From 533e4db9f531ed714f9bc64174838d04c86a7689 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 02:03:34 +0800 Subject: [PATCH 01/17] refactor(packaging): Remove deprecated test configuration from setup.py The `test_suite` and `tests_require` arguments in `setup()` are legacy setuptools features that have been deprecated. Modern test runners like `pytest` and `tox` handle test discovery and dependency management externally. This commit removes these obsolete arguments to modernize the packaging configuration, reduce clutter, and silence deprecation warnings. Signed-off-by: acture --- setup.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/setup.py b/setup.py index c62cf183..825b49f0 100644 --- a/setup.py +++ b/setup.py @@ -61,8 +61,6 @@ "pandas>=1.0.1, <=1.1.5; python_version<='3.7'", ], setup_requires=[CYTHON_STR], - test_suite="nose.collector", - tests_require=[], ext_modules=[ setuptools.Extension( "cpp_easygraph", sources, optional=True, extra_compile_args=compileArgs From 7d61aa7cd44936fffb8552c97284216cb648f873 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 02:07:15 +0800 Subject: [PATCH 02/17] style(packaging): Use SPDX license identifier 'BSD-3-Clause' The `setup.py` file used the deprecated license classifier `License :: OSI Approved :: BSD License`. Modern Python packaging standards (PyPA) recommend using specific, machine-readable SPDX identifiers. This commit replaces the old classifier with the precise `BSD-3-Clause` identifier in the `license` field. This aligns the project with best practices and silences setuptools deprecation warnings. Signed-off-by: acture --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 825b49f0..b7cac426 100644 --- a/setup.py +++ b/setup.py @@ -33,7 +33,7 @@ "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", - "License :: OSI Approved :: BSD License", + "BSD-3-Clause", "Operating System :: OS Independent", ], python_requires=">=3.6, <3.11", From a9ef56bfbdb014e1af41e83f08eae5959ba249bd Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 12:42:53 +0800 Subject: [PATCH 03/17] refactor(packaging): Migrate from `setup.py` to `pyproject.toml` and restructure project Replaced the legacy `setup.py` with modern `pyproject.toml` following PEP 517 and PEP 518 standards. Updated the project structure to move source files into a `src/` directory. Also, introduced `scikit-build` for efficient handling of C++ extensions. This change modernizes the project's packaging approach, aligns with best practices, and simplifies dependency management. Signed-off-by: acture --- .python-version | 1 + CMakeLists.txt | 15 ++ pyproject.toml | 215 +++++------------- setup.py | 69 ------ .../cpp_easygraph}/classes/__init__.h | 0 .../cpp_easygraph}/classes/directed_graph.cpp | 0 .../cpp_easygraph}/classes/directed_graph.h | 0 .../cpp_easygraph}/classes/graph.cpp | 0 .../cpp_easygraph}/classes/graph.h | 0 .../cpp_easygraph}/classes/operation.cpp | 0 .../cpp_easygraph}/classes/operation.h | 0 .../cpp_easygraph}/common/common.h | 0 .../cpp_easygraph}/common/utils.cpp | 0 .../cpp_easygraph}/common/utils.h | 0 .../cpp_easygraph}/cpp_easygraph.cpp | 0 .../cpp_easygraph}/functions/__init__.h | 0 .../functions/components/__init__.h | 0 .../functions/components/biconnected.cpp | 0 .../functions/components/biconnected.h | 0 .../functions/not_sorted/__init__.h | 0 .../functions/not_sorted/cluster.cpp | 0 .../functions/not_sorted/cluster.h | 0 .../cpp_easygraph}/functions/path/__init__.h | 0 .../cpp_easygraph}/functions/path/path.cpp | 0 .../cpp_easygraph}/functions/path/path.h | 0 .../functions/structural_holes/__init__.h | 0 .../functions/structural_holes/evaluation.cpp | 0 .../functions/structural_holes/evaluation.h | 0 {easygraph => src/easygraph}/__init__.py | 0 .../easygraph}/classes/__init__.py | 0 .../easygraph}/classes/directed_graph.py | 0 .../easygraph}/classes/directed_multigraph.py | 0 {easygraph => src/easygraph}/classes/graph.py | 0 .../easygraph}/classes/graphviews.py | 0 .../easygraph}/classes/multigraph.py | 0 .../easygraph}/classes/operation.py | 0 .../easygraph}/classes/tests/__init__.py | 0 .../classes/tests/test_multidigraph.py | 0 .../classes/tests/test_multigraph.py | 0 .../classes/tests/test_operation.py | 0 {easygraph => src/easygraph}/convert.py | 0 .../easygraph}/datasets/__init__.py | 2 +- .../easygraph}/datasets/get_sample_graph.py | 0 .../datasets/samples/blogcatalog.mat | Bin .../easygraph}/functions/__init__.py | 0 .../functions/centrality/__init__.py | 0 .../functions/centrality/betweenness.py | 0 .../functions/centrality/clossness.py | 0 .../easygraph}/functions/centrality/degree.py | 0 .../functions/centrality/flowbetweenness.py | 0 .../functions/centrality/tests/__init__.py | 0 .../centrality/tests/test_betweenness.py | 0 .../centrality/tests/test_clossness.py | 0 .../centrality/tests/test_flowbetweenness.py | 0 .../easygraph}/functions/community/LPA.py | 0 .../functions/community/__init__.py | 0 .../functions/community/modularity.py | 0 .../community/modularity_max_detection.py | 0 .../easygraph}/functions/community/motif.py | 0 .../functions/community/tests/__init__.py | 0 .../tests/test_ modularity_max_detection.py | 0 .../functions/community/tests/test_LPA.py | 0 .../community/tests/test_modularity.py | 0 .../functions/community/tests/test_motif.py | 0 .../functions/components/__init__.py | 0 .../functions/components/biconnected.py | 0 .../functions/components/connected.py | 0 .../functions/components/ego_betweenness.py | 0 .../functions/components/tests/__init__.py | 0 .../components/tests/test_biconnected.py | 0 .../easygraph}/functions/drawing/__init__.py | 0 .../easygraph}/functions/drawing/drawing.py | 0 .../easygraph}/functions/drawing/plot.py | 0 .../functions/drawing/positioning.py | 0 .../functions/drawing/tests/__init__.py | 0 .../drawing/tests/test_positioning.py | 0 .../functions/graph_embedding/NOBE.py | 0 .../functions/graph_embedding/__init__.py | 0 .../functions/graph_embedding/deepwalk.py | 0 .../functions/graph_embedding/line.py | 0 .../functions/graph_embedding/node2vec.py | 0 .../functions/graph_embedding/sdne.py | 0 .../graph_generator/RandomNetwork.py | 0 .../functions/graph_generator/__init__.py | 0 .../functions/graph_generator/classic.py | 0 .../functions/not_sorted/__init__.py | 0 .../functions/not_sorted/bridges.py | 0 .../functions/not_sorted/cluster.py | 0 .../functions/not_sorted/laplacian.py | 0 .../easygraph}/functions/not_sorted/mst.py | 0 .../functions/not_sorted/pagerank.py | 0 .../functions/not_sorted/tests/__init__.py | 0 .../not_sorted/tests/test_cluster.py | 0 .../functions/not_sorted/tests/test_mst.py | 0 .../not_sorted/tests/test_pagerank.py | 0 .../easygraph}/functions/path/__init__.py | 2 +- .../easygraph}/functions/path/path.py | 0 .../functions/structural_holes/AP_Greedy.py | 0 .../functions/structural_holes/HAM.py | 0 .../functions/structural_holes/HIS.py | 0 .../functions/structural_holes/ICC.py | 0 .../functions/structural_holes/MaxD.py | 0 .../functions/structural_holes/NOBE.py | 0 .../functions/structural_holes/SHII_metric.py | 0 .../functions/structural_holes/__init__.py | 0 .../functions/structural_holes/evaluation.py | 0 .../functions/structural_holes/maxBlock.py | 0 .../functions/structural_holes/metrics.py | 0 .../strong_connected_component.py | 0 .../structural_holes/tests/__init__.py | 0 .../structural_holes/tests/test_AP_Greedy.py | 0 .../structural_holes/tests/test_HAM.py | 0 .../structural_holes/tests/test_HIS.py | 0 .../structural_holes/tests/test_ICC.py | 0 .../structural_holes/tests/test_NOBE.py | 0 .../structural_holes/tests/test_evaluation.py | 0 .../tests/test_strong_connected_component.py | 0 .../structural_holes/tests/test_weakTie.py | 0 .../functions/structural_holes/weakTie.py | 0 .../easygraph}/readwrite/__init__.py | 0 .../easygraph}/readwrite/edgelist.py | 0 .../easygraph}/readwrite/gexf.py | 0 {easygraph => src/easygraph}/readwrite/gml.py | 0 .../easygraph}/readwrite/graphml.py | 0 .../easygraph}/readwrite/graphviz.py | 0 .../easygraph}/readwrite/pajek.py | 0 .../easygraph}/readwrite/pickle.py | 0 .../easygraph}/readwrite/tests/__init__.py | 0 .../readwrite/tests/test_edgelist.py | 0 .../easygraph}/readwrite/tests/test_gexf.py | 0 .../easygraph}/readwrite/tests/test_gml.py | 0 .../readwrite/tests/test_graphml.py | 0 .../readwrite/tests/test_graphviz.py | 0 .../easygraph}/readwrite/tests/test_pajek.py | 0 .../easygraph}/readwrite/tests/test_pickle.py | 0 .../easygraph}/readwrite/tests/test_ucinet.py | 0 .../easygraph}/readwrite/ucinet.py | 0 .../easygraph}/tests/__init__.py | 0 .../easygraph}/tests/test_convert.py | 0 .../easygraph}/utils/__init__.py | 0 {easygraph => src/easygraph}/utils/alias.py | 0 .../easygraph}/utils/convert_class.py | 0 .../easygraph}/utils/convert_to_matrix.py | 0 .../easygraph}/utils/decorators.py | 0 .../easygraph}/utils/exception.py | 0 .../easygraph}/utils/index_of_node.py | 0 .../easygraph}/utils/mapped_queue.py | 0 {easygraph => src/easygraph}/utils/misc.py | 0 {easygraph => src/easygraph}/utils/relabel.py | 0 .../easygraph}/utils/tests/__init__.py | 0 .../utils/tests/test_convert_to_matrix.py | 0 .../utils/tests/test_mapped_queue.py | 0 .../easygraph}/utils/type_change.py | 0 tox-conda-test.ini | 9 - tox-conda.ini | 14 -- tox-test.ini | 8 - tox.ini | 38 +++- 157 files changed, 100 insertions(+), 273 deletions(-) create mode 100644 .python-version create mode 100644 CMakeLists.txt delete mode 100644 setup.py rename {cpp_easygraph => src/cpp_easygraph}/classes/__init__.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/classes/directed_graph.cpp (100%) rename {cpp_easygraph => src/cpp_easygraph}/classes/directed_graph.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/classes/graph.cpp (100%) rename {cpp_easygraph => src/cpp_easygraph}/classes/graph.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/classes/operation.cpp (100%) rename {cpp_easygraph => src/cpp_easygraph}/classes/operation.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/common/common.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/common/utils.cpp (100%) rename {cpp_easygraph => src/cpp_easygraph}/common/utils.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/cpp_easygraph.cpp (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/__init__.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/components/__init__.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/components/biconnected.cpp (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/components/biconnected.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/not_sorted/__init__.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/not_sorted/cluster.cpp (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/not_sorted/cluster.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/path/__init__.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/path/path.cpp (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/path/path.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/structural_holes/__init__.h (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/structural_holes/evaluation.cpp (100%) rename {cpp_easygraph => src/cpp_easygraph}/functions/structural_holes/evaluation.h (100%) rename {easygraph => src/easygraph}/__init__.py (100%) rename {easygraph => src/easygraph}/classes/__init__.py (100%) rename {easygraph => src/easygraph}/classes/directed_graph.py (100%) rename {easygraph => src/easygraph}/classes/directed_multigraph.py (100%) rename {easygraph => src/easygraph}/classes/graph.py (100%) rename {easygraph => src/easygraph}/classes/graphviews.py (100%) rename {easygraph => src/easygraph}/classes/multigraph.py (100%) rename {easygraph => src/easygraph}/classes/operation.py (100%) rename {easygraph => src/easygraph}/classes/tests/__init__.py (100%) rename {easygraph => src/easygraph}/classes/tests/test_multidigraph.py (100%) rename {easygraph => src/easygraph}/classes/tests/test_multigraph.py (100%) rename {easygraph => src/easygraph}/classes/tests/test_operation.py (100%) rename {easygraph => src/easygraph}/convert.py (100%) rename {easygraph => src/easygraph}/datasets/__init__.py (98%) rename {easygraph => src/easygraph}/datasets/get_sample_graph.py (100%) rename {easygraph => src/easygraph}/datasets/samples/blogcatalog.mat (100%) rename {easygraph => src/easygraph}/functions/__init__.py (100%) rename {easygraph => src/easygraph}/functions/centrality/__init__.py (100%) rename {easygraph => src/easygraph}/functions/centrality/betweenness.py (100%) rename {easygraph => src/easygraph}/functions/centrality/clossness.py (100%) rename {easygraph => src/easygraph}/functions/centrality/degree.py (100%) rename {easygraph => src/easygraph}/functions/centrality/flowbetweenness.py (100%) rename {easygraph => src/easygraph}/functions/centrality/tests/__init__.py (100%) rename {easygraph => src/easygraph}/functions/centrality/tests/test_betweenness.py (100%) rename {easygraph => src/easygraph}/functions/centrality/tests/test_clossness.py (100%) rename {easygraph => src/easygraph}/functions/centrality/tests/test_flowbetweenness.py (100%) rename {easygraph => src/easygraph}/functions/community/LPA.py (100%) rename {easygraph => src/easygraph}/functions/community/__init__.py (100%) rename {easygraph => src/easygraph}/functions/community/modularity.py (100%) rename {easygraph => src/easygraph}/functions/community/modularity_max_detection.py (100%) rename {easygraph => src/easygraph}/functions/community/motif.py (100%) rename {easygraph => src/easygraph}/functions/community/tests/__init__.py (100%) rename {easygraph => src/easygraph}/functions/community/tests/test_ modularity_max_detection.py (100%) rename {easygraph => src/easygraph}/functions/community/tests/test_LPA.py (100%) rename {easygraph => src/easygraph}/functions/community/tests/test_modularity.py (100%) rename {easygraph => src/easygraph}/functions/community/tests/test_motif.py (100%) rename {easygraph => src/easygraph}/functions/components/__init__.py (100%) rename {easygraph => src/easygraph}/functions/components/biconnected.py (100%) rename {easygraph => src/easygraph}/functions/components/connected.py (100%) rename {easygraph => src/easygraph}/functions/components/ego_betweenness.py (100%) rename {easygraph => src/easygraph}/functions/components/tests/__init__.py (100%) rename {easygraph => src/easygraph}/functions/components/tests/test_biconnected.py (100%) rename {easygraph => src/easygraph}/functions/drawing/__init__.py (100%) rename {easygraph => src/easygraph}/functions/drawing/drawing.py (100%) rename {easygraph => src/easygraph}/functions/drawing/plot.py (100%) rename {easygraph => src/easygraph}/functions/drawing/positioning.py (100%) rename {easygraph => src/easygraph}/functions/drawing/tests/__init__.py (100%) rename {easygraph => src/easygraph}/functions/drawing/tests/test_positioning.py (100%) rename {easygraph => src/easygraph}/functions/graph_embedding/NOBE.py (100%) rename {easygraph => src/easygraph}/functions/graph_embedding/__init__.py (100%) rename {easygraph => src/easygraph}/functions/graph_embedding/deepwalk.py (100%) rename {easygraph => src/easygraph}/functions/graph_embedding/line.py (100%) rename {easygraph => src/easygraph}/functions/graph_embedding/node2vec.py (100%) rename {easygraph => src/easygraph}/functions/graph_embedding/sdne.py (100%) rename {easygraph => src/easygraph}/functions/graph_generator/RandomNetwork.py (100%) rename {easygraph => src/easygraph}/functions/graph_generator/__init__.py (100%) rename {easygraph => src/easygraph}/functions/graph_generator/classic.py (100%) rename {easygraph => src/easygraph}/functions/not_sorted/__init__.py (100%) rename {easygraph => src/easygraph}/functions/not_sorted/bridges.py (100%) rename {easygraph => src/easygraph}/functions/not_sorted/cluster.py (100%) rename {easygraph => src/easygraph}/functions/not_sorted/laplacian.py (100%) rename {easygraph => src/easygraph}/functions/not_sorted/mst.py (100%) rename {easygraph => src/easygraph}/functions/not_sorted/pagerank.py (100%) rename {easygraph => src/easygraph}/functions/not_sorted/tests/__init__.py (100%) rename {easygraph => src/easygraph}/functions/not_sorted/tests/test_cluster.py (100%) rename {easygraph => src/easygraph}/functions/not_sorted/tests/test_mst.py (100%) rename {easygraph => src/easygraph}/functions/not_sorted/tests/test_pagerank.py (100%) rename {easygraph => src/easygraph}/functions/path/__init__.py (95%) rename {easygraph => src/easygraph}/functions/path/path.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/AP_Greedy.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/HAM.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/HIS.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/ICC.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/MaxD.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/NOBE.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/SHII_metric.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/__init__.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/evaluation.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/maxBlock.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/metrics.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/strong_connected_component.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/tests/__init__.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/tests/test_AP_Greedy.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/tests/test_HAM.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/tests/test_HIS.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/tests/test_ICC.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/tests/test_NOBE.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/tests/test_evaluation.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/tests/test_strong_connected_component.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/tests/test_weakTie.py (100%) rename {easygraph => src/easygraph}/functions/structural_holes/weakTie.py (100%) rename {easygraph => src/easygraph}/readwrite/__init__.py (100%) rename {easygraph => src/easygraph}/readwrite/edgelist.py (100%) rename {easygraph => src/easygraph}/readwrite/gexf.py (100%) rename {easygraph => src/easygraph}/readwrite/gml.py (100%) rename {easygraph => src/easygraph}/readwrite/graphml.py (100%) rename {easygraph => src/easygraph}/readwrite/graphviz.py (100%) rename {easygraph => src/easygraph}/readwrite/pajek.py (100%) rename {easygraph => src/easygraph}/readwrite/pickle.py (100%) rename {easygraph => src/easygraph}/readwrite/tests/__init__.py (100%) rename {easygraph => src/easygraph}/readwrite/tests/test_edgelist.py (100%) rename {easygraph => src/easygraph}/readwrite/tests/test_gexf.py (100%) rename {easygraph => src/easygraph}/readwrite/tests/test_gml.py (100%) rename {easygraph => src/easygraph}/readwrite/tests/test_graphml.py (100%) rename {easygraph => src/easygraph}/readwrite/tests/test_graphviz.py (100%) rename {easygraph => src/easygraph}/readwrite/tests/test_pajek.py (100%) rename {easygraph => src/easygraph}/readwrite/tests/test_pickle.py (100%) rename {easygraph => src/easygraph}/readwrite/tests/test_ucinet.py (100%) rename {easygraph => src/easygraph}/readwrite/ucinet.py (100%) rename {easygraph => src/easygraph}/tests/__init__.py (100%) rename {easygraph => src/easygraph}/tests/test_convert.py (100%) rename {easygraph => src/easygraph}/utils/__init__.py (100%) rename {easygraph => src/easygraph}/utils/alias.py (100%) rename {easygraph => src/easygraph}/utils/convert_class.py (100%) rename {easygraph => src/easygraph}/utils/convert_to_matrix.py (100%) rename {easygraph => src/easygraph}/utils/decorators.py (100%) rename {easygraph => src/easygraph}/utils/exception.py (100%) rename {easygraph => src/easygraph}/utils/index_of_node.py (100%) rename {easygraph => src/easygraph}/utils/mapped_queue.py (100%) rename {easygraph => src/easygraph}/utils/misc.py (100%) rename {easygraph => src/easygraph}/utils/relabel.py (100%) rename {easygraph => src/easygraph}/utils/tests/__init__.py (100%) rename {easygraph => src/easygraph}/utils/tests/test_convert_to_matrix.py (100%) rename {easygraph => src/easygraph}/utils/tests/test_mapped_queue.py (100%) rename {easygraph => src/easygraph}/utils/type_change.py (100%) delete mode 100644 tox-conda-test.ini delete mode 100644 tox-conda.ini delete mode 100644 tox-test.ini diff --git a/.python-version b/.python-version new file mode 100644 index 00000000..e4fba218 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.12 diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 00000000..357c4a1d --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,15 @@ +cmake_minimum_required(VERSION 3.15) +project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX) + +cmake_policy(SET CMP0167 NEW) + +set(PYBIND11_FINDPYTHON ON) +find_package(pybind11 CONFIG REQUIRED) +find_package(Boost REQUIRED COMPONENTS python3) + +pybind11_add_module(cpp_easygraph MODULE src/cpp_easygraph/cpp_easygraph.cpp) + +target_include_directories(cpp_easygraph PRIVATE ${Boost_INCLUDE_DIRS}) +target_link_libraries(cpp_easygraph PRIVATE ${Boost_LIBRARIES}) + +install(TARGETS cpp_easygraph DESTINATION ${SKBUILD_PROJECT_NAME}) diff --git a/pyproject.toml b/pyproject.toml index e3c81922..65335894 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,168 +1,63 @@ -# [tool.poetry] -# name = "python-easygraph" -# version = "1.2.0rc1.dev0" -# description = "Python Graph Library" -# authors = [ -# "Teddy Xinyuan Chen <45612704+tddschn@users.noreply.github.com>", -# ] -# maintainers = [ -# "Teddy Xinyuan Chen <45612704+tddschn@users.noreply.github.com>" -# ] -# license = "MIT" - -# readme = "README.md" - -# packages = [ -# { include = "poetry", from = "src" } -# ] -# include = [ -# { path = "tests", format = "sdist" } -# ] - -# homepage = "https://python-poetry.org/" -# repository = "https://github.com/python-poetry/poetry" -# documentation = "https://python-poetry.org/docs" - -# keywords = ["packaging", "dependency", "poetry"] - -# classifiers = [ -# "Topic :: Software Development :: Build Tools", -# "Topic :: Software Development :: Libraries :: Python Modules" -# ] - -# [tool.poetry.build] -# generate-setup-file = false - -# # Requirements -# [tool.poetry.dependencies] -# python = "^3.7" - -# poetry-core = "^1.1.0b3" -# poetry-plugin-export = "^1.0.5" -# cachecontrol = { version = "^0.12.9", extras = ["filecache"] } -# cachy = "^0.3.0" -# cleo = "^1.0.0a5" -# crashtest = "^0.3.0" -# html5lib = "^1.0" -# importlib-metadata = { version = "^4.4", python = "<3.10" } -# # keyring uses calver, so version is unclamped -# keyring = ">=21.2.0" -# # packaging uses calver, so version is unclamped -# packaging = ">=20.4" -# pexpect = "^4.7.0" -# pkginfo = "^1.5" -# platformdirs = "^2.5.2" -# requests = "^2.18" -# requests-toolbelt = "^0.9.1" -# shellingham = "^1.1" -# tomlkit = ">=0.11.1,<1.0.0" -# # exclude 20.4.5 - 20.4.6 due to https://github.com/pypa/pip/issues/9953 -# virtualenv = "(>=20.4.3,<20.4.5 || >=20.4.7)" -# xattr = { version = "^0.9.7", markers = "sys_platform == 'darwin'" } -# urllib3 = "^1.26.0" -# dulwich = "^0.20.44" - -# [tool.poetry.dev-dependencies] -# tox = "^3.18" -# pytest = "^7.1" -# pytest-cov = "^3.0" -# pytest-mock = "^3.5" -# pytest-randomly = "^3.10" -# pytest-sugar = "^0.9" -# pytest-xdist = { version = "^2.5", extras = ["psutil"] } -# pre-commit = "^2.6" -# deepdiff = "^5.0" -# httpretty = "^1.0" -# typing-extensions = { version = "^4.0.0", python = "<3.8" } -# zipp = { version = "^3.4", python = "<3.8" } -# flatdict = "^4.0.1" -# mypy = ">=0.960" -# types-html5lib = ">=1.1.7" -# types-jsonschema = ">=4.4.4" -# types-requests = ">=2.27.11" - -# [tool.poetry.scripts] -# poetry = "poetry.console.application:main" - - -# [build-system] -# requires = ["poetry-core>=1.0.0"] -# build-backend = "poetry.core.masonry.api" - - -[tool.isort] -py_version = 37 -profile = "black" -force_single_line = true -combine_as_imports = true -lines_between_types = 1 -lines_after_imports = 2 -src_paths = ["src", "tests"] -extend_skip = ["setup.py"] -known_third_party = ["poetry.core"] - +[project] +name = "Python-EasyGraph" +version = "0.2a40" +authors = [ + { name = "Fudan MSN Group", email = "easygraph@163.com" }, +] +description = "Easy Graph" +readme = "README.rst" +requires-python = ">=3.10" +license = "BSD-3-Clause" +classifiers = [ + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Operating System :: OS Independent", +] +dependencies = [ + "gensim>=4.2.0", + "joblib>=1.1.1", + "matplotlib>=3.3.4", + "nose>=1.3.7", + "numpy>=1.19.5", + "pandas>=0.25.3", + "progressbar>=2.5", + "progressbar33>=2.4", + "scikit-learn>=0.24.2", + "scipy>=1.5.4", + "six>=1.17.0", + "statsmodels>=0.12.2", + "tqdm>=4.64.1", +] -[tool.black] -target-version = ['py37'] -preview = true -force-exclude = ''' -.*/setup\.py$ -''' +[project.scripts] +easy-graph = "easy_graph:main" +[tool.scikit-build] +minimum-version = "build-system.requires" +build-dir = "build/{wheel_tag}" -# [tool.mypy] -# files = "src" -# mypy_path = "src" -# namespace_packages = true -# explicit_package_bases = true -# show_error_codes = true -# strict = true -# enable_error_code = [ -# "ignore-without-code", -# "redundant-expr", -# "truthy-bool", -# ] +[tool.uv] +cache-keys = [{ file = "pyproject.toml" }, { file = "src/**/*.{h,c,hpp,cpp}" }, { file = "src/cpp_easygraph/CMakeLists.txt" }] -# use of importlib-metadata backport at python3.7 makes it impossible to -# satisfy mypy without some ignores: but we get a different set of ignores at -# different python versions. -# -# , meanwhile suppress that -# warning. -# [[tool.mypy.overrides]] -# module = [ -# 'poetry.console.commands.self.show.plugins', -# 'poetry.installation.executor', -# 'poetry.mixology.version_solver', -# 'poetry.plugins.plugin_manager', -# 'poetry.repositories.installed_repository', -# 'poetry.utils.env', -# ] -# warn_unused_ignores = false +[build-system] +requires = ["scikit-build-core>=0.10", "pybind11"] +build-backend = "scikit_build_core.build" -# [[tool.mypy.overrides]] -# module = [ -# 'cachecontrol.*', -# 'cachy.*', -# 'cleo.*', -# 'crashtest.*', -# 'pexpect.*', -# 'pkginfo.*', -# 'requests_toolbelt.*', -# 'shellingham.*', -# 'virtualenv.*', -# 'xattr.*', -# ] -# ignore_missing_imports = true +[tool.setuptools.packages.find] +# 告诉 setuptools 你的包在 "src" 目录下 +where = ["src"] -[tool.coverage.run] -branch = true -source = [ "easygraph/"] -relative_files = true +[dependency-groups] +dev = [ + "pytest>=8.4.2", + "ruff>=0.14.1", + "scikit-build-core>=0.11.6", +] -[tool.coverage.report] -exclude_lines = [ - "pragma: no cover", - "if TYPE_CHECKING:" -] +[tool.pytest.ini_options] +python_files = "**/tests/test_*.py" +addopts = "-ra --disable-warnings" diff --git a/setup.py b/setup.py deleted file mode 100644 index b7cac426..00000000 --- a/setup.py +++ /dev/null @@ -1,69 +0,0 @@ -import platform - -from pathlib import Path - -import setuptools - - -with open("README.rst") as fh: - long_description = fh.read() - -cpp_source_dir = Path(__file__).parent / "cpp_easygraph" -sources = list(str(x) for x in cpp_source_dir.rglob("*.cpp")) - -uname = platform.uname() -compileArgs = [] -if uname[0] == "Darwin" or uname[0] == "Linux": - compileArgs = ["-std=c++11"] -CYTHON_STR = "Cython" - -setuptools.setup( - name="Python-EasyGraph", - version="0.2a40", - author="Fudan MSN Group", - author_email="easygraph@163.com", - description="Easy Graph", - long_description=long_description, - long_description_content_type="text/x-rst", - url="https://github.com/easy-graph/Easy-Graph", - packages=setuptools.find_packages(), - classifiers=[ - "Programming Language :: Python :: 3.6", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "BSD-3-Clause", - "Operating System :: OS Independent", - ], - python_requires=">=3.6, <3.11", - install_requires=[ - "numpy>=1.18.5, <=1.19.5; python_version=='3.6'", - "numpy>=1.18.5; python_version>='3.7'", - "tqdm>=4.49.0", - "joblib>=0.16.0", - "six>=1.15.0, <1.16.0", - "gensim<=4.1.2; python_version=='3.6'", - "gensim>=4.1.2; python_version>='3.7'", - "progressbar33>=2.4", - "scikit-learn>=0.23.0, <=0.24.2; python_version=='3.6'", - "scikit-learn>=0.24.0, <=1.0.2; python_version=='3.7'", - "scikit-learn>=1.1; python_version>='3.8'", - "scipy>=1.5.0, <=1.5.4; python_version=='3.6'", - "scipy>=1.5.0, <=1.7.3; python_version=='3.7'", - "scipy>=1.8.0; python_version>='3.8'", - "matplotlib>=3.3.0, <=3.3.4; python_version<'3.10'", - "matplotlib>=3.5.2; python_version>='3.10'", - "statsmodels>=0.12.0, <=0.12.2; python_version=='3.6'", - "statsmodels>=0.12.0; python_version>='3.7'", - "progressbar>=2.5", - "nose>=0.10.1", - "pandas>=1.0.1, <=1.1.5; python_version<='3.7'", - ], - setup_requires=[CYTHON_STR], - ext_modules=[ - setuptools.Extension( - "cpp_easygraph", sources, optional=True, extra_compile_args=compileArgs - ) - ], -) diff --git a/cpp_easygraph/classes/__init__.h b/src/cpp_easygraph/classes/__init__.h similarity index 100% rename from cpp_easygraph/classes/__init__.h rename to src/cpp_easygraph/classes/__init__.h diff --git a/cpp_easygraph/classes/directed_graph.cpp b/src/cpp_easygraph/classes/directed_graph.cpp similarity index 100% rename from cpp_easygraph/classes/directed_graph.cpp rename to src/cpp_easygraph/classes/directed_graph.cpp diff --git a/cpp_easygraph/classes/directed_graph.h b/src/cpp_easygraph/classes/directed_graph.h similarity index 100% rename from cpp_easygraph/classes/directed_graph.h rename to src/cpp_easygraph/classes/directed_graph.h diff --git a/cpp_easygraph/classes/graph.cpp b/src/cpp_easygraph/classes/graph.cpp similarity index 100% rename from cpp_easygraph/classes/graph.cpp rename to src/cpp_easygraph/classes/graph.cpp diff --git a/cpp_easygraph/classes/graph.h b/src/cpp_easygraph/classes/graph.h similarity index 100% rename from cpp_easygraph/classes/graph.h rename to src/cpp_easygraph/classes/graph.h diff --git a/cpp_easygraph/classes/operation.cpp b/src/cpp_easygraph/classes/operation.cpp similarity index 100% rename from cpp_easygraph/classes/operation.cpp rename to src/cpp_easygraph/classes/operation.cpp diff --git a/cpp_easygraph/classes/operation.h b/src/cpp_easygraph/classes/operation.h similarity index 100% rename from cpp_easygraph/classes/operation.h rename to src/cpp_easygraph/classes/operation.h diff --git a/cpp_easygraph/common/common.h b/src/cpp_easygraph/common/common.h similarity index 100% rename from cpp_easygraph/common/common.h rename to src/cpp_easygraph/common/common.h diff --git a/cpp_easygraph/common/utils.cpp b/src/cpp_easygraph/common/utils.cpp similarity index 100% rename from cpp_easygraph/common/utils.cpp rename to src/cpp_easygraph/common/utils.cpp diff --git a/cpp_easygraph/common/utils.h b/src/cpp_easygraph/common/utils.h similarity index 100% rename from cpp_easygraph/common/utils.h rename to src/cpp_easygraph/common/utils.h diff --git a/cpp_easygraph/cpp_easygraph.cpp b/src/cpp_easygraph/cpp_easygraph.cpp similarity index 100% rename from cpp_easygraph/cpp_easygraph.cpp rename to src/cpp_easygraph/cpp_easygraph.cpp diff --git a/cpp_easygraph/functions/__init__.h b/src/cpp_easygraph/functions/__init__.h similarity index 100% rename from cpp_easygraph/functions/__init__.h rename to src/cpp_easygraph/functions/__init__.h diff --git a/cpp_easygraph/functions/components/__init__.h b/src/cpp_easygraph/functions/components/__init__.h similarity index 100% rename from cpp_easygraph/functions/components/__init__.h rename to src/cpp_easygraph/functions/components/__init__.h diff --git a/cpp_easygraph/functions/components/biconnected.cpp b/src/cpp_easygraph/functions/components/biconnected.cpp similarity index 100% rename from cpp_easygraph/functions/components/biconnected.cpp rename to src/cpp_easygraph/functions/components/biconnected.cpp diff --git a/cpp_easygraph/functions/components/biconnected.h b/src/cpp_easygraph/functions/components/biconnected.h similarity index 100% rename from cpp_easygraph/functions/components/biconnected.h rename to src/cpp_easygraph/functions/components/biconnected.h diff --git a/cpp_easygraph/functions/not_sorted/__init__.h b/src/cpp_easygraph/functions/not_sorted/__init__.h similarity index 100% rename from cpp_easygraph/functions/not_sorted/__init__.h rename to src/cpp_easygraph/functions/not_sorted/__init__.h diff --git a/cpp_easygraph/functions/not_sorted/cluster.cpp b/src/cpp_easygraph/functions/not_sorted/cluster.cpp similarity index 100% rename from cpp_easygraph/functions/not_sorted/cluster.cpp rename to src/cpp_easygraph/functions/not_sorted/cluster.cpp diff --git a/cpp_easygraph/functions/not_sorted/cluster.h b/src/cpp_easygraph/functions/not_sorted/cluster.h similarity index 100% rename from cpp_easygraph/functions/not_sorted/cluster.h rename to src/cpp_easygraph/functions/not_sorted/cluster.h diff --git a/cpp_easygraph/functions/path/__init__.h b/src/cpp_easygraph/functions/path/__init__.h similarity index 100% rename from cpp_easygraph/functions/path/__init__.h rename to src/cpp_easygraph/functions/path/__init__.h diff --git a/cpp_easygraph/functions/path/path.cpp b/src/cpp_easygraph/functions/path/path.cpp similarity index 100% rename from cpp_easygraph/functions/path/path.cpp rename to src/cpp_easygraph/functions/path/path.cpp diff --git a/cpp_easygraph/functions/path/path.h b/src/cpp_easygraph/functions/path/path.h similarity index 100% rename from cpp_easygraph/functions/path/path.h rename to src/cpp_easygraph/functions/path/path.h diff --git a/cpp_easygraph/functions/structural_holes/__init__.h b/src/cpp_easygraph/functions/structural_holes/__init__.h similarity index 100% rename from cpp_easygraph/functions/structural_holes/__init__.h rename to src/cpp_easygraph/functions/structural_holes/__init__.h diff --git a/cpp_easygraph/functions/structural_holes/evaluation.cpp b/src/cpp_easygraph/functions/structural_holes/evaluation.cpp similarity index 100% rename from cpp_easygraph/functions/structural_holes/evaluation.cpp rename to src/cpp_easygraph/functions/structural_holes/evaluation.cpp diff --git a/cpp_easygraph/functions/structural_holes/evaluation.h b/src/cpp_easygraph/functions/structural_holes/evaluation.h similarity index 100% rename from cpp_easygraph/functions/structural_holes/evaluation.h rename to src/cpp_easygraph/functions/structural_holes/evaluation.h diff --git a/easygraph/__init__.py b/src/easygraph/__init__.py similarity index 100% rename from easygraph/__init__.py rename to src/easygraph/__init__.py diff --git a/easygraph/classes/__init__.py b/src/easygraph/classes/__init__.py similarity index 100% rename from easygraph/classes/__init__.py rename to src/easygraph/classes/__init__.py diff --git a/easygraph/classes/directed_graph.py b/src/easygraph/classes/directed_graph.py similarity index 100% rename from easygraph/classes/directed_graph.py rename to src/easygraph/classes/directed_graph.py diff --git a/easygraph/classes/directed_multigraph.py b/src/easygraph/classes/directed_multigraph.py similarity index 100% rename from easygraph/classes/directed_multigraph.py rename to src/easygraph/classes/directed_multigraph.py diff --git a/easygraph/classes/graph.py b/src/easygraph/classes/graph.py similarity index 100% rename from easygraph/classes/graph.py rename to src/easygraph/classes/graph.py diff --git a/easygraph/classes/graphviews.py b/src/easygraph/classes/graphviews.py similarity index 100% rename from easygraph/classes/graphviews.py rename to src/easygraph/classes/graphviews.py diff --git a/easygraph/classes/multigraph.py b/src/easygraph/classes/multigraph.py similarity index 100% rename from easygraph/classes/multigraph.py rename to src/easygraph/classes/multigraph.py diff --git a/easygraph/classes/operation.py b/src/easygraph/classes/operation.py similarity index 100% rename from easygraph/classes/operation.py rename to src/easygraph/classes/operation.py diff --git a/easygraph/classes/tests/__init__.py b/src/easygraph/classes/tests/__init__.py similarity index 100% rename from easygraph/classes/tests/__init__.py rename to src/easygraph/classes/tests/__init__.py diff --git a/easygraph/classes/tests/test_multidigraph.py b/src/easygraph/classes/tests/test_multidigraph.py similarity index 100% rename from easygraph/classes/tests/test_multidigraph.py rename to src/easygraph/classes/tests/test_multidigraph.py diff --git a/easygraph/classes/tests/test_multigraph.py b/src/easygraph/classes/tests/test_multigraph.py similarity index 100% rename from easygraph/classes/tests/test_multigraph.py rename to src/easygraph/classes/tests/test_multigraph.py diff --git a/easygraph/classes/tests/test_operation.py b/src/easygraph/classes/tests/test_operation.py similarity index 100% rename from easygraph/classes/tests/test_operation.py rename to src/easygraph/classes/tests/test_operation.py diff --git a/easygraph/convert.py b/src/easygraph/convert.py similarity index 100% rename from easygraph/convert.py rename to src/easygraph/convert.py diff --git a/easygraph/datasets/__init__.py b/src/easygraph/datasets/__init__.py similarity index 98% rename from easygraph/datasets/__init__.py rename to src/easygraph/datasets/__init__.py index db2ab2d1..aebbc746 100644 --- a/easygraph/datasets/__init__.py +++ b/src/easygraph/datasets/__init__.py @@ -1 +1 @@ -from easygraph.datasets.get_sample_graph import * +from easygraph.datasets.get_sample_graph import * diff --git a/easygraph/datasets/get_sample_graph.py b/src/easygraph/datasets/get_sample_graph.py similarity index 100% rename from easygraph/datasets/get_sample_graph.py rename to src/easygraph/datasets/get_sample_graph.py diff --git a/easygraph/datasets/samples/blogcatalog.mat b/src/easygraph/datasets/samples/blogcatalog.mat similarity index 100% rename from easygraph/datasets/samples/blogcatalog.mat rename to src/easygraph/datasets/samples/blogcatalog.mat diff --git a/easygraph/functions/__init__.py b/src/easygraph/functions/__init__.py similarity index 100% rename from easygraph/functions/__init__.py rename to src/easygraph/functions/__init__.py diff --git a/easygraph/functions/centrality/__init__.py b/src/easygraph/functions/centrality/__init__.py similarity index 100% rename from easygraph/functions/centrality/__init__.py rename to src/easygraph/functions/centrality/__init__.py diff --git a/easygraph/functions/centrality/betweenness.py b/src/easygraph/functions/centrality/betweenness.py similarity index 100% rename from easygraph/functions/centrality/betweenness.py rename to src/easygraph/functions/centrality/betweenness.py diff --git a/easygraph/functions/centrality/clossness.py b/src/easygraph/functions/centrality/clossness.py similarity index 100% rename from easygraph/functions/centrality/clossness.py rename to src/easygraph/functions/centrality/clossness.py diff --git a/easygraph/functions/centrality/degree.py b/src/easygraph/functions/centrality/degree.py similarity index 100% rename from easygraph/functions/centrality/degree.py rename to src/easygraph/functions/centrality/degree.py diff --git a/easygraph/functions/centrality/flowbetweenness.py b/src/easygraph/functions/centrality/flowbetweenness.py similarity index 100% rename from easygraph/functions/centrality/flowbetweenness.py rename to src/easygraph/functions/centrality/flowbetweenness.py diff --git a/easygraph/functions/centrality/tests/__init__.py b/src/easygraph/functions/centrality/tests/__init__.py similarity index 100% rename from easygraph/functions/centrality/tests/__init__.py rename to src/easygraph/functions/centrality/tests/__init__.py diff --git a/easygraph/functions/centrality/tests/test_betweenness.py b/src/easygraph/functions/centrality/tests/test_betweenness.py similarity index 100% rename from easygraph/functions/centrality/tests/test_betweenness.py rename to src/easygraph/functions/centrality/tests/test_betweenness.py diff --git a/easygraph/functions/centrality/tests/test_clossness.py b/src/easygraph/functions/centrality/tests/test_clossness.py similarity index 100% rename from easygraph/functions/centrality/tests/test_clossness.py rename to src/easygraph/functions/centrality/tests/test_clossness.py diff --git a/easygraph/functions/centrality/tests/test_flowbetweenness.py b/src/easygraph/functions/centrality/tests/test_flowbetweenness.py similarity index 100% rename from easygraph/functions/centrality/tests/test_flowbetweenness.py rename to src/easygraph/functions/centrality/tests/test_flowbetweenness.py diff --git a/easygraph/functions/community/LPA.py b/src/easygraph/functions/community/LPA.py similarity index 100% rename from easygraph/functions/community/LPA.py rename to src/easygraph/functions/community/LPA.py diff --git a/easygraph/functions/community/__init__.py b/src/easygraph/functions/community/__init__.py similarity index 100% rename from easygraph/functions/community/__init__.py rename to src/easygraph/functions/community/__init__.py diff --git a/easygraph/functions/community/modularity.py b/src/easygraph/functions/community/modularity.py similarity index 100% rename from easygraph/functions/community/modularity.py rename to src/easygraph/functions/community/modularity.py diff --git a/easygraph/functions/community/modularity_max_detection.py b/src/easygraph/functions/community/modularity_max_detection.py similarity index 100% rename from easygraph/functions/community/modularity_max_detection.py rename to src/easygraph/functions/community/modularity_max_detection.py diff --git a/easygraph/functions/community/motif.py b/src/easygraph/functions/community/motif.py similarity index 100% rename from easygraph/functions/community/motif.py rename to src/easygraph/functions/community/motif.py diff --git a/easygraph/functions/community/tests/__init__.py b/src/easygraph/functions/community/tests/__init__.py similarity index 100% rename from easygraph/functions/community/tests/__init__.py rename to src/easygraph/functions/community/tests/__init__.py diff --git a/easygraph/functions/community/tests/test_ modularity_max_detection.py b/src/easygraph/functions/community/tests/test_ modularity_max_detection.py similarity index 100% rename from easygraph/functions/community/tests/test_ modularity_max_detection.py rename to src/easygraph/functions/community/tests/test_ modularity_max_detection.py diff --git a/easygraph/functions/community/tests/test_LPA.py b/src/easygraph/functions/community/tests/test_LPA.py similarity index 100% rename from easygraph/functions/community/tests/test_LPA.py rename to src/easygraph/functions/community/tests/test_LPA.py diff --git a/easygraph/functions/community/tests/test_modularity.py b/src/easygraph/functions/community/tests/test_modularity.py similarity index 100% rename from easygraph/functions/community/tests/test_modularity.py rename to src/easygraph/functions/community/tests/test_modularity.py diff --git a/easygraph/functions/community/tests/test_motif.py b/src/easygraph/functions/community/tests/test_motif.py similarity index 100% rename from easygraph/functions/community/tests/test_motif.py rename to src/easygraph/functions/community/tests/test_motif.py diff --git a/easygraph/functions/components/__init__.py b/src/easygraph/functions/components/__init__.py similarity index 100% rename from easygraph/functions/components/__init__.py rename to src/easygraph/functions/components/__init__.py diff --git a/easygraph/functions/components/biconnected.py b/src/easygraph/functions/components/biconnected.py similarity index 100% rename from easygraph/functions/components/biconnected.py rename to src/easygraph/functions/components/biconnected.py diff --git a/easygraph/functions/components/connected.py b/src/easygraph/functions/components/connected.py similarity index 100% rename from easygraph/functions/components/connected.py rename to src/easygraph/functions/components/connected.py diff --git a/easygraph/functions/components/ego_betweenness.py b/src/easygraph/functions/components/ego_betweenness.py similarity index 100% rename from easygraph/functions/components/ego_betweenness.py rename to src/easygraph/functions/components/ego_betweenness.py diff --git a/easygraph/functions/components/tests/__init__.py b/src/easygraph/functions/components/tests/__init__.py similarity index 100% rename from easygraph/functions/components/tests/__init__.py rename to src/easygraph/functions/components/tests/__init__.py diff --git a/easygraph/functions/components/tests/test_biconnected.py b/src/easygraph/functions/components/tests/test_biconnected.py similarity index 100% rename from easygraph/functions/components/tests/test_biconnected.py rename to src/easygraph/functions/components/tests/test_biconnected.py diff --git a/easygraph/functions/drawing/__init__.py b/src/easygraph/functions/drawing/__init__.py similarity index 100% rename from easygraph/functions/drawing/__init__.py rename to src/easygraph/functions/drawing/__init__.py diff --git a/easygraph/functions/drawing/drawing.py b/src/easygraph/functions/drawing/drawing.py similarity index 100% rename from easygraph/functions/drawing/drawing.py rename to src/easygraph/functions/drawing/drawing.py diff --git a/easygraph/functions/drawing/plot.py b/src/easygraph/functions/drawing/plot.py similarity index 100% rename from easygraph/functions/drawing/plot.py rename to src/easygraph/functions/drawing/plot.py diff --git a/easygraph/functions/drawing/positioning.py b/src/easygraph/functions/drawing/positioning.py similarity index 100% rename from easygraph/functions/drawing/positioning.py rename to src/easygraph/functions/drawing/positioning.py diff --git a/easygraph/functions/drawing/tests/__init__.py b/src/easygraph/functions/drawing/tests/__init__.py similarity index 100% rename from easygraph/functions/drawing/tests/__init__.py rename to src/easygraph/functions/drawing/tests/__init__.py diff --git a/easygraph/functions/drawing/tests/test_positioning.py b/src/easygraph/functions/drawing/tests/test_positioning.py similarity index 100% rename from easygraph/functions/drawing/tests/test_positioning.py rename to src/easygraph/functions/drawing/tests/test_positioning.py diff --git a/easygraph/functions/graph_embedding/NOBE.py b/src/easygraph/functions/graph_embedding/NOBE.py similarity index 100% rename from easygraph/functions/graph_embedding/NOBE.py rename to src/easygraph/functions/graph_embedding/NOBE.py diff --git a/easygraph/functions/graph_embedding/__init__.py b/src/easygraph/functions/graph_embedding/__init__.py similarity index 100% rename from easygraph/functions/graph_embedding/__init__.py rename to src/easygraph/functions/graph_embedding/__init__.py diff --git a/easygraph/functions/graph_embedding/deepwalk.py b/src/easygraph/functions/graph_embedding/deepwalk.py similarity index 100% rename from easygraph/functions/graph_embedding/deepwalk.py rename to src/easygraph/functions/graph_embedding/deepwalk.py diff --git a/easygraph/functions/graph_embedding/line.py b/src/easygraph/functions/graph_embedding/line.py similarity index 100% rename from easygraph/functions/graph_embedding/line.py rename to src/easygraph/functions/graph_embedding/line.py diff --git a/easygraph/functions/graph_embedding/node2vec.py b/src/easygraph/functions/graph_embedding/node2vec.py similarity index 100% rename from easygraph/functions/graph_embedding/node2vec.py rename to src/easygraph/functions/graph_embedding/node2vec.py diff --git a/easygraph/functions/graph_embedding/sdne.py b/src/easygraph/functions/graph_embedding/sdne.py similarity index 100% rename from easygraph/functions/graph_embedding/sdne.py rename to src/easygraph/functions/graph_embedding/sdne.py diff --git a/easygraph/functions/graph_generator/RandomNetwork.py b/src/easygraph/functions/graph_generator/RandomNetwork.py similarity index 100% rename from easygraph/functions/graph_generator/RandomNetwork.py rename to src/easygraph/functions/graph_generator/RandomNetwork.py diff --git a/easygraph/functions/graph_generator/__init__.py b/src/easygraph/functions/graph_generator/__init__.py similarity index 100% rename from easygraph/functions/graph_generator/__init__.py rename to src/easygraph/functions/graph_generator/__init__.py diff --git a/easygraph/functions/graph_generator/classic.py b/src/easygraph/functions/graph_generator/classic.py similarity index 100% rename from easygraph/functions/graph_generator/classic.py rename to src/easygraph/functions/graph_generator/classic.py diff --git a/easygraph/functions/not_sorted/__init__.py b/src/easygraph/functions/not_sorted/__init__.py similarity index 100% rename from easygraph/functions/not_sorted/__init__.py rename to src/easygraph/functions/not_sorted/__init__.py diff --git a/easygraph/functions/not_sorted/bridges.py b/src/easygraph/functions/not_sorted/bridges.py similarity index 100% rename from easygraph/functions/not_sorted/bridges.py rename to src/easygraph/functions/not_sorted/bridges.py diff --git a/easygraph/functions/not_sorted/cluster.py b/src/easygraph/functions/not_sorted/cluster.py similarity index 100% rename from easygraph/functions/not_sorted/cluster.py rename to src/easygraph/functions/not_sorted/cluster.py diff --git a/easygraph/functions/not_sorted/laplacian.py b/src/easygraph/functions/not_sorted/laplacian.py similarity index 100% rename from easygraph/functions/not_sorted/laplacian.py rename to src/easygraph/functions/not_sorted/laplacian.py diff --git a/easygraph/functions/not_sorted/mst.py b/src/easygraph/functions/not_sorted/mst.py similarity index 100% rename from easygraph/functions/not_sorted/mst.py rename to src/easygraph/functions/not_sorted/mst.py diff --git a/easygraph/functions/not_sorted/pagerank.py b/src/easygraph/functions/not_sorted/pagerank.py similarity index 100% rename from easygraph/functions/not_sorted/pagerank.py rename to src/easygraph/functions/not_sorted/pagerank.py diff --git a/easygraph/functions/not_sorted/tests/__init__.py b/src/easygraph/functions/not_sorted/tests/__init__.py similarity index 100% rename from easygraph/functions/not_sorted/tests/__init__.py rename to src/easygraph/functions/not_sorted/tests/__init__.py diff --git a/easygraph/functions/not_sorted/tests/test_cluster.py b/src/easygraph/functions/not_sorted/tests/test_cluster.py similarity index 100% rename from easygraph/functions/not_sorted/tests/test_cluster.py rename to src/easygraph/functions/not_sorted/tests/test_cluster.py diff --git a/easygraph/functions/not_sorted/tests/test_mst.py b/src/easygraph/functions/not_sorted/tests/test_mst.py similarity index 100% rename from easygraph/functions/not_sorted/tests/test_mst.py rename to src/easygraph/functions/not_sorted/tests/test_mst.py diff --git a/easygraph/functions/not_sorted/tests/test_pagerank.py b/src/easygraph/functions/not_sorted/tests/test_pagerank.py similarity index 100% rename from easygraph/functions/not_sorted/tests/test_pagerank.py rename to src/easygraph/functions/not_sorted/tests/test_pagerank.py diff --git a/easygraph/functions/path/__init__.py b/src/easygraph/functions/path/__init__.py similarity index 95% rename from easygraph/functions/path/__init__.py rename to src/easygraph/functions/path/__init__.py index a09c6127..67d731a3 100644 --- a/easygraph/functions/path/__init__.py +++ b/src/easygraph/functions/path/__init__.py @@ -1 +1 @@ -from .path import * +from .path import * diff --git a/easygraph/functions/path/path.py b/src/easygraph/functions/path/path.py similarity index 100% rename from easygraph/functions/path/path.py rename to src/easygraph/functions/path/path.py diff --git a/easygraph/functions/structural_holes/AP_Greedy.py b/src/easygraph/functions/structural_holes/AP_Greedy.py similarity index 100% rename from easygraph/functions/structural_holes/AP_Greedy.py rename to src/easygraph/functions/structural_holes/AP_Greedy.py diff --git a/easygraph/functions/structural_holes/HAM.py b/src/easygraph/functions/structural_holes/HAM.py similarity index 100% rename from easygraph/functions/structural_holes/HAM.py rename to src/easygraph/functions/structural_holes/HAM.py diff --git a/easygraph/functions/structural_holes/HIS.py b/src/easygraph/functions/structural_holes/HIS.py similarity index 100% rename from easygraph/functions/structural_holes/HIS.py rename to src/easygraph/functions/structural_holes/HIS.py diff --git a/easygraph/functions/structural_holes/ICC.py b/src/easygraph/functions/structural_holes/ICC.py similarity index 100% rename from easygraph/functions/structural_holes/ICC.py rename to src/easygraph/functions/structural_holes/ICC.py diff --git a/easygraph/functions/structural_holes/MaxD.py b/src/easygraph/functions/structural_holes/MaxD.py similarity index 100% rename from easygraph/functions/structural_holes/MaxD.py rename to src/easygraph/functions/structural_holes/MaxD.py diff --git a/easygraph/functions/structural_holes/NOBE.py b/src/easygraph/functions/structural_holes/NOBE.py similarity index 100% rename from easygraph/functions/structural_holes/NOBE.py rename to src/easygraph/functions/structural_holes/NOBE.py diff --git a/easygraph/functions/structural_holes/SHII_metric.py b/src/easygraph/functions/structural_holes/SHII_metric.py similarity index 100% rename from easygraph/functions/structural_holes/SHII_metric.py rename to src/easygraph/functions/structural_holes/SHII_metric.py diff --git a/easygraph/functions/structural_holes/__init__.py b/src/easygraph/functions/structural_holes/__init__.py similarity index 100% rename from easygraph/functions/structural_holes/__init__.py rename to src/easygraph/functions/structural_holes/__init__.py diff --git a/easygraph/functions/structural_holes/evaluation.py b/src/easygraph/functions/structural_holes/evaluation.py similarity index 100% rename from easygraph/functions/structural_holes/evaluation.py rename to src/easygraph/functions/structural_holes/evaluation.py diff --git a/easygraph/functions/structural_holes/maxBlock.py b/src/easygraph/functions/structural_holes/maxBlock.py similarity index 100% rename from easygraph/functions/structural_holes/maxBlock.py rename to src/easygraph/functions/structural_holes/maxBlock.py diff --git a/easygraph/functions/structural_holes/metrics.py b/src/easygraph/functions/structural_holes/metrics.py similarity index 100% rename from easygraph/functions/structural_holes/metrics.py rename to src/easygraph/functions/structural_holes/metrics.py diff --git a/easygraph/functions/structural_holes/strong_connected_component.py b/src/easygraph/functions/structural_holes/strong_connected_component.py similarity index 100% rename from easygraph/functions/structural_holes/strong_connected_component.py rename to src/easygraph/functions/structural_holes/strong_connected_component.py diff --git a/easygraph/functions/structural_holes/tests/__init__.py b/src/easygraph/functions/structural_holes/tests/__init__.py similarity index 100% rename from easygraph/functions/structural_holes/tests/__init__.py rename to src/easygraph/functions/structural_holes/tests/__init__.py diff --git a/easygraph/functions/structural_holes/tests/test_AP_Greedy.py b/src/easygraph/functions/structural_holes/tests/test_AP_Greedy.py similarity index 100% rename from easygraph/functions/structural_holes/tests/test_AP_Greedy.py rename to src/easygraph/functions/structural_holes/tests/test_AP_Greedy.py diff --git a/easygraph/functions/structural_holes/tests/test_HAM.py b/src/easygraph/functions/structural_holes/tests/test_HAM.py similarity index 100% rename from easygraph/functions/structural_holes/tests/test_HAM.py rename to src/easygraph/functions/structural_holes/tests/test_HAM.py diff --git a/easygraph/functions/structural_holes/tests/test_HIS.py b/src/easygraph/functions/structural_holes/tests/test_HIS.py similarity index 100% rename from easygraph/functions/structural_holes/tests/test_HIS.py rename to src/easygraph/functions/structural_holes/tests/test_HIS.py diff --git a/easygraph/functions/structural_holes/tests/test_ICC.py b/src/easygraph/functions/structural_holes/tests/test_ICC.py similarity index 100% rename from easygraph/functions/structural_holes/tests/test_ICC.py rename to src/easygraph/functions/structural_holes/tests/test_ICC.py diff --git a/easygraph/functions/structural_holes/tests/test_NOBE.py b/src/easygraph/functions/structural_holes/tests/test_NOBE.py similarity index 100% rename from easygraph/functions/structural_holes/tests/test_NOBE.py rename to src/easygraph/functions/structural_holes/tests/test_NOBE.py diff --git a/easygraph/functions/structural_holes/tests/test_evaluation.py b/src/easygraph/functions/structural_holes/tests/test_evaluation.py similarity index 100% rename from easygraph/functions/structural_holes/tests/test_evaluation.py rename to src/easygraph/functions/structural_holes/tests/test_evaluation.py diff --git a/easygraph/functions/structural_holes/tests/test_strong_connected_component.py b/src/easygraph/functions/structural_holes/tests/test_strong_connected_component.py similarity index 100% rename from easygraph/functions/structural_holes/tests/test_strong_connected_component.py rename to src/easygraph/functions/structural_holes/tests/test_strong_connected_component.py diff --git a/easygraph/functions/structural_holes/tests/test_weakTie.py b/src/easygraph/functions/structural_holes/tests/test_weakTie.py similarity index 100% rename from easygraph/functions/structural_holes/tests/test_weakTie.py rename to src/easygraph/functions/structural_holes/tests/test_weakTie.py diff --git a/easygraph/functions/structural_holes/weakTie.py b/src/easygraph/functions/structural_holes/weakTie.py similarity index 100% rename from easygraph/functions/structural_holes/weakTie.py rename to src/easygraph/functions/structural_holes/weakTie.py diff --git a/easygraph/readwrite/__init__.py b/src/easygraph/readwrite/__init__.py similarity index 100% rename from easygraph/readwrite/__init__.py rename to src/easygraph/readwrite/__init__.py diff --git a/easygraph/readwrite/edgelist.py b/src/easygraph/readwrite/edgelist.py similarity index 100% rename from easygraph/readwrite/edgelist.py rename to src/easygraph/readwrite/edgelist.py diff --git a/easygraph/readwrite/gexf.py b/src/easygraph/readwrite/gexf.py similarity index 100% rename from easygraph/readwrite/gexf.py rename to src/easygraph/readwrite/gexf.py diff --git a/easygraph/readwrite/gml.py b/src/easygraph/readwrite/gml.py similarity index 100% rename from easygraph/readwrite/gml.py rename to src/easygraph/readwrite/gml.py diff --git a/easygraph/readwrite/graphml.py b/src/easygraph/readwrite/graphml.py similarity index 100% rename from easygraph/readwrite/graphml.py rename to src/easygraph/readwrite/graphml.py diff --git a/easygraph/readwrite/graphviz.py b/src/easygraph/readwrite/graphviz.py similarity index 100% rename from easygraph/readwrite/graphviz.py rename to src/easygraph/readwrite/graphviz.py diff --git a/easygraph/readwrite/pajek.py b/src/easygraph/readwrite/pajek.py similarity index 100% rename from easygraph/readwrite/pajek.py rename to src/easygraph/readwrite/pajek.py diff --git a/easygraph/readwrite/pickle.py b/src/easygraph/readwrite/pickle.py similarity index 100% rename from easygraph/readwrite/pickle.py rename to src/easygraph/readwrite/pickle.py diff --git a/easygraph/readwrite/tests/__init__.py b/src/easygraph/readwrite/tests/__init__.py similarity index 100% rename from easygraph/readwrite/tests/__init__.py rename to src/easygraph/readwrite/tests/__init__.py diff --git a/easygraph/readwrite/tests/test_edgelist.py b/src/easygraph/readwrite/tests/test_edgelist.py similarity index 100% rename from easygraph/readwrite/tests/test_edgelist.py rename to src/easygraph/readwrite/tests/test_edgelist.py diff --git a/easygraph/readwrite/tests/test_gexf.py b/src/easygraph/readwrite/tests/test_gexf.py similarity index 100% rename from easygraph/readwrite/tests/test_gexf.py rename to src/easygraph/readwrite/tests/test_gexf.py diff --git a/easygraph/readwrite/tests/test_gml.py b/src/easygraph/readwrite/tests/test_gml.py similarity index 100% rename from easygraph/readwrite/tests/test_gml.py rename to src/easygraph/readwrite/tests/test_gml.py diff --git a/easygraph/readwrite/tests/test_graphml.py b/src/easygraph/readwrite/tests/test_graphml.py similarity index 100% rename from easygraph/readwrite/tests/test_graphml.py rename to src/easygraph/readwrite/tests/test_graphml.py diff --git a/easygraph/readwrite/tests/test_graphviz.py b/src/easygraph/readwrite/tests/test_graphviz.py similarity index 100% rename from easygraph/readwrite/tests/test_graphviz.py rename to src/easygraph/readwrite/tests/test_graphviz.py diff --git a/easygraph/readwrite/tests/test_pajek.py b/src/easygraph/readwrite/tests/test_pajek.py similarity index 100% rename from easygraph/readwrite/tests/test_pajek.py rename to src/easygraph/readwrite/tests/test_pajek.py diff --git a/easygraph/readwrite/tests/test_pickle.py b/src/easygraph/readwrite/tests/test_pickle.py similarity index 100% rename from easygraph/readwrite/tests/test_pickle.py rename to src/easygraph/readwrite/tests/test_pickle.py diff --git a/easygraph/readwrite/tests/test_ucinet.py b/src/easygraph/readwrite/tests/test_ucinet.py similarity index 100% rename from easygraph/readwrite/tests/test_ucinet.py rename to src/easygraph/readwrite/tests/test_ucinet.py diff --git a/easygraph/readwrite/ucinet.py b/src/easygraph/readwrite/ucinet.py similarity index 100% rename from easygraph/readwrite/ucinet.py rename to src/easygraph/readwrite/ucinet.py diff --git a/easygraph/tests/__init__.py b/src/easygraph/tests/__init__.py similarity index 100% rename from easygraph/tests/__init__.py rename to src/easygraph/tests/__init__.py diff --git a/easygraph/tests/test_convert.py b/src/easygraph/tests/test_convert.py similarity index 100% rename from easygraph/tests/test_convert.py rename to src/easygraph/tests/test_convert.py diff --git a/easygraph/utils/__init__.py b/src/easygraph/utils/__init__.py similarity index 100% rename from easygraph/utils/__init__.py rename to src/easygraph/utils/__init__.py diff --git a/easygraph/utils/alias.py b/src/easygraph/utils/alias.py similarity index 100% rename from easygraph/utils/alias.py rename to src/easygraph/utils/alias.py diff --git a/easygraph/utils/convert_class.py b/src/easygraph/utils/convert_class.py similarity index 100% rename from easygraph/utils/convert_class.py rename to src/easygraph/utils/convert_class.py diff --git a/easygraph/utils/convert_to_matrix.py b/src/easygraph/utils/convert_to_matrix.py similarity index 100% rename from easygraph/utils/convert_to_matrix.py rename to src/easygraph/utils/convert_to_matrix.py diff --git a/easygraph/utils/decorators.py b/src/easygraph/utils/decorators.py similarity index 100% rename from easygraph/utils/decorators.py rename to src/easygraph/utils/decorators.py diff --git a/easygraph/utils/exception.py b/src/easygraph/utils/exception.py similarity index 100% rename from easygraph/utils/exception.py rename to src/easygraph/utils/exception.py diff --git a/easygraph/utils/index_of_node.py b/src/easygraph/utils/index_of_node.py similarity index 100% rename from easygraph/utils/index_of_node.py rename to src/easygraph/utils/index_of_node.py diff --git a/easygraph/utils/mapped_queue.py b/src/easygraph/utils/mapped_queue.py similarity index 100% rename from easygraph/utils/mapped_queue.py rename to src/easygraph/utils/mapped_queue.py diff --git a/easygraph/utils/misc.py b/src/easygraph/utils/misc.py similarity index 100% rename from easygraph/utils/misc.py rename to src/easygraph/utils/misc.py diff --git a/easygraph/utils/relabel.py b/src/easygraph/utils/relabel.py similarity index 100% rename from easygraph/utils/relabel.py rename to src/easygraph/utils/relabel.py diff --git a/easygraph/utils/tests/__init__.py b/src/easygraph/utils/tests/__init__.py similarity index 100% rename from easygraph/utils/tests/__init__.py rename to src/easygraph/utils/tests/__init__.py diff --git a/easygraph/utils/tests/test_convert_to_matrix.py b/src/easygraph/utils/tests/test_convert_to_matrix.py similarity index 100% rename from easygraph/utils/tests/test_convert_to_matrix.py rename to src/easygraph/utils/tests/test_convert_to_matrix.py diff --git a/easygraph/utils/tests/test_mapped_queue.py b/src/easygraph/utils/tests/test_mapped_queue.py similarity index 100% rename from easygraph/utils/tests/test_mapped_queue.py rename to src/easygraph/utils/tests/test_mapped_queue.py diff --git a/easygraph/utils/type_change.py b/src/easygraph/utils/type_change.py similarity index 100% rename from easygraph/utils/type_change.py rename to src/easygraph/utils/type_change.py diff --git a/tox-conda-test.ini b/tox-conda-test.ini deleted file mode 100644 index 8fb355f4..00000000 --- a/tox-conda-test.ini +++ /dev/null @@ -1,9 +0,0 @@ -[tox] -requires = tox-conda -envlist = py36, py37, py38, py39 - -skipsdist = true - -[testenv] -commands = - python --version diff --git a/tox-conda.ini b/tox-conda.ini deleted file mode 100644 index 36627e72..00000000 --- a/tox-conda.ini +++ /dev/null @@ -1,14 +0,0 @@ -# content of: tox.ini , put in same dir as setup.py -[tox] -requires = tox-conda -envlist = py36, py37, py38, py39 - -[testenv] -# install pytest in the virtualenv where commands will be executed -deps = - pytest - . - -commands = - # NOTE: you can run any command line tool here - not just tests - pytest diff --git a/tox-test.ini b/tox-test.ini deleted file mode 100644 index 5f5ebe00..00000000 --- a/tox-test.ini +++ /dev/null @@ -1,8 +0,0 @@ -[tox] -envlist = py36, py37, py38, py39 - -skipsdist = true - -[testenv] -commands = - python --version diff --git a/tox.ini b/tox.ini index 2ae04401..81aad477 100644 --- a/tox.ini +++ b/tox.ini @@ -1,19 +1,35 @@ -# content of: tox.ini , put in same dir as setup.py [tox] -; envlist = py36, py37, py38, py39 -; py36 is really old https://endoflife.date/python -; and I can't install it on my machine without using pyenv. +# Define all Python versions you want to test against envlist = py36, py37, py38, py39, py310 +# Use tox-uv to make environment creation extremely fast +# This replaces the need for tox-conda +requires = tox-uv +provision = .tox-uv + +# By default, build the package once and use it for all environments +skipsdist = false + [testenv] -# install pytest in the virtualenv where commands will be executed +# Define the dependencies needed for testing. +# `uv` will install these from your lock file if it exists. deps = - ; Pillow - ; kiwisolver - ; genism lxml pytest - ; . + # The "." is crucial: it tells tox to install your + # Easy-Graph project (using setup.py) into the test env + . + +# Define the command to run the tests +# {posargs} allows you to pass extra arguments, e.g., tox -e py310 -- -k "test_something" commands = - # NOTE: you can run any command line tool here - not just tests - pytest + pytest {posargs} + +# This section is for your "version check" use case +[testenv:pyver] +description = "Simply check the Python version, do not install the package" +# Don't build or install the package +skipsdist = true +# Just run the version command +commands = + python --version From 35f8a2386d782b5d4bebc54905f01df3eab71349 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 12:55:21 +0800 Subject: [PATCH 04/17] feat(env): Add `.envrc` for automated virtual environment management Introduced a `.envrc` file to automate virtual environment setup using `direnv`. This inclusion ensures that the virtual environment is automatically initialized on directory entry and the necessary environment is activated. Signed-off-by: acture --- .envrc | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 .envrc diff --git a/.envrc b/.envrc new file mode 100644 index 00000000..eff7387f --- /dev/null +++ b/.envrc @@ -0,0 +1,2 @@ +[[ -d '.venv' ]] || uv venv +source .venv/bin/activate From 1a2f23f6695e13de31e1e0b19e4fd5bde1cc926f Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 12:58:18 +0800 Subject: [PATCH 05/17] refactor(codebase): Remove unused imports and improve variable naming for clarity This commit removes redundant imports, such as `deepcopy` and others from several modules, to reduce unnecessary dependencies. Additionally, improved the variable naming for better readability (e.g., `l` renamed to `length`). The changes optimize the codebase and enhance code clarity while preserving current functionality. Signed-off-by: acture --- src/easygraph/classes/directed_graph.py | 1 - src/easygraph/classes/directed_multigraph.py | 2 - src/easygraph/classes/graph.py | 2 - src/easygraph/classes/multigraph.py | 2 - src/easygraph/readwrite/gexf.py | 2 +- src/easygraph/readwrite/gml.py | 1 - src/easygraph/utils/alias.py | 6 +- src/easygraph/utils/decorators.py | 4 +- src/easygraph/utils/misc.py | 138 +++++++++--------- .../utils/tests/test_convert_to_matrix.py | 1 - 10 files changed, 75 insertions(+), 84 deletions(-) diff --git a/src/easygraph/classes/directed_graph.py b/src/easygraph/classes/directed_graph.py index 9515972b..98f97178 100644 --- a/src/easygraph/classes/directed_graph.py +++ b/src/easygraph/classes/directed_graph.py @@ -1,4 +1,3 @@ -from copy import deepcopy from typing import Dict from typing import List diff --git a/src/easygraph/classes/directed_multigraph.py b/src/easygraph/classes/directed_multigraph.py index c0cfeadd..9ca78519 100644 --- a/src/easygraph/classes/directed_multigraph.py +++ b/src/easygraph/classes/directed_multigraph.py @@ -1,6 +1,4 @@ from copy import deepcopy -from typing import Dict -from typing import List import easygraph as eg import easygraph.convert as convert diff --git a/src/easygraph/classes/graph.py b/src/easygraph/classes/graph.py index 73687985..b5ac5166 100644 --- a/src/easygraph/classes/graph.py +++ b/src/easygraph/classes/graph.py @@ -1,8 +1,6 @@ -from copy import deepcopy from typing import Dict from typing import List -import easygraph as eg import easygraph.convert as convert from easygraph.utils.exception import EasyGraphError diff --git a/src/easygraph/classes/multigraph.py b/src/easygraph/classes/multigraph.py index fbe6b55b..a2522ea9 100644 --- a/src/easygraph/classes/multigraph.py +++ b/src/easygraph/classes/multigraph.py @@ -1,7 +1,5 @@ """Base class for MultiGraph.""" from copy import deepcopy -from typing import Dict -from typing import List import easygraph as eg import easygraph.convert as convert diff --git a/src/easygraph/readwrite/gexf.py b/src/easygraph/readwrite/gexf.py index aea2edb6..f75c7cb6 100644 --- a/src/easygraph/readwrite/gexf.py +++ b/src/easygraph/readwrite/gexf.py @@ -252,7 +252,7 @@ def __init__( # Make meta element a non-graph element # Also add lastmodifieddate as attribute, not tag meta_element = Element("meta") - subelement_text = f"EasyGraph" + subelement_text = "EasyGraph" SubElement(meta_element, "creator").text = subelement_text meta_element.set("lastmodifieddate", time.strftime("%Y-%m-%d")) self.xml.append(meta_element) diff --git a/src/easygraph/readwrite/gml.py b/src/easygraph/readwrite/gml.py index d9815195..df44b037 100644 --- a/src/easygraph/readwrite/gml.py +++ b/src/easygraph/readwrite/gml.py @@ -39,7 +39,6 @@ from io import StringIO from typing import Any from typing import NamedTuple -from unicodedata import category import easygraph as eg diff --git a/src/easygraph/utils/alias.py b/src/easygraph/utils/alias.py index 4fe2651d..43f91b6e 100644 --- a/src/easygraph/utils/alias.py +++ b/src/easygraph/utils/alias.py @@ -16,10 +16,10 @@ def create_alias_table(area_ratio): """ import numpy as np - l = len(area_ratio) - accept, alias = [0] * l, [0] * l + length = len(area_ratio) + accept, alias = [0] * length, [0] * length small, large = [], [] - area_ratio_ = np.array(area_ratio) * l + area_ratio_ = np.array(area_ratio) * length for i, prob in enumerate(area_ratio_): if prob < 1.0: small.append(i) diff --git a/src/easygraph/utils/decorators.py b/src/easygraph/utils/decorators.py index 75a04c7e..a685547a 100644 --- a/src/easygraph/utils/decorators.py +++ b/src/easygraph/utils/decorators.py @@ -85,8 +85,8 @@ def sp_np_function(G): ) # 3-way logic: True if "directed" input, False if "undirected" input, else None - dval = ("directed" in graph_types) or not ("undirected" in graph_types) and None - mval = ("multigraph" in graph_types) or not ("graph" in graph_types) and None + dval = ("directed" in graph_types) or "undirected" not in graph_types and None + mval = ("multigraph" in graph_types) or "graph" not in graph_types and None errmsg = f"not implemented for {' '.join(graph_types)} type" def _not_implemented_for(g): diff --git a/src/easygraph/utils/misc.py b/src/easygraph/utils/misc.py index 0108dbbe..61ecac7e 100644 --- a/src/easygraph/utils/misc.py +++ b/src/easygraph/utils/misc.py @@ -6,27 +6,27 @@ def split_len(nodes, step=30000): - ret = [] - length = len(nodes) - for i in range(0, length, step): - ret.append(nodes[i : i + step]) - if len(ret[-1]) * 3 < step: - ret[-2] = ret[-2] + ret[-1] - ret = ret[:-1] - return ret + ret = [] + length = len(nodes) + for i in range(0, length, step): + ret.append(nodes[i : i + step]) + if len(ret[-1]) * 3 < step: + ret[-2] = ret[-2] + ret[-1] + ret = ret[:-1] + return ret def split(nodes, n): - ret = [] - length = len(nodes) # 总长 - step = int(length / n) + 1 # 每份的长度 - for i in range(0, length, step): - ret.append(nodes[i : i + step]) - return ret + ret = [] + length = len(nodes) # 总长 + step = int(length / n) + 1 # 每份的长度 + for i in range(0, length, step): + ret.append(nodes[i : i + step]) + return ret def nodes_equal(nodes1, nodes2): - """Check if nodes are equal. + """Check if nodes are equal. Equality here means equal as Python objects. Node data must match if included. @@ -41,19 +41,19 @@ def nodes_equal(nodes1, nodes2): bool True if nodes are equal, False otherwise. """ - nlist1 = list(nodes1) - nlist2 = list(nodes2) - try: - d1 = dict(nlist1) - d2 = dict(nlist2) - except (ValueError, TypeError): - d1 = dict.fromkeys(nlist1) - d2 = dict.fromkeys(nlist2) - return d1 == d2 + nlist1 = list(nodes1) + nlist2 = list(nodes2) + try: + d1 = dict(nlist1) + d2 = dict(nlist2) + except (ValueError, TypeError): + d1 = dict.fromkeys(nlist1) + d2 = dict.fromkeys(nlist2) + return d1 == d2 def edges_equal(edges1, edges2, need_data=True): - """Check if edges are equal. + """Check if edges are equal. Equality here means equal as Python objects. Edge data must match if included. @@ -71,51 +71,51 @@ def edges_equal(edges1, edges2, need_data=True): bool True if edges are equal, False otherwise. """ - from collections import defaultdict - - d1 = defaultdict(dict) - d2 = defaultdict(dict) - c1 = 0 - for c1, e in enumerate(edges1): - u, v = e[0], e[1] - data = [] - if need_data == True: - data = [e[2:]] - if v in d1[u]: - data = d1[u][v] + data - d1[u][v] = data - d1[v][u] = data - c2 = 0 - for c2, e in enumerate(edges2): - u, v = e[0], e[1] - data = [] - if need_data == True: - data = [e[2:]] - if v in d2[u]: - data = d2[u][v] + data - d2[u][v] = data - d2[v][u] = data - if c1 != c2: - return False - # can check one direction because lengths are the same. - for n, nbrdict in d1.items(): - for nbr, datalist in nbrdict.items(): - if n not in d2: - return False - if nbr not in d2[n]: - return False - d2datalist = d2[n][nbr] - for data in datalist: - if datalist.count(data) != d2datalist.count(data): - return False - return True + from collections import defaultdict + + d1 = defaultdict(dict) + d2 = defaultdict(dict) + c1 = 0 + for c1, e in enumerate(edges1): + u, v = e[0], e[1] + data = [] + if need_data: + data = [e[2:]] + if v in d1[u]: + data = d1[u][v] + data + d1[u][v] = data + d1[v][u] = data + c2 = 0 + for c2, e in enumerate(edges2): + u, v = e[0], e[1] + data = [] + if need_data: + data = [e[2:]] + if v in d2[u]: + data = d2[u][v] + data + d2[u][v] = data + d2[v][u] = data + if c1 != c2: + return False + # can check one direction because lengths are the same. + for n, nbrdict in d1.items(): + for nbr, datalist in nbrdict.items(): + if n not in d2: + return False + if nbr not in d2[n]: + return False + d2datalist = d2[n][nbr] + for data in datalist: + if datalist.count(data) != d2datalist.count(data): + return False + return True # Recipe from the itertools documentation. def pairwise(iterable, cyclic=False): - "s -> (s0, s1), (s1, s2), (s2, s3), ..." - a, b = tee(iterable) - first = next(b, None) - if cyclic is True: - return zip(a, chain(b, (first,))) - return zip(a, b) + "s -> (s0, s1), (s1, s2), (s2, s3), ..." + a, b = tee(iterable) + first = next(b, None) + if cyclic is True: + return zip(a, chain(b, (first,))) + return zip(a, b) diff --git a/src/easygraph/utils/tests/test_convert_to_matrix.py b/src/easygraph/utils/tests/test_convert_to_matrix.py index 5093dfd9..59fc645d 100644 --- a/src/easygraph/utils/tests/test_convert_to_matrix.py +++ b/src/easygraph/utils/tests/test_convert_to_matrix.py @@ -1,4 +1,3 @@ -import sys import unittest import easygraph as eg From 130b41f003832a8b74017487dca2d85bf32dd777 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 13:21:42 +0800 Subject: [PATCH 06/17] refactor(cpp_binding): Replace Boost.Python with pybind11 for bindings Migrated from `Boost.Python` to `pybind11` for Python bindings, removing the dependency on Boost. Updated `CMakeLists.txt` to drop Boost requirements and refactored binding definitions to align with the pybind11 API. This includes updating function signatures and argument handling for consistency with pybind11. This migration simplifies the build process and reduces external dependencies while maintaining existing functionality. Signed-off-by: acture --- CMakeLists.txt | 6 -- src/cpp_easygraph/classes/directed_graph.cpp | 2 +- src/cpp_easygraph/classes/directed_graph.h | 13 ++- src/cpp_easygraph/common/common.h | 6 +- src/cpp_easygraph/cpp_easygraph.cpp | 105 ++++++++++--------- 5 files changed, 63 insertions(+), 69 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 357c4a1d..47610c47 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,15 +1,9 @@ cmake_minimum_required(VERSION 3.15) project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX) -cmake_policy(SET CMP0167 NEW) - set(PYBIND11_FINDPYTHON ON) find_package(pybind11 CONFIG REQUIRED) -find_package(Boost REQUIRED COMPONENTS python3) pybind11_add_module(cpp_easygraph MODULE src/cpp_easygraph/cpp_easygraph.cpp) -target_include_directories(cpp_easygraph PRIVATE ${Boost_INCLUDE_DIRS}) -target_link_libraries(cpp_easygraph PRIVATE ${Boost_LIBRARIES}) - install(TARGETS cpp_easygraph DESTINATION ${SKBUILD_PROJECT_NAME}) diff --git a/src/cpp_easygraph/classes/directed_graph.cpp b/src/cpp_easygraph/classes/directed_graph.cpp index a08312d5..a99bef9a 100644 --- a/src/cpp_easygraph/classes/directed_graph.cpp +++ b/src/cpp_easygraph/classes/directed_graph.cpp @@ -97,4 +97,4 @@ py::object DiGraph_number_of_edges(py::object self, py::object u, py::object v) node_t u_id = py::extract(G.node_to_id[u]); node_t v_id = py::extract(G.node_to_id.get(v, -1)); return py::object(int(v != -1 && G.adj[u_id].count(v_id))); -} \ No newline at end of file +} diff --git a/src/cpp_easygraph/classes/directed_graph.h b/src/cpp_easygraph/classes/directed_graph.h index ea6bb6b4..8fed7ac3 100644 --- a/src/cpp_easygraph/classes/directed_graph.h +++ b/src/cpp_easygraph/classes/directed_graph.h @@ -9,10 +9,9 @@ struct DiGraph: public Graph DiGraph(); }; -py::object DiGraph__init__(py::tuple args, py::dict kwargs); - -py::object DiGraph_out_degree(py::object self, py::object weight); -py::object DiGraph_in_degree(py::object self, py::object weight); -py::object DiGraph_degree(py::object self, py::object weight); -py::object DiGraph_size(py::object self, py::object weight); -py::object DiGraph_number_of_edges(py::object self, py::object u, py::object v); \ No newline at end of file +py::object DiGraph__init__(DiGraph *self, py::args args, py::kwargs kwargs); +py::object DiGraph_out_degree(DiGraph &self, py::object weight); +py::object DiGraph_in_degree(DiGraph &self, py::object weight); +py::object DiGraph_degree(DiGraph &self, py::object weight); +py::object DiGraph_size(DiGraph &self, py::object weight); +py::object DiGraph_number_of_edges(DiGraph &self, py::object u, py::object v); diff --git a/src/cpp_easygraph/common/common.h b/src/cpp_easygraph/common/common.h index 096b7552..c8e8556a 100644 --- a/src/cpp_easygraph/common/common.h +++ b/src/cpp_easygraph/common/common.h @@ -1,7 +1,5 @@ #pragma once -#define BOOST_PYTHON_STATIC_LIB -#include #include #include #include @@ -14,7 +12,7 @@ #include #include -namespace py = boost::python; +namespace py = pybind11; typedef int node_t; typedef float weight_t; @@ -22,4 +20,4 @@ typedef std::map node_attr_dict_factory; //(weight_key, v typedef std::map edge_attr_dict_factory; //(weight_key, value) typedef std::unordered_map node_dict_factory; //(node, node_attr) typedef std::unordered_map adj_attr_dict_factory; //(out_node, (weight_key, value)) -typedef std::unordered_map adj_dict_factory; //(node, edge_attr) \ No newline at end of file +typedef std::unordered_map adj_dict_factory; //(node, edge_attr) diff --git a/src/cpp_easygraph/cpp_easygraph.cpp b/src/cpp_easygraph/cpp_easygraph.cpp index 5c7c1be1..221b8839 100644 --- a/src/cpp_easygraph/cpp_easygraph.cpp +++ b/src/cpp_easygraph/cpp_easygraph.cpp @@ -1,65 +1,68 @@ +#include +#include + #include "classes/__init__.h" #include "functions/__init__.h" -BOOST_PYTHON_MODULE(cpp_easygraph) +PYBIND11_MODULE(cpp_easygraph, m) { - py::class_("Graph", py::no_init) - .def("__init__", py::raw_function(&Graph__init__)) + py::class_(m, "Graph") + .def("__init__", &Graph__init__) .def(py::init<>()) .def("__iter__", &Graph__iter__) .def("__len__", &Graph__len__) - .def("__contains__", &Graph__contains__, (py::arg("node"))) - .def("__getitem__", &Graph__getitem__, (py::arg("node"))) - .def("add_node", py::raw_function(&Graph_add_node)) - .def("add_nodes", &Graph_add_nodes, (py::arg("nodes_for_adding"), py::arg("nodes_attr") = py::list())) - .def("add_nodes_from", py::raw_function(&Graph_add_nodes_from)) - .def("remove_node", &Graph_remove_node, (py::arg("node_to_remove"))) - .def("remove_nodes", &Graph_remove_nodes, (py::arg("nodes_to_remove"))) + .def("__contains__", &Graph__contains__, py::arg("node")) + .def("__getitem__", &Graph__getitem__, py::arg("node")) + .def("add_node", &Graph_add_node) + .def("add_nodes", &Graph_add_nodes, py::arg("nodes_for_adding"), py::arg("nodes_attr") = py::list()) + .def("add_nodes_from", &Graph_add_nodes_from) + .def("remove_node", &Graph_remove_node, py::arg("node_to_remove")) + .def("remove_nodes", &Graph_remove_nodes, py::arg("nodes_to_remove")) .def("number_of_nodes", &Graph_number_of_nodes) - .def("has_node", &Graph_has_node, (py::arg("node"))) - .def("nbunch_iter", &Graph_nbunch_iter, (py::arg("nbunch") = py::object())) - .def("add_edge", py::raw_function(&Graph_add_edge)) - .def("add_edges", &Graph_add_edges, (py::arg("edges_for_adding"), py::arg("edges_attr") = py::list())) - .def("add_edges_from", py::raw_function(&Graph_add_edges_from)) - .def("add_edges_from_file", &Graph_add_edges_from_file, (py::arg("file"), py::arg("weighted") = false)) - .def("add_weighted_edge", &Graph_add_weighted_edge, (py::arg("u_of_edge"), py::arg("v_of_edge"), py::arg("weight"))) - .def("remove_edge", &Graph_remove_edge, (py::arg("u"), py::arg("v"))) - .def("remove_edges", &Graph_remove_edges, (py::arg("edges_to_remove"))) - .def("number_of_edges", &Graph_number_of_edges, (py::arg("u") = py::object(), py::arg("v") = py::object())) - .def("has_edge", &Graph_has_edge, (py::arg("u"), py::arg("y"))) + .def("has_node", &Graph_has_node, py::arg("node")) + .def("nbunch_iter", &Graph_nbunch_iter, py::arg("nbunch") = py::none()) + .def("add_edge", &Graph_add_edge) + .def("add_edges", &Graph_add_edges, py::arg("edges_for_adding"), py::arg("edges_attr") = py::list()) + .def("add_edges_from", &Graph_add_edges_from) + .def("add_edges_from_file", &Graph_add_edges_from_file, py::arg("file"), py::arg("weighted") = false) + .def("add_weighted_edge", &Graph_add_weighted_edge, py::arg("u_of_edge"), py::arg("v_of_edge"), py::arg("weight")) + .def("remove_edge", &Graph_remove_edge, py::arg("u"), py::arg("v")) + .def("remove_edges", &Graph_remove_edges, py::arg("edges_to_remove")) + .def("number_of_edges", &Graph_number_of_edges, py::arg("u") = py::none(), py::arg("v") = py::none()) + .def("has_edge", &Graph_has_edge, py::arg("u"), py::arg("y")) .def("copy", &Graph_copy) - .def("degree", &Graph_degree, (py::arg("weight") = py::object("weight"))) - .def("neighbors", &Graph_neighbors, (py::arg("node"))) - .def("all_neighbors", &Graph_neighbors, (py::arg("node"))) - .def("nodes_subgraph", &Graph_nodes_subgraph, (py::arg("from_nodes"))) - .def("ego_subgraph", &Graph_ego_subgraph, (py::arg("center"))) - .def("size", &Graph_size, (py::arg("weight") = py::object())) + .def("degree", &Graph_degree, py::arg("weight") = "weight") + .def("neighbors", &Graph_neighbors, py::arg("node")) + .def("all_neighbors", &Graph_neighbors, py::arg("node")) + .def("nodes_subgraph", &Graph_nodes_subgraph, py::arg("from_nodes")) + .def("ego_subgraph", &Graph_ego_subgraph, py::arg("center")) + .def("size", &Graph_size, py::arg("weight") = py::none()) .def("is_directed", &Graph_is_directed) .def("is_multigraph", &Graph_is_multigraph) - .add_property("graph", &Graph::get_graph) - .add_property("nodes", &Graph::get_nodes) - .add_property("name", &Graph::get_name) - .add_property("adj", &Graph::get_adj) - .add_property("edges", &Graph::get_edges); - - py::class_>("DiGraph", py::no_init) - .def("__init__", py::raw_function(&DiGraph__init__)) + .def_property_readonly("graph", &Graph::get_graph) + .def_property_readonly("nodes", &Graph::get_nodes) + .def_property_readonly("name", &Graph::get_name) + .def_property_readonly("adj", &Graph::get_adj) + .def_property_readonly("edges", &Graph::get_edges); + + py::class_(m, "DiGraph") + .def("__init__", &DiGraph__init__) .def(py::init<>()) - .def("out_degree", &DiGraph_out_degree, (py::arg("weight") = "weight")) - .def("in_degree", &DiGraph_in_degree, (py::arg("weight") = "weight")) - .def("degree", &DiGraph_degree, (py::arg("weight") = "weight")) - .def("size", &DiGraph_size, (py::arg("weight") = py::object())) - .def("number_of_edges", &DiGraph_number_of_edges, (py::arg("u") = py::object(), py::arg("v") = py::object())); + .def("out_degree", &DiGraph_out_degree, py::arg("weight") = "weight") + .def("in_degree", &DiGraph_in_degree, py::arg("weight") = "weight") + .def("degree", &DiGraph_degree, py::arg("weight") = "weight") + .def("size", &DiGraph_size, py::arg("weight") = py::none()) + .def("number_of_edges", &DiGraph_number_of_edges, py::arg("u") = py::none(), py::arg("v") = py::none()); - py::def("cpp_density",&density,(py::arg("G"))); - py::def("cpp_constraint", &constraint, (py::arg("G"), py::arg("nodes") = py::object(), py::arg("weight") = py::object(), py::arg("n_workers") = py::object())); - py::def("cpp_effective_size", &effective_size, (py::arg("G"), py::arg("nodes") = py::object(), py::arg("weight") = py::object(), py::arg("n_workers") = py::object())); - py::def("cpp_hierarchy", &hierarchy, (py::arg("G"), py::arg("nodes") = py::object(), py::arg("weight") = py::object(), py::arg("n_workers") = py::object())); - py::def("cpp_dijkstra_multisource", &_dijkstra_multisource, (py::arg("G"), py::arg("sources"), py::arg("weight") = "weight", py::arg("target") = py::object())); - py::def("cpp_clustering", &clustering, (py::arg("G"), py::arg("nodes") = py::object(), py::arg("weight") = py::object())); - py::def("cpp_biconnected_dfs_record_edges", &_biconnected_dfs_record_edges, (py::arg("G"), py::arg("need_components") = true)); - py::def("cpp_Floyd", &Floyd, (py::arg("G"))); - py::def("cpp_Prim", &Prim, (py::arg("G"))); - py::def("cpp_Kruskal", &Kruskal, (py::arg("G"))); -} \ No newline at end of file + m.def("cpp_density",&density,py::arg("G")); + m.def("cpp_constraint", &constraint, py::arg("G"), py::arg("nodes") = py::none(), py::arg("weight") = py::none(), py::arg("n_workers") = py::none()); + m.def("cpp_effective_size", &effective_size, py::arg("G"), py::arg("nodes") = py::none(), py::arg("weight") = py::none(), py::arg("n_workers") = py::none()); + m.def("cpp_hierarchy", &hierarchy, py::arg("G"), py::arg("nodes") = py::none(), py::arg("weight") = py::none(), py::arg("n_workers") = py::none()); + m.def("cpp_dijkstra_multisource", &_dijkstra_multisource, py::arg("G"), py::arg("sources"), py::arg("weight") = "weight", py::arg("target") = py::none()); + m.def("cpp_clustering", &clustering, py::arg("G"), py::arg("nodes") = py::none(), py::arg("weight") = py::none()); + m.def("cpp_biconnected_dfs_record_edges", &_biconnected_dfs_record_edges, py::arg("G"), py::arg("need_components") = true); + m.def("cpp_Floyd", &Floyd, py::arg("G")); + m.def("cpp_Prim", &Prim, py::arg("G")); + m.def("cpp_Kruskal", &Kruskal, py::arg("G")); +} From 67e6ab587aae6e8f31a6e55dac22cafef3ee4f7f Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 15:52:40 +0800 Subject: [PATCH 07/17] refactor(project): modernize project structure and update dependencies - Renamed `blogcatalog.mat` for consistency in the dataset samples. - Updated `.gitignore` by adding IDE-specific build directory patterns (e.g., `**/cmake-build-debug`). - Removed support for Python versions <3.10 in `pyproject.toml`. - Adjusted `pyproject.toml` to include `scikit-build`-specific details (`source-dir` added under `[tool.scikit-build.cmake]`). - Simplified package structure by modifying `setuptools.packages.find.where`. These changes streamline project organization, enhance compatibility with modern packaging standards, and refine dependency management. Signed-off-by: acture --- .gitignore | 1 + {src/easygraph => easygraph}/__init__.py | 0 {src/easygraph => easygraph}/classes/__init__.py | 0 .../classes/directed_graph.py | 0 .../classes/directed_multigraph.py | 0 {src/easygraph => easygraph}/classes/graph.py | 0 {src/easygraph => easygraph}/classes/graphviews.py | 0 {src/easygraph => easygraph}/classes/multigraph.py | 0 {src/easygraph => easygraph}/classes/operation.py | 0 .../classes/tests/__init__.py | 0 .../classes/tests/test_multidigraph.py | 0 .../classes/tests/test_multigraph.py | 0 .../classes/tests/test_operation.py | 0 {src/easygraph => easygraph}/convert.py | 0 {src/easygraph => easygraph}/datasets/__init__.py | 0 .../datasets/get_sample_graph.py | 0 .../datasets/samples/blogcatalog.mat | Bin {src/easygraph => easygraph}/functions/__init__.py | 0 .../functions/centrality/__init__.py | 0 .../functions/centrality/betweenness.py | 0 .../functions/centrality/clossness.py | 0 .../functions/centrality/degree.py | 0 .../functions/centrality/flowbetweenness.py | 0 .../functions/centrality/tests/__init__.py | 0 .../functions/centrality/tests/test_betweenness.py | 0 .../functions/centrality/tests/test_clossness.py | 0 .../centrality/tests/test_flowbetweenness.py | 0 .../functions/community/LPA.py | 0 .../functions/community/__init__.py | 0 .../functions/community/modularity.py | 0 .../community/modularity_max_detection.py | 0 .../functions/community/motif.py | 0 .../functions/community/tests/__init__.py | 0 .../tests/test_ modularity_max_detection.py | 0 .../functions/community/tests/test_LPA.py | 0 .../functions/community/tests/test_modularity.py | 0 .../functions/community/tests/test_motif.py | 0 .../functions/components/__init__.py | 0 .../functions/components/biconnected.py | 0 .../functions/components/connected.py | 0 .../functions/components/ego_betweenness.py | 0 .../functions/components/tests/__init__.py | 0 .../functions/components/tests/test_biconnected.py | 0 .../functions/drawing/__init__.py | 0 .../functions/drawing/drawing.py | 0 .../functions/drawing/plot.py | 0 .../functions/drawing/positioning.py | 0 .../functions/drawing/tests/__init__.py | 0 .../functions/drawing/tests/test_positioning.py | 0 .../functions/graph_embedding/NOBE.py | 0 .../functions/graph_embedding/__init__.py | 0 .../functions/graph_embedding/deepwalk.py | 0 .../functions/graph_embedding/line.py | 0 .../functions/graph_embedding/node2vec.py | 0 .../functions/graph_embedding/sdne.py | 0 .../functions/graph_generator/RandomNetwork.py | 0 .../functions/graph_generator/__init__.py | 0 .../functions/graph_generator/classic.py | 0 .../functions/not_sorted/__init__.py | 0 .../functions/not_sorted/bridges.py | 0 .../functions/not_sorted/cluster.py | 0 .../functions/not_sorted/laplacian.py | 0 .../functions/not_sorted/mst.py | 0 .../functions/not_sorted/pagerank.py | 0 .../functions/not_sorted/tests/__init__.py | 0 .../functions/not_sorted/tests/test_cluster.py | 0 .../functions/not_sorted/tests/test_mst.py | 0 .../functions/not_sorted/tests/test_pagerank.py | 0 .../functions/path/__init__.py | 0 .../easygraph => easygraph}/functions/path/path.py | 0 .../functions/structural_holes/AP_Greedy.py | 0 .../functions/structural_holes/HAM.py | 0 .../functions/structural_holes/HIS.py | 0 .../functions/structural_holes/ICC.py | 0 .../functions/structural_holes/MaxD.py | 0 .../functions/structural_holes/NOBE.py | 0 .../functions/structural_holes/SHII_metric.py | 0 .../functions/structural_holes/__init__.py | 0 .../functions/structural_holes/evaluation.py | 0 .../functions/structural_holes/maxBlock.py | 0 .../functions/structural_holes/metrics.py | 0 .../structural_holes/strong_connected_component.py | 0 .../functions/structural_holes/tests/__init__.py | 0 .../structural_holes/tests/test_AP_Greedy.py | 0 .../functions/structural_holes/tests/test_HAM.py | 0 .../functions/structural_holes/tests/test_HIS.py | 0 .../functions/structural_holes/tests/test_ICC.py | 0 .../functions/structural_holes/tests/test_NOBE.py | 0 .../structural_holes/tests/test_evaluation.py | 0 .../tests/test_strong_connected_component.py | 0 .../structural_holes/tests/test_weakTie.py | 0 .../functions/structural_holes/weakTie.py | 0 {src/easygraph => easygraph}/readwrite/__init__.py | 0 {src/easygraph => easygraph}/readwrite/edgelist.py | 0 {src/easygraph => easygraph}/readwrite/gexf.py | 0 {src/easygraph => easygraph}/readwrite/gml.py | 0 {src/easygraph => easygraph}/readwrite/graphml.py | 0 {src/easygraph => easygraph}/readwrite/graphviz.py | 0 {src/easygraph => easygraph}/readwrite/pajek.py | 0 {src/easygraph => easygraph}/readwrite/pickle.py | 0 .../readwrite/tests/__init__.py | 0 .../readwrite/tests/test_edgelist.py | 0 .../readwrite/tests/test_gexf.py | 0 .../readwrite/tests/test_gml.py | 0 .../readwrite/tests/test_graphml.py | 0 .../readwrite/tests/test_graphviz.py | 0 .../readwrite/tests/test_pajek.py | 0 .../readwrite/tests/test_pickle.py | 0 .../readwrite/tests/test_ucinet.py | 0 {src/easygraph => easygraph}/readwrite/ucinet.py | 0 {src/easygraph => easygraph}/tests/__init__.py | 0 {src/easygraph => easygraph}/tests/test_convert.py | 0 {src/easygraph => easygraph}/utils/__init__.py | 0 {src/easygraph => easygraph}/utils/alias.py | 0 .../easygraph => easygraph}/utils/convert_class.py | 0 .../utils/convert_to_matrix.py | 0 {src/easygraph => easygraph}/utils/decorators.py | 0 {src/easygraph => easygraph}/utils/exception.py | 0 .../easygraph => easygraph}/utils/index_of_node.py | 0 {src/easygraph => easygraph}/utils/mapped_queue.py | 0 {src/easygraph => easygraph}/utils/misc.py | 0 {src/easygraph => easygraph}/utils/relabel.py | 0 .../utils/tests/__init__.py | 0 .../utils/tests/test_convert_to_matrix.py | 0 .../utils/tests/test_mapped_queue.py | 0 {src/easygraph => easygraph}/utils/type_change.py | 0 pyproject.toml | 13 ++++--------- 127 files changed, 5 insertions(+), 9 deletions(-) rename {src/easygraph => easygraph}/__init__.py (100%) rename {src/easygraph => easygraph}/classes/__init__.py (100%) rename {src/easygraph => easygraph}/classes/directed_graph.py (100%) rename {src/easygraph => easygraph}/classes/directed_multigraph.py (100%) rename {src/easygraph => easygraph}/classes/graph.py (100%) rename {src/easygraph => easygraph}/classes/graphviews.py (100%) rename {src/easygraph => easygraph}/classes/multigraph.py (100%) rename {src/easygraph => easygraph}/classes/operation.py (100%) rename {src/easygraph => easygraph}/classes/tests/__init__.py (100%) rename {src/easygraph => easygraph}/classes/tests/test_multidigraph.py (100%) rename {src/easygraph => easygraph}/classes/tests/test_multigraph.py (100%) rename {src/easygraph => easygraph}/classes/tests/test_operation.py (100%) rename {src/easygraph => easygraph}/convert.py (100%) rename {src/easygraph => easygraph}/datasets/__init__.py (100%) rename {src/easygraph => easygraph}/datasets/get_sample_graph.py (100%) rename {src/easygraph => easygraph}/datasets/samples/blogcatalog.mat (100%) rename {src/easygraph => easygraph}/functions/__init__.py (100%) rename {src/easygraph => easygraph}/functions/centrality/__init__.py (100%) rename {src/easygraph => easygraph}/functions/centrality/betweenness.py (100%) rename {src/easygraph => easygraph}/functions/centrality/clossness.py (100%) rename {src/easygraph => easygraph}/functions/centrality/degree.py (100%) rename {src/easygraph => easygraph}/functions/centrality/flowbetweenness.py (100%) rename {src/easygraph => easygraph}/functions/centrality/tests/__init__.py (100%) rename {src/easygraph => easygraph}/functions/centrality/tests/test_betweenness.py (100%) rename {src/easygraph => easygraph}/functions/centrality/tests/test_clossness.py (100%) rename {src/easygraph => easygraph}/functions/centrality/tests/test_flowbetweenness.py (100%) rename {src/easygraph => easygraph}/functions/community/LPA.py (100%) rename {src/easygraph => easygraph}/functions/community/__init__.py (100%) rename {src/easygraph => easygraph}/functions/community/modularity.py (100%) rename {src/easygraph => easygraph}/functions/community/modularity_max_detection.py (100%) rename {src/easygraph => easygraph}/functions/community/motif.py (100%) rename {src/easygraph => easygraph}/functions/community/tests/__init__.py (100%) rename {src/easygraph => easygraph}/functions/community/tests/test_ modularity_max_detection.py (100%) rename {src/easygraph => easygraph}/functions/community/tests/test_LPA.py (100%) rename {src/easygraph => easygraph}/functions/community/tests/test_modularity.py (100%) rename {src/easygraph => easygraph}/functions/community/tests/test_motif.py (100%) rename {src/easygraph => easygraph}/functions/components/__init__.py (100%) rename {src/easygraph => easygraph}/functions/components/biconnected.py (100%) rename {src/easygraph => easygraph}/functions/components/connected.py (100%) rename {src/easygraph => easygraph}/functions/components/ego_betweenness.py (100%) rename {src/easygraph => easygraph}/functions/components/tests/__init__.py (100%) rename {src/easygraph => easygraph}/functions/components/tests/test_biconnected.py (100%) rename {src/easygraph => easygraph}/functions/drawing/__init__.py (100%) rename {src/easygraph => easygraph}/functions/drawing/drawing.py (100%) rename {src/easygraph => easygraph}/functions/drawing/plot.py (100%) rename {src/easygraph => easygraph}/functions/drawing/positioning.py (100%) rename {src/easygraph => easygraph}/functions/drawing/tests/__init__.py (100%) rename {src/easygraph => easygraph}/functions/drawing/tests/test_positioning.py (100%) rename {src/easygraph => easygraph}/functions/graph_embedding/NOBE.py (100%) rename {src/easygraph => easygraph}/functions/graph_embedding/__init__.py (100%) rename {src/easygraph => easygraph}/functions/graph_embedding/deepwalk.py (100%) rename {src/easygraph => easygraph}/functions/graph_embedding/line.py (100%) rename {src/easygraph => easygraph}/functions/graph_embedding/node2vec.py (100%) rename {src/easygraph => easygraph}/functions/graph_embedding/sdne.py (100%) rename {src/easygraph => easygraph}/functions/graph_generator/RandomNetwork.py (100%) rename {src/easygraph => easygraph}/functions/graph_generator/__init__.py (100%) rename {src/easygraph => easygraph}/functions/graph_generator/classic.py (100%) rename {src/easygraph => easygraph}/functions/not_sorted/__init__.py (100%) rename {src/easygraph => easygraph}/functions/not_sorted/bridges.py (100%) rename {src/easygraph => easygraph}/functions/not_sorted/cluster.py (100%) rename {src/easygraph => easygraph}/functions/not_sorted/laplacian.py (100%) rename {src/easygraph => easygraph}/functions/not_sorted/mst.py (100%) rename {src/easygraph => easygraph}/functions/not_sorted/pagerank.py (100%) rename {src/easygraph => easygraph}/functions/not_sorted/tests/__init__.py (100%) rename {src/easygraph => easygraph}/functions/not_sorted/tests/test_cluster.py (100%) rename {src/easygraph => easygraph}/functions/not_sorted/tests/test_mst.py (100%) rename {src/easygraph => easygraph}/functions/not_sorted/tests/test_pagerank.py (100%) rename {src/easygraph => easygraph}/functions/path/__init__.py (100%) rename {src/easygraph => easygraph}/functions/path/path.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/AP_Greedy.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/HAM.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/HIS.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/ICC.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/MaxD.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/NOBE.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/SHII_metric.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/__init__.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/evaluation.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/maxBlock.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/metrics.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/strong_connected_component.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/tests/__init__.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/tests/test_AP_Greedy.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/tests/test_HAM.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/tests/test_HIS.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/tests/test_ICC.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/tests/test_NOBE.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/tests/test_evaluation.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/tests/test_strong_connected_component.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/tests/test_weakTie.py (100%) rename {src/easygraph => easygraph}/functions/structural_holes/weakTie.py (100%) rename {src/easygraph => easygraph}/readwrite/__init__.py (100%) rename {src/easygraph => easygraph}/readwrite/edgelist.py (100%) rename {src/easygraph => easygraph}/readwrite/gexf.py (100%) rename {src/easygraph => easygraph}/readwrite/gml.py (100%) rename {src/easygraph => easygraph}/readwrite/graphml.py (100%) rename {src/easygraph => easygraph}/readwrite/graphviz.py (100%) rename {src/easygraph => easygraph}/readwrite/pajek.py (100%) rename {src/easygraph => easygraph}/readwrite/pickle.py (100%) rename {src/easygraph => easygraph}/readwrite/tests/__init__.py (100%) rename {src/easygraph => easygraph}/readwrite/tests/test_edgelist.py (100%) rename {src/easygraph => easygraph}/readwrite/tests/test_gexf.py (100%) rename {src/easygraph => easygraph}/readwrite/tests/test_gml.py (100%) rename {src/easygraph => easygraph}/readwrite/tests/test_graphml.py (100%) rename {src/easygraph => easygraph}/readwrite/tests/test_graphviz.py (100%) rename {src/easygraph => easygraph}/readwrite/tests/test_pajek.py (100%) rename {src/easygraph => easygraph}/readwrite/tests/test_pickle.py (100%) rename {src/easygraph => easygraph}/readwrite/tests/test_ucinet.py (100%) rename {src/easygraph => easygraph}/readwrite/ucinet.py (100%) rename {src/easygraph => easygraph}/tests/__init__.py (100%) rename {src/easygraph => easygraph}/tests/test_convert.py (100%) rename {src/easygraph => easygraph}/utils/__init__.py (100%) rename {src/easygraph => easygraph}/utils/alias.py (100%) rename {src/easygraph => easygraph}/utils/convert_class.py (100%) rename {src/easygraph => easygraph}/utils/convert_to_matrix.py (100%) rename {src/easygraph => easygraph}/utils/decorators.py (100%) rename {src/easygraph => easygraph}/utils/exception.py (100%) rename {src/easygraph => easygraph}/utils/index_of_node.py (100%) rename {src/easygraph => easygraph}/utils/mapped_queue.py (100%) rename {src/easygraph => easygraph}/utils/misc.py (100%) rename {src/easygraph => easygraph}/utils/relabel.py (100%) rename {src/easygraph => easygraph}/utils/tests/__init__.py (100%) rename {src/easygraph => easygraph}/utils/tests/test_convert_to_matrix.py (100%) rename {src/easygraph => easygraph}/utils/tests/test_mapped_queue.py (100%) rename {src/easygraph => easygraph}/utils/type_change.py (100%) diff --git a/.gitignore b/.gitignore index 0c55db21..818accaa 100644 --- a/.gitignore +++ b/.gitignore @@ -171,3 +171,4 @@ x64/ *.vcxproj *.vcxproj.filters *.vcxproj.user +**/cmake-build-debug diff --git a/src/easygraph/__init__.py b/easygraph/__init__.py similarity index 100% rename from src/easygraph/__init__.py rename to easygraph/__init__.py diff --git a/src/easygraph/classes/__init__.py b/easygraph/classes/__init__.py similarity index 100% rename from src/easygraph/classes/__init__.py rename to easygraph/classes/__init__.py diff --git a/src/easygraph/classes/directed_graph.py b/easygraph/classes/directed_graph.py similarity index 100% rename from src/easygraph/classes/directed_graph.py rename to easygraph/classes/directed_graph.py diff --git a/src/easygraph/classes/directed_multigraph.py b/easygraph/classes/directed_multigraph.py similarity index 100% rename from src/easygraph/classes/directed_multigraph.py rename to easygraph/classes/directed_multigraph.py diff --git a/src/easygraph/classes/graph.py b/easygraph/classes/graph.py similarity index 100% rename from src/easygraph/classes/graph.py rename to easygraph/classes/graph.py diff --git a/src/easygraph/classes/graphviews.py b/easygraph/classes/graphviews.py similarity index 100% rename from src/easygraph/classes/graphviews.py rename to easygraph/classes/graphviews.py diff --git a/src/easygraph/classes/multigraph.py b/easygraph/classes/multigraph.py similarity index 100% rename from src/easygraph/classes/multigraph.py rename to easygraph/classes/multigraph.py diff --git a/src/easygraph/classes/operation.py b/easygraph/classes/operation.py similarity index 100% rename from src/easygraph/classes/operation.py rename to easygraph/classes/operation.py diff --git a/src/easygraph/classes/tests/__init__.py b/easygraph/classes/tests/__init__.py similarity index 100% rename from src/easygraph/classes/tests/__init__.py rename to easygraph/classes/tests/__init__.py diff --git a/src/easygraph/classes/tests/test_multidigraph.py b/easygraph/classes/tests/test_multidigraph.py similarity index 100% rename from src/easygraph/classes/tests/test_multidigraph.py rename to easygraph/classes/tests/test_multidigraph.py diff --git a/src/easygraph/classes/tests/test_multigraph.py b/easygraph/classes/tests/test_multigraph.py similarity index 100% rename from src/easygraph/classes/tests/test_multigraph.py rename to easygraph/classes/tests/test_multigraph.py diff --git a/src/easygraph/classes/tests/test_operation.py b/easygraph/classes/tests/test_operation.py similarity index 100% rename from src/easygraph/classes/tests/test_operation.py rename to easygraph/classes/tests/test_operation.py diff --git a/src/easygraph/convert.py b/easygraph/convert.py similarity index 100% rename from src/easygraph/convert.py rename to easygraph/convert.py diff --git a/src/easygraph/datasets/__init__.py b/easygraph/datasets/__init__.py similarity index 100% rename from src/easygraph/datasets/__init__.py rename to easygraph/datasets/__init__.py diff --git a/src/easygraph/datasets/get_sample_graph.py b/easygraph/datasets/get_sample_graph.py similarity index 100% rename from src/easygraph/datasets/get_sample_graph.py rename to easygraph/datasets/get_sample_graph.py diff --git a/src/easygraph/datasets/samples/blogcatalog.mat b/easygraph/datasets/samples/blogcatalog.mat similarity index 100% rename from src/easygraph/datasets/samples/blogcatalog.mat rename to easygraph/datasets/samples/blogcatalog.mat diff --git a/src/easygraph/functions/__init__.py b/easygraph/functions/__init__.py similarity index 100% rename from src/easygraph/functions/__init__.py rename to easygraph/functions/__init__.py diff --git a/src/easygraph/functions/centrality/__init__.py b/easygraph/functions/centrality/__init__.py similarity index 100% rename from src/easygraph/functions/centrality/__init__.py rename to easygraph/functions/centrality/__init__.py diff --git a/src/easygraph/functions/centrality/betweenness.py b/easygraph/functions/centrality/betweenness.py similarity index 100% rename from src/easygraph/functions/centrality/betweenness.py rename to easygraph/functions/centrality/betweenness.py diff --git a/src/easygraph/functions/centrality/clossness.py b/easygraph/functions/centrality/clossness.py similarity index 100% rename from src/easygraph/functions/centrality/clossness.py rename to easygraph/functions/centrality/clossness.py diff --git a/src/easygraph/functions/centrality/degree.py b/easygraph/functions/centrality/degree.py similarity index 100% rename from src/easygraph/functions/centrality/degree.py rename to easygraph/functions/centrality/degree.py diff --git a/src/easygraph/functions/centrality/flowbetweenness.py b/easygraph/functions/centrality/flowbetweenness.py similarity index 100% rename from src/easygraph/functions/centrality/flowbetweenness.py rename to easygraph/functions/centrality/flowbetweenness.py diff --git a/src/easygraph/functions/centrality/tests/__init__.py b/easygraph/functions/centrality/tests/__init__.py similarity index 100% rename from src/easygraph/functions/centrality/tests/__init__.py rename to easygraph/functions/centrality/tests/__init__.py diff --git a/src/easygraph/functions/centrality/tests/test_betweenness.py b/easygraph/functions/centrality/tests/test_betweenness.py similarity index 100% rename from src/easygraph/functions/centrality/tests/test_betweenness.py rename to easygraph/functions/centrality/tests/test_betweenness.py diff --git a/src/easygraph/functions/centrality/tests/test_clossness.py b/easygraph/functions/centrality/tests/test_clossness.py similarity index 100% rename from src/easygraph/functions/centrality/tests/test_clossness.py rename to easygraph/functions/centrality/tests/test_clossness.py diff --git a/src/easygraph/functions/centrality/tests/test_flowbetweenness.py b/easygraph/functions/centrality/tests/test_flowbetweenness.py similarity index 100% rename from src/easygraph/functions/centrality/tests/test_flowbetweenness.py rename to easygraph/functions/centrality/tests/test_flowbetweenness.py diff --git a/src/easygraph/functions/community/LPA.py b/easygraph/functions/community/LPA.py similarity index 100% rename from src/easygraph/functions/community/LPA.py rename to easygraph/functions/community/LPA.py diff --git a/src/easygraph/functions/community/__init__.py b/easygraph/functions/community/__init__.py similarity index 100% rename from src/easygraph/functions/community/__init__.py rename to easygraph/functions/community/__init__.py diff --git a/src/easygraph/functions/community/modularity.py b/easygraph/functions/community/modularity.py similarity index 100% rename from src/easygraph/functions/community/modularity.py rename to easygraph/functions/community/modularity.py diff --git a/src/easygraph/functions/community/modularity_max_detection.py b/easygraph/functions/community/modularity_max_detection.py similarity index 100% rename from src/easygraph/functions/community/modularity_max_detection.py rename to easygraph/functions/community/modularity_max_detection.py diff --git a/src/easygraph/functions/community/motif.py b/easygraph/functions/community/motif.py similarity index 100% rename from src/easygraph/functions/community/motif.py rename to easygraph/functions/community/motif.py diff --git a/src/easygraph/functions/community/tests/__init__.py b/easygraph/functions/community/tests/__init__.py similarity index 100% rename from src/easygraph/functions/community/tests/__init__.py rename to easygraph/functions/community/tests/__init__.py diff --git a/src/easygraph/functions/community/tests/test_ modularity_max_detection.py b/easygraph/functions/community/tests/test_ modularity_max_detection.py similarity index 100% rename from src/easygraph/functions/community/tests/test_ modularity_max_detection.py rename to easygraph/functions/community/tests/test_ modularity_max_detection.py diff --git a/src/easygraph/functions/community/tests/test_LPA.py b/easygraph/functions/community/tests/test_LPA.py similarity index 100% rename from src/easygraph/functions/community/tests/test_LPA.py rename to easygraph/functions/community/tests/test_LPA.py diff --git a/src/easygraph/functions/community/tests/test_modularity.py b/easygraph/functions/community/tests/test_modularity.py similarity index 100% rename from src/easygraph/functions/community/tests/test_modularity.py rename to easygraph/functions/community/tests/test_modularity.py diff --git a/src/easygraph/functions/community/tests/test_motif.py b/easygraph/functions/community/tests/test_motif.py similarity index 100% rename from src/easygraph/functions/community/tests/test_motif.py rename to easygraph/functions/community/tests/test_motif.py diff --git a/src/easygraph/functions/components/__init__.py b/easygraph/functions/components/__init__.py similarity index 100% rename from src/easygraph/functions/components/__init__.py rename to easygraph/functions/components/__init__.py diff --git a/src/easygraph/functions/components/biconnected.py b/easygraph/functions/components/biconnected.py similarity index 100% rename from src/easygraph/functions/components/biconnected.py rename to easygraph/functions/components/biconnected.py diff --git a/src/easygraph/functions/components/connected.py b/easygraph/functions/components/connected.py similarity index 100% rename from src/easygraph/functions/components/connected.py rename to easygraph/functions/components/connected.py diff --git a/src/easygraph/functions/components/ego_betweenness.py b/easygraph/functions/components/ego_betweenness.py similarity index 100% rename from src/easygraph/functions/components/ego_betweenness.py rename to easygraph/functions/components/ego_betweenness.py diff --git a/src/easygraph/functions/components/tests/__init__.py b/easygraph/functions/components/tests/__init__.py similarity index 100% rename from src/easygraph/functions/components/tests/__init__.py rename to easygraph/functions/components/tests/__init__.py diff --git a/src/easygraph/functions/components/tests/test_biconnected.py b/easygraph/functions/components/tests/test_biconnected.py similarity index 100% rename from src/easygraph/functions/components/tests/test_biconnected.py rename to easygraph/functions/components/tests/test_biconnected.py diff --git a/src/easygraph/functions/drawing/__init__.py b/easygraph/functions/drawing/__init__.py similarity index 100% rename from src/easygraph/functions/drawing/__init__.py rename to easygraph/functions/drawing/__init__.py diff --git a/src/easygraph/functions/drawing/drawing.py b/easygraph/functions/drawing/drawing.py similarity index 100% rename from src/easygraph/functions/drawing/drawing.py rename to easygraph/functions/drawing/drawing.py diff --git a/src/easygraph/functions/drawing/plot.py b/easygraph/functions/drawing/plot.py similarity index 100% rename from src/easygraph/functions/drawing/plot.py rename to easygraph/functions/drawing/plot.py diff --git a/src/easygraph/functions/drawing/positioning.py b/easygraph/functions/drawing/positioning.py similarity index 100% rename from src/easygraph/functions/drawing/positioning.py rename to easygraph/functions/drawing/positioning.py diff --git a/src/easygraph/functions/drawing/tests/__init__.py b/easygraph/functions/drawing/tests/__init__.py similarity index 100% rename from src/easygraph/functions/drawing/tests/__init__.py rename to easygraph/functions/drawing/tests/__init__.py diff --git a/src/easygraph/functions/drawing/tests/test_positioning.py b/easygraph/functions/drawing/tests/test_positioning.py similarity index 100% rename from src/easygraph/functions/drawing/tests/test_positioning.py rename to easygraph/functions/drawing/tests/test_positioning.py diff --git a/src/easygraph/functions/graph_embedding/NOBE.py b/easygraph/functions/graph_embedding/NOBE.py similarity index 100% rename from src/easygraph/functions/graph_embedding/NOBE.py rename to easygraph/functions/graph_embedding/NOBE.py diff --git a/src/easygraph/functions/graph_embedding/__init__.py b/easygraph/functions/graph_embedding/__init__.py similarity index 100% rename from src/easygraph/functions/graph_embedding/__init__.py rename to easygraph/functions/graph_embedding/__init__.py diff --git a/src/easygraph/functions/graph_embedding/deepwalk.py b/easygraph/functions/graph_embedding/deepwalk.py similarity index 100% rename from src/easygraph/functions/graph_embedding/deepwalk.py rename to easygraph/functions/graph_embedding/deepwalk.py diff --git a/src/easygraph/functions/graph_embedding/line.py b/easygraph/functions/graph_embedding/line.py similarity index 100% rename from src/easygraph/functions/graph_embedding/line.py rename to easygraph/functions/graph_embedding/line.py diff --git a/src/easygraph/functions/graph_embedding/node2vec.py b/easygraph/functions/graph_embedding/node2vec.py similarity index 100% rename from src/easygraph/functions/graph_embedding/node2vec.py rename to easygraph/functions/graph_embedding/node2vec.py diff --git a/src/easygraph/functions/graph_embedding/sdne.py b/easygraph/functions/graph_embedding/sdne.py similarity index 100% rename from src/easygraph/functions/graph_embedding/sdne.py rename to easygraph/functions/graph_embedding/sdne.py diff --git a/src/easygraph/functions/graph_generator/RandomNetwork.py b/easygraph/functions/graph_generator/RandomNetwork.py similarity index 100% rename from src/easygraph/functions/graph_generator/RandomNetwork.py rename to easygraph/functions/graph_generator/RandomNetwork.py diff --git a/src/easygraph/functions/graph_generator/__init__.py b/easygraph/functions/graph_generator/__init__.py similarity index 100% rename from src/easygraph/functions/graph_generator/__init__.py rename to easygraph/functions/graph_generator/__init__.py diff --git a/src/easygraph/functions/graph_generator/classic.py b/easygraph/functions/graph_generator/classic.py similarity index 100% rename from src/easygraph/functions/graph_generator/classic.py rename to easygraph/functions/graph_generator/classic.py diff --git a/src/easygraph/functions/not_sorted/__init__.py b/easygraph/functions/not_sorted/__init__.py similarity index 100% rename from src/easygraph/functions/not_sorted/__init__.py rename to easygraph/functions/not_sorted/__init__.py diff --git a/src/easygraph/functions/not_sorted/bridges.py b/easygraph/functions/not_sorted/bridges.py similarity index 100% rename from src/easygraph/functions/not_sorted/bridges.py rename to easygraph/functions/not_sorted/bridges.py diff --git a/src/easygraph/functions/not_sorted/cluster.py b/easygraph/functions/not_sorted/cluster.py similarity index 100% rename from src/easygraph/functions/not_sorted/cluster.py rename to easygraph/functions/not_sorted/cluster.py diff --git a/src/easygraph/functions/not_sorted/laplacian.py b/easygraph/functions/not_sorted/laplacian.py similarity index 100% rename from src/easygraph/functions/not_sorted/laplacian.py rename to easygraph/functions/not_sorted/laplacian.py diff --git a/src/easygraph/functions/not_sorted/mst.py b/easygraph/functions/not_sorted/mst.py similarity index 100% rename from src/easygraph/functions/not_sorted/mst.py rename to easygraph/functions/not_sorted/mst.py diff --git a/src/easygraph/functions/not_sorted/pagerank.py b/easygraph/functions/not_sorted/pagerank.py similarity index 100% rename from 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b/easygraph/functions/not_sorted/tests/test_pagerank.py similarity index 100% rename from src/easygraph/functions/not_sorted/tests/test_pagerank.py rename to easygraph/functions/not_sorted/tests/test_pagerank.py diff --git a/src/easygraph/functions/path/__init__.py b/easygraph/functions/path/__init__.py similarity index 100% rename from src/easygraph/functions/path/__init__.py rename to easygraph/functions/path/__init__.py diff --git a/src/easygraph/functions/path/path.py b/easygraph/functions/path/path.py similarity index 100% rename from src/easygraph/functions/path/path.py rename to easygraph/functions/path/path.py diff --git a/src/easygraph/functions/structural_holes/AP_Greedy.py b/easygraph/functions/structural_holes/AP_Greedy.py similarity index 100% rename from src/easygraph/functions/structural_holes/AP_Greedy.py rename to easygraph/functions/structural_holes/AP_Greedy.py diff --git a/src/easygraph/functions/structural_holes/HAM.py b/easygraph/functions/structural_holes/HAM.py similarity index 100% rename from src/easygraph/functions/structural_holes/HAM.py rename to easygraph/functions/structural_holes/HAM.py diff --git a/src/easygraph/functions/structural_holes/HIS.py b/easygraph/functions/structural_holes/HIS.py similarity index 100% rename from src/easygraph/functions/structural_holes/HIS.py rename to easygraph/functions/structural_holes/HIS.py diff --git a/src/easygraph/functions/structural_holes/ICC.py b/easygraph/functions/structural_holes/ICC.py similarity index 100% rename from src/easygraph/functions/structural_holes/ICC.py rename to easygraph/functions/structural_holes/ICC.py diff --git a/src/easygraph/functions/structural_holes/MaxD.py b/easygraph/functions/structural_holes/MaxD.py similarity index 100% rename from src/easygraph/functions/structural_holes/MaxD.py rename to easygraph/functions/structural_holes/MaxD.py diff --git a/src/easygraph/functions/structural_holes/NOBE.py b/easygraph/functions/structural_holes/NOBE.py similarity index 100% rename from src/easygraph/functions/structural_holes/NOBE.py rename to easygraph/functions/structural_holes/NOBE.py diff --git a/src/easygraph/functions/structural_holes/SHII_metric.py b/easygraph/functions/structural_holes/SHII_metric.py similarity index 100% rename from src/easygraph/functions/structural_holes/SHII_metric.py rename to easygraph/functions/structural_holes/SHII_metric.py diff --git a/src/easygraph/functions/structural_holes/__init__.py b/easygraph/functions/structural_holes/__init__.py similarity index 100% rename from src/easygraph/functions/structural_holes/__init__.py rename to easygraph/functions/structural_holes/__init__.py diff --git a/src/easygraph/functions/structural_holes/evaluation.py b/easygraph/functions/structural_holes/evaluation.py similarity index 100% rename from src/easygraph/functions/structural_holes/evaluation.py rename to easygraph/functions/structural_holes/evaluation.py diff --git a/src/easygraph/functions/structural_holes/maxBlock.py b/easygraph/functions/structural_holes/maxBlock.py similarity index 100% rename from src/easygraph/functions/structural_holes/maxBlock.py rename to easygraph/functions/structural_holes/maxBlock.py diff --git a/src/easygraph/functions/structural_holes/metrics.py b/easygraph/functions/structural_holes/metrics.py similarity index 100% rename from src/easygraph/functions/structural_holes/metrics.py rename to easygraph/functions/structural_holes/metrics.py diff --git a/src/easygraph/functions/structural_holes/strong_connected_component.py b/easygraph/functions/structural_holes/strong_connected_component.py similarity index 100% rename from src/easygraph/functions/structural_holes/strong_connected_component.py rename to easygraph/functions/structural_holes/strong_connected_component.py diff --git a/src/easygraph/functions/structural_holes/tests/__init__.py b/easygraph/functions/structural_holes/tests/__init__.py similarity index 100% rename from src/easygraph/functions/structural_holes/tests/__init__.py rename to easygraph/functions/structural_holes/tests/__init__.py diff --git a/src/easygraph/functions/structural_holes/tests/test_AP_Greedy.py b/easygraph/functions/structural_holes/tests/test_AP_Greedy.py similarity index 100% rename from src/easygraph/functions/structural_holes/tests/test_AP_Greedy.py rename to easygraph/functions/structural_holes/tests/test_AP_Greedy.py diff --git a/src/easygraph/functions/structural_holes/tests/test_HAM.py b/easygraph/functions/structural_holes/tests/test_HAM.py similarity index 100% rename from src/easygraph/functions/structural_holes/tests/test_HAM.py rename to easygraph/functions/structural_holes/tests/test_HAM.py diff --git a/src/easygraph/functions/structural_holes/tests/test_HIS.py b/easygraph/functions/structural_holes/tests/test_HIS.py similarity index 100% rename from src/easygraph/functions/structural_holes/tests/test_HIS.py rename to easygraph/functions/structural_holes/tests/test_HIS.py diff --git a/src/easygraph/functions/structural_holes/tests/test_ICC.py b/easygraph/functions/structural_holes/tests/test_ICC.py similarity index 100% rename from src/easygraph/functions/structural_holes/tests/test_ICC.py rename to easygraph/functions/structural_holes/tests/test_ICC.py diff --git a/src/easygraph/functions/structural_holes/tests/test_NOBE.py b/easygraph/functions/structural_holes/tests/test_NOBE.py similarity index 100% rename from src/easygraph/functions/structural_holes/tests/test_NOBE.py rename to easygraph/functions/structural_holes/tests/test_NOBE.py diff --git a/src/easygraph/functions/structural_holes/tests/test_evaluation.py b/easygraph/functions/structural_holes/tests/test_evaluation.py similarity index 100% rename from src/easygraph/functions/structural_holes/tests/test_evaluation.py rename to easygraph/functions/structural_holes/tests/test_evaluation.py diff --git a/src/easygraph/functions/structural_holes/tests/test_strong_connected_component.py b/easygraph/functions/structural_holes/tests/test_strong_connected_component.py similarity index 100% rename from src/easygraph/functions/structural_holes/tests/test_strong_connected_component.py rename to easygraph/functions/structural_holes/tests/test_strong_connected_component.py diff --git a/src/easygraph/functions/structural_holes/tests/test_weakTie.py b/easygraph/functions/structural_holes/tests/test_weakTie.py similarity index 100% rename from src/easygraph/functions/structural_holes/tests/test_weakTie.py rename to easygraph/functions/structural_holes/tests/test_weakTie.py diff --git a/src/easygraph/functions/structural_holes/weakTie.py b/easygraph/functions/structural_holes/weakTie.py similarity index 100% rename from src/easygraph/functions/structural_holes/weakTie.py rename to easygraph/functions/structural_holes/weakTie.py diff --git a/src/easygraph/readwrite/__init__.py b/easygraph/readwrite/__init__.py similarity index 100% rename from src/easygraph/readwrite/__init__.py rename to easygraph/readwrite/__init__.py diff --git a/src/easygraph/readwrite/edgelist.py b/easygraph/readwrite/edgelist.py similarity index 100% rename from src/easygraph/readwrite/edgelist.py rename to easygraph/readwrite/edgelist.py diff --git a/src/easygraph/readwrite/gexf.py b/easygraph/readwrite/gexf.py similarity index 100% rename from src/easygraph/readwrite/gexf.py rename to easygraph/readwrite/gexf.py diff --git a/src/easygraph/readwrite/gml.py b/easygraph/readwrite/gml.py similarity index 100% rename from src/easygraph/readwrite/gml.py rename to easygraph/readwrite/gml.py diff --git a/src/easygraph/readwrite/graphml.py b/easygraph/readwrite/graphml.py similarity index 100% rename from src/easygraph/readwrite/graphml.py rename to easygraph/readwrite/graphml.py diff --git a/src/easygraph/readwrite/graphviz.py b/easygraph/readwrite/graphviz.py similarity index 100% rename from src/easygraph/readwrite/graphviz.py rename to easygraph/readwrite/graphviz.py diff --git a/src/easygraph/readwrite/pajek.py b/easygraph/readwrite/pajek.py similarity index 100% rename from src/easygraph/readwrite/pajek.py rename to easygraph/readwrite/pajek.py diff --git a/src/easygraph/readwrite/pickle.py b/easygraph/readwrite/pickle.py similarity index 100% rename from src/easygraph/readwrite/pickle.py rename to easygraph/readwrite/pickle.py diff --git a/src/easygraph/readwrite/tests/__init__.py b/easygraph/readwrite/tests/__init__.py similarity index 100% rename from src/easygraph/readwrite/tests/__init__.py rename to easygraph/readwrite/tests/__init__.py diff --git a/src/easygraph/readwrite/tests/test_edgelist.py b/easygraph/readwrite/tests/test_edgelist.py similarity index 100% rename from src/easygraph/readwrite/tests/test_edgelist.py rename to easygraph/readwrite/tests/test_edgelist.py diff --git a/src/easygraph/readwrite/tests/test_gexf.py b/easygraph/readwrite/tests/test_gexf.py similarity index 100% rename from src/easygraph/readwrite/tests/test_gexf.py rename to easygraph/readwrite/tests/test_gexf.py diff --git a/src/easygraph/readwrite/tests/test_gml.py b/easygraph/readwrite/tests/test_gml.py similarity index 100% rename from src/easygraph/readwrite/tests/test_gml.py rename to easygraph/readwrite/tests/test_gml.py diff --git a/src/easygraph/readwrite/tests/test_graphml.py b/easygraph/readwrite/tests/test_graphml.py similarity index 100% rename from src/easygraph/readwrite/tests/test_graphml.py rename to easygraph/readwrite/tests/test_graphml.py diff --git a/src/easygraph/readwrite/tests/test_graphviz.py b/easygraph/readwrite/tests/test_graphviz.py similarity index 100% rename from src/easygraph/readwrite/tests/test_graphviz.py rename to easygraph/readwrite/tests/test_graphviz.py diff --git a/src/easygraph/readwrite/tests/test_pajek.py b/easygraph/readwrite/tests/test_pajek.py similarity index 100% rename from src/easygraph/readwrite/tests/test_pajek.py rename to easygraph/readwrite/tests/test_pajek.py diff --git a/src/easygraph/readwrite/tests/test_pickle.py b/easygraph/readwrite/tests/test_pickle.py similarity index 100% rename from src/easygraph/readwrite/tests/test_pickle.py rename to easygraph/readwrite/tests/test_pickle.py diff --git a/src/easygraph/readwrite/tests/test_ucinet.py b/easygraph/readwrite/tests/test_ucinet.py similarity index 100% rename from src/easygraph/readwrite/tests/test_ucinet.py rename to easygraph/readwrite/tests/test_ucinet.py diff --git a/src/easygraph/readwrite/ucinet.py b/easygraph/readwrite/ucinet.py similarity index 100% rename from src/easygraph/readwrite/ucinet.py rename to easygraph/readwrite/ucinet.py diff --git a/src/easygraph/tests/__init__.py b/easygraph/tests/__init__.py similarity index 100% rename from src/easygraph/tests/__init__.py rename to easygraph/tests/__init__.py diff --git a/src/easygraph/tests/test_convert.py b/easygraph/tests/test_convert.py similarity index 100% rename from src/easygraph/tests/test_convert.py rename to easygraph/tests/test_convert.py diff --git a/src/easygraph/utils/__init__.py b/easygraph/utils/__init__.py similarity index 100% rename from src/easygraph/utils/__init__.py rename to easygraph/utils/__init__.py diff --git a/src/easygraph/utils/alias.py b/easygraph/utils/alias.py similarity index 100% rename from src/easygraph/utils/alias.py rename to easygraph/utils/alias.py diff --git a/src/easygraph/utils/convert_class.py b/easygraph/utils/convert_class.py similarity index 100% rename from src/easygraph/utils/convert_class.py rename to easygraph/utils/convert_class.py diff --git a/src/easygraph/utils/convert_to_matrix.py b/easygraph/utils/convert_to_matrix.py similarity index 100% rename from src/easygraph/utils/convert_to_matrix.py rename to easygraph/utils/convert_to_matrix.py diff --git a/src/easygraph/utils/decorators.py b/easygraph/utils/decorators.py similarity index 100% rename from src/easygraph/utils/decorators.py rename to easygraph/utils/decorators.py diff --git a/src/easygraph/utils/exception.py b/easygraph/utils/exception.py similarity index 100% rename from src/easygraph/utils/exception.py rename to easygraph/utils/exception.py diff --git a/src/easygraph/utils/index_of_node.py b/easygraph/utils/index_of_node.py similarity index 100% rename from src/easygraph/utils/index_of_node.py rename to easygraph/utils/index_of_node.py diff --git a/src/easygraph/utils/mapped_queue.py b/easygraph/utils/mapped_queue.py similarity index 100% rename from src/easygraph/utils/mapped_queue.py rename to easygraph/utils/mapped_queue.py diff --git a/src/easygraph/utils/misc.py b/easygraph/utils/misc.py similarity index 100% rename from src/easygraph/utils/misc.py rename to easygraph/utils/misc.py diff --git a/src/easygraph/utils/relabel.py b/easygraph/utils/relabel.py similarity index 100% rename from src/easygraph/utils/relabel.py rename to easygraph/utils/relabel.py diff --git a/src/easygraph/utils/tests/__init__.py b/easygraph/utils/tests/__init__.py similarity index 100% rename from src/easygraph/utils/tests/__init__.py rename to easygraph/utils/tests/__init__.py diff --git a/src/easygraph/utils/tests/test_convert_to_matrix.py b/easygraph/utils/tests/test_convert_to_matrix.py similarity index 100% rename from src/easygraph/utils/tests/test_convert_to_matrix.py rename to easygraph/utils/tests/test_convert_to_matrix.py diff --git a/src/easygraph/utils/tests/test_mapped_queue.py b/easygraph/utils/tests/test_mapped_queue.py similarity index 100% rename from src/easygraph/utils/tests/test_mapped_queue.py rename to easygraph/utils/tests/test_mapped_queue.py diff --git a/src/easygraph/utils/type_change.py b/easygraph/utils/type_change.py similarity index 100% rename from src/easygraph/utils/type_change.py rename to easygraph/utils/type_change.py diff --git a/pyproject.toml b/pyproject.toml index 65335894..0416c02c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,10 +9,6 @@ readme = "README.rst" requires-python = ">=3.10" license = "BSD-3-Clause" classifiers = [ - "Programming Language :: Python :: 3.6", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Operating System :: OS Independent", ] @@ -39,16 +35,12 @@ easy-graph = "easy_graph:main" minimum-version = "build-system.requires" build-dir = "build/{wheel_tag}" -[tool.uv] -cache-keys = [{ file = "pyproject.toml" }, { file = "src/**/*.{h,c,hpp,cpp}" }, { file = "src/cpp_easygraph/CMakeLists.txt" }] - [build-system] requires = ["scikit-build-core>=0.10", "pybind11"] build-backend = "scikit_build_core.build" [tool.setuptools.packages.find] -# 告诉 setuptools 你的包在 "src" 目录下 -where = ["src"] +where = ["."] [dependency-groups] dev = [ @@ -61,3 +53,6 @@ dev = [ [tool.pytest.ini_options] python_files = "**/tests/test_*.py" addopts = "-ra --disable-warnings" + +[tool.scikit-build.cmake] +source-dir = "cpp_easygraph" From dec852ede20244ece449b251d2f553dd08eff495 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 15:53:42 +0800 Subject: [PATCH 08/17] refactor(graph): migrate from Boost.Python to pybind11 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Completely replaced all Boost.Python bindings with modern pybind11 equivalents. All modules, method bindings, and function wrappers were rewritten to use pybind11’s C++17 interface (py::object, py::dict, py::list, etc.). Removed Boost.Python headers and adjusted build/CMake configuration accordingly. Signed-off-by: acture --- CMakeLists.txt | 9 - cpp_easygraph/CMakeLists.txt | 23 + .../include}/biconnected.h | 7 +- cpp_easygraph/include/cluster.h | 8 + cpp_easygraph/include/common.h | 30 + cpp_easygraph/include/directed_graph.h | 17 + cpp_easygraph/include/evaluation.h | 15 + cpp_easygraph/include/graph.h | 52 ++ cpp_easygraph/include/operation.h | 6 + cpp_easygraph/include/path.h | 13 + cpp_easygraph/include/utils.h | 7 + cpp_easygraph/src/biconnected.cpp | 135 +++ cpp_easygraph/src/cluster.cpp | 195 ++++ cpp_easygraph/src/cpp_easygraph.cpp | 86 ++ cpp_easygraph/src/directed_graph.cpp | 174 ++++ cpp_easygraph/src/evaluation.cpp | 295 ++++++ cpp_easygraph/src/graph.cpp | 865 ++++++++++++++++++ cpp_easygraph/src/operation.cpp | 18 + cpp_easygraph/src/path.cpp | 371 ++++++++ cpp_easygraph/src/utils.cpp | 30 + src/cpp_easygraph/classes/__init__.h | 6 - src/cpp_easygraph/classes/directed_graph.cpp | 100 -- src/cpp_easygraph/classes/directed_graph.h | 17 - src/cpp_easygraph/classes/graph.cpp | 643 ------------- src/cpp_easygraph/classes/graph.h | 54 -- src/cpp_easygraph/classes/operation.cpp | 17 - src/cpp_easygraph/classes/operation.h | 6 - src/cpp_easygraph/common/common.h | 23 - src/cpp_easygraph/common/utils.cpp | 26 - src/cpp_easygraph/common/utils.h | 8 - src/cpp_easygraph/cpp_easygraph.cpp | 68 -- src/cpp_easygraph/functions/__init__.h | 7 - .../functions/components/__init__.h | 4 - .../functions/components/biconnected.cpp | 108 --- .../functions/not_sorted/__init__.h | 4 - .../functions/not_sorted/cluster.cpp | 113 --- .../functions/not_sorted/cluster.h | 6 - src/cpp_easygraph/functions/path/__init__.h | 4 - src/cpp_easygraph/functions/path/path.cpp | 226 ----- src/cpp_easygraph/functions/path/path.h | 9 - .../functions/structural_holes/__init__.h | 4 - .../functions/structural_holes/evaluation.cpp | 205 ----- .../functions/structural_holes/evaluation.h | 8 - 43 files changed, 2344 insertions(+), 1678 deletions(-) delete mode 100644 CMakeLists.txt create mode 100644 cpp_easygraph/CMakeLists.txt rename {src/cpp_easygraph/functions/components => cpp_easygraph/include}/biconnected.h (83%) create mode 100644 cpp_easygraph/include/cluster.h create mode 100644 cpp_easygraph/include/common.h create mode 100644 cpp_easygraph/include/directed_graph.h create mode 100644 cpp_easygraph/include/evaluation.h create mode 100644 cpp_easygraph/include/graph.h create mode 100644 cpp_easygraph/include/operation.h create mode 100644 cpp_easygraph/include/path.h create mode 100644 cpp_easygraph/include/utils.h create mode 100644 cpp_easygraph/src/biconnected.cpp create mode 100644 cpp_easygraph/src/cluster.cpp create mode 100644 cpp_easygraph/src/cpp_easygraph.cpp create mode 100644 cpp_easygraph/src/directed_graph.cpp create mode 100644 cpp_easygraph/src/evaluation.cpp create mode 100644 cpp_easygraph/src/graph.cpp create mode 100644 cpp_easygraph/src/operation.cpp create mode 100644 cpp_easygraph/src/path.cpp create mode 100644 cpp_easygraph/src/utils.cpp delete mode 100644 src/cpp_easygraph/classes/__init__.h delete mode 100644 src/cpp_easygraph/classes/directed_graph.cpp delete mode 100644 src/cpp_easygraph/classes/directed_graph.h delete mode 100644 src/cpp_easygraph/classes/graph.cpp delete mode 100644 src/cpp_easygraph/classes/graph.h delete mode 100644 src/cpp_easygraph/classes/operation.cpp delete mode 100644 src/cpp_easygraph/classes/operation.h delete mode 100644 src/cpp_easygraph/common/common.h delete mode 100644 src/cpp_easygraph/common/utils.cpp delete mode 100644 src/cpp_easygraph/common/utils.h delete mode 100644 src/cpp_easygraph/cpp_easygraph.cpp delete mode 100644 src/cpp_easygraph/functions/__init__.h delete mode 100644 src/cpp_easygraph/functions/components/__init__.h delete mode 100644 src/cpp_easygraph/functions/components/biconnected.cpp delete mode 100644 src/cpp_easygraph/functions/not_sorted/__init__.h delete mode 100644 src/cpp_easygraph/functions/not_sorted/cluster.cpp delete mode 100644 src/cpp_easygraph/functions/not_sorted/cluster.h delete mode 100644 src/cpp_easygraph/functions/path/__init__.h delete mode 100644 src/cpp_easygraph/functions/path/path.cpp delete mode 100644 src/cpp_easygraph/functions/path/path.h delete mode 100644 src/cpp_easygraph/functions/structural_holes/__init__.h delete mode 100644 src/cpp_easygraph/functions/structural_holes/evaluation.cpp delete mode 100644 src/cpp_easygraph/functions/structural_holes/evaluation.h diff --git a/CMakeLists.txt b/CMakeLists.txt deleted file mode 100644 index 47610c47..00000000 --- a/CMakeLists.txt +++ /dev/null @@ -1,9 +0,0 @@ -cmake_minimum_required(VERSION 3.15) -project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX) - -set(PYBIND11_FINDPYTHON ON) -find_package(pybind11 CONFIG REQUIRED) - -pybind11_add_module(cpp_easygraph MODULE src/cpp_easygraph/cpp_easygraph.cpp) - -install(TARGETS cpp_easygraph DESTINATION ${SKBUILD_PROJECT_NAME}) diff --git a/cpp_easygraph/CMakeLists.txt b/cpp_easygraph/CMakeLists.txt new file mode 100644 index 00000000..151394a6 --- /dev/null +++ b/cpp_easygraph/CMakeLists.txt @@ -0,0 +1,23 @@ +cmake_minimum_required(VERSION 3.15) +if(NOT DEFINED SKBUILD_PROJECT_NAME) + set(SKBUILD_PROJECT_NAME "cpp_easygraph_standalone") +endif() + +project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX) + +set(CMAKE_CXX_STANDARD 17) +set(CMAKE_CXX_STANDARD_REQUIRED ON) + +set(PYBIND11_FINDPYTHON ON) +find_package(pybind11 CONFIG REQUIRED) + +file(GLOB_RECURSE EASYGRAPH_SOURCES "src/*.cpp") + + +pybind11_add_module(cpp_easygraph MODULE ${EASYGRAPH_SOURCES}) + +target_include_directories(cpp_easygraph PUBLIC "include") + +if(SKBUILD) + install(TARGETS cpp_easygraph DESTINATION ${SKBUILD_PROJECT_NAME}) +endif () diff --git a/src/cpp_easygraph/functions/components/biconnected.h b/cpp_easygraph/include/biconnected.h similarity index 83% rename from src/cpp_easygraph/functions/components/biconnected.h rename to cpp_easygraph/include/biconnected.h index 889173e9..6350391e 100644 --- a/src/cpp_easygraph/functions/components/biconnected.h +++ b/cpp_easygraph/include/biconnected.h @@ -1,7 +1,8 @@ #pragma once -#define BOOST_PYTHON_STATIC_LIB -#include "../../common/common.h" + +#include "common.h" +#include "graph.h" class NeighborIterator { public: @@ -32,4 +33,4 @@ typedef struct stackNode { } }stack_node; -py::object _biconnected_dfs_record_edges(py::object G, py::object need_components); +py::list _biconnected_dfs_record_edges(Graph& G, bool need_components); diff --git a/cpp_easygraph/include/cluster.h b/cpp_easygraph/include/cluster.h new file mode 100644 index 00000000..856b87b1 --- /dev/null +++ b/cpp_easygraph/include/cluster.h @@ -0,0 +1,8 @@ +#pragma once + + +#include "common.h" + +py::object clustering(py::object G, + py::object nodes = py::none(), + py::object weight = py::none()); diff --git a/cpp_easygraph/include/common.h b/cpp_easygraph/include/common.h new file mode 100644 index 00000000..774f8c7d --- /dev/null +++ b/cpp_easygraph/include/common.h @@ -0,0 +1,30 @@ +#pragma once + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace py = pybind11; + +using node_t = int; +using weight_t = float; +using node_attr_dict_factory = + std::map; //(weight_key, value) +using edge_attr_dict_factory = + std::map; //(weight_key, value) +using node_dict_factory = + std::unordered_map; //(node, node_attr) +using adj_attr_dict_factory = + std::unordered_map; //(out_node, (weight_key, value)) +using adj_dict_factory = + std::unordered_map; //(node, edge_attr) diff --git a/cpp_easygraph/include/directed_graph.h b/cpp_easygraph/include/directed_graph.h new file mode 100644 index 00000000..08287a0f --- /dev/null +++ b/cpp_easygraph/include/directed_graph.h @@ -0,0 +1,17 @@ +#pragma once + + +#include "graph.h" +#include "common.h" + +struct DiGraph: public Graph +{ + DiGraph(); +}; + +void DiGraph__init__(DiGraph &self, py::kwargs kwargs); +py::dict DiGraph_out_degree(const py::object& self, const py::object& weight); +py::dict DiGraph_in_degree(const py::object& self, const py::object& weight); +py::dict DiGraph_degree(const py::object &self,const py::object &weight); +py::object DiGraph_size(const py::object& self, const py::object& weight); +py::object DiGraph_number_of_edges(const py::object &self,const py::object &u,const py::object &v); diff --git a/cpp_easygraph/include/evaluation.h b/cpp_easygraph/include/evaluation.h new file mode 100644 index 00000000..b632c049 --- /dev/null +++ b/cpp_easygraph/include/evaluation.h @@ -0,0 +1,15 @@ +#pragma once +#include "common.h" +#include "graph.h" + +py::dict constraint(const py::object &G, py::object nodes, + const py::object &weight, + const py::object &n_workers /*未使用但保留签名*/); +py::object effective_size(py::object G, py::object nodes, py::object weight, + py::object n_workers); + + +py::dict hierarchy(Graph& G, + py::object nodes = py::none(), + py::object weight = py::none(), + py::object n_workers = py::none()); diff --git a/cpp_easygraph/include/graph.h b/cpp_easygraph/include/graph.h new file mode 100644 index 00000000..a1d84d08 --- /dev/null +++ b/cpp_easygraph/include/graph.h @@ -0,0 +1,52 @@ +#pragma once + + +#include "common.h" + +struct Graph +{ + node_dict_factory node; + adj_dict_factory adj; + py::dict node_to_id, id_to_node, graph; + node_t id; + bool dirty_nodes, dirty_adj; + py::object nodes_cache, adj_cache; + + Graph(); + py::object get_nodes(); + py::object get_name(); + py::object get_graph(); + py::object get_adj(); + py::object get_edges(); +}; + +void Graph__init__(Graph &self, py::kwargs kwargs); +py::object Graph__iter__(py::object self); +py::object Graph__len__(const py::object& self); +py::object Graph__contains__(const py::object& self, const py::object& node); +py::object Graph__getitem__(py::object self, py::object node); +py::object Graph_add_node(const py::tuple& args, const py::dict& kwargs); +py::object Graph_add_nodes(Graph& self,const py::list& nodes_for_adding,const py::list& nodes_attr); +void Graph_add_nodes_from(Graph& self, const py::iterable& nodes_for_adding, const py::kwargs& kwargs); +void Graph_remove_node(Graph& self, const py::object& node_to_remove); +void Graph_remove_nodes(Graph& self, const py::sequence& nodes_to_remove); +py::object Graph_number_of_nodes(Graph& self); +bool Graph_has_node(Graph &self, py::object node); +py::object Graph_nbunch_iter(py::object self, py::object nbunch); +void Graph_add_edge(Graph& self, const py::object& u_of_edge, const py::object& v_of_edge, const py::kwargs& kwargs); +void Graph_add_edges(Graph& self, const py::sequence& edges_for_adding, const py::sequence& edges_attr) ; +void Graph_add_edges_from(Graph& self, const py::iterable& ebunch, const py::kwargs& attr); +void Graph_add_edges_from_file(Graph& self, const py::str& file, bool weighted); +py::object Graph_add_weighted_edge(Graph& self, py::object u_of_edge, py::object v_of_edge, weight_t weight); +void Graph_remove_edge(Graph& self, const py::object& u, const py::object& v); +void Graph_remove_edges(Graph& self, const py::sequence& edges_to_remove); +int Graph_number_of_edges(const Graph& self, py::object u = py::none(), py::object v = py::none()); +bool Graph_has_edge(const Graph& self, const py::object& u, const py::object& v); +py::object Graph_copy(py::handle self_h); +py::dict Graph_degree(const Graph& self, py::object weight = py::none()); +py::list Graph_neighbors(const Graph& self, const py::object& node); +py::object Graph_nodes_subgraph(py::object self, py::list from_nodes); +py::object Graph_ego_subgraph(py::object self, py::object center); +py::object Graph_size(const Graph& G, py::object weight = py::none()); +bool Graph_is_directed(const Graph& self); +bool Graph_is_multigraph(const Graph& self); diff --git a/cpp_easygraph/include/operation.h b/cpp_easygraph/include/operation.h new file mode 100644 index 00000000..d7816136 --- /dev/null +++ b/cpp_easygraph/include/operation.h @@ -0,0 +1,6 @@ +#pragma once + + +#include "graph.h" + +double density(const Graph& G); diff --git a/cpp_easygraph/include/path.h b/cpp_easygraph/include/path.h new file mode 100644 index 00000000..55be34ac --- /dev/null +++ b/cpp_easygraph/include/path.h @@ -0,0 +1,13 @@ +#pragma once + + +#include "common.h" +#include "graph.h" + +py::dict _dijkstra_multisource(const py::object &G, + const py::object &sources, + const py::object &weight, + const py::object &target); +py::dict Floyd(Graph& G); +py::dict Prim(Graph& G); +py::dict Kruskal(Graph& G); diff --git a/cpp_easygraph/include/utils.h b/cpp_easygraph/include/utils.h new file mode 100644 index 00000000..70f7c9d9 --- /dev/null +++ b/cpp_easygraph/include/utils.h @@ -0,0 +1,7 @@ +#pragma once + +#include "common.h" + +py::dict attr_to_dict(const node_attr_dict_factory& attr); +std::string weight_to_string(py::handle weight); +py::object py_sum(const py::object& o); diff --git a/cpp_easygraph/src/biconnected.cpp b/cpp_easygraph/src/biconnected.cpp new file mode 100644 index 00000000..1b5f4821 --- /dev/null +++ b/cpp_easygraph/src/biconnected.cpp @@ -0,0 +1,135 @@ +#include "biconnected.h" +#include "graph.h" +#include "utils.h" + +node_t index_edge(std::vector>& edges, const std::pair& target) { + for (int i = edges.size() - 1;i >= 0;i--) { + if ((edges[i].first == target.first) && (edges[i].second == target.second)) { + return i; + } + } + return -1; +} + + +py::list _biconnected_dfs_record_edges(Graph& G, bool need_components) { + py::list ret; + std::unordered_set visited; + + auto& nodes = G.node; // id -> node attributes + auto& adj = G.adj; // id -> (neighbor id -> edge attrs) + + for (auto it = nodes.begin(); it != nodes.end(); ++it) { + const node_t start_id = it->first; + if (visited.find(start_id) != visited.end()) { + continue; + } + + std::unordered_map discovery; + std::unordered_map low; + node_t root_children = 0; + + discovery.emplace(start_id, 0); + low.emplace(start_id, 0); + visited.emplace(start_id); + + std::vector> edge_stack; + std::vector stack; + + // 注意：这里与原实现一致，使用 operator[] 获取邻接（如无则创建空条目） + adj_attr_dict_factory start_adj = adj[start_id]; + NeighborIterator neighbors_iter(start_adj); + stack.emplace_back(stack_node{start_id, start_id, neighbors_iter}); + + while (!stack.empty()) { + stack_node& node_info = stack.back(); + const node_t node_grandparent_id = node_info.grandparent; + const node_t node_parent_id = node_info.parent; + + try { + const node_t node_child_id = node_info.neighbors_iter.next(); + + if (node_grandparent_id == node_child_id) { + continue; + } + + if (visited.find(node_child_id) != visited.end()) { + // 回边：更新 low值 + if (discovery[node_child_id] <= discovery[node_parent_id]) { + low[node_parent_id] = std::min(low[node_parent_id], discovery[node_child_id]); + if (need_components) { + edge_stack.emplace_back(node_parent_id, node_child_id); + } + } + } else { + // 树边：首次发现 + low[node_child_id] = discovery[node_child_id] = static_cast(discovery.size()); + visited.emplace(node_child_id); + + // 子节点邻居迭代器 + NeighborIterator child_neighbors_iter(adj[node_child_id]); + + // 压栈：当前 parent 变为 grandparent，新 child 为 parent + stack.emplace_back(stack_node{node_parent_id, node_child_id, child_neighbors_iter}); + + if (need_components) { + edge_stack.emplace_back(node_parent_id, node_child_id); + } + } + } catch (int) { + // 当前迭代器穷尽：弹栈并做割点/双连通分量处理 + stack.pop_back(); + + if (stack.size() > 1) { + // 非根结点情况：检查割点条件 + if (low[node_parent_id] >= discovery[node_grandparent_id]) { + if (need_components) { + py::list tmp_ret; + std::pair iter_edge(-1, -1); + while (iter_edge.first != node_grandparent_id || iter_edge.second != node_parent_id) { + iter_edge = edge_stack.back(); + edge_stack.pop_back(); + // 通过 id_to_node 还原 Python 节点对象 + py::object u = G.id_to_node.attr("__getitem__")(py::cast(iter_edge.first)); + py::object v = G.id_to_node.attr("__getitem__")(py::cast(iter_edge.second)); + tmp_ret.append(py::make_tuple(u, v)); + } + ret.append(tmp_ret); + } else { + py::object ap = G.id_to_node.attr("__getitem__")(py::cast(node_grandparent_id)); + ret.append(ap); // 记录割点 + } + } + // 回溯时更新祖父节点的 low + low[node_grandparent_id] = std::min(low[node_grandparent_id], low[node_parent_id]); + } else if (!stack.empty()) { + // 根的一个子树处理完毕 + ++root_children; + if (need_components) { + const std::pair target(node_grandparent_id, node_parent_id); + const node_t ind = index_edge(edge_stack, target); + if (ind != static_cast(-1)) { + py::list tmp_ret; + for (node_t z = ind; z < edge_stack.size(); ++z) { + const auto& e = edge_stack[z]; + py::object u = G.id_to_node.attr("__getitem__")(py::cast(e.first)); + py::object v = G.id_to_node.attr("__getitem__")(py::cast(e.second)); + tmp_ret.append(py::make_tuple(u, v)); + } + ret.append(tmp_ret); + } + } + } + } + } // while stack + + if (!need_components) { + if (root_children > 1) { + py::object root = G.id_to_node.attr("__getitem__")(py::cast(start_id)); + ret.append(root); // 根是割点 + } + } + } // for nodes + + return ret; +} diff --git a/cpp_easygraph/src/cluster.cpp b/cpp_easygraph/src/cluster.cpp new file mode 100644 index 00000000..30bc8fca --- /dev/null +++ b/cpp_easygraph/src/cluster.cpp @@ -0,0 +1,195 @@ +#include "graph.h" +#include "utils.h" + +inline weight_t wt(adj_dict_factory& adj, node_t u, node_t v, std::string weight, weight_t max_weight = 1) { + auto& attr = adj[u][v]; + return (attr.count(weight) ? attr[weight] : 1) / max_weight; +} + +py::list _weighted_triangles_and_degree(Graph& G, + py::object nodes = py::none(), + py::object weight = py::none()) { + // ---- 0) 权重键 & 最大权重 ---- + std::string weight_key; + bool use_weight = !weight.is_none(); + if (use_weight) { + weight_key = weight_to_string(weight); + } + + // 统计是否有边 + bool has_edges = false; + for (auto it = G.adj.begin(); it != G.adj.end() && !has_edges; ++it) { + if (!it->second.empty()) has_edges = true; + } + + weight_t max_weight = 1; + if (use_weight && has_edges) { + bool assigned = false; + for (auto uit = G.adj.begin(); uit != G.adj.end(); ++uit) { + auto &nbrs = uit->second; + for (auto vit = nbrs.begin(); vit != nbrs.end(); ++vit) { + const auto &d = vit->second; // 属性 map + weight_t cur = 1; + auto dit = d.find(weight_key); + if (dit != d.end()) cur = dit->second; + if (assigned) { + max_weight = std::max(max_weight, cur); + } else { + assigned = true; + max_weight = cur; + } + } + } + } + + // ---- 1) 确定要遍历的节点列表（Python 对象）---- + std::vector nodes_vec; + if (nodes.is_none()) { + // 遍历 G.node（以 id 为键），通过 id_to_node 还原 Python 节点对象 + nodes_vec.reserve(G.node.size()); + for (auto it = G.node.begin(); it != G.node.end(); ++it) { + node_t nid = it->first; + py::object node_obj = G.id_to_node.attr("__getitem__")(py::cast(nid)); + nodes_vec.push_back(std::move(node_obj)); + } + } else { + // 遍历传入的可迭代对象，过滤不存在的节点 + for (py::handle h : nodes) { + py::object n = py::reinterpret_borrow(h); + if (G.node_to_id.contains(n)) { + nodes_vec.push_back(std::move(n)); + } + } + } + + // ---- 2) 主循环：每个节点的度与加权三角形数 ---- + py::list ret; + for (const py::object &node_obj : nodes_vec) { + // node -> id + node_t i_id = py::cast(G.node_to_id[node_obj]); + + // inbrs = 邻居集合（去掉自环） + std::unordered_set inbrs; + auto itAdjI = G.adj.find(i_id); + if (itAdjI != G.adj.end()) { + auto &nbrs = itAdjI->second; + for (auto kv = nbrs.begin(); kv != nbrs.end(); ++kv) { + if (kv->first != i_id) inbrs.insert(kv->first); + } + } + + // 统计加权三角形 + std::unordered_set seen; + weight_t weighted_triangles = 0; + + for (const auto &j_id : inbrs) { + seen.insert(j_id); + weight_t wij = wt(G.adj, i_id, j_id, weight_key, max_weight); + + // 只考虑 k 不在 seen 中（避免 j-k, k-j 双计） + for (const auto &k_id : inbrs) { + if (seen.count(k_id)) continue; + // 需要 j-k 相邻 + auto itAdjJ = G.adj.find(j_id); + if (itAdjJ == G.adj.end()) continue; + if (!itAdjJ->second.count(k_id)) continue; + + weight_t wjk = wt(G.adj, j_id, k_id, weight_key, max_weight); + weight_t wki = wt(G.adj, k_id, i_id, weight_key, max_weight); + + weighted_triangles += std::cbrt(static_cast(wij) * + static_cast(wjk) * + static_cast(wki)); + } + } + + // 结果条目：(python_node, degree, 2 * weighted_triangles) + // 注意：degree = inbrs.size() + ret.append(py::make_tuple(node_obj, + static_cast(inbrs.size()), + 2.0 * static_cast(weighted_triangles))); + } + + return ret; +} +py::list _triangles_and_degree(Graph& G, py::object nodes = py::none()) { + auto& adj = G.adj; + + // 1) 确定要处理的节点集合（Python 对象形式） + std::vector nodes_vec; + if (nodes.is_none()) { + nodes_vec.reserve(G.node.size()); + for (const auto& kv : G.node) { + const node_t nid = kv.first; + nodes_vec.emplace_back(G.id_to_node.attr("__getitem__")(py::cast(nid))); + } + } else { + for (py::handle h : nodes) { + py::object obj = py::reinterpret_borrow(h); + if (G.node_to_id.contains(obj)) nodes_vec.emplace_back(std::move(obj)); + } + } + + // 2) 主循环 + py::list ret; + for (const py::object& node_obj : nodes_vec) { + // node -> id + const node_t v = py::cast(G.node_to_id[node_obj]); + + // 邻居集合（去掉自环） + std::unordered_set vs; + if (auto it = adj.find(v); it != adj.end()) { + for (const auto& kv : it->second) vs.insert(kv.first); + } + vs.erase(v); + + // 统计邻居之间的连边数（按原逻辑：有序对计数） + weight_t ntriangles = 0; // 原实现是对 (w,node) 有序对计数 + for (const node_t w : vs) { + auto itW = adj.find(w); + if (itW == adj.end()) continue; + const auto& nbrW = itW->second; + + for (const node_t u : vs) { + if (u == w) continue; + ntriangles += static_cast(nbrW.count(u)); + } + } + + // (python_node, degree, ntriangles) + // 注意：原代码未除以 2，这里保持一致 + py::object py_node = G.id_to_node.attr("__getitem__")(py::cast(v)); + ret.append(py::make_tuple(py_node, static_cast(vs.size()), ntriangles)); + } + + return ret; +} +py::object clustering(py::object G, + py::object nodes, + py::object weight) { + if (py::bool_(G.attr("is_directed")())) { + throw py::value_error("Not implemented yet"); + } + + Graph& G_ = py::cast(G); // 用 py::cast 而不是 extract + + py::list td_list = weight.is_none() + ? _triangles_and_degree(G_, nodes) + : _weighted_triangles_and_degree(G_, nodes, weight); + + py::dict clusterc; + const std::size_t n = py::len(td_list); + for (std::size_t i = 0; i < n; ++i) { + py::tuple t = td_list[i].cast(); + py::object v = t[0]; + int d = t[1].cast(); + double tri = t[2].cast(); + double c = (tri != 0.0 && d >= 2) ? (tri / (double(d) * double(d - 1))) : 0.0; + clusterc[v] = c; + } + + if (!nodes.is_none() && G_.node_to_id.contains(nodes)) { + return clusterc.attr("__getitem__")(nodes); + } + return clusterc; +} diff --git a/cpp_easygraph/src/cpp_easygraph.cpp b/cpp_easygraph/src/cpp_easygraph.cpp new file mode 100644 index 00000000..7fb2bc45 --- /dev/null +++ b/cpp_easygraph/src/cpp_easygraph.cpp @@ -0,0 +1,86 @@ +#include "biconnected.h" +#include "cluster.h" +#include "common.h" +#include "directed_graph.h" +#include "evaluation.h" +#include "graph.h" +#include "operation.h" +#include "path.h" + +PYBIND11_MODULE(cpp_easygraph, m) { + + py::class_(m, "Graph") + .def("__init__", &Graph__init__) + .def(py::init<>()) + .def("__iter__", &Graph__iter__) + .def("__len__", &Graph__len__) + .def("__contains__", &Graph__contains__, py::arg("node")) + .def("__getitem__", &Graph__getitem__, py::arg("node")) + .def("add_node", &Graph_add_node) + .def("add_nodes", &Graph_add_nodes, py::arg("nodes_for_adding"), + py::arg("nodes_attr") = py::list()) + .def("add_nodes_from", &Graph_add_nodes_from) + .def("remove_node", &Graph_remove_node, py::arg("node_to_remove")) + .def("remove_nodes", &Graph_remove_nodes, py::arg("nodes_to_remove")) + .def("number_of_nodes", &Graph_number_of_nodes) + .def("has_node", &Graph_has_node, py::arg("node")) + .def("nbunch_iter", &Graph_nbunch_iter, py::arg("nbunch") = py::none()) + .def("add_edge", &Graph_add_edge) + .def("add_edges", &Graph_add_edges, py::arg("edges_for_adding"), + py::arg("edges_attr") = py::list()) + .def("add_edges_from", &Graph_add_edges_from) + .def("add_edges_from_file", &Graph_add_edges_from_file, py::arg("file"), + py::arg("weighted") = false) + .def("add_weighted_edge", &Graph_add_weighted_edge, py::arg("u_of_edge"), + py::arg("v_of_edge"), py::arg("weight")) + .def("remove_edge", &Graph_remove_edge, py::arg("u"), py::arg("v")) + .def("remove_edges", &Graph_remove_edges, py::arg("edges_to_remove")) + .def("number_of_edges", &Graph_number_of_edges, py::arg("u") = py::none(), + py::arg("v") = py::none()) + .def("has_edge", &Graph_has_edge, py::arg("u"), py::arg("y")) + .def("copy", &Graph_copy) + .def("degree", &Graph_degree, py::arg("weight") = py::str("weight")) + .def("neighbors", &Graph_neighbors, py::arg("node")) + .def("all_neighbors", &Graph_neighbors, py::arg("node")) + .def("nodes_subgraph", &Graph_nodes_subgraph, py::arg("from_nodes")) + .def("ego_subgraph", &Graph_ego_subgraph, py::arg("center")) + .def("size", &Graph_size, py::arg("weight") = py::none()) + .def("is_directed", &Graph_is_directed) + .def("is_multigraph", &Graph_is_multigraph) + .def_property_readonly("graph", &Graph::get_graph) + .def_property_readonly("nodes", &Graph::get_nodes) + .def_property_readonly("name", &Graph::get_name) + .def_property_readonly("adj", &Graph::get_adj) + .def_property_readonly("edges", &Graph::get_edges); + + py::class_(m, "DiGraph") + .def("__init__", &DiGraph__init__) + .def(py::init<>()) + .def("out_degree", &DiGraph_out_degree, py::arg("weight") = "weight") + .def("in_degree", &DiGraph_in_degree, py::arg("weight") = "weight") + .def("degree", &DiGraph_degree, py::arg("weight") = "weight") + .def("size", &DiGraph_size, py::arg("weight") = py::none()) + .def("number_of_edges", &DiGraph_number_of_edges, + py::arg("u") = py::none(), py::arg("v") = py::none()); + + m.def("cpp_density", &density, py::arg("G")); + m.def("cpp_constraint", &constraint, py::arg("G"), + py::arg("nodes") = py::none(), py::arg("weight") = py::none(), + py::arg("n_workers") = py::none()); + m.def("cpp_effective_size", &effective_size, py::arg("G"), + py::arg("nodes") = py::none(), py::arg("weight") = py::none(), + py::arg("n_workers") = py::none()); + m.def("cpp_hierarchy", &hierarchy, py::arg("G"), + py::arg("nodes") = py::none(), py::arg("weight") = py::none(), + py::arg("n_workers") = py::none()); + m.def("cpp_dijkstra_multisource", &_dijkstra_multisource, py::arg("G"), + py::arg("sources"), py::arg("weight") = "weight", + py::arg("target") = py::none()); + m.def("cpp_clustering", &clustering, py::arg("G"), + py::arg("nodes") = py::none(), py::arg("weight") = py::none()); + m.def("cpp_biconnected_dfs_record_edges", &_biconnected_dfs_record_edges, + py::arg("G"), py::arg("need_components") = true); + m.def("cpp_Floyd", &Floyd, py::arg("G")); + m.def("cpp_Prim", &Prim, py::arg("G")); + m.def("cpp_Kruskal", &Kruskal, py::arg("G")); +} diff --git a/cpp_easygraph/src/directed_graph.cpp b/cpp_easygraph/src/directed_graph.cpp new file mode 100644 index 00000000..2053998f --- /dev/null +++ b/cpp_easygraph/src/directed_graph.cpp @@ -0,0 +1,174 @@ +#include "directed_graph.h" +#include "common.h" +#include "utils.h" + +DiGraph::DiGraph() : Graph() {} + +void DiGraph___init__(DiGraph &self, py::kwargs kwargs) { + new (&self) DiGraph(); + + py::object MappingProxyType = + py::module_::import("types").attr("MappingProxyType"); + + if (kwargs) { + for (auto &item : kwargs) { + self.graph[py::str(item.first)] = item.second; + } + } + + self.nodes_cache = MappingProxyType(py::dict()); + self.adj_cache = MappingProxyType(py::dict()); +} + +py::dict DiGraph_out_degree(const py::object &self, + const py::object &weight) { + py::dict degree; + + // edges 既可能是属性(list/iterable)，也可能是方法（如 edges(data=True)） + py::object edges_obj = self.attr("edges"); + + py::list edges = py::isinstance(edges_obj) + ? py::list(edges_obj()) + : py::list(edges_obj); + + // 遍历边：(u, v, d) + for (py::ssize_t i = 0; i < py::len(edges); ++i) { + py::tuple edge = edges[i].cast(); + py::object u = edge[0]; + // v 在本函数中未使用，但保留一致性 + // py::object v = edge[1]; + py::dict d = (edge.size() >= 3) ? edge[2].cast() : py::dict(); + + py::object w = d.attr("get")(weight, 1); // d.get(weight, 1) + + if (degree.contains(u)) { + // degree[u] += w —— 用 Python 的 __add__ 避免数值类型分歧 + degree[u] = degree[u].attr("__add__")(w); + } else { + degree[u] = w; + } + } + + // 确保所有节点都有条目：不存在则补 0 + py::object nodes_obj = self.attr("nodes"); + py::list nodes = py::isinstance(nodes_obj) + ? py::list(nodes_obj()) + : py::list(nodes_obj); + for (py::ssize_t i = 0; i < py::len(nodes); ++i) { + py::object node = nodes[i]; + if (!degree.contains(node)) { + degree[node] = 0; + } + } + + return degree; +} + +py::dict DiGraph_in_degree(const py::object &self, + const py::object &weight) { + py::dict degree; + + // edges 可能是属性(list/iterable)或方法（如 edges(data=True)） + py::object edges_obj = self.attr("edges"); + py::list edges = py::isinstance(edges_obj) + ? py::list(edges_obj()) + : py::list(edges_obj); + + // 遍历边：(u, v, d) + for (py::ssize_t i = 0; i < py::len(edges); ++i) { + py::tuple edge = edges[i].cast(); + // u 未使用，但保留对齐 + // py::object u = edge[0]; + py::object v = edge[1]; + py::dict d = (edge.size() >= 3) ? edge[2].cast() : py::dict(); + + // d.get(weight, 1) + py::object w = d.attr("get")(weight, 1); + + if (degree.contains(v)) { + // degree[v] += w —— 用 Python 的 __add__ 以避免数值类型差异 + degree[v] = degree[v].attr("__add__")(w); + } else { + degree[v] = w; + } + } + + // 确保所有节点都有条目：不存在则补 0 + py::object nodes_obj = self.attr("nodes"); + py::list nodes = py::isinstance(nodes_obj) + ? py::list(nodes_obj()) + : py::list(nodes_obj); + for (py::ssize_t i = 0; i < py::len(nodes); ++i) { + py::object node = nodes[i]; + if (!degree.contains(node)) { + degree[node] = 0; + } + } + + return degree; +} + +py::dict DiGraph_degree(const py::object &self, + const py::object &weight) { + py::dict degree; + + // out_degree / in_degree 都应返回 dict + py::dict out_degree = self.attr("out_degree")(weight).cast(); + py::dict in_degree = self.attr("in_degree")(weight).cast(); + + // nodes 可能是属性或方法 + py::object nodes_obj = self.attr("nodes"); + + py::list nodes = py::isinstance(nodes_obj) + ? py::list(nodes_obj()) + : py::list(nodes_obj); + + for (py::ssize_t i = 0; i < py::len(nodes); ++i) { + py::object u = nodes[i]; + + // 取度值：若不存在则当 0 + py::object out_v = out_degree.contains(u) ? out_degree[u] : py::int_(0); + py::object in_v = in_degree.contains(u) ? in_degree[u] : py::int_(0); + + // degree[u] = out_v + in_v （用 Python 的 __add__ 以兼容 int/float/Decimal + // 等） + degree[u] = out_v.attr("__add__")(in_v); + } + return degree; +} + +py::object DiGraph_size(const py::object &self, + const py::object &weight) { + py::dict out_degree = self.attr("out_degree")(weight).cast(); + + py::object values = out_degree.attr("values")(); // dict_values 视图 + py::object s = py::module_::import("builtins").attr("sum")(values); + + return weight.is_none() ? py::int_(s) : s; +} + +py::object DiGraph_number_of_edges(const py::object &self, + const py::object &u, + const py::object &v) { + // 若未指定 u（与原先 u == py::object() 等价），直接返回 size() + if (u.is_none()) { + return self.attr("size")(); + } + + // 将 self 视为 Graph 的引用 + Graph &G = self.cast(); + + // node_to_id: Python dict（与原代码保持一致） + py::dict node_to_id = G.node_to_id; + + // u_id = node_to_id[u] + node_t u_id = node_to_id[u].cast(); + + // v_id = node_to_id.get(v, -1) + node_t v_id = node_to_id.attr("get")(v, py::int_(-1)).cast(); + + // 计算是否存在边 (u, v) + int exists = + (v_id != static_cast(-1)) && (G.adj[u_id].count(v_id) ? 1 : 0); + return py::int_(exists); // 与原实现保持返回 0/1 的 int +} diff --git a/cpp_easygraph/src/evaluation.cpp b/cpp_easygraph/src/evaluation.cpp new file mode 100644 index 00000000..023d07be --- /dev/null +++ b/cpp_easygraph/src/evaluation.cpp @@ -0,0 +1,295 @@ +#include "evaluation.h" +#include "graph.h" +#include "utils.h" + +struct pair_hash { + template + std::size_t operator()(const std::pair &p) const { + auto h1 = std::hash()(p.first); + auto h2 = std::hash()(p.second); + return h1 ^ h2; + } +}; + +std::unordered_map, weight_t, pair_hash> sum_nmw_rec, + max_nmw_rec, local_constraint_rec; + +enum norm_t { sum, max }; + +weight_t mutual_weight(adj_dict_factory &G, node_t u, node_t v, + std::string weight) { + weight_t a_uv = 0, a_vu = 0; + if (G.count(u) && G[u].count(v)) { + edge_attr_dict_factory &guv = G[u][v]; + a_uv = guv.count(weight) ? guv[weight] : 1; + } + if (G.count(v) && G[v].count(u)) { + edge_attr_dict_factory &gvu = G[v][u]; + a_uv = gvu.count(weight) ? gvu[weight] : 1; + } + return a_uv + a_vu; +} + +weight_t normalized_mutual_weight(adj_dict_factory &G, node_t u, node_t v, + std::string weight, norm_t norm = sum) { + std::pair edge = std::make_pair(u, v); + auto &nmw_rec = (norm == sum) ? sum_nmw_rec : max_nmw_rec; + if (nmw_rec.count(edge)) { + return nmw_rec[edge]; + } else { + weight_t scale = 0; + for (auto &w : G[u]) { + weight_t temp_weight = mutual_weight(G, u, w.first, weight); + scale = + (norm == sum) ? (scale + temp_weight) : std::max(scale, temp_weight); + } + weight_t nmw = scale ? (mutual_weight(G, u, v, weight) / scale) : 0; + nmw_rec[edge] = nmw; + return nmw; + } +} + +weight_t local_constraint(adj_dict_factory &G, node_t u, node_t v, + std::string weight = "None") { + std::pair edge = std::make_pair(u, v); + if (local_constraint_rec.count(edge)) { + return local_constraint_rec[edge]; + } else { + weight_t direct = normalized_mutual_weight(G, u, v, weight); + weight_t indirect = 0; + for (auto &w : G[u]) { + indirect += normalized_mutual_weight(G, u, w.first, weight) * + normalized_mutual_weight(G, w.first, v, weight); + } + weight_t result = pow((direct + indirect), 2); + local_constraint_rec[edge] = result; + return result; + } +} + +std::pair +compute_constraint_of_v(adj_dict_factory &G, node_t v, std::string weight) { + weight_t constraint_of_v = 0; + if (G[v].size() == 0) { + constraint_of_v = Py_NAN; + } else { + for (const auto &n : G[v]) { + constraint_of_v += local_constraint(G, v, n.first, weight); + } + } + return std::make_pair(v, constraint_of_v); +} + +py::dict constraint(const py::object &G, py::object nodes, + const py::object &weight, + const py::object &n_workers /*未使用但保留签名*/) { + // 1) 预处理 + std::string weight_key = weight_to_string(weight); + sum_nmw_rec.clear(); + max_nmw_rec.clear(); + local_constraint_rec.clear(); + + // 2) nodes 缺省：从 G.nodes 获取；兼容属性或方法 + if (nodes.is_none()) { + nodes = G.attr("nodes"); + } + py::list nodes_list; + if (py::isinstance(nodes) || PyCallable_Check(nodes.ptr())) + nodes_list = py::list(nodes()); + else + nodes_list = py::list(nodes); + + // 3) 主循环 + py::dict result; + Graph &G_ = G.cast(); + + for (py::ssize_t i = 0; i < py::len(nodes_list); ++i) { + py::object v = nodes_list[i]; + + // v_id = G_.node_to_id[v] + // 若 node_to_id 是 py::dict + node_t v_id = G_.node_to_id[v].cast(); + + // 计算 (best_id, value) + std::pair p = + compute_constraint_of_v(G_.adj, v_id, weight_key); + + // key = G_.id_to_node[p.first] + py::object key = G_.id_to_node.attr("get")(py::int_(p.first)); + + // result[key] = p.second + result[key] = py::cast(p.second); + } + + return result; +} + +weight_t redundancy(adj_dict_factory &G, node_t u, node_t v, + std::string weight = "None") { + weight_t r = 0; + for (const auto &neighbor_info : G[u]) { + node_t w = neighbor_info.first; + r += normalized_mutual_weight(G, u, w, weight) * + normalized_mutual_weight(G, v, w, weight, max); + } + return 1 - r; +} + +py::dict effective_size(const py::object &G, py::object nodes, + const py::object &weight, + const py::object &n_workers /*未用，保留签名*/) { + Graph &G_ = G.cast(); + + // 与原逻辑一致的全局缓存清理 + sum_nmw_rec.clear(); + max_nmw_rec.clear(); + + py::dict eff; + + // nodes 缺省：迭代整个图 + if (nodes.is_none()) { + nodes = G; // 假定 G 可迭代出节点 + } + py::list nodes_list(nodes); + + // 为了兼容 G[v] 的写法 + py::object getitem = G.attr("__getitem__"); + py::object py_nan = py::module_::import("math").attr("nan"); + + // 无向图 + 无权：使用 ego_subgraph 的闭式公式 + if (!G.attr("is_directed")().cast() && weight.is_none()) { + for (py::ssize_t i = 0; i < py::len(nodes_list); ++i) { + py::object v = nodes_list[i]; + + // 度为 0 → NaN + if (py::len(getitem(v)) == 0) { + eff[v] = py_nan; + continue; + } + + py::object E = G.attr("ego_subgraph")(v); + auto n = py::len(E); + if (n > 1) { + weight_t size = E.attr("size")().cast(); + // val = n - 1 - (2 * size) / (n - 1) + double nd = static_cast(n); + double val = nd - 1.0 - (2.0 * static_cast(size)) / (nd - 1.0); + eff[v] = py::float_(val); + } else { + eff[v] = py::int_(0); + } + } + } else { + // 有向或有权：按邻接表+redundancy 求和 + const std::string weight_key = weight_to_string(weight); + + for (py::ssize_t i = 0; i < py::len(nodes_list); ++i) { + py::object v = nodes_list[i]; + + if (py::len(getitem(v)) == 0) { + eff[v] = py_nan; + continue; + } + + weight_t redundancy_sum = weight_t(0); + + // v_id = node_to_id[v] + // （pybind11 的 py::dict 不建议用 operator[] 取值，改用 get） + node_t v_id = G_.node_to_id.attr("get")(v, py::none()).cast(); + + for (const auto &nbr : G_.adj[v_id]) { + node_t u_id = nbr.first; + redundancy_sum += redundancy(G_.adj, v_id, u_id, weight_key); + } + eff[v] = py::cast(redundancy_sum); + } + } + + return eff; +} + +py::dict hierarchy(Graph& G, + py::object nodes, + py::object weight, + py::object n_workers) { + sum_nmw_rec.clear(); + max_nmw_rec.clear(); + local_constraint_rec.clear(); + + // 权重键（允许 None；你的 local_constraint/取权重逻辑应能在缺失时回退到 1） + const std::string weight_key = weight_to_string(weight); + + // 构造要处理的节点列表（Python 对象形式） + std::vector nodes_vec; + if (nodes.is_none()) { + nodes_vec.reserve(G.node.size()); + for (const auto &kv : G.node) { + const node_t nid = kv.first; + // 从 id_to_node 取回 Python 节点对象（const 情况下用 __getitem__） + nodes_vec.emplace_back(G.id_to_node.attr("__getitem__")(py::cast(nid))); + } + } else { + for (py::handle h : nodes) { + py::object v = py::reinterpret_borrow(h); + if (G.node_to_id.contains(v)) + nodes_vec.emplace_back(std::move(v)); + } + } + + py::dict result; + + for (const py::object &v_obj : nodes_vec) { + // v -> id；若节点不在图中（并发修改等），跳过 + if (!G.node_to_id.contains(v_obj)) { + result[v_obj] = 0.0; + continue; + } + const node_t v_id = py::cast(G.node_to_id[v_obj]); + + // 邻居集合（去掉自环） + std::vector nbrs_vec; + if (auto it = G.adj.find(v_id); it != G.adj.end()) { + nbrs_vec.reserve(it->second.size()); + for (const auto &kv : it->second) { + const node_t w_id = kv.first; + if (w_id != v_id) + nbrs_vec.push_back(w_id); + } + } + const int n = static_cast(nbrs_vec.size()); + if (n <= 1) { + result[v_obj] = 0.0; + continue; + } + + // 计算每个邻居的 local_constraint 以及总和 C + std::vector c_vals; + c_vals.reserve(n); + + double C = 0.0; + for (const node_t w_id : nbrs_vec) { + const double cw = + static_cast(local_constraint(G.adj, v_id, w_id, weight_key)); + c_vals.push_back(cw); + C += cw; + } + + double h_sum = 0.0; + if (C > 0.0) { + // hierarchy_sum = sum_{w in N(v)} ( (c_w/C)*n * log((c_w/C)*n) ) / (n*log + // n) + const double n_log_n = + static_cast(n) * std::log(static_cast(n)); + for (double cw : c_vals) { + const double p = cw / C; // 归一化权重 + const double t = p * static_cast(n); + if (t > 0.0) { + h_sum += (t * std::log(t)) / n_log_n; + } + } + } + result[v_obj] = h_sum; // 若 C==0 则为 0 + } + + return result; +} diff --git a/cpp_easygraph/src/graph.cpp b/cpp_easygraph/src/graph.cpp new file mode 100644 index 00000000..43567e6b --- /dev/null +++ b/cpp_easygraph/src/graph.cpp @@ -0,0 +1,865 @@ +#include "graph.h" +#include "common.h" +#include "utils.h" + +Graph::Graph() { + py::object MappingProxyType = py::module_::import("types").attr("MappingProxyType"); + this->id = 0; + this->dirty_nodes = true; + this->dirty_adj = true; + this->node_to_id = py::dict(); + this->id_to_node = py::dict(); + this->graph = py::dict(); + this->nodes_cache = MappingProxyType(py::dict()); + this->adj_cache = MappingProxyType(py::dict()); +} + +void Graph___init__(Graph &self, py::kwargs kwargs) { + // 可选：防止重复初始化，placement-new 复位 + new (&self) Graph(); + + // graph.update(kwargs) + if (kwargs && py::len(kwargs) > 0) { + self.graph.attr("update")(kwargs); + // 也可手动拷贝键值： + // for (auto &item : kwargs) self.graph[py::str(item.first)] = item.second; + } + + // 重新创建只读 cache + py::object MappingProxyType = py::module_::import("types").attr("MappingProxyType"); + self.nodes_cache = MappingProxyType(py::dict()); + self.adj_cache = MappingProxyType(py::dict()); +} + +py::object Graph__iter__(py::object self) { + return self.attr("nodes").attr("__iter__")(); +} + +py::object Graph__len__(const py::object& self) { + // 将 self 转成 Graph& + Graph& self_ = self.cast(); + + // 计算 Python 层 len(node_to_id) + py::ssize_t n = py::len(self_.node_to_id); + + // 返回 Python int + return py::int_(n); +} + +py::object Graph__contains__(const py::object& self, const py::object& node) { + Graph& self_ = self.cast(); + + try { + // 若 node_to_id 是 Python dict，可直接调用 contains() + bool has = self_.node_to_id.attr("__contains__")(node).cast(); + return py::bool_(has); + } + catch (const py::error_already_set& e) { + // 捕获 Python 异常 + if (e.matches(PyExc_TypeError)) { + // TypeError: 节点类型不匹配 → 返回 False + PyErr_Clear(); + return py::bool_(false); + } else { + // 重新抛出其他异常，让 Python 层能看到原始错误 + throw; + } + } +} + +py::object Graph__getitem__(py::object self, py::object node) { + return self.attr("adj")[node]; +} + +node_t _add_one_node(Graph& self, + const py::object& one_node_for_adding, + py::object node_attr /* = None */) { + if (node_attr.is_none()) { + node_attr = py::dict(); + } + + node_t id; + // if self.node_to_id.contains(one_node_for_adding) + const bool has = + self.node_to_id.attr("__contains__")(one_node_for_adding).cast(); + + if (has) { + // id = self.node_to_id[one_node_for_adding] + id = self.node_to_id.attr("__getitem__")(one_node_for_adding).cast(); + } else { + id = ++(self.id); + + // self.id_to_node[id] = one_node_for_adding + self.id_to_node.attr("__setitem__")(py::int_(id), one_node_for_adding); + + // self.node_to_id[one_node_for_adding] = id + self.node_to_id.attr("__setitem__")(one_node_for_adding, py::int_(id)); + } + + // items = list(node_attr.items()) + py::list items = py::list(node_attr.attr("items")()); + + // 初始化 C++ 侧的属性/邻接容器 + self.node[id] = node_attr_dict_factory(); + self.adj[id] = adj_attr_dict_factory(); + + for (py::ssize_t i = 0; i < py::len(items); ++i) { + py::tuple kv = items[i].cast(); + py::object pkey = kv[0]; + std::string weight_key = weight_to_string(pkey); + weight_t value = kv[1].cast(); + self.node[id].insert({weight_key, value}); + } + + return id; +} + +py::object Graph_add_node(const py::tuple& args, const py::dict& kwargs) { + // args: [self, node] + Graph& self = args[0].cast(); + py::object one_node_for_adding = args[1]; + + self.dirty_nodes = true; + self.dirty_adj = true; + + // kwargs 直接当作属性字典传入 + py::object node_attr = kwargs; // kwargs 本身就是 dict-like + _add_one_node(self, one_node_for_adding, node_attr); + + return py::none(); // 等价于原来的 py::object() +} + + +py::object Graph_add_nodes(Graph& self, + const py::list& nodes_for_adding, + const py::list& nodes_attr) { + self.dirty_nodes = true; + self.dirty_adj = true; + + if (py::len(nodes_attr) != 0 && + py::len(nodes_for_adding) != py::len(nodes_attr)) { + throw py::value_error("Nodes and attributes lists must have the same length."); + } + + for (py::ssize_t i = 0; i < py::len(nodes_for_adding); ++i) { + py::object one_node_for_adding = nodes_for_adding[i]; + + py::dict node_attr; + if (py::len(nodes_attr) != 0) { + node_attr = nodes_attr[i].cast(); // 若不是 dict，会抛 TypeError + } else { + node_attr = py::dict(); + } + + _add_one_node(self, one_node_for_adding, node_attr); + } + + return py::none(); +} + +void Graph_add_nodes_from(Graph& self, const py::iterable& nodes_for_adding, const py::kwargs& kwargs) { + self.dirty_nodes = true; + self.dirty_adj = true; + + // 预先把 kwargs 复制到一个 dict（避免原地修改 kwargs） + py::dict base_attrs; + for (auto item : kwargs) { + base_attrs[item.first] = item.second; + } + + for (py::handle h : nodes_for_adding) { + py::object n_obj = py::reinterpret_borrow(h); + py::dict merged_attrs = py::dict(base_attrs); // 每个节点的属性从 kwargs 起步 + + // 支持形如 (node, {attr...}) 的二元组 + if (py::isinstance(n_obj)) { + py::tuple t = n_obj.cast(); + if (py::len(t) != 2) + throw py::type_error("Each tuple must be (node, dict)."); + + py::object node = t[0]; + py::object maybe_dict = t[1]; + + if (!py::isinstance(maybe_dict)) + throw py::type_error("Second element of tuple must be a dict."); + + py::dict ndict = maybe_dict.cast(); + // 合并 per-node 属性：kwargs < ndict（ndict 覆盖同名键） + for (auto kv : ndict) { + merged_attrs[kv.first] = kv.second; + } + n_obj = std::move(node); + } + + // 禁止 None 作为节点 + if (n_obj.is_none()) + throw py::value_error("None cannot be a node."); + + // 如为新节点则先添加 + bool newnode = !self.node_to_id.contains(n_obj); + if (newnode) { + _add_one_node(self, n_obj, py::none()); + } + + // 获取 node id；若你的 map 直接存的是 node_t，可去掉 cast + node_t id = py::cast(self.node_to_id[n_obj]); + + // 写入属性 + for (auto kv : merged_attrs) { + py::handle k = kv.first; + py::handle v = kv.second; + + // 若你的 weight_to_string 接受 py::object： + std::string weight_key = weight_to_string(py::reinterpret_borrow(k)); + weight_t weight_val = py::cast(v); + + self.node[id].insert(std::make_pair(std::move(weight_key), std::move(weight_val))); + } + } +} +void Graph_remove_node(Graph& self, const py::object& node_to_remove) { + self.dirty_nodes = true; + self.dirty_adj = true; + + if (!self.node_to_id.contains(node_to_remove)) { + // KeyError: 带上对象 repr + throw py::key_error(py::str("No node {} in graph.").format(node_to_remove)); + } + + // 从 Python dict 中取出 id 并转为 node_t + node_t node_id = py::cast(self.node_to_id[node_to_remove]); + + // 先从所有邻居的邻接表中删除该节点 + // 注：这里修改的是 neighbor 的容器，不会使对 self.adj[node_id] 的遍历失效 + for (const auto& kv : self.adj[node_id]) { + const node_t neighbor_id = kv.first; + self.adj[neighbor_id].erase(node_id); + } + + // 再删掉该节点的邻接表与节点属性 + self.adj.erase(node_id); + self.node.erase(node_id); + + // 同步 Python 侧的映射（与原代码一致使用 pop） + self.node_to_id.attr("pop")(node_to_remove); + self.id_to_node.attr("pop")(node_id); +} + +void Graph_remove_nodes(Graph& self, const py::sequence& nodes_to_remove) { + self.dirty_nodes = true; + self.dirty_adj = true; + + const std::size_t n = py::len(nodes_to_remove); + + // 先整体校验（与原逻辑一致：任一不存在则立即报错并不做部分删除） + for (std::size_t i = 0; i < n; ++i) { + py::object node = nodes_to_remove[i]; + if (!self.node_to_id.contains(node)) { + throw py::key_error(py::str("No node {} in graph.").format(node)); + } + } + + // 再逐个删除（若输入包含重复节点，第二次删除会抛 KeyError，与原行为一致） + for (std::size_t i = 0; i < n; ++i) { + py::object node = nodes_to_remove[i]; + Graph_remove_node(self, node); // 直接调 C++ 实现，避免 Python 回调开销 + } +} + +py::object Graph_number_of_nodes(Graph& self) { + return py::int_(self.node.size()); +} + +bool Graph_has_node(Graph &self, py::object node) { + return self.node_to_id.contains(node); +} + +py::object Graph_nbunch_iter(py::object self, py::object nbunch) { + py::object bunch = py::object(); + if (nbunch.is_none()) { + bunch = self.attr("adj").attr("__iter__")(); + } + else if (self.contains(nbunch)) { + py::list nbunch_wrapper = py::list(); + nbunch_wrapper.append(nbunch); + bunch = nbunch_wrapper.attr("__iter__")(); + } + else { + py::list nbunch_list = py::list(nbunch), nodes_list = py::list(); + for (int i = 0;i < py::len(nbunch_list);i++) { + py::object n = nbunch_list[i]; + if (self.contains(n)) { + nodes_list.append(n); + } + } + bunch = nbunch_list.attr("__iter__")(); + } + return bunch; +} + +void _add_one_edge(Graph& self, const py::object& u_of_edge, const py::object& v_of_edge, const py::object& edge_attr) { + // 1) 端点确保存在并取得 id + node_t u, v; + + if (self.node_to_id.contains(u_of_edge)) { + u = py::cast(self.node_to_id[u_of_edge]); + } else { + // 这里给新节点空属性（与原始代码传 py::none() 等价） + u = _add_one_node(self, u_of_edge, py::dict{}); + } + + if (self.node_to_id.contains(v_of_edge)) { + v = py::cast(self.node_to_id[v_of_edge]); + } else { + v = _add_one_node(self, v_of_edge, py::dict{}); + } + + // 2) 规范化边属性：None -> 空 dict；否则必须是 dict + py::dict attrs; + if (edge_attr.is_none()) { + attrs = py::dict{}; + } else if (py::isinstance(edge_attr)) { + attrs = edge_attr.cast(); + } else { + throw py::type_error("edge_attr must be a dict or None."); + } + + // 3) 初始化双向邻接条目 + self.adj[u][v] = node_attr_dict_factory(); + self.adj[v][u] = node_attr_dict_factory(); + + // 4) 填充属性（dict 直接可迭代：kv.first, kv.second） + for (auto kv : attrs) { + std::string key = weight_to_string(py::reinterpret_borrow(kv.first)); + weight_t val = py::cast(kv.second); + self.adj[u][v].insert(std::make_pair(key, val)); + self.adj[v][u].insert(std::make_pair(std::move(key), val)); + // 注意：上面对 key 复用/移动若底层容器需要独立 key，可改为两次构造字符串 + } +} +void Graph_add_edge(Graph& self, const py::object& u_of_edge, const py::object& v_of_edge, const py::kwargs& kwargs) { + self.dirty_nodes = true; + self.dirty_adj = true; + + // 将 **kwargs 复制为独立 dict，避免在 _add_one_edge 内修改到调用方对象 + py::dict edge_attr; + for (auto kv : kwargs) { + edge_attr[kv.first] = kv.second; + } + + _add_one_edge(self, u_of_edge, v_of_edge, edge_attr); // 其内部负责建点与属性合并 +} + +void Graph_add_edges(Graph& self, const py::sequence& edges_for_adding, const py::sequence& edges_attr) { + self.dirty_nodes = true; + self.dirty_adj = true; + + const std::size_t n = py::len(edges_for_adding); + const std::size_t m = py::len(edges_attr); + + if (m != 0 && n != m) { + // 原代码抛 AssertionError；pybind11 无内建 assertion_error，这里用 value_error 更合适 + throw py::value_error("Edges and Attributes lists must have same length."); + } + + for (std::size_t i = 0; i < n; ++i) { + // 1) 取出一条边，要求是 (u, v) + py::object edge_obj = edges_for_adding[i]; + if (!py::isinstance(edge_obj)) { + throw py::type_error("Each edge must be a tuple (u, v)."); + } + py::tuple e = edge_obj.cast(); + if (py::len(e) != 2) { + throw py::type_error("Each edge tuple must have length 2: (u, v)."); + } + py::object u = e[0]; + py::object v = e[1]; + + // 2) 选择该边对应的属性 + py::dict attr; + if (m != 0) { + attr = edges_attr[i].cast(); // 若不是 dict 会抛 type_error + } else { + attr = py::dict{}; + } + + // 3) 添加该边（_add_one_edge 内部负责必要的建点与属性赋值） + _add_one_edge(self, u, v, attr); + } +} + +void Graph_add_edges_from(Graph& self, const py::iterable& ebunch, const py::kwargs& attr) { + self.dirty_nodes = true; + self.dirty_adj = true; + + // 1) 复制全局属性 kwargs + py::dict base_attrs; + for (auto kv : attr) base_attrs[kv.first] = kv.second; + + // 2) 遍历边集合 + for (py::handle h : ebunch) { + py::object eobj = py::reinterpret_borrow(h); + + // 允许 list/tuple/任意可序列化为 sequence 的对象 + py::sequence e = eobj.cast(); + const std::size_t L = py::len(e); + if (L != 2 && L != 3) { + throw py::value_error(py::str("Edge tuple {} must be a 2-tuple or 3-tuple.").format(eobj)); + } + + py::object u = e[0]; + py::object v = e[1]; + if (u.is_none() || v.is_none()) { + throw py::value_error("None cannot be a node."); + } + + // 每边的局部属性（kwargs < per-edge dict） + py::dict per_edge = py::dict(base_attrs); + if (L == 3) { + py::object maybe_dict = e[2]; + if (!py::isinstance(maybe_dict)) { + throw py::type_error("Edge data (3rd element) must be a dict."); + } + py::dict dd = maybe_dict.cast(); + for (auto kv : dd) per_edge[kv.first] = kv.second; + } + + // 3) 确保端点存在并获得 id + node_t uid, vid; + if (self.node_to_id.contains(u)) { + uid = py::cast(self.node_to_id[u]); + } else { + uid = _add_one_node(self, u, py::dict{}); + } + if (self.node_to_id.contains(v)) { + vid = py::cast(self.node_to_id[v]); + } else { + vid = _add_one_node(self, v, py::dict{}); + } + + // 4) 初始化（若不存在则创建）边属性容器 + if (!self.adj[uid].count(vid)) self.adj[uid][vid] = node_attr_dict_factory(); + if (!self.adj[vid].count(uid)) self.adj[vid][uid] = node_attr_dict_factory(); + + auto& uv = self.adj[uid][vid]; + auto& vu = self.adj[vid][uid]; + + // 5) 写入属性：赋值语义（覆盖旧值），两向一致 + for (auto kv : per_edge) { + std::string k = weight_to_string(py::reinterpret_borrow(kv.first)); + weight_t vval = py::cast(kv.second); + uv[k] = vval; + vu[k] = vval; + } + } +} + +struct commactype : std::ctype { + commactype() : std::ctype(get_table()) {} + + static const std::ctype_base::mask* get_table() { + using mask = std::ctype_base::mask; + static std::vector table(std::ctype::table_size, mask()); // 静态存储期 + static bool inited = false; + if (!inited) { + table[','] = std::ctype_base::space; + table[' '] = std::ctype_base::space; + table['\t'] = std::ctype_base::space; + table['\n'] = std::ctype_base::space; + table['\r'] = std::ctype_base::space; + inited = true; + } + return table.data(); + } +}; + +void Graph_add_edges_from_file(Graph& self, const py::str& file, bool weighted) { + self.dirty_nodes = true; + self.dirty_adj = true; + + std::ios::sync_with_stdio(false); + + const std::string file_path = py::cast(file); + std::ifstream in(file_path); + if (!in.is_open()) { + throw py::value_error("File not found: " + file_path); + } + in.imbue(std::locale(std::locale(), new commactype)); + + std::string su, sv; + const std::string key = "weight"; + weight_t w{}; + + while (in >> su >> sv) { + py::str pu(su), pv(sv); + + // 取得/创建端点 id + node_t uid, vid; + if (self.node_to_id.contains(pu)) { + uid = py::cast(self.node_to_id[pu]); + } else { + uid = _add_one_node(self, pu, py::dict{}); + } + if (self.node_to_id.contains(pv)) { + vid = py::cast(self.node_to_id[pv]); + } else { + vid = _add_one_node(self, pv, py::dict{}); + } + + // 初始化两向邻接条目（若尚不存在） + if (!self.adj[uid].count(vid)) self.adj[uid][vid] = node_attr_dict_factory(); + if (!self.adj[vid].count(uid)) self.adj[vid][uid] = node_attr_dict_factory(); + + if (weighted) { + if (!(in >> w)) { + throw py::value_error("Weighted file format error: missing/invalid weight after edge (" + su + ", " + sv + ")."); + } + self.adj[uid][vid][key] = w; + self.adj[vid][uid][key] = w; + } + // 无权重：仅保证邻接存在，属性留空 + } +} +py::object Graph_add_weighted_edge(Graph& self, py::object u_of_edge, py::object v_of_edge, weight_t weight) { + self.dirty_nodes = true; + self.dirty_adj = true; + py::dict edge_attr; + edge_attr["weight"] = weight; + _add_one_edge(self, u_of_edge, v_of_edge, edge_attr); + return py::object(); +} + +void Graph_remove_edge(Graph& self, const py::object& u, const py::object& v) { + self.dirty_nodes = true; + self.dirty_adj = true; + + if (!self.node_to_id.contains(u) || !self.node_to_id.contains(v)) { + throw py::key_error(py::str("No edge {}-{} in graph.").format(u, v)); + } + + const node_t uid = py::cast(self.node_to_id[u]); + const node_t vid = py::cast(self.node_to_id[v]); + + // 不创建默认邻接表：用 find 检查 + auto it_u = self.adj.find(uid); + if (it_u == self.adj.end()) { + throw py::key_error(py::str("No edge {}-{} in graph.").format(u, v)); + } + auto& nbrs_u = it_u->second; + + auto it_uv = nbrs_u.find(vid); + if (it_uv == nbrs_u.end()) { + throw py::key_error(py::str("No edge {}-{} in graph.").format(u, v)); + } + + // 删除 u->v + nbrs_u.erase(it_uv); + + // 无向图对称删除 v->u（若自环则不重复） + if (uid != vid) { + auto it_v = self.adj.find(vid); + if (it_v != self.adj.end()) { + it_v->second.erase(uid); + } + } +} +void Graph_remove_edges(Graph& self, const py::sequence& edges_to_remove) { + self.dirty_nodes = true; + self.dirty_adj = true; + + const std::size_t n = py::len(edges_to_remove); + for (std::size_t i = 0; i < n; ++i) { + py::object edge_obj = edges_to_remove[i]; + if (!py::isinstance(edge_obj)) { + throw py::type_error("Each edge must be a tuple (u, v)."); + } + py::tuple edge = edge_obj.cast(); + if (py::len(edge) != 2) { + throw py::type_error("Each edge tuple must have length 2: (u, v)."); + } + py::object u = edge[0]; + py::object v = edge[1]; + + Graph_remove_edge(self, u, v); + } +} + +int Graph_number_of_edges(const Graph& self, py::object u, py::object v) { + // 1) 全图边数 + if (u.is_none()) { + std::size_t total = 0; + for (const auto& kv : self.adj) total += kv.second.size(); + return static_cast(total / 2); + } + + // 2) 指定 (u, v) 是否存在：不存在节点 → 0 + if (!self.node_to_id.contains(u) || !self.node_to_id.contains(v)) { + return 0; + } + + const node_t uid = py::cast(self.node_to_id[u]); + const node_t vid = py::cast(self.node_to_id[v]); + + // 不要用 self.adj[uid] 以免创建空条目 + auto it_u = self.adj.find(uid); + if (it_u == self.adj.end()) return 0; + + const auto& nbrs_u = it_u->second; + return static_cast(nbrs_u.count(vid) ? 1 : 0); +} + +bool Graph_has_edge(const Graph& self, const py::object& u, const py::object& v) { + if (!self.node_to_id.contains(u) || !self.node_to_id.contains(v)) + return false; + + const node_t uid = py::cast(self.node_to_id[u]); + const node_t vid = py::cast(self.node_to_id[v]); + + auto it_u = self.adj.find(uid); + if (it_u == self.adj.end()) + return false; + + const auto& nbrs_u = it_u->second; + return nbrs_u.find(vid) != nbrs_u.end(); +} + +py::object Graph_copy(py::handle self_h) { + // 取 C++ 引用 + const Graph& self = py::cast(self_h); + + // 使用 self.__class__() 构造同类型实例 + py::object cls = py::type::of(self_h); + py::object Gobj = cls(); // 调用该类型的无参构造；需在绑定里暴露默认构造 + + // 取得其 C++ 引用，拷贝字段 + Graph& G = py::cast(Gobj); + + G.graph = py::dict(self.graph); + G.id_to_node = py::dict(self.id_to_node); + G.node_to_id = py::dict(self.node_to_id); + G.node = self.node; + G.adj = self.adj; + G.dirty_nodes = self.dirty_nodes; + G.dirty_adj = self.dirty_adj; + + return Gobj; // 返回 Python 对象（保持动态类型） +} + +py::dict Graph_degree(const Graph& self, py::object weight) { + // 1) 预处理权重键 + const bool use_weight = !weight.is_none(); + std::string wkey; + if (use_weight) { + wkey = weight_to_string(py::reinterpret_borrow(weight)); + } + + // 2) 累加度数：用临时 map，避免反复操作 py::dict + std::unordered_map deg; + + // 先为所有节点置 0（保证孤立点也在结果里） + for (const auto& kv : self.node) { + deg.emplace(kv.first, 0.0); + } + + // 3) 遍历边（避免双计：仅在 uid <= vid 时计一次） + for (const auto& [uid, nbrs] : self.adj) { + for (const auto& [vid, attrs] : nbrs) { + if (uid > vid) continue; // 无向图去重 + double w = 1.0; + if (use_weight) { + auto it = attrs.find(wkey); + if (it != attrs.end()) { + w = static_cast(it->second); + } + } + deg[uid] += w; + deg[vid] += w; + } + } + + // 4) 生成 Python dict：键为原始 Python 节点对象 + py::dict degree; + for (const auto& [nid, val] : deg) { + // self.id_to_node[nid] -> py::object + py::object node_obj = self.id_to_node.attr("__getitem__")(py::cast(nid)); + degree[node_obj] = val; + } + + return degree; +} + +py::list Graph_neighbors(const Graph& self, const py::object& node) { + if (!self.node_to_id.contains(node)) { + throw py::key_error(py::str("No node {}").format(node)); + } + + const node_t uid = py::cast(self.node_to_id[node]); + + py::list out; + auto it = self.adj.find(uid); + if (it == self.adj.end()) { + return out; // 没有邻居 + } + + const auto& nbrs = it->second; // map + for (const auto& kv : nbrs) { + const node_t vid = kv.first; + // 从 id_to_node 取回 Python 节点对象（const 上用 __getitem__ 避免 operator[]） + py::object v = self.id_to_node.attr("__getitem__")(py::cast(vid)); + out.append(v); + } + return out; +} + +py::object Graph_nodes_subgraph(py::handle self_h, const py::sequence& from_nodes) { + const Graph& self = py::cast(self_h); + + // 1) 构造“同类”实例：等价于 Python 的 self.__class__() + py::object cls = py::type::of(self_h); + py::object Gobj = cls(); // 需要 Graph 在绑定里有无参构造 + Graph& G = py::cast(Gobj); + + // 2) 复制元数据 graph（浅拷贝） + G.graph = py::dict(self.graph); + + // 3) 收集子集节点（只加入存在于原图的节点） + std::unordered_set subset; + const std::size_t n = py::len(from_nodes); + for (std::size_t i = 0; i < n; ++i) { + py::object node = from_nodes[i]; + if (!self.node_to_id.contains(node)) continue; + + node_t nid = py::cast(self.node_to_id[node]); + subset.insert(nid); + + // 取该节点属性 -> py::dict + py::dict node_attr; + auto it = self.node.find(nid); + if (it != self.node.end()) { + for (const auto& kv : it->second) { + node_attr[py::str(kv.first)] = kv.second; // weight_t 可隐式/显式 cast + } + } + + // 在子图中建点（保持原 Python 节点对象） + _add_one_node(G, node, node_attr); + } + + // 4) 子集诱导边：仅当两端都在 subset 中；无向图用 uid <= vid 去重 + for (node_t uid : subset) { + auto it_u = self.adj.find(uid); + if (it_u == self.adj.end()) continue; + + for (const auto& kv : it_u->second) { + node_t vid = kv.first; + if (!subset.count(vid)) continue; + if (uid > vid) continue; // 无向图避免重复添加 + + // 边属性 -> py::dict + py::dict edge_attr; + for (const auto& e : kv.second) { + edge_attr[py::str(e.first)] = e.second; + } + + // 从 id 取回 Python 节点对象 + py::object u_obj = self.id_to_node.attr("__getitem__")(py::cast(uid)); + py::object v_obj = self.id_to_node.attr("__getitem__")(py::cast(vid)); + + _add_one_edge(G, u_obj, v_obj, edge_attr); + } + } + + return Gobj; +} +py::object Graph_ego_subgraph(py::object self, py::object center) { + py::list neighbors_of_center = py::list(self.attr("all_neighbors")(center)); + neighbors_of_center.append(center); + return self.attr("nodes_subgraph")(neighbors_of_center); +} + +py::object Graph_size(const Graph& G, py::object weight ) { + py::dict deg = Graph_degree(G, weight); // {node_obj: degree_value} + + double sum_deg = 0.0; + for (auto kv : deg) { + sum_deg += py::cast(kv.second); + } + + if (weight.is_none()) { + // 与原逻辑一致：先转整型再除 2（整数除法） + // 这里 sum_deg 应该是偶数（无向图），做一次显式截断 + long long m2 = static_cast(sum_deg); + return py::int_(m2 / 2); + } else { + return py::float_(sum_deg / 2.0); + } +} + +bool Graph_is_directed(const Graph& self) { + return false; +} + +bool Graph_is_multigraph(const Graph& self) { + return false; +} + +py::object Graph::get_nodes() { + py::object MappingProxyType = py::module_::import("types").attr("MappingProxyType"); + if (this->dirty_nodes) { + py::dict nodes = py::dict(); + for (const auto& node_info : node) { + node_t id = node_info.first; + const auto& node_attr = node_info.second; + nodes[this->id_to_node[py::int_(id)]] = MappingProxyType(attr_to_dict(node_attr)); + } + this->nodes_cache = MappingProxyType(nodes); + this->dirty_nodes = false; + } + return this->nodes_cache; +} + +py::object Graph::get_name() { + return this->graph.attr("get")("name", ""); +} + +py::object Graph::get_graph() { + return this->graph; +} + +py::object Graph::get_adj() { + py::object MappingProxyType = py::module_::import("types").attr("MappingProxyType"); + if (this->dirty_adj) { + py::dict adj = py::dict(); + for (const auto& ego_edges : this->adj) { + node_t start_point = ego_edges.first; + py::dict ego_edges_dict = py::dict(); + for (const auto& edge_info : ego_edges.second) { + node_t end_point = edge_info.first; + const auto& edge_attr = edge_info.second; + ego_edges_dict[this->id_to_node[py::int_(end_point)]] = MappingProxyType(attr_to_dict(edge_attr)); + } + adj[this->id_to_node[py::int_(start_point)]] = MappingProxyType(ego_edges_dict); + } + this->adj_cache = MappingProxyType(adj); + this->dirty_adj = false; + } + return this->adj_cache; +} + +py::object Graph::get_edges() { + py::list edges = py::list(); + std::set > seen; + for (const auto& ego_edges : this->adj) { + node_t u = ego_edges.first; + for (const auto& edge_info : ego_edges.second) { + node_t v = edge_info.first; + const auto& edge_attr = edge_info.second; + if (seen.find(std::make_pair(u,v)) == seen.end()) { + seen.insert(std::make_pair(u,v)); + seen.insert(std::make_pair(v,u)); + edges.append(py::make_tuple(this->id_to_node[py::int_(u)], this->id_to_node[py::int_(v)], attr_to_dict(edge_attr))); + } + } + } + return edges; +} diff --git a/cpp_easygraph/src/operation.cpp b/cpp_easygraph/src/operation.cpp new file mode 100644 index 00000000..5904ea49 --- /dev/null +++ b/cpp_easygraph/src/operation.cpp @@ -0,0 +1,18 @@ +#include "operation.h" +#include "graph.h" +double density(const Graph& G) { + const std::size_t n = G.node.size(); + if (n <= 1) return 0.0; + + // m2 为度数总和；无向图中 m2 = 2 * |E| + std::size_t m2 = 0; + for (const auto& kv : G.adj) { + m2 += kv.second.size(); + } + if (m2 == 0) return 0.0; + + // 与原实现一致：d = m2 / (n*(n-1)) + // 对无向简单图，这等价于 2|E| / (n*(n-1)) + return static_cast(m2) / + (static_cast(n) * static_cast(n - 1)); +} diff --git a/cpp_easygraph/src/path.cpp b/cpp_easygraph/src/path.cpp new file mode 100644 index 00000000..4fd80dff --- /dev/null +++ b/cpp_easygraph/src/path.cpp @@ -0,0 +1,371 @@ +#include "path.h" +#include "graph.h" +#include "utils.h" + +#include + +py::dict _dijkstra_multisource(const py::object &G, + const py::object &sources, + const py::object &weight, + const py::object &target) { + Graph &G_ = G.cast(); + const std::string weight_key = weight_to_string(weight); + + // target_id = G_.node_to_id.get(target, -1) + const node_t target_id = + G_.node_to_id.attr("get")(target, py::int_(-1)).cast(); + + std::map dist; + std::map seen; + + using QItem = std::pair; + std::priority_queue, std::greater> Q; + + // sources 列表 + py::list sources_list = py::list(sources); + for (py::ssize_t i = 0; i < py::len(sources_list); ++i) { + const node_t s_id = G_.node_to_id[sources_list[i]].cast(); + seen[s_id] = weight_t(0); + Q.emplace(weight_t(0), s_id); + } + + // Dijkstra + while (!Q.empty()) { + const auto node = Q.top(); + Q.pop(); + const weight_t d = node.first; + const node_t v = node.second; + + if (dist.count(v)) { + continue; + } + dist[v] = d; + + if (v == target_id) { + break; // 已到目标 + } + + auto &adj = G_.adj; // 邻接结构 + for (auto &neighbor_info : adj[v]) { // neighbor_info: (u, attr) + const node_t u = neighbor_info.first; + + // attr: 例如 std::unordered_map + auto &attr = neighbor_info.second; + const weight_t cost = + (attr.count(weight_key) ? attr[weight_key] : weight_t(1)); + + const weight_t vu_dist = dist[v] + cost; + + if (dist.count(u)) { + if (vu_dist < dist[u]) { + throw py::value_error("Contradictory paths found: negative weights?"); + } + // 否则已是最优，跳过 + } else if (!seen.count(u) || vu_dist < seen[u]) { + seen[u] = vu_dist; + Q.emplace(vu_dist, u); + } else { + // 已有更优 seen[u] + } + } + } + + // 转回 Python 映射：node_obj -> distance + py::dict pydist; + for (const auto &kv : dist) { + const node_t vid = kv.first; + const weight_t d = kv.second; + py::object key = G_.id_to_node.attr("__getitem__")(py::cast(vid)); + pydist[key] = py::cast(d); + } + return pydist; +} +py::dict Prim(Graph& G) { + py::dict result_dict; + + // 结果图（临时存：id -> (id -> weight)） + std::unordered_map> res_dict; + + auto& nodes = G.node; + auto& adj = G.adj; + + // 收集节点，初始化 selected/candidate + std::vector selected; + std::vector candidate; + selected.reserve(nodes.size()); + candidate.reserve(nodes.size()); + + for (node_dict_factory::const_iterator it = nodes.begin(); it != nodes.end(); ++it) { + node_t node_id = it->first; + // 先在结果字典中为每个 python 节点放一个空 dict + py::object node_obj = G.id_to_node.attr("__getitem__")(py::cast(node_id)); + result_dict[node_obj] = py::dict(); + + if (selected.empty()) { + selected.emplace_back(node_id); + } else { + candidate.emplace_back(node_id); + } + } + + if (selected.empty()) { + // 空图 + return result_dict; + } + + const weight_t INF = std::numeric_limits::infinity(); + + // 朴素 Prim：每次在 selected 与 candidate 间找最小权边 + while (!candidate.empty()) { + node_t best_u = static_cast(-1); + node_t best_v = static_cast(-1); + weight_t best_w = INF; + + for (std::size_t i = 0; i < selected.size(); ++i) { + const node_t u = selected[i]; + + // 找 u 的邻接 + adj_attr_dict_factory node_adj; + if (adj.find(u) != adj.end()) { + node_adj = adj.at(u); + } else { + continue; + } + + for (std::size_t j = 0; j < candidate.size(); ++j) { + const node_t v = candidate[j]; + + weight_t edge_weight = INF; + // 是否存在 u->v 边 + adj_attr_dict_factory::const_iterator it_uv = node_adj.find(v); + if (it_uv != node_adj.end()) { + const edge_attr_dict_factory& eattr = it_uv->second; + edge_attr_dict_factory::const_iterator wit = eattr.find("weight"); + edge_weight = (wit != eattr.end()) ? wit->second : static_cast(1); + } + + if (nodes.find(u) != nodes.end() && edge_weight < best_w) { + best_u = u; best_v = v; best_w = edge_weight; + } + } + } + + if (best_u != static_cast(-1) && best_v != static_cast(-1)) { + // 选入最小边 (best_u, best_v) + res_dict[best_u][best_v] = best_w; + + // v 从 candidate -> selected + selected.emplace_back(best_v); + std::vector::iterator it = std::find(candidate.begin(), candidate.end(), best_v); + if (it != candidate.end()) candidate.erase(it); + } else { + // 剩余节点与 selected 之间不连通（图不连通，Prim 停止） + break; + } + } + + // 将 res_dict 中的 id 映射成 python 节点对象，并写回 result_dict + for (std::unordered_map>::const_iterator it = res_dict.begin(); + it != res_dict.end(); ++it) { + const node_t u = it->first; + const std::unordered_map& nbrs = it->second; + + py::object u_obj = G.id_to_node.attr("__getitem__")(py::cast(u)); + py::dict u_dict = result_dict.attr("__getitem__")(u_obj).cast(); + + for (std::unordered_map::const_iterator jt = nbrs.begin(); + jt != nbrs.end(); ++jt) { + const node_t v = jt->first; + const weight_t w = jt->second; + + py::object v_obj = G.id_to_node.attr("__getitem__")(py::cast(v)); + u_dict[v_obj] = w; + } + } + + return result_dict; +}bool comp(const std::pair, weight_t> &a, + const std::pair, weight_t> &b) { + return a.second < b.second; +} +py::dict Kruskal(Graph& G) { + py::dict result_dict; + + auto& nodes = G.node; + auto& adj = G.adj; + + // 1) 为每个节点在结果字典中放一个空 dict + std::vector ids; + ids.reserve(nodes.size()); + for (auto it = nodes.begin(); it != nodes.end(); ++it) { + node_t u = it->first; + ids.push_back(u); + py::object u_obj = G.id_to_node.attr("__getitem__")(py::cast(u)); + result_dict[u_obj] = py::dict(); + } + if (ids.empty()) return result_dict; + + // 2) 收集边列表 (u,v,w) + // 若是无向图：仅收集 u < v 侧以去重；若是有向图，请移除 "if (u < v)"。 + struct Edge { node_t u, v; weight_t w; }; + std::vector edges; + for (auto uit = adj.begin(); uit != adj.end(); ++uit) { + node_t u = uit->first; + const auto& nbrs = uit->second; + for (auto vit = nbrs.begin(); vit != nbrs.end(); ++vit) { + node_t v = vit->first; + const edge_attr_dict_factory& eattr = vit->second; + auto w_it = eattr.find("weight"); + weight_t w = (w_it != eattr.end()) ? w_it->second : static_cast(1); + + if (u < v) { // 无向图去重；有向图请删除此行条件 + edges.push_back({u, v, w}); + } + } + } + + // 3) Kruskal：边按权升序 + std::sort(edges.begin(), edges.end(), + [](const Edge& a, const Edge& b) { return a.w < b.w; }); + + // 4) 并查集（DSU） + // 将 node_t 映射到 0..N-1 索引 + std::unordered_map idx; + idx.reserve(ids.size()); + for (int i = 0; i < static_cast(ids.size()); ++i) idx[ids[i]] = i; + + std::vector parent(ids.size()), rank_(ids.size(), 0); + std::iota(parent.begin(), parent.end(), 0); + + auto find = [&](int x) { + while (parent[x] != x) { + parent[x] = parent[parent[x]]; + x = parent[x]; + } + return x; + }; + auto unite = [&](int a, int b) { + a = find(a); b = find(b); + if (a == b) return false; + if (rank_[a] < rank_[b]) std::swap(a, b); + parent[b] = a; + if (rank_[a] == rank_[b]) ++rank_[a]; + return true; + }; + + // 5) 选择 MST 边（以 id->id->weight 暂存） + std::unordered_map> res_dict; + + for (const auto& e : edges) { + auto it_u = idx.find(e.u); + auto it_v = idx.find(e.v); + if (it_u == idx.end() || it_v == idx.end()) continue; // 安全性 + if (unite(it_u->second, it_v->second)) { + // 只写一个方向；若你想对称写入，可在最终输出时补回另一侧 + res_dict[e.u][e.v] = e.w; + } + } + + // 6) 将 id -> Python 节点对象，并写回 result_dict + for (auto it = res_dict.begin(); it != res_dict.end(); ++it) { + node_t u = it->first; + py::object u_obj = G.id_to_node.attr("__getitem__")(py::cast(u)); + py::dict u_dict = result_dict.attr("__getitem__")(u_obj).cast(); + + const auto& nbrs = it->second; + for (auto jt = nbrs.begin(); jt != nbrs.end(); ++jt) { + node_t v = jt->first; + weight_t w = jt->second; + + py::object v_obj = G.id_to_node.attr("__getitem__")(py::cast(v)); + u_dict[v_obj] = w; + + // 如需无向对称输出，取消下面两行注释： + // py::dict v_dict = result_dict.attr("__getitem__")(v_obj).cast(); + // v_dict[u_obj] = w; + } + } + + return result_dict; +} +py::dict Floyd(Graph& G) { + py::dict result_dict; + + auto& nodes = G.node; + auto& adj = G.adj; + + // 节点 id 列表 + std::vector ids; + ids.reserve(nodes.size()); + for (auto it = nodes.begin(); it != nodes.end(); ++it) { + ids.push_back(it->first); + // 先为每个节点放一个空 dict + py::object u_obj = G.id_to_node.attr("__getitem__")(py::cast(it->first)); + result_dict[u_obj] = py::dict(); + } + if (ids.empty()) return result_dict; + + const weight_t INF = std::numeric_limits::infinity(); + + // 距离矩阵（用哈希映射表示） + std::unordered_map> dist; + dist.reserve(ids.size()); + for (node_t u : ids) { + auto& row = dist[u]; // 创建一行 + row.reserve(ids.size()); + for (node_t v : ids) { + // 自环距离 0 + if (u == v) { + row[v] = static_cast(0); + continue; + } + // 有边则取权重，否则 INF + weight_t w = INF; + auto it_u = adj.find(u); + if (it_u != adj.end()) { + const auto& nbrs = it_u->second; + auto it_uv = nbrs.find(v); + if (it_uv != nbrs.end()) { + const auto& eattr = it_uv->second; + auto wit = eattr.find("weight"); + w = (wit != eattr.end()) ? wit->second : static_cast(1); + } + } + row[v] = w; + } + } + + // Floyd–Warshall：O(n^3) + for (node_t k : ids) { + for (node_t i : ids) { + // 小优化：如果 i->k 已不可达，跳过内层 + weight_t dik = dist[i][k]; + if (dik == INF) continue; + + for (node_t j : ids) { + weight_t kj = dist[k][j]; + if (kj == INF) continue; + + weight_t through = static_cast(dik + kj); + weight_t& ij = dist[i][j]; + if (through < ij) ij = through; + } + } + } + + // 写出为 {py_node: {py_node: distance}} + for (const auto& row : dist) { + node_t u = row.first; + py::object u_obj = G.id_to_node.attr("__getitem__")(py::cast(u)); + py::dict u_dict = result_dict.attr("__getitem__")(u_obj).cast(); + + for (const auto& kv : row.second) { + node_t v = kv.first; + weight_t d = kv.second; + py::object v_obj = G.id_to_node.attr("__getitem__")(py::cast(v)); + u_dict[v_obj] = d; + } + } + + return result_dict; +} diff --git a/cpp_easygraph/src/utils.cpp b/cpp_easygraph/src/utils.cpp new file mode 100644 index 00000000..b58fe398 --- /dev/null +++ b/cpp_easygraph/src/utils.cpp @@ -0,0 +1,30 @@ +#include "utils.h" + +py::dict attr_to_dict(const node_attr_dict_factory& attr) { + py::dict attr_dict; + for (const auto& kv : attr) { + // kv.first 是 std::string，kv.second 是 weight_t + attr_dict[py::str(kv.first)] = py::cast(kv.second); + } + return attr_dict; +} + +std::string weight_to_string(py::handle weight) { + // 如果 weight 不是 str，则尝试转换为 str，并在 None 情况下发警告 + if (!py::isinstance(weight)) { + if (weight.is_none()) { + py::module_::import("warnings") + .attr("warn")("None will be transformed into an instance of str."); + } + // 强制转为 Python 字符串 + weight = py::str(weight); + } + + // 转成 std::string + return py::cast(weight); +} + +py::object py_sum(const py::object& o) { + py::object sum_func = py::module_::import("builtins").attr("sum"); + return sum_func(o); +} diff --git a/src/cpp_easygraph/classes/__init__.h b/src/cpp_easygraph/classes/__init__.h deleted file mode 100644 index 939a4309..00000000 --- a/src/cpp_easygraph/classes/__init__.h +++ /dev/null @@ -1,6 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "graph.h" -#include "directed_graph.h" -#include "operation.h" \ No newline at end of file diff --git a/src/cpp_easygraph/classes/directed_graph.cpp b/src/cpp_easygraph/classes/directed_graph.cpp deleted file mode 100644 index a99bef9a..00000000 --- a/src/cpp_easygraph/classes/directed_graph.cpp +++ /dev/null @@ -1,100 +0,0 @@ -#include "directed_graph.h" -#include "../common/utils.h" - -DiGraph::DiGraph(): Graph() { - -} - -py::object DiGraph__init__(py::tuple args, py::dict kwargs) { - py::object MappingProxyType = py::import("types").attr("MappingProxyType"); - py::object self = args[0]; - self.attr("__init__")(); - DiGraph& self_ = py::extract(self); - py::dict graph_attr = kwargs; - self_.graph.update(graph_attr); - self_.nodes_cache = MappingProxyType(py::dict()); - self_.adj_cache = MappingProxyType(py::dict()); - return py::object(); -} - -py::object DiGraph_out_degree(py::object self, py::object weight) { - py::dict degree = py::dict(); - py::list edges = py::extract(self.attr("edges")); - py::object u, v; - py::dict d; - for (int i = 0;i < py::len(edges);i++) { - py::tuple edge = py::extract(edges[i]); - u = edge[0]; - v = edge[1]; - d = py::extract(edge[2]); - if (degree.contains(u)) { - degree[u] += d.get(weight, 1); - } - else { - degree[u] = d.get(weight, 1); - } - } - py::list nodes = py::list(self.attr("nodes")); - for (int i = 0;i < py::len(nodes);i++) { - py::object node = nodes[i]; - if (!degree.contains(node)) { - degree[node] = 0; - } - } - return degree; -} - -py::object DiGraph_in_degree(py::object self, py::object weight) { - py::dict degree = py::dict(); - py::list edges = py::extract(self.attr("edges")); - py::object u, v; - py::dict d; - for (int i = 0;i < py::len(edges);i++) { - py::tuple edge = py::extract(edges[i]); - u = edge[0]; - v = edge[1]; - d = py::extract(edge[2]); - if (degree.contains(v)) { - degree[v] += d.get(weight, 1); - } - else { - degree[v] = d.get(weight, 1); - } - } - py::list nodes = py::list(self.attr("nodes")); - for (int i = 0;i < py::len(nodes);i++) { - py::object node = nodes[i]; - if (!degree.contains(node)) { - degree[node] = 0; - } - } - return degree; -} - -py::object DiGraph_degree(py::object self, py::object weight) { - py::dict degree = py::dict(); - py::dict out_degree = py::extract(self.attr("out_degree")(weight)); - py::dict in_degree = py::extract(self.attr("in_degree")(weight)); - py::list nodes = py::list(self.attr("nodes")); - for (int i = 0;i < py::len(nodes);i++) { - py::object u = nodes[i]; - degree[u] = out_degree[u] + in_degree[u]; - } - return degree; -} - -py::object DiGraph_size(py::object self, py::object weight) { - py::dict out_degree = py::extract(self.attr("out_degree")(weight)); - py::object s = py_sum(out_degree.values()); - return (weight == py::object()) ? py::object(py::extract(s)) : s; -} - -py::object DiGraph_number_of_edges(py::object self, py::object u, py::object v) { - if (u == py::object()) { - return self.attr("size")(); - } - Graph& G = py::extract(self); - node_t u_id = py::extract(G.node_to_id[u]); - node_t v_id = py::extract(G.node_to_id.get(v, -1)); - return py::object(int(v != -1 && G.adj[u_id].count(v_id))); -} diff --git a/src/cpp_easygraph/classes/directed_graph.h b/src/cpp_easygraph/classes/directed_graph.h deleted file mode 100644 index 8fed7ac3..00000000 --- a/src/cpp_easygraph/classes/directed_graph.h +++ /dev/null @@ -1,17 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "graph.h" -#include "../common/common.h" - -struct DiGraph: public Graph -{ - DiGraph(); -}; - -py::object DiGraph__init__(DiGraph *self, py::args args, py::kwargs kwargs); -py::object DiGraph_out_degree(DiGraph &self, py::object weight); -py::object DiGraph_in_degree(DiGraph &self, py::object weight); -py::object DiGraph_degree(DiGraph &self, py::object weight); -py::object DiGraph_size(DiGraph &self, py::object weight); -py::object DiGraph_number_of_edges(DiGraph &self, py::object u, py::object v); diff --git a/src/cpp_easygraph/classes/graph.cpp b/src/cpp_easygraph/classes/graph.cpp deleted file mode 100644 index 343387b6..00000000 --- a/src/cpp_easygraph/classes/graph.cpp +++ /dev/null @@ -1,643 +0,0 @@ -#include "graph.h" -#include "../common/utils.h" - -Graph::Graph() { - py::object MappingProxyType = py::import("types").attr("MappingProxyType"); - this->id = 0; - this->dirty_nodes = true; - this->dirty_adj = true; - this->node_to_id = py::dict(); - this->id_to_node = py::dict(); - this->graph = py::dict(); - this->nodes_cache = MappingProxyType(py::dict()); - this->adj_cache = MappingProxyType(py::dict()); -} - -py::object Graph__init__(py::tuple args, py::dict kwargs) { - py::object MappingProxyType = py::import("types").attr("MappingProxyType"); - py::object self = args[0]; - self.attr("__init__")(); - Graph& self_ = py::extract(self); - py::dict graph_attr = kwargs; - self_.graph.update(graph_attr); - self_.nodes_cache = MappingProxyType(py::dict()); - self_.adj_cache = MappingProxyType(py::dict()); - return py::object(); -} - -py::object Graph__iter__(py::object self) { - return self.attr("nodes").attr("__iter__")(); -} - -py::object Graph__len__(py::object self) { - Graph& self_ = py::extract(self); - return py::object(py::len(self_.node_to_id)); -} - -py::object Graph__contains__(py::object self, py::object node) { - Graph& self_ = py::extract(self); - try { - return self_.node_to_id.contains(node); - } - catch (const py::error_already_set&) { - PyObject* type, * value, * traceback; - PyErr_Fetch(&type, &value, &traceback); - if (PyErr_GivenExceptionMatches(PyExc_TypeError, type)) { - return py::object(false); - } - else { - PyErr_Restore(type, value, traceback); - return py::object(); - } - } -} - -py::object Graph__getitem__(py::object self, py::object node) { - return self.attr("adj")[node]; -} - -node_t _add_one_node(Graph& self, py::object one_node_for_adding, py::object node_attr = py::dict()) { - node_t id; - if (self.node_to_id.contains(one_node_for_adding)) { - id = py::extract(self.node_to_id[one_node_for_adding]); - } - else { - id = ++(self.id); - self.id_to_node[id] = one_node_for_adding; - self.node_to_id[one_node_for_adding] = id; - } - py::list items = py::list(node_attr.attr("items")()); - self.node[id] = node_attr_dict_factory(); - self.adj[id] = adj_attr_dict_factory(); - for (int i = 0; i < len(items);i++) { - py::tuple kv = py::extract(items[i]); - py::object pkey = kv[0]; - std::string weight_key = weight_to_string(pkey); - weight_t value = py::extract(kv[1]); - self.node[id].insert(std::make_pair(weight_key, value)); - } - return id; -} - -py::object Graph_add_node(py::tuple args, py::dict kwargs) { - Graph& self = py::extract(args[0]); - self.dirty_nodes = true; - self.dirty_adj = true; - py::object one_node_for_adding = args[1]; - py::dict node_attr = kwargs; - _add_one_node(self, one_node_for_adding, node_attr); - return py::object(); -} - -py::object Graph_add_nodes(Graph& self, py::list nodes_for_adding, py::list nodes_attr) { - self.dirty_nodes = true; - self.dirty_adj = true; - if (py::len(nodes_attr) != 0) { - if (py::len(nodes_for_adding) != py::len(nodes_attr)) { - PyErr_Format(PyExc_AssertionError, "Nodes and Attributes lists must have same length."); - return py::object(); - } - } - for (int i = 0;i < py::len(nodes_for_adding);i++) { - py::object one_node_for_adding = nodes_for_adding[i]; - py::dict node_attr; - if (py::len(nodes_attr)) { - node_attr = py::extract(nodes_attr[i]); - } - else { - node_attr = py::dict(); - } - _add_one_node(self, one_node_for_adding, node_attr); - } - return py::object(); -} - -py::object Graph_add_nodes_from(py::tuple args, py::dict kwargs) { - Graph& self = py::extract(args[0]); - self.dirty_nodes = true; - self.dirty_adj = true; - py::list nodes_for_adding = py::list(args[1]); - for (int i = 0;i < py::len(nodes_for_adding);i++) { - bool newnode; - py::dict attr = kwargs; - py::dict newdict, ndict; - py::object n = nodes_for_adding[i]; - try { - newnode = !self.node_to_id.contains(n); - newdict = attr; - } - catch (const py::error_already_set&) { - PyObject* type, * value, * traceback; - PyErr_Fetch(&type, &value, &traceback); - if (PyErr_GivenExceptionMatches(PyExc_TypeError, type)) { - py::tuple n_pair = py::extract(n); - n = n_pair[0]; - ndict = py::extract(n_pair[1]); - newnode = !self.node_to_id.contains(n); - newdict = attr.copy(); - newdict.update(ndict); - } - else { - PyErr_Restore(type, value, traceback); - return py::object(); - } - } - if (newnode) { - if (n == py::object()) { - PyErr_Format(PyExc_ValueError, "None cannot be a node"); - return py::object(); - } - _add_one_node(self, n); - } - node_t id = py::extract(self.node_to_id[n]); - py::list items = py::list(newdict.items()); - for (int i = 0; i < len(items);i++) { - py::tuple kv = py::extract(items[i]); - py::object pkey = kv[0]; - std::string weight_key = weight_to_string(pkey); - weight_t value = py::extract(kv[1]); - self.node[id].insert(std::make_pair(weight_key, value)); - } - } - return py::object(); -} - -py::object Graph_remove_node(Graph& self, py::object node_to_remove) { - self.dirty_nodes = true; - self.dirty_adj = true; - if (!self.node_to_id.contains(node_to_remove)) { - PyErr_Format(PyExc_KeyError, "No node %R in graph.", node_to_remove.ptr()); - return py::object(); - } - node_t node_id = py::extract(self.node_to_id[node_to_remove]); - for (const auto& neighbor_info : self.adj[node_id]) { - node_t neighbor_id = neighbor_info.first; - self.adj[neighbor_id].erase(node_id); - } - self.adj.erase(node_id); - self.node.erase(node_id); - self.node_to_id.attr("pop")(node_to_remove); - self.id_to_node.attr("pop")(node_id); - return py::object(); -} - -py::object Graph_remove_nodes(py::object self, py::list nodes_to_remove) { - Graph& self_ = py::extract(self); - self_.dirty_nodes = true; - self_.dirty_adj = true; - for (int i = 0;i < py::len(nodes_to_remove);i++) { - py::object node_to_remove = nodes_to_remove[i]; - if (!self_.node_to_id.contains(node_to_remove)) { - PyErr_Format(PyExc_KeyError, "No node %R in graph.", node_to_remove.ptr()); - return py::object(); - } - } - for (int i = 0;i < py::len(nodes_to_remove);i++) { - py::object node_to_remove = nodes_to_remove[i]; - self.attr("remove_node")(node_to_remove); - } - return py::object(); -} - -py::object Graph_number_of_nodes(Graph& self) { - return py::object(int(self.node.size())); -} - -py::object Graph_has_node(Graph& self, py::object node) { - return self.node_to_id.contains(node); -} - -py::object Graph_nbunch_iter(py::object self, py::object nbunch) { - py::object bunch = py::object(); - if (nbunch == py::object()) { - bunch = self.attr("adj").attr("__iter__")(); - } - else if (self.contains(nbunch)) { - py::list nbunch_wrapper = py::list(); - nbunch_wrapper.append(nbunch); - bunch = nbunch_wrapper.attr("__iter__")(); - } - else { - py::list nbunch_list = py::list(nbunch), nodes_list = py::list(); - for (int i = 0;i < py::len(nbunch_list);i++) { - py::object n = nbunch_list[i]; - if (self.contains(n)) { - nodes_list.append(n); - } - } - bunch = nbunch_list.attr("__iter__")(); - } - return bunch; -} - -void _add_one_edge(Graph& self, py::object u_of_edge, py::object v_of_edge, py::object edge_attr) { - node_t u, v; - if (!self.node_to_id.contains(u_of_edge)) { - u = _add_one_node(self, u_of_edge); - } - else { - u = py::extract(self.node_to_id[u_of_edge]); - } - if (!self.node_to_id.contains(v_of_edge)) { - v = _add_one_node(self, v_of_edge); - } - else { - v = py::extract(self.node_to_id[v_of_edge]); - } - py::list items = py::list(edge_attr.attr("items")()); - self.adj[u][v] = node_attr_dict_factory(); - self.adj[v][u] = node_attr_dict_factory(); - for (int i = 0; i < len(items);i++) { - py::tuple kv = py::extract(items[i]); - py::object pkey = kv[0]; - std::string weight_key = weight_to_string(pkey); - weight_t value = py::extract(kv[1]); - self.adj[u][v].insert(std::make_pair(weight_key, value)); - self.adj[v][u].insert(std::make_pair(weight_key, value)); - } -} - -py::object Graph_add_edge(py::tuple args, py::dict kwargs) { - Graph& self = py::extract(args[0]); - self.dirty_nodes = true; - self.dirty_adj = true; - py::object u_of_edge = args[1], v_of_edge = args[2]; - py::dict edge_attr = kwargs; - _add_one_edge(self, u_of_edge, v_of_edge, edge_attr); - return py::object(); -} - -py::object Graph_add_edges(Graph& self, py::list edges_for_adding, py::list edges_attr) { - self.dirty_nodes = true; - self.dirty_adj = true; - if (py::len(edges_attr) != 0) { - if (py::len(edges_for_adding) != py::len(edges_attr)) { - PyErr_Format(PyExc_AssertionError, "Edges and Attributes lists must have same length."); - return py::object(); - } - } - for (int i = 0;i < py::len(edges_for_adding);i++) { - py::tuple one_edge_for_adding = py::extract(edges_for_adding[i]); - py::dict edge_attr; - if (py::len(edges_attr)) { - edge_attr = py::extract(edges_attr[i]); - } - else { - edge_attr = py::dict(); - } - _add_one_edge(self, one_edge_for_adding[0], one_edge_for_adding[1], edge_attr); - } - return py::object(); -} - -py::object Graph_add_edges_from(py::tuple args, py::dict attr) { - Graph& self = py::extract(args[0]); - self.dirty_nodes = true; - self.dirty_adj = true; - py::list ebunch_to_add = py::list(args[1]); - for (int i = 0;i < len(ebunch_to_add);i++) { - py::list e = py::list(ebunch_to_add[i]); - py::object u, v; - py::dict dd; - switch (len(e)) { - case 2: { - u = e[0]; - v = e[1]; - break; - } - case 3: { - u = e[0]; - v = e[1]; - dd = py::extract(e[2]); - break; - } - default: { - PyErr_Format(PyExc_ValueError, "Edge tuple %R must be a 2 - tuple or 3 - tuple.", e.ptr()); - return py::object(); - } - } - node_t u_id, v_id; - if (!self.node_to_id.contains(u)) { - if (u == py::object()) { - PyErr_Format(PyExc_ValueError, "None cannot be a node"); - return py::object(); - } - u_id = _add_one_node(self, u); - } - if (!self.node_to_id.contains(v)) { - if (v == py::object()) { - PyErr_Format(PyExc_ValueError, "None cannot be a node"); - return py::object(); - } - v_id = _add_one_node(self, v); - } - auto datadict = self.adj[u_id].count(v_id) ? self.adj[u_id][v_id] : node_attr_dict_factory(); - py::list items = py::list(attr); - items.extend(py::list(dd)); - for (int i = 0;i < py::len(items);i++) { - py::tuple kv = py::extract(items[i]); - py::object pkey = kv[0]; - std::string weight_key = weight_to_string(pkey); - weight_t value = py::extract(kv[1]); - datadict.insert(std::make_pair(weight_key, value)); - } - //Warning: in Graph.py the edge attr is directed assigned by the dict extended from the original attr - self.adj[u_id][v_id].insert(datadict.begin(), datadict.end()); - self.adj[v_id][u_id].insert(datadict.begin(), datadict.end()); - } - return py::object(); -} - -py::object Graph_add_edges_from_file(Graph& self, py::str file, py::object weighted) { - self.dirty_nodes = true; - self.dirty_adj = true; - struct commactype : std::ctype { - commactype() : std::ctype(get_table()) {} - std::ctype_base::mask const* get_table() { - std::ctype_base::mask* rc = 0; - if (rc == 0) { - rc = new std::ctype_base::mask[std::ctype::table_size]; - std::fill_n(rc, std::ctype::table_size, std::ctype_base::mask()); - rc[','] = std::ctype_base::space; - rc[' '] = std::ctype_base::space; - rc['\t'] = std::ctype_base::space; - rc['\n'] = std::ctype_base::space; - rc['\r'] = std::ctype_base::space; - } - return rc; - } - }; - - std::ios::sync_with_stdio(0); - std::string file_path = py::extract(file); - std::ifstream in; - in.open(file_path); - if (!in.is_open()) { - PyErr_Format(PyExc_FileNotFoundError, "Please check the file and make sure the path only contains English"); - return py::object(); - } - in.imbue(std::locale(std::locale(), new commactype)); - std::string data, key("weight"); - std::string su, sv; - weight_t weight; - while (in >> su >> sv) { - py::object pu(su), pv(sv); - node_t u, v; - if (!self.node_to_id.contains(pu)) { - u = _add_one_node(self, pu); - } - else { - u = py::extract(self.node_to_id[pu]); - } - if (!self.node_to_id.contains(pv)) { - v = _add_one_node(self, pv); - } - else { - v = py::extract(self.node_to_id[pv]); - } - if (weighted) { - in >> weight; - self.adj[u][v][key] = self.adj[v][u][key] = weight; - } - else { - if (!self.adj[u].count(v)) { - self.adj[u][v] = node_attr_dict_factory(); - } - if (!self.adj[v].count(u)) { - self.adj[v][u] = node_attr_dict_factory(); - } - } - } - in.close(); - return py::object(); -} - -py::object Graph_add_weighted_edge(Graph& self, py::object u_of_edge, py::object v_of_edge, weight_t weight) { - self.dirty_nodes = true; - self.dirty_adj = true; - py::dict edge_attr; - edge_attr["weight"] = weight; - _add_one_edge(self, u_of_edge, v_of_edge, edge_attr); - return py::object(); -} - -py::object Graph_remove_edge(Graph& self, py::object u, py::object v) { - self.dirty_nodes = true; - self.dirty_adj = true; - if (self.node_to_id.contains(u) && self.node_to_id.contains(v)) { - node_t u_id = py::extract(self.node_to_id[u]); - node_t v_id = py::extract(self.node_to_id[v]); - auto& v_neighbors_info = self.adj[u_id]; - if (v_neighbors_info.find(v_id) != v_neighbors_info.end()) { - v_neighbors_info.erase(v_id); - if (u_id != v_id) { - self.adj[v_id].erase(u_id); - } - return py::object(); - } - } - PyErr_Format(PyExc_KeyError, "No edge %R-%R in graph.", u.ptr(), v.ptr()); - return py::object(); -} - -py::object Graph_remove_edges(py::object self, py::list edges_to_remove) { - Graph& self_ = py::extract(self); - for (int i = 0;i < py::len(edges_to_remove);i++) { - py::tuple edge = py::extract(edges_to_remove[i]); - py::object u = edge[0], v = edge[1]; - self.attr("remove_edge")(u, v); - } - self_.dirty_nodes = true; - self_.dirty_adj = true; - return py::object(); -} - -py::object Graph_number_of_edges(py::object self, py::object u, py::object v) { - if (u == py::object()) { - return self.attr("size")(); - } - Graph& self_ = py::extract(self); - node_t u_id = py::extract(self_.node_to_id.get(u, -1)); - node_t v_id = py::extract(self_.node_to_id.get(v, -1)); - return py::object(int(self_.adj.count(u_id) && self_.adj[u_id].count(v_id))); -} - -py::object Graph_has_edge(Graph& self, py::object u, py::object v) { - if (self.node_to_id.contains(u) && self.node_to_id.contains(v)) { - node_t u_id = py::extract(self.node_to_id[u]); - node_t v_id = py::extract(self.node_to_id[v]); - auto& v_neighbors_info = self.adj[u_id]; - if (v_neighbors_info.find(v_id) != v_neighbors_info.end()) { - return py::object(true); - } - } - return py::object(false); -} - -py::object Graph_copy(py::object self) { - Graph& self_ = py::extract(self); - py::object G = self.attr("__class__")(); - Graph& G_ = py::extract(G); - G_.graph.update(self_.graph); - G_.id_to_node.update(self_.id_to_node); - G_.node_to_id.update(self_.node_to_id); - G_.node = self_.node; - G_.adj = self_.adj; - return py::object(G); -} - -py::object Graph_degree(py::object self, py::object weight) { - py::dict degree; - py::list edges = py::extract(self.attr("edges")); - py::object u, v; - py::dict d; - for (int i = 0;i < py::len(edges);i++) { - py::tuple edge = py::extract(edges[i]); - u = edge[0]; - v = edge[1]; - d = py::extract(edge[2]); - if (degree.contains(u)) { - degree[u] += d.get(weight, 1); - } - else { - degree[u] = d.get(weight, 1); - } - if (degree.contains(v)) { - degree[v] += d.get(weight, 1); - } - else { - degree[v] = d.get(weight, 1); - } - } - py::list nodes = py::list(self.attr("nodes")); - for (int i = 0;i < py::len(nodes);i++) { - py::object node = nodes[i]; - if (!degree.contains(node)) { - degree[node] = 0; - } - } - return degree; -} - -py::object Graph_neighbors(py::object self, py::object node) { - Graph& self_ = py::extract(self); - if (self_.node_to_id.contains(node)) { - return self.attr("adj")[node].attr("__iter__")(); - } - else { - PyErr_Format(PyExc_KeyError, "No node %R", node.ptr()); - return py::object(); - } -} - -py::object Graph_nodes_subgraph(py::object self, py::list from_nodes) { - py::object G = self.attr("__class__")(); - Graph& self_ = py::extract(self); - Graph& G_ = py::extract(G); - G_.graph.update(self_.graph); - py::object nodes = self.attr("nodes"); - py::object adj = self.attr("adj"); - for (int i = 0;i < py::len(from_nodes);i++) { - py::object node = from_nodes[i]; - if (self_.node_to_id.contains(node)) { - py::object node_attr = nodes[node]; - _add_one_node(G_, node, node_attr); - } - py::object out_edges = adj[node]; - py::list edge_items = py::list(out_edges.attr("items")()); - for (int j = 0;j < py::len(edge_items);j++) { - py::tuple item = py::extract(edge_items[j]); - py::object v = item[0]; - py::object edge_attr = item[1]; - if (from_nodes.contains(v)) { - _add_one_edge(G_, node, v, edge_attr); - } - } - } - return G; -} - -py::object Graph_ego_subgraph(py::object self, py::object center) { - py::list neighbors_of_center = py::list(self.attr("all_neighbors")(center)); - neighbors_of_center.append(center); - return self.attr("nodes_subgraph")(neighbors_of_center); -} - -py::object Graph_size(py::object self, py::object weight) { - py::dict degree = py::extract(self.attr("degree")(weight)); - py::list items = degree.items(); - weight_t s = 0; - for (int i = 0;i < py::len(items);i++) { - s += py::extract(items[i][1]); - } - return (weight == py::object()) ? py::object(int(s) / 2) : py::object(s / 2); -} - -py::object Graph_is_directed(py::object self) { - return py::object(false); -} - -py::object Graph_is_multigraph(py::object self) { - return py::object(false); -} - -py::object Graph::get_nodes() { - py::object MappingProxyType = py::import("types").attr("MappingProxyType"); - if (this->dirty_nodes) { - py::dict nodes = py::dict(); - for (const auto& node_info : node) { - node_t id = node_info.first; - const auto& node_attr = node_info.second; - nodes[this->id_to_node[id]] = MappingProxyType(attr_to_dict(node_attr)); - } - this->nodes_cache = MappingProxyType(nodes); - this->dirty_nodes = false; - } - return this->nodes_cache; -} - -py::object Graph::get_name() { - return this->graph.attr("get")("name", ""); -} - -py::object Graph::get_graph() { - return this->graph; -} - -py::object Graph::get_adj() { - py::object MappingProxyType = py::import("types").attr("MappingProxyType"); - if (this->dirty_adj) { - py::dict adj = py::dict(); - for (const auto& ego_edges : this->adj) { - node_t start_point = ego_edges.first; - py::dict ego_edges_dict = py::dict(); - for (const auto& edge_info : ego_edges.second) { - node_t end_point = edge_info.first; - const auto& edge_attr = edge_info.second; - ego_edges_dict[this->id_to_node[end_point]] = MappingProxyType(attr_to_dict(edge_attr)); - } - adj[this->id_to_node[start_point]] = MappingProxyType(ego_edges_dict); - } - this->adj_cache = MappingProxyType(adj); - this->dirty_adj = false; - } - return this->adj_cache; -} - -py::object Graph::get_edges() { - py::list edges = py::list(); - std::set > seen; - for (const auto& ego_edges : this->adj) { - node_t u = ego_edges.first; - for (const auto& edge_info : ego_edges.second) { - node_t v = edge_info.first; - const auto& edge_attr = edge_info.second; - if (seen.find(std::make_pair(u,v)) == seen.end()) { - seen.insert(std::make_pair(u,v)); - seen.insert(std::make_pair(v,u)); - edges.append(py::make_tuple(this->id_to_node[u], this->id_to_node[v], attr_to_dict(edge_attr))); - } - } - } - return edges; -} diff --git a/src/cpp_easygraph/classes/graph.h b/src/cpp_easygraph/classes/graph.h deleted file mode 100644 index b7b1e931..00000000 --- a/src/cpp_easygraph/classes/graph.h +++ /dev/null @@ -1,54 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "../common/common.h" - -struct Graph -{ - node_dict_factory node; - adj_dict_factory adj; - py::dict node_to_id, id_to_node, graph; - node_t id; - bool dirty_nodes, dirty_adj; - py::object nodes_cache, adj_cache; - - Graph(); - py::object get_nodes(); - py::object get_name(); - py::object get_graph(); - py::object get_adj(); - py::object get_edges(); -}; - - -py::object Graph__init__(py::tuple args, py::dict kwargs); -py::object Graph__iter__(py::object self); -py::object Graph__len__(py::object self); -py::object Graph__contains__(py::object self, py::object node); -py::object Graph__getitem__(py::object self, py::object node); -py::object Graph_add_node(py::tuple args, py::dict kwargs); -py::object Graph_add_nodes(Graph& self, py::list nodes_for_adding, py::list nodes_attr); -py::object Graph_add_nodes_from(py::tuple args, py::dict kwargs); -py::object Graph_remove_node(Graph& self, py::object node_to_remove); -py::object Graph_remove_nodes(py::object self, py::list nodes_to_remove); -py::object Graph_number_of_nodes(Graph& self); -py::object Graph_has_node(Graph& self, py::object node); -py::object Graph_nbunch_iter(py::object self, py::object nbunch); -py::object Graph_add_edge(py::tuple args, py::dict kwargs); -py::object Graph_add_edges(Graph& self, py::list edges_for_adding, py::list edges_attr); -py::object Graph_add_edges_from(py::tuple args, py::dict attr); -py::object Graph_add_edges_from_file(Graph& self, py::str file, py::object weighted); -py::object Graph_add_weighted_edge(Graph& self, py::object u_of_edge, py::object v_of_edge, weight_t weight); -py::object Graph_remove_edge(Graph& self, py::object u, py::object v); -py::object Graph_remove_edges(py::object self, py::list edges_to_remove); -py::object Graph_number_of_edges(py::object self, py::object u, py::object v); -py::object Graph_has_edge(Graph& self, py::object u, py::object v); -py::object Graph_copy(py::object self); -py::object Graph_degree(py::object self, py::object weight); -py::object Graph_neighbors(py::object self, py::object node); -py::object Graph_nodes_subgraph(py::object self, py::list from_nodes); -py::object Graph_ego_subgraph(py::object self, py::object center); -py::object Graph_size(py::object self, py::object weight); -py::object Graph_is_directed(py::object self); -py::object Graph_is_multigraph(py::object self); - diff --git a/src/cpp_easygraph/classes/operation.cpp b/src/cpp_easygraph/classes/operation.cpp deleted file mode 100644 index 7e15c08f..00000000 --- a/src/cpp_easygraph/classes/operation.cpp +++ /dev/null @@ -1,17 +0,0 @@ -#include "operation.h" -#include "graph.h" -py::object density(py::object G) { - Graph &G_ = py::extract(G); - node_t n = G_.node.size(); - adj_dict_factory adj=G_.adj; - node_t m=0; - for(adj_dict_factory::iterator i=adj.begin();i!=adj.end();i++){ - adj_attr_dict_factory node_edge=i->second; - m+=node_edge.size(); - } - if (m == 0 || n <= 1) { - return py::object(0); - } - weight_t d = m * 1.0 / (n * (n - 1)); - return py::object(d); -} diff --git a/src/cpp_easygraph/classes/operation.h b/src/cpp_easygraph/classes/operation.h deleted file mode 100644 index 619ac629..00000000 --- a/src/cpp_easygraph/classes/operation.h +++ /dev/null @@ -1,6 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "../common/common.h" - -py::object density(py::object G); \ No newline at end of file diff --git a/src/cpp_easygraph/common/common.h b/src/cpp_easygraph/common/common.h deleted file mode 100644 index c8e8556a..00000000 --- a/src/cpp_easygraph/common/common.h +++ /dev/null @@ -1,23 +0,0 @@ -#pragma once - -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include - -namespace py = pybind11; - -typedef int node_t; -typedef float weight_t; -typedef std::map node_attr_dict_factory; //(weight_key, value) -typedef std::map edge_attr_dict_factory; //(weight_key, value) -typedef std::unordered_map node_dict_factory; //(node, node_attr) -typedef std::unordered_map adj_attr_dict_factory; //(out_node, (weight_key, value)) -typedef std::unordered_map adj_dict_factory; //(node, edge_attr) diff --git a/src/cpp_easygraph/common/utils.cpp b/src/cpp_easygraph/common/utils.cpp deleted file mode 100644 index 5c488280..00000000 --- a/src/cpp_easygraph/common/utils.cpp +++ /dev/null @@ -1,26 +0,0 @@ -#include "utils.h" - -py::object attr_to_dict(const node_attr_dict_factory& attr) { - py::dict attr_dict = py::dict(); - for (const auto& kv : attr) { - attr_dict[kv.first] = kv.second; - } - return attr_dict; -} - -std::string weight_to_string(py::object weight) { - py::object warn = py::import("warnings").attr("warn"); - if (weight.attr("__class__") != py::str().attr("__class__")) { - if (weight != py::object()) { - warn(py::str(weight) + py::str(" would be transformed into an instance of str.")); - } - weight = py::str(weight); - } - std::string weight_key = py::extract(weight); - return weight_key; -} - -py::object py_sum(py::object o) { - py::object sum = py::import("builtins").attr("sum"); - return sum(o); -} \ No newline at end of file diff --git a/src/cpp_easygraph/common/utils.h b/src/cpp_easygraph/common/utils.h deleted file mode 100644 index f41d7931..00000000 --- a/src/cpp_easygraph/common/utils.h +++ /dev/null @@ -1,8 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "common.h" - -py::object attr_to_dict(const node_attr_dict_factory& attr); -std::string weight_to_string(py::object weight); -py::object py_sum(py::object o); \ No newline at end of file diff --git a/src/cpp_easygraph/cpp_easygraph.cpp b/src/cpp_easygraph/cpp_easygraph.cpp deleted file mode 100644 index 221b8839..00000000 --- a/src/cpp_easygraph/cpp_easygraph.cpp +++ /dev/null @@ -1,68 +0,0 @@ -#include -#include - -#include "classes/__init__.h" -#include "functions/__init__.h" - -PYBIND11_MODULE(cpp_easygraph, m) -{ - - py::class_(m, "Graph") - .def("__init__", &Graph__init__) - .def(py::init<>()) - .def("__iter__", &Graph__iter__) - .def("__len__", &Graph__len__) - .def("__contains__", &Graph__contains__, py::arg("node")) - .def("__getitem__", &Graph__getitem__, py::arg("node")) - .def("add_node", &Graph_add_node) - .def("add_nodes", &Graph_add_nodes, py::arg("nodes_for_adding"), py::arg("nodes_attr") = py::list()) - .def("add_nodes_from", &Graph_add_nodes_from) - .def("remove_node", &Graph_remove_node, py::arg("node_to_remove")) - .def("remove_nodes", &Graph_remove_nodes, py::arg("nodes_to_remove")) - .def("number_of_nodes", &Graph_number_of_nodes) - .def("has_node", &Graph_has_node, py::arg("node")) - .def("nbunch_iter", &Graph_nbunch_iter, py::arg("nbunch") = py::none()) - .def("add_edge", &Graph_add_edge) - .def("add_edges", &Graph_add_edges, py::arg("edges_for_adding"), py::arg("edges_attr") = py::list()) - .def("add_edges_from", &Graph_add_edges_from) - .def("add_edges_from_file", &Graph_add_edges_from_file, py::arg("file"), py::arg("weighted") = false) - .def("add_weighted_edge", &Graph_add_weighted_edge, py::arg("u_of_edge"), py::arg("v_of_edge"), py::arg("weight")) - .def("remove_edge", &Graph_remove_edge, py::arg("u"), py::arg("v")) - .def("remove_edges", &Graph_remove_edges, py::arg("edges_to_remove")) - .def("number_of_edges", &Graph_number_of_edges, py::arg("u") = py::none(), py::arg("v") = py::none()) - .def("has_edge", &Graph_has_edge, py::arg("u"), py::arg("y")) - .def("copy", &Graph_copy) - .def("degree", &Graph_degree, py::arg("weight") = "weight") - .def("neighbors", &Graph_neighbors, py::arg("node")) - .def("all_neighbors", &Graph_neighbors, py::arg("node")) - .def("nodes_subgraph", &Graph_nodes_subgraph, py::arg("from_nodes")) - .def("ego_subgraph", &Graph_ego_subgraph, py::arg("center")) - .def("size", &Graph_size, py::arg("weight") = py::none()) - .def("is_directed", &Graph_is_directed) - .def("is_multigraph", &Graph_is_multigraph) - .def_property_readonly("graph", &Graph::get_graph) - .def_property_readonly("nodes", &Graph::get_nodes) - .def_property_readonly("name", &Graph::get_name) - .def_property_readonly("adj", &Graph::get_adj) - .def_property_readonly("edges", &Graph::get_edges); - - py::class_(m, "DiGraph") - .def("__init__", &DiGraph__init__) - .def(py::init<>()) - .def("out_degree", &DiGraph_out_degree, py::arg("weight") = "weight") - .def("in_degree", &DiGraph_in_degree, py::arg("weight") = "weight") - .def("degree", &DiGraph_degree, py::arg("weight") = "weight") - .def("size", &DiGraph_size, py::arg("weight") = py::none()) - .def("number_of_edges", &DiGraph_number_of_edges, py::arg("u") = py::none(), py::arg("v") = py::none()); - - m.def("cpp_density",&density,py::arg("G")); - m.def("cpp_constraint", &constraint, py::arg("G"), py::arg("nodes") = py::none(), py::arg("weight") = py::none(), py::arg("n_workers") = py::none()); - m.def("cpp_effective_size", &effective_size, py::arg("G"), py::arg("nodes") = py::none(), py::arg("weight") = py::none(), py::arg("n_workers") = py::none()); - m.def("cpp_hierarchy", &hierarchy, py::arg("G"), py::arg("nodes") = py::none(), py::arg("weight") = py::none(), py::arg("n_workers") = py::none()); - m.def("cpp_dijkstra_multisource", &_dijkstra_multisource, py::arg("G"), py::arg("sources"), py::arg("weight") = "weight", py::arg("target") = py::none()); - m.def("cpp_clustering", &clustering, py::arg("G"), py::arg("nodes") = py::none(), py::arg("weight") = py::none()); - m.def("cpp_biconnected_dfs_record_edges", &_biconnected_dfs_record_edges, py::arg("G"), py::arg("need_components") = true); - m.def("cpp_Floyd", &Floyd, py::arg("G")); - m.def("cpp_Prim", &Prim, py::arg("G")); - m.def("cpp_Kruskal", &Kruskal, py::arg("G")); -} diff --git a/src/cpp_easygraph/functions/__init__.h b/src/cpp_easygraph/functions/__init__.h deleted file mode 100644 index 485b9381..00000000 --- a/src/cpp_easygraph/functions/__init__.h +++ /dev/null @@ -1,7 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "components/__init__.h" -#include "not_sorted/__init__.h" -#include "path/__init__.h" -#include "structural_holes/__init__.h" \ No newline at end of file diff --git a/src/cpp_easygraph/functions/components/__init__.h b/src/cpp_easygraph/functions/components/__init__.h deleted file mode 100644 index 1b91d451..00000000 --- a/src/cpp_easygraph/functions/components/__init__.h +++ /dev/null @@ -1,4 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "biconnected.h" \ No newline at end of file diff --git a/src/cpp_easygraph/functions/components/biconnected.cpp b/src/cpp_easygraph/functions/components/biconnected.cpp deleted file mode 100644 index ffd2001c..00000000 --- a/src/cpp_easygraph/functions/components/biconnected.cpp +++ /dev/null @@ -1,108 +0,0 @@ -#include "biconnected.h" -#include "../../classes/graph.h" -#include "../../common/utils.h" - -node_t index_edge(std::vector>& edges, const std::pair& target) { - for (int i = edges.size() - 1;i >= 0;i--) { - if ((edges[i].first == target.first) && (edges[i].second == target.second)) { - return i; - } - } - return -1; -} - - -py::object _biconnected_dfs_record_edges(py::object G, py::object need_components) { - py::list ret = py::list(); - std::unordered_set visited; - Graph& G_ = py::extract(G); - node_dict_factory nodes_list = G_.node; - for (node_dict_factory::iterator iter = nodes_list.begin();iter != nodes_list.end();iter++) { - node_t start_id = iter->first; - if (visited.find(start_id) != visited.end()) { - continue; - } - std::unordered_map discovery; - std::unordered_map low; - node_t root_children = 0; - discovery.emplace(start_id, 0); - low.emplace(start_id, 0); - visited.emplace(start_id); - std::vector> edge_stack; - std::vector stack; - adj_attr_dict_factory start_adj = G_.adj[start_id]; - NeighborIterator neighbors_iter = NeighborIterator(start_adj); - stack_node initial_stack_node(start_id, start_id, neighbors_iter); - stack.emplace_back(initial_stack_node); - while (!stack.empty()) { - stack_node& node_info = stack.back(); - node_t node_grandparent_id = node_info.grandparent; - node_t node_parent_id = node_info.parent; - try { - node_t node_child_id = node_info.neighbors_iter.next(); - if (node_grandparent_id == node_child_id) { - continue; - } - if (visited.find(node_child_id) != visited.end()) { - if (discovery[node_child_id] <= discovery[node_parent_id]) { - low[node_parent_id] = std::min(low[node_parent_id], discovery[node_child_id]); - if (need_components) { - edge_stack.emplace_back(std::make_pair(node_parent_id, node_child_id)); - } - } - } - else { - low[node_child_id] = discovery[node_child_id] = discovery.size(); - visited.emplace(node_child_id); - adj_attr_dict_factory node_child_adj = G_.adj[node_child_id]; - NeighborIterator child_neighbors_iter = NeighborIterator(G_.adj[node_child_id]); - stack.emplace_back(node_parent_id, node_child_id, child_neighbors_iter); - if (need_components) { - edge_stack.emplace_back(std::make_pair(node_parent_id, node_child_id)); - } - } - } - catch (int) { - stack.pop_back(); - if (stack.size() > 1) { - if (low[node_parent_id] >= discovery[node_grandparent_id]) { - if (need_components) { - py::list tmp_ret = py::list(); - std::pair iter_edge = std::make_pair(-1, -1); - while ((iter_edge.first != node_grandparent_id || iter_edge.second != node_parent_id)) { - iter_edge = edge_stack.back(); - edge_stack.pop_back(); - tmp_ret.append(py::make_tuple(G_.id_to_node[iter_edge.first], G_.id_to_node[iter_edge.second])); - } - ret.append(tmp_ret); - } - else { - ret.append(G_.id_to_node[node_grandparent_id]); - } - } - low[node_grandparent_id] = std::min(low[node_grandparent_id], low[node_parent_id]); - } - else if (stack.size() > 0) { - root_children += 1; - if (need_components == true) { - std::pair target = std::make_pair(node_grandparent_id, node_parent_id); - node_t ind = index_edge(edge_stack, target); - if (ind != -1) { - py::list tmp_ret = py::list(); - for (node_t z = ind;z < edge_stack.size();z++) { - tmp_ret.append(py::make_tuple(G_.id_to_node[edge_stack[z].first], G_.id_to_node[edge_stack[z].second])); - } - ret.append(tmp_ret); - } - } - } - } - } - if (!need_components) { - if (root_children > 1) { - ret.append(G_.id_to_node(start_id)); - } - } - } - return ret; -} diff --git a/src/cpp_easygraph/functions/not_sorted/__init__.h b/src/cpp_easygraph/functions/not_sorted/__init__.h deleted file mode 100644 index b3f8406a..00000000 --- a/src/cpp_easygraph/functions/not_sorted/__init__.h +++ /dev/null @@ -1,4 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "cluster.h" \ No newline at end of file diff --git a/src/cpp_easygraph/functions/not_sorted/cluster.cpp b/src/cpp_easygraph/functions/not_sorted/cluster.cpp deleted file mode 100644 index f823f0ad..00000000 --- a/src/cpp_easygraph/functions/not_sorted/cluster.cpp +++ /dev/null @@ -1,113 +0,0 @@ -#include "cluster.h" -#include "../../classes/graph.h" -#include "../../common/utils.h" - -inline weight_t wt(adj_dict_factory& adj, node_t u, node_t v, std::string weight, weight_t max_weight = 1) { - auto& attr = adj[u][v]; - return (attr.count(weight) ? attr[weight] : 1) / max_weight; -} - -py::list _weighted_triangles_and_degree(py::object G, py::object nodes, py::object weight) { - std::string weight_key = weight_to_string(weight); - Graph& G_ = py::extract(G); - weight_t max_weight = 1; - if (weight == py::object() || G.attr("number_of_edges")() == 0) { - max_weight = 1; - } - else { - int assigned = 0; - for (auto& u_info : G_.adj) { - for (auto& v_info : u_info.second) { - auto& d = v_info.second; - if (assigned) { - max_weight = std::max(max_weight, d.count(weight_key) ? d[weight_key] : 1); - } - else { - assigned = 1; - max_weight = d.count(weight_key) ? d[weight_key] : 1; - } - } - } - } - py::list nodes_list = py::list(nodes == py::object() ? G.attr("nodes") : G.attr("nbunch_iter")(nodes)); - py::list ret = py::list(); - for (int i = 0;i < py::len(nodes_list);i++) { - node_t i_id = py::extract(G_.node_to_id[nodes_list[i]]); - std::unordered_set inbrs, seen; - auto& adj = G_.adj; - for (const auto& pair : adj[i_id]) { - inbrs.insert(pair.first); - } - inbrs.erase(i_id); - weight_t weighted_triangles = 0; - for (const auto& j_id : inbrs) { - seen.insert(j_id); - weight_t wij = wt(adj, i_id, j_id, weight_key, max_weight); - for (const auto& k_id : inbrs) { - if (adj[j_id].count(k_id) && !seen.count(k_id)) { - weight_t wjk = wt(adj, j_id, k_id, weight_key, max_weight); - weight_t wki = wt(adj, k_id, i_id, weight_key, max_weight); - weighted_triangles += std::cbrt(wij * wjk * wki); - } - } - } - ret.append(py::make_tuple(G_.id_to_node[i_id], inbrs.size(), 2 * weighted_triangles)); - } - return ret; -} - -py::list _triangles_and_degree(py::object G, py::object nodes = py::object()) { - Graph& G_ = py::extract(G); - auto& adj = G_.adj; - py::list nodes_list = py::list(nodes == py::object() ? G.attr("nodes") : G.attr("nbunch_iter")(nodes)); - py::list ret = py::list(); - for (int i = 0;i < py::len(nodes_list);i++) { - node_t v = py::extract(G_.node_to_id[nodes_list[i]]); - std::unordered_set vs; - for (const auto& pair : adj[v]) { - vs.insert(pair.first); - } - vs.erase(v); - weight_t ntriangles = 0; - for (const auto& w : vs) { - for (const auto& node : vs) { - ntriangles += node != w && adj[w].count(node); - } - } - ret.append(py::make_tuple(G_.id_to_node[v], vs.size(), ntriangles)); - } - return ret; -} - -py::object clustering(py::object G, py::object nodes, py::object weight) { - py::dict clusterc = py::dict(); - if (G.attr("is_directed")()) { - PyErr_Format(PyExc_RuntimeError, "Not implemented yet"); - return py::object(); - } - else { - py::list td_list; - if (weight != py::object()) { - td_list = _weighted_triangles_and_degree(G, nodes, weight); - } - else { - td_list = _triangles_and_degree(G, nodes); - } - for (int i = 0;i < py::len(td_list);i++) { - py::tuple tuple = py::extract(td_list[i]); - py::object v = tuple[0]; - int d = py::extract(tuple[1]); - weight_t t = py::extract(tuple[2]); - if (t == 0) { - clusterc[v] = 0; - } - else { - clusterc[v] = t / (d * (d - 1)); - } - } - } - if (G.contains(nodes)) { - return clusterc[nodes]; - } - return clusterc; -} \ No newline at end of file diff --git a/src/cpp_easygraph/functions/not_sorted/cluster.h b/src/cpp_easygraph/functions/not_sorted/cluster.h deleted file mode 100644 index 2a547c6d..00000000 --- a/src/cpp_easygraph/functions/not_sorted/cluster.h +++ /dev/null @@ -1,6 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "../../common/common.h" - -py::object clustering(py::object G, py::object nodes, py::object weight); \ No newline at end of file diff --git a/src/cpp_easygraph/functions/path/__init__.h b/src/cpp_easygraph/functions/path/__init__.h deleted file mode 100644 index f09fd758..00000000 --- a/src/cpp_easygraph/functions/path/__init__.h +++ /dev/null @@ -1,4 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "path.h" \ No newline at end of file diff --git a/src/cpp_easygraph/functions/path/path.cpp b/src/cpp_easygraph/functions/path/path.cpp deleted file mode 100644 index 75761c8c..00000000 --- a/src/cpp_easygraph/functions/path/path.cpp +++ /dev/null @@ -1,226 +0,0 @@ -#include "path.h" -#include "../../classes/graph.h" -#include "../../common/utils.h" - -py::object _dijkstra_multisource(py::object G, py::object sources, py::object weight, py::object target) { - Graph& G_ = py::extract(G); - std::string weight_key = weight_to_string(weight); - node_t target_id = py::extract(G_.node_to_id.get(target, -1)); - std::map dist, seen; - std::priority_queue, std::vector>, std::greater>> Q; - py::list sources_list = py::list(sources); - for (int i = 0;i < py::len(sources_list);i++) { - node_t source = py::extract(G_.node_to_id[sources_list[i]]); - seen[source] = 0; - Q.push(std::make_pair(0, source)); - } - while (!Q.empty()) { - std::pair node = Q.top(); - Q.pop(); - weight_t d = node.first; - node_t v = node.second; - if (dist.count(v)) { - continue; - } - dist[v] = d; - if (v == target_id) { - break; - } - adj_dict_factory& adj = G_.adj; - for (auto& neighbor_info : adj[v]) { - node_t u = neighbor_info.first; - weight_t cost = neighbor_info.second.count(weight_key) ? neighbor_info.second[weight_key] : 1; - weight_t vu_dist = dist[v] + cost; - if (dist.count(u)) { - if (vu_dist < dist[u]) { - PyErr_Format(PyExc_ValueError, "Contradictory paths found: negative weights?"); - return py::object(); - } - } - else if (!seen.count(u) || vu_dist < seen[u]) { - seen[u] = vu_dist; - Q.push(std::make_pair(vu_dist, u)); - } - else { - continue; - } - } - } - py::dict pydist = py::dict(); - for (const auto& kv : dist) { - pydist[G_.id_to_node[kv.first]] = kv.second; - } - return pydist; -} - -py::object Prim(py::object G) { - std::unordered_map> res_dict; - py::dict result_dict = py::dict(); - Graph& G_ = py::extract(G); - adj_dict_factory adj = G_.adj; - std::vector selected; - std::vector candidate; - node_dict_factory node_list = G_.node; - for (node_dict_factory::iterator i = node_list.begin();i != node_list.end();i++) { - node_t node_id = i->first; - result_dict[G_.id_to_node[node_id]] = py::dict(); - if (selected.size() == 0) { - selected.emplace_back(node_id); - } - else { - candidate.emplace_back(node_id); - } - } - while (candidate.size() > 0) { - node_t start_id = -1; - node_t end_id = -1; - weight_t min_weight = INFINITY; - for (node_t i = 0;i < selected.size();i++) { - for (node_t j = 0;j < candidate.size();j++) { - adj_attr_dict_factory node_adj = G_.adj[selected[i]]; - edge_attr_dict_factory edge_attr; - weight_t edge_weight = INFINITY; - bool j_exist = false; - if (node_adj.find(candidate[j]) != node_adj.end()) { - edge_attr = node_adj[candidate[j]]; - edge_weight = edge_attr.find("weight") != edge_attr.end() ? edge_attr["weight"] : 1; - j_exist = true; - } - if ((node_list.find(selected[i]) != node_list.end()) && - j_exist && - (edge_weight < min_weight)) { - start_id = selected[i]; - end_id = candidate[j]; - min_weight = edge_weight; - } - } - } - if (start_id != -1 && end_id != -1) { - res_dict[start_id][end_id] = min_weight; - selected.emplace_back(end_id); - std::vector::iterator temp_iter; - temp_iter = std::find(candidate.begin(), candidate.end(), end_id); - candidate.erase(temp_iter); - } - else { - break; - } - } - for (std::unordered_map>::iterator k = res_dict.begin(); - k != res_dict.end();k++) { - py::object res_node = G_.id_to_node[k->first]; - for (std::unordered_map::iterator z = k->second.begin();z != k->second.end();z++) { - py::object res_adj_node = G_.id_to_node[z->first]; - result_dict[res_node][res_adj_node] = z->second; - } - } - return result_dict; - -} -bool comp(const std::pair, weight_t>& a, const std::pair, weight_t>& b) { - return a.second < b.second; -} -py::object Kruskal(py::object G) { - std::unordered_map> res_dict; - py::dict result_dict = py::dict(); - std::vector> group; - Graph& G_ = py::extract(G); - adj_dict_factory adj = G_.adj; - node_dict_factory node_list = G_.node; - std::vector, weight_t>>edge_list; - for (node_dict_factory::iterator i = node_list.begin();i != node_list.end();i++) { - node_t i_id = i->first; - result_dict[G_.id_to_node[i_id]] = py::dict(); - std::vector temp_vector; - temp_vector.emplace_back(i_id); - group.emplace_back(temp_vector); - adj_attr_dict_factory i_adj = adj[i_id]; - for (adj_attr_dict_factory::iterator j = i_adj.begin();j != i_adj.end();j++) { - node_t j_id = j->first; - weight_t weight = adj[i_id][j_id].find("weight") != adj[i_id][j_id].end() ? adj[i_id][j_id]["weight"] : 1; - edge_list.emplace_back(std::make_pair(std::make_pair(i_id, j_id), weight)); - } - } - std::sort(edge_list.begin(), edge_list.end(), comp); - node_t m, n; - for (auto edge : edge_list) { - for (node_t i = 0;i < group.size();i++) { - for (node_t j = 0;j < group[i].size();j++) { - if (group[i][j] == edge.first.first) { - m = i; - break; - } - } - for (node_t j = 0;j < group[i].size();j++) { - if (group[i][j] == edge.first.second) { - n = i; - break; - } - } - } - if (m != n) { - - res_dict[edge.first.first][edge.first.second] = edge.second; - std::vector temp_vector; - group[m].insert(group[m].end(), group[n].begin(), group[n].end()); - group[n].clear(); - } - } - for (std::unordered_map>::iterator k = res_dict.begin(); - k != res_dict.end();k++) { - py::object res_node = G_.id_to_node[k->first]; - for (std::unordered_map::iterator z = k->second.begin();z != k->second.end();z++) { - py::object res_adj_node = G_.id_to_node[z->first]; - result_dict[res_node][res_adj_node] = z->second; - } - } - return result_dict; -} - -py::object Floyd(py::object G) { - std::unordered_map> res_dict; - Graph& G_ = py::extract(G); - adj_dict_factory adj = G_.adj; - py::dict result_dict = py::dict(); - node_dict_factory node_list = G_.node; - for (node_dict_factory::iterator i = node_list.begin();i != node_list.end();i++) { - result_dict[G_.id_to_node[i->first]] = py::dict(); - adj_attr_dict_factory temp_key = adj[i->first]; - for (node_dict_factory::iterator j = node_list.begin();j != node_list.end();j++) { - if (temp_key.find(j->first) != temp_key.end()) { - if (adj[i->first][j->first].count("weight") == 0) { - adj[i->first][j->first]["weight"] = 1; - } - res_dict[i->first][j->first] = adj[i->first][j->first]["weight"]; - } - else { - res_dict[i->first][j->first] = INFINITY; - } - if (i->first == j->first) { - res_dict[i->first][i->first] = 0; - } - } - } - - for (node_dict_factory::iterator k = node_list.begin();k != node_list.end();k++) { - for (node_dict_factory::iterator i = node_list.begin();i != node_list.end();i++) { - for (node_dict_factory::iterator j = node_list.begin();j != node_list.end();j++) { - weight_t temp = res_dict[i->first][k->first] + res_dict[k->first][j->first]; - weight_t i_j_weight = res_dict[i->first][j->first]; - if (i_j_weight > temp) { - res_dict[i->first][j->first] = temp; - } - } - } - } - - for (std::unordered_map>::iterator k = res_dict.begin(); - k != res_dict.end();k++) { - py::object res_node = G_.id_to_node[k->first]; - for (std::unordered_map::iterator z = k->second.begin();z != k->second.end();z++) { - py::object res_adj_node = G_.id_to_node[z->first]; - result_dict[res_node][res_adj_node] = z->second; - } - } - return result_dict; -} diff --git a/src/cpp_easygraph/functions/path/path.h b/src/cpp_easygraph/functions/path/path.h deleted file mode 100644 index a125184b..00000000 --- a/src/cpp_easygraph/functions/path/path.h +++ /dev/null @@ -1,9 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "../../common/common.h" - -py::object _dijkstra_multisource(py::object G, py::object sources, py::object weight, py::object target); -py::object Floyd(py::object G); -py::object Prim(py::object G); -py::object Kruskal(py::object G); \ No newline at end of file diff --git a/src/cpp_easygraph/functions/structural_holes/__init__.h b/src/cpp_easygraph/functions/structural_holes/__init__.h deleted file mode 100644 index 62eb0f9c..00000000 --- a/src/cpp_easygraph/functions/structural_holes/__init__.h +++ /dev/null @@ -1,4 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "evaluation.h" \ No newline at end of file diff --git a/src/cpp_easygraph/functions/structural_holes/evaluation.cpp b/src/cpp_easygraph/functions/structural_holes/evaluation.cpp deleted file mode 100644 index 1799999b..00000000 --- a/src/cpp_easygraph/functions/structural_holes/evaluation.cpp +++ /dev/null @@ -1,205 +0,0 @@ -#include "evaluation.h" -#include "../../classes/graph.h" -#include "../../common/utils.h" - -struct pair_hash -{ - template - std::size_t operator() (const std::pair& p) const - { - auto h1 = std::hash()(p.first); - auto h2 = std::hash()(p.second); - return h1 ^ h2; - } -}; - -std::unordered_map, weight_t, pair_hash> sum_nmw_rec, max_nmw_rec, local_constraint_rec; - -enum norm_t { - sum, max -}; - - -weight_t mutual_weight(adj_dict_factory& G, node_t u, node_t v, std::string weight) { - weight_t a_uv = 0, a_vu = 0; - if (G.count(u) && G[u].count(v)) { - edge_attr_dict_factory& guv = G[u][v]; - a_uv = guv.count(weight) ? guv[weight] : 1; - } - if (G.count(v) && G[v].count(u)) { - edge_attr_dict_factory& gvu = G[v][u]; - a_uv = gvu.count(weight) ? gvu[weight] : 1; - } - return a_uv + a_vu; -} - -weight_t normalized_mutual_weight(adj_dict_factory& G, node_t u, node_t v, std::string weight, norm_t norm = sum) { - std::pair edge = std::make_pair(u, v); - auto& nmw_rec = (norm == sum) ? sum_nmw_rec : max_nmw_rec; - if (nmw_rec.count(edge)) { - return nmw_rec[edge]; - } - else { - weight_t scale = 0; - for (auto& w : G[u]) { - weight_t temp_weight = mutual_weight(G, u, w.first, weight); - scale = (norm == sum) ? (scale + temp_weight) : std::max(scale, temp_weight); - } - weight_t nmw = scale ? (mutual_weight(G, u, v, weight) / scale) : 0; - nmw_rec[edge] = nmw; - return nmw; - } -} - -weight_t local_constraint(adj_dict_factory& G, node_t u, node_t v, std::string weight = "None") { - std::pair edge = std::make_pair(u, v); - if (local_constraint_rec.count(edge)) { - return local_constraint_rec[edge]; - } - else { - weight_t direct = normalized_mutual_weight(G, u, v, weight); - weight_t indirect = 0; - for (auto& w : G[u]) { - indirect += normalized_mutual_weight(G, u, w.first, weight) * normalized_mutual_weight(G, w.first, v, weight); - } - weight_t result = pow((direct + indirect), 2); - local_constraint_rec[edge] = result; - return result; - } -} - -std::pair compute_constraint_of_v(adj_dict_factory& G, node_t v, std::string weight) { - weight_t constraint_of_v = 0; - if (G[v].size() == 0) { - constraint_of_v = Py_NAN; - } - else { - for (const auto& n : G[v]) { - constraint_of_v += local_constraint(G, v, n.first, weight); - } - } - return std::make_pair(v, constraint_of_v); -} - -py::object constraint(py::object G, py::object nodes, py::object weight, py::object n_workers) { - std::string weight_key = weight_to_string(weight); - sum_nmw_rec.clear(); - max_nmw_rec.clear(); - local_constraint_rec.clear(); - if (nodes == py::object()) { - nodes = G.attr("nodes"); - } - py::list nodes_list = py::list(nodes); - py::list constraint_results = py::list(); - Graph& G_ = py::extract(G); - for (int i = 0;i < py::len(nodes_list);i++) { - py::object v = nodes_list[i]; - node_t v_id = py::extract(G_.node_to_id[v]); - std::pair constraint_pair = compute_constraint_of_v(G_.adj, v_id, weight_key); - py::tuple constraint_of_v = py::make_tuple(G_.id_to_node[constraint_pair.first], constraint_pair.second); - constraint_results.append(constraint_of_v); - } - py::dict constraint = py::dict(constraint_results); - return constraint; -} - -weight_t redundancy(adj_dict_factory& G, node_t u, node_t v, std::string weight = "None") { - weight_t r = 0; - for (const auto& neighbor_info : G[u]) { - node_t w = neighbor_info.first; - r += normalized_mutual_weight(G, u, w, weight) * normalized_mutual_weight(G, v, w, weight, max); - } - return 1 - r; -} - -py::object effective_size(py::object G, py::object nodes, py::object weight, py::object n_workers) { - Graph& G_ = py::extract(G); - sum_nmw_rec.clear(); - max_nmw_rec.clear(); - py::dict effective_size = py::dict(); - if (nodes == py::object()) { - nodes = G; - } - nodes = py::list(nodes); - if (!G.attr("is_directed")() && weight == py::object()) { - for (int i = 0;i < py::len(nodes);i++) { - py::object v = nodes[i]; - if (py::len(G[v]) == 0) { - effective_size[v] = py::object(Py_NAN); - continue; - } - py::object E = G.attr("ego_subgraph")(v); - if (py::len(E) > 1) { - weight_t size = py::extract(E.attr("size")()); - effective_size[v] = py::len(E) - 1 - (2.0 * size) / (py::len(E) - 1); - } - else { - effective_size[v] = 0; - } - } - } - else { - std::string weight_key = weight_to_string(weight); - for (int i = 0;i < py::len(nodes);i++) { - py::object v = nodes[i]; - if (py::len(G[v]) == 0) { - effective_size[v] = py::object(Py_NAN); - continue; - } - weight_t redundancy_sum = 0; - node_t v_id = py::extract(G_.node_to_id[v]); - for (const auto& neighbor_info : G_.adj[v_id]) { - node_t u_id = neighbor_info.first; - redundancy_sum += redundancy(G_.adj, v_id, u_id, weight_key); - } - effective_size[v] = redundancy_sum; - } - } - return effective_size; -} - -py::object hierarchy(py::object G, py::object nodes, py::object weight, py::object n_workers) { - sum_nmw_rec.clear(); - max_nmw_rec.clear(); - local_constraint_rec.clear(); - std::string weight_key = weight_to_string(weight); - if (nodes == py::object()) { - nodes = G.attr("nodes"); - } - py::list nodes_list = py::list(nodes); - - Graph& G_ = py::extract(G); - py::dict hierarchy = py::dict(); - - for (int i = 0;i < py::len(nodes_list);i++) { - py::object v = nodes_list[i]; - py::object E = G.attr("ego_subgraph")(v); - - int n = py::len(E) - 1; - - weight_t C = 0; - std::map c; - py::list neighbors_of_v = py::list(G.attr("neighbors")(v)); - - for (int j = 0;j < py::len(neighbors_of_v);j++) { - py::object w = neighbors_of_v[j]; - node_t v_id = py::extract(G_.node_to_id[v]); - node_t w_id = py::extract(G_.node_to_id[w]); - C += local_constraint(G_.adj, v_id, w_id, weight_key); - c[w_id] = local_constraint(G_.adj, v_id, w_id, weight_key); - } - if (n > 1) { - weight_t hierarchy_sum = 0; - for (int k = 0;k < py::len(neighbors_of_v);k++) { - py::object w = neighbors_of_v[k]; - node_t w_id = py::extract(G_.node_to_id[w]); - hierarchy_sum += c[w_id] / C * n * log(c[w_id] / C * n) / (n * log(n)); - } - hierarchy[v] = hierarchy_sum; - } - if (!hierarchy.has_key(v)) { - hierarchy[v] = 0; - } - } - return hierarchy; -} \ No newline at end of file diff --git a/src/cpp_easygraph/functions/structural_holes/evaluation.h b/src/cpp_easygraph/functions/structural_holes/evaluation.h deleted file mode 100644 index 2695079c..00000000 --- a/src/cpp_easygraph/functions/structural_holes/evaluation.h +++ /dev/null @@ -1,8 +0,0 @@ -#pragma once -#define BOOST_PYTHON_STATIC_LIB - -#include "../../common/common.h" - -py::object constraint(py::object G, py::object nodes, py::object weight, py::object n_workers); -py::object effective_size(py::object G, py::object nodes, py::object weight, py::object n_workers); -py::object hierarchy(py::object G, py::object nodes, py::object weight, py::object n_workers); \ No newline at end of file From 070ffdfe3f6ff0df73c5de73f51579099d9d0a11 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 16:16:31 +0800 Subject: [PATCH 09/17] refactor(project): remove legacy test and config files, enhance project structure - Removed `pytest.ini`, `tox.ini`, and `.flake8` as part of the configuration cleanup. - Updated and reorganized `pyproject.toml` with modern configurations for dependency management, linting, and testing. - Migrated build-related files from `cpp_easygraph` to `_cpp_easygraph` to align with updated CMake project structure. - Introduced Ruff linting with detailed rule selection and customization. - Consolidated `tox` configurations into `pyproject.toml`. These updates simplify project setup, align with modern tooling practices, and improve maintainability. Signed-off-by: acture --- .flake8 | 69 ---------- .../CMakeLists.txt | 0 .../include/biconnected.h | 0 .../include/cluster.h | 0 .../include/common.h | 0 .../include/directed_graph.h | 0 .../include/evaluation.h | 0 .../include/graph.h | 0 .../include/operation.h | 0 .../include/path.h | 0 .../include/utils.h | 0 .../src/biconnected.cpp | 0 .../src/cluster.cpp | 0 .../src/cpp_easygraph.cpp | 0 .../src/directed_graph.cpp | 0 .../src/evaluation.cpp | 0 .../src/graph.cpp | 0 .../src/operation.cpp | 0 .../src/path.cpp | 0 .../src/utils.cpp | 0 pyproject.toml | 130 ++++++++++++++---- pytest.ini | 4 - tox.ini | 35 ----- 23 files changed, 107 insertions(+), 131 deletions(-) delete mode 100644 .flake8 rename {cpp_easygraph => _cpp_easygraph}/CMakeLists.txt (100%) rename {cpp_easygraph => _cpp_easygraph}/include/biconnected.h (100%) rename {cpp_easygraph => _cpp_easygraph}/include/cluster.h (100%) rename {cpp_easygraph => _cpp_easygraph}/include/common.h (100%) rename {cpp_easygraph => _cpp_easygraph}/include/directed_graph.h (100%) rename {cpp_easygraph => _cpp_easygraph}/include/evaluation.h (100%) rename {cpp_easygraph => _cpp_easygraph}/include/graph.h (100%) rename {cpp_easygraph => _cpp_easygraph}/include/operation.h (100%) rename {cpp_easygraph => _cpp_easygraph}/include/path.h (100%) rename {cpp_easygraph => _cpp_easygraph}/include/utils.h (100%) rename {cpp_easygraph => _cpp_easygraph}/src/biconnected.cpp (100%) rename {cpp_easygraph => _cpp_easygraph}/src/cluster.cpp (100%) rename {cpp_easygraph => _cpp_easygraph}/src/cpp_easygraph.cpp (100%) rename {cpp_easygraph => _cpp_easygraph}/src/directed_graph.cpp (100%) rename {cpp_easygraph => _cpp_easygraph}/src/evaluation.cpp (100%) rename {cpp_easygraph => _cpp_easygraph}/src/graph.cpp (100%) rename {cpp_easygraph => _cpp_easygraph}/src/operation.cpp (100%) rename {cpp_easygraph => _cpp_easygraph}/src/path.cpp (100%) rename {cpp_easygraph => _cpp_easygraph}/src/utils.cpp (100%) delete mode 100644 pytest.ini delete mode 100644 tox.ini diff --git a/.flake8 b/.flake8 deleted file mode 100644 index daa7560e..00000000 --- a/.flake8 +++ /dev/null @@ -1,69 +0,0 @@ -[flake8] -min_python_version = 3.7.0 -max-line-length = 88 -ban-relative-imports = true -# flake8-use-fstring: https://github.com/MichaelKim0407/flake8-use-fstring#--percent-greedy-and---format-greedy -format-greedy = 1 -inline-quotes = double -enable-extensions = TC, TC1 -type-checking-exempt-modules = typing, typing-extensions -eradicate-whitelist-extend = ^-.*; -extend-ignore = - # E203: Whitespace before ':' (pycqa/pycodestyle#373) - E203, - # SIM106: Handle error-cases first - SIM106, - # ANN101: Missing type annotation for self in method - ANN101, - # ANN102: Missing type annotation for cls in classmethod - ANN102, - F401, - F403, - I252, - SIM115, - N806, - N803, - B007, - E501, - C408, - SIM113, - N802, - N400, - E501, - E802, - E800, - B001, - B006, - B020, - C414, - C416, - E402, - E711, - E712, - E722, - E741, - F405, - F541, - F811, - F821, - F841, - FS001, - FS002, - I250, - N801, - N804, - N812, - N816, - Q002, - SIM102, - SIM105, - SIM111, - SIM114, - SIM118, - SIM201, - SIM203, - SIM300, - SIM401, - TC002 - - diff --git a/cpp_easygraph/CMakeLists.txt b/_cpp_easygraph/CMakeLists.txt similarity index 100% rename from cpp_easygraph/CMakeLists.txt rename to _cpp_easygraph/CMakeLists.txt diff --git a/cpp_easygraph/include/biconnected.h b/_cpp_easygraph/include/biconnected.h similarity index 100% rename from cpp_easygraph/include/biconnected.h rename to _cpp_easygraph/include/biconnected.h diff --git a/cpp_easygraph/include/cluster.h b/_cpp_easygraph/include/cluster.h similarity index 100% rename from cpp_easygraph/include/cluster.h rename to _cpp_easygraph/include/cluster.h diff --git a/cpp_easygraph/include/common.h b/_cpp_easygraph/include/common.h similarity index 100% rename from cpp_easygraph/include/common.h rename to _cpp_easygraph/include/common.h diff --git a/cpp_easygraph/include/directed_graph.h b/_cpp_easygraph/include/directed_graph.h similarity index 100% rename from cpp_easygraph/include/directed_graph.h rename to _cpp_easygraph/include/directed_graph.h diff --git a/cpp_easygraph/include/evaluation.h b/_cpp_easygraph/include/evaluation.h similarity index 100% rename from cpp_easygraph/include/evaluation.h rename to _cpp_easygraph/include/evaluation.h diff --git a/cpp_easygraph/include/graph.h b/_cpp_easygraph/include/graph.h similarity index 100% rename from cpp_easygraph/include/graph.h rename to _cpp_easygraph/include/graph.h diff --git a/cpp_easygraph/include/operation.h b/_cpp_easygraph/include/operation.h similarity index 100% rename from cpp_easygraph/include/operation.h rename to _cpp_easygraph/include/operation.h diff --git a/cpp_easygraph/include/path.h b/_cpp_easygraph/include/path.h similarity index 100% rename from cpp_easygraph/include/path.h rename to _cpp_easygraph/include/path.h diff --git a/cpp_easygraph/include/utils.h b/_cpp_easygraph/include/utils.h similarity index 100% rename from cpp_easygraph/include/utils.h rename to _cpp_easygraph/include/utils.h diff --git a/cpp_easygraph/src/biconnected.cpp b/_cpp_easygraph/src/biconnected.cpp similarity index 100% rename from cpp_easygraph/src/biconnected.cpp rename to _cpp_easygraph/src/biconnected.cpp diff --git a/cpp_easygraph/src/cluster.cpp b/_cpp_easygraph/src/cluster.cpp similarity index 100% rename from cpp_easygraph/src/cluster.cpp rename to _cpp_easygraph/src/cluster.cpp diff --git a/cpp_easygraph/src/cpp_easygraph.cpp b/_cpp_easygraph/src/cpp_easygraph.cpp similarity index 100% rename from cpp_easygraph/src/cpp_easygraph.cpp rename to _cpp_easygraph/src/cpp_easygraph.cpp diff --git a/cpp_easygraph/src/directed_graph.cpp b/_cpp_easygraph/src/directed_graph.cpp similarity index 100% rename from cpp_easygraph/src/directed_graph.cpp rename to _cpp_easygraph/src/directed_graph.cpp diff --git a/cpp_easygraph/src/evaluation.cpp b/_cpp_easygraph/src/evaluation.cpp similarity index 100% rename from cpp_easygraph/src/evaluation.cpp rename to _cpp_easygraph/src/evaluation.cpp diff --git a/cpp_easygraph/src/graph.cpp b/_cpp_easygraph/src/graph.cpp similarity index 100% rename from cpp_easygraph/src/graph.cpp rename to _cpp_easygraph/src/graph.cpp diff --git a/cpp_easygraph/src/operation.cpp b/_cpp_easygraph/src/operation.cpp similarity index 100% rename from cpp_easygraph/src/operation.cpp rename to _cpp_easygraph/src/operation.cpp diff --git a/cpp_easygraph/src/path.cpp b/_cpp_easygraph/src/path.cpp similarity index 100% rename from cpp_easygraph/src/path.cpp rename to _cpp_easygraph/src/path.cpp diff --git a/cpp_easygraph/src/utils.cpp b/_cpp_easygraph/src/utils.cpp similarity index 100% rename from cpp_easygraph/src/utils.cpp rename to _cpp_easygraph/src/utils.cpp diff --git a/pyproject.toml b/pyproject.toml index 0416c02c..2ce4eba1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,30 +2,29 @@ name = "Python-EasyGraph" version = "0.2a40" authors = [ - { name = "Fudan MSN Group", email = "easygraph@163.com" }, + { name = "Fudan MSN Group", email = "easygraph@163.com" }, ] description = "Easy Graph" readme = "README.rst" requires-python = ">=3.10" license = "BSD-3-Clause" classifiers = [ - "Programming Language :: Python :: 3.10", - "Operating System :: OS Independent", + "Programming Language :: Python :: 3.10", + "Operating System :: OS Independent", ] dependencies = [ - "gensim>=4.2.0", - "joblib>=1.1.1", - "matplotlib>=3.3.4", - "nose>=1.3.7", - "numpy>=1.19.5", - "pandas>=0.25.3", - "progressbar>=2.5", - "progressbar33>=2.4", - "scikit-learn>=0.24.2", - "scipy>=1.5.4", - "six>=1.17.0", - "statsmodels>=0.12.2", - "tqdm>=4.64.1", + "gensim>=4.2.0", + "joblib>=1.1.1", + "matplotlib>=3.3.4", + "numpy>=1.19.5", + "pandas>=0.25.3", + "progressbar>=2.5", + "progressbar33>=2.4", + "scikit-learn>=0.24.2", + "scipy>=1.5.4", + "six>=1.17.0", + "statsmodels>=0.12.2", + "tqdm>=4.64.1", ] [project.scripts] @@ -39,14 +38,18 @@ build-dir = "build/{wheel_tag}" requires = ["scikit-build-core>=0.10", "pybind11"] build-backend = "scikit_build_core.build" -[tool.setuptools.packages.find] -where = ["."] +[tool.setuptools] +packages = ["easygraph"] + +[tool.scikit-build.cmake] +source-dir = "_cpp_easygraph" [dependency-groups] dev = [ - "pytest>=8.4.2", - "ruff>=0.14.1", - "scikit-build-core>=0.11.6", + "pandas-stubs>=2.3.2.250926", + "pytest>=8.4.2", + "ruff>=0.14.1", + "scikit-build-core>=0.11.6", ] @@ -54,5 +57,86 @@ dev = [ python_files = "**/tests/test_*.py" addopts = "-ra --disable-warnings" -[tool.scikit-build.cmake] -source-dir = "cpp_easygraph" + +# pyproject.toml +[tool.ruff] +target-version = "py310" # 原 min_python_version +line-length = 88 # 原 max-line-length + +[tool.ruff.lint] +# 只启用你确实想要的规则族： +# - E/F/W: pycodestyle/pyflakes +# - I: isort（导入排序） +# - B: flake8-bugbear +# - UP: pyupgrade（含“优先 f-string”） +# - Q: flake8-quotes（引号风格） +# - SIM: flake8-simplify +# - TID: flake8-tidy-imports（含 TID252 禁止相对导入） +# - TCH: flake8-type-checking（类型导入移动到 if TYPE_CHECKING） +# - ERA: eradicate（清理注释死码） +select = [ + "E", "F", "W", + "I", + "B", + "UP", + "Q", + "SIM", + "TID", + "TCH", + "ERA", +] + +# 仅保留你确实需要的忽略。E203 与 Black 冲突通常忽略。 +ignore = [ + "E203", + # 你若不想启用某个规则族，就别放进 select；无需在 ignore 里罗列一堆。 +] + +# （可选）按文件忽略 +# per-file-ignores = { "tests/**.py" = ["S101"] } + +# —— 各插件的细化配置 —— # + +[tool.ruff.lint.flake8-quotes] +# 原 flake8: inline-quotes = double +inline-quotes = "double" +# 若想统一 docstring/多行字符串： +# multiline-quotes = "double" +# docstring-quotes = "double" + +[tool.ruff.lint.flake8-tidy-imports] +# 原 flake8: ban-relative-imports = true ==> TID252 +ban-relative-imports = "all" + +[tool.ruff.lint.flake8-type-checking] +# 原: type-checking-exempt-modules = typing, typing-extensions +exempt-modules = ["typing", "typing_extensions"] + +# eradicate（清理注释死码） +[tool.ruff.lint.flake8-eradicate] +# 原 flake8-eradicate 的 whitelist-extend 在 Ruff 中没有等价项； +# 如果你需要排除某些模式，建议用 per-file-ignores 或者在 ERA 里关闭对应规则。 +# aggressive = true #（可选）更激进清理 + +[tool.tox] +# 定义通用配置 +requires = ["tox-uv>=1.0"] +provision = ".tox-uv" +skipsdist = false +env_list = ["py36", "py37", "py38", "py39", "py310"] + +[tool.tox.env] +# 默认环境配置 +deps = [ + "lxml", + "pytest", + "." +] +commands = [ + "pytest {posargs}" +] + +[tool.tox.env.pyver] +description = "Simply check the Python version, do not install the package" +skipsdist = true +commands = ["python --version"] diff --git a/pytest.ini b/pytest.ini deleted file mode 100644 index f7054a48..00000000 --- a/pytest.ini +++ /dev/null @@ -1,4 +0,0 @@ -[pytest] -# to speed up tests collection -python_files = **/tests/test_*.py -addopts=-ra --disable-warnings diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 81aad477..00000000 --- a/tox.ini +++ /dev/null @@ -1,35 +0,0 @@ -[tox] -# Define all Python versions you want to test against -envlist = py36, py37, py38, py39, py310 - -# Use tox-uv to make environment creation extremely fast -# This replaces the need for tox-conda -requires = tox-uv -provision = .tox-uv - -# By default, build the package once and use it for all environments -skipsdist = false - -[testenv] -# Define the dependencies needed for testing. -# `uv` will install these from your lock file if it exists. -deps = - lxml - pytest - # The "." is crucial: it tells tox to install your - # Easy-Graph project (using setup.py) into the test env - . - -# Define the command to run the tests -# {posargs} allows you to pass extra arguments, e.g., tox -e py310 -- -k "test_something" -commands = - pytest {posargs} - -# This section is for your "version check" use case -[testenv:pyver] -description = "Simply check the Python version, do not install the package" -# Don't build or install the package -skipsdist = true -# Just run the version command -commands = - python --version From 9a93dde5371c8bb6337a4915858fabfc4bc05468 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 16:16:46 +0800 Subject: [PATCH 10/17] chore(tests): remove legacy `nose` dependency MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Replaced `from nose import SkipTest` with `from unittest import SkipTest` for compatibility with Python ≥3.12. - Removed all residual `nose` imports and related code paths. - Ensures pytest-native skip handling (`pytest.importorskip`, `pytest.skip`) is used consistently. This change removes an unmaintained dependency (`nose`) and restores compatibility with modern Python versions. Signed-off-by: acture --- easygraph/readwrite/tests/test_ucinet.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easygraph/readwrite/tests/test_ucinet.py b/easygraph/readwrite/tests/test_ucinet.py index 3c91c87b..cfbf7539 100644 --- a/easygraph/readwrite/tests/test_ucinet.py +++ b/easygraph/readwrite/tests/test_ucinet.py @@ -6,8 +6,6 @@ import easygraph as eg -from nose import SkipTest -from nose.tools import * def filterEdges(edges): @@ -35,10 +33,6 @@ def setup_class(self): ("e", "a"), ] ) - try: - pass - except ImportError: - raise SkipTest("NumPy not available.") def test_generate_ucinet(self): Gout = eg.generate_ucinet(self.G) From d51208d14ebee147990d16b7393193cea8151e53 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 16:21:22 +0800 Subject: [PATCH 11/17] feat(packaging): add optional Graphviz dependency - Introduced `graphviz` as an optional dependency in `pyproject.toml`, requiring `lxml>=6.0.2`. - Enables additional functionality for users needing Graphviz-related features. This addition improves the flexibility of the package by allowing optional integration with Graphviz. Signed-off-by: acture --- pyproject.toml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 2ce4eba1..b3bc86e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,6 +30,11 @@ dependencies = [ [project.scripts] easy-graph = "easy_graph:main" +[project.optional-dependencies] +graphviz = [ + "lxml>=6.0.2", +] + [tool.scikit-build] minimum-version = "build-system.requires" build-dir = "build/{wheel_tag}" From 9d95287cdac47a98d56469c42d8b97c46c4d59b4 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 16:21:38 +0800 Subject: [PATCH 12/17] fix(graphml,gexf): replace deprecated `np.float_` with `np.float64` - Updated instances of `np.float_` to `np.float64` in `graphml.py`, `gexf.py`, and associated tests. - Ensures compatibility with newer NumPy versions where `np.float_` is deprecated. Signed-off-by: acture --- easygraph/readwrite/gexf.py | 2 +- easygraph/readwrite/graphml.py | 2 +- easygraph/readwrite/tests/test_graphml.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easygraph/readwrite/gexf.py b/easygraph/readwrite/gexf.py index f75c7cb6..e86f1350 100644 --- a/easygraph/readwrite/gexf.py +++ b/easygraph/readwrite/gexf.py @@ -187,7 +187,7 @@ def construct_types(self): (np.float64, "float"), (np.float32, "float"), (np.float16, "float"), - (np.float_, "float"), + (np.float64, "float"), (np.int_, "int"), (np.int8, "int"), (np.int16, "int"), diff --git a/easygraph/readwrite/graphml.py b/easygraph/readwrite/graphml.py index 8f577105..61e39070 100644 --- a/easygraph/readwrite/graphml.py +++ b/easygraph/readwrite/graphml.py @@ -418,7 +418,7 @@ def construct_types(self): (np.float64, "float"), (np.float32, "float"), (np.float16, "float"), - (np.float_, "float"), + (np.float64, "float"), (np.int_, "int"), (np.int8, "int"), (np.int16, "int"), diff --git a/easygraph/readwrite/tests/test_graphml.py b/easygraph/readwrite/tests/test_graphml.py index 88ec32ef..a3a58c92 100644 --- a/easygraph/readwrite/tests/test_graphml.py +++ b/easygraph/readwrite/tests/test_graphml.py @@ -1283,7 +1283,7 @@ def test_mixed_int_type_number_attributes(self): def test_numpy_float(self): np = pytest.importorskip("numpy") - wt = np.float_(3.4) + wt = np.float64(3.4) G = eg.Graph([(1, 2, {"weight": wt})]) fd, fname = tempfile.mkstemp() self.writer(G, fname) From 9c0f243d4010394c4ff6b87d3cf44d27d267a7d7 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 16:26:09 +0800 Subject: [PATCH 13/17] fix(packaging): update Graphviz optional dependency to `pygraphviz>=1.14` - Replaced `lxml>=6.0.2` with `pygraphviz>=1.14` in `pyproject.toml` under `[project.optional-dependencies]`. - Ensures compatibility and better alignment with Graphviz-related features. Signed-off-by: acture --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b3bc86e6..57037543 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,7 +32,7 @@ easy-graph = "easy_graph:main" [project.optional-dependencies] graphviz = [ - "lxml>=6.0.2", + "pygraphviz>=1.14", ] [tool.scikit-build] From 37e898e80eb88687403c46c7c63767105491aa8d Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 16:31:02 +0800 Subject: [PATCH 14/17] fix(tests): replace deprecated `DataFrame.append` with `pd.concat` - Updated `test_convert.py` to replace the deprecated `DataFrame.append` method with `pd.concat` for constructing dataframes. - Ensures compatibility with newer pandas versions where `DataFrame.append` is deprecated. Signed-off-by: acture --- easygraph/tests/test_convert.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easygraph/tests/test_convert.py b/easygraph/tests/test_convert.py index 1c869b8f..c237c57d 100644 --- a/easygraph/tests/test_convert.py +++ b/easygraph/tests/test_convert.py @@ -43,7 +43,7 @@ def setup_method(self): self.df = df mdf = pd.DataFrame([[4, 16, "A", "D"]], columns=["weight", "cost", 0, "b"]) - self.mdf = df.append(mdf) + self.mdf = pd.concat([df, mdf], ignore_index=True) def assert_equal(self, G1, G2): assert nodes_equal(G1.nodes, G2.nodes) From 6de337dccdedcce1ec060c929365c9169e358335 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 17:04:31 +0800 Subject: [PATCH 15/17] refactor(readwrite): remove warnings, fix indentation, and clean up parsing logic - Removed unnecessary `warnings` imports and deprecated warnings in the GML parsing module (`gml.py`). - Fixed inconsistent indentation across GML and GraphML modules to adhere to PEP 8 standards. - Improved readability by cleaning up GML parsing logic, particularly around `parse_gml_lines` and helper functions. - Minor fix in GraphML Signed-off-by: acture --- easygraph/readwrite/gml.py | 759 ++++++++++++++++----------------- easygraph/readwrite/graphml.py | 2 +- pyproject.toml | 2 +- 3 files changed, 379 insertions(+), 384 deletions(-) diff --git a/easygraph/readwrite/gml.py b/easygraph/readwrite/gml.py index df44b037..a6d3acb6 100644 --- a/easygraph/readwrite/gml.py +++ b/easygraph/readwrite/gml.py @@ -31,7 +31,6 @@ import html.entities as htmlentitydefs import re -import warnings from ast import literal_eval from collections import defaultdict @@ -52,43 +51,43 @@ def escape(text): - """Use XML character references to escape characters. + """Use XML character references to escape characters. Use XML character references for unprintable or non-ASCII characters, double quotes and ampersands in a string """ - def fixup(m): - ch = m.group(0) - return "&#" + str(ord(ch)) + ";" + def fixup(m): + ch = m.group(0) + return "&#" + str(ord(ch)) + ";" - text = re.sub('[^ -~]|[&"]', fixup, text) - return text if isinstance(text, str) else str(text) + text = re.sub('[^ -~]|[&"]', fixup, text) + return text if isinstance(text, str) else str(text) def unescape(text): - """Replace XML character references with the referenced characters""" - - def fixup(m): - text = m.group(0) - if text[1] == "#": - # Character reference - if text[2] == "x": - code = int(text[3:-1], 16) - else: - code = int(text[2:-1]) - else: - # Named entity - try: - code = htmlentitydefs.name2codepoint[text[1:-1]] - except KeyError: - return text # leave unchanged - try: - return chr(code) - except (ValueError, OverflowError): - return text # leave unchanged - - return re.sub("&(?:[0-9A-Za-z]+|#(?:[0-9]+|x[0-9A-Fa-f]+));", fixup, text) + """Replace XML character references with the referenced characters""" + + def fixup(m): + text = m.group(0) + if text[1] == "#": + # Character reference + if text[2] == "x": + code = int(text[3:-1], 16) + else: + code = int(text[2:-1]) + else: + # Named entity + try: + code = htmlentitydefs.name2codepoint[text[1:-1]] + except KeyError: + return text # leave unchanged + try: + return chr(code) + except (ValueError, OverflowError): + return text # leave unchanged + + return re.sub("&(?:[0-9A-Za-z]+|#(?:[0-9]+|x[0-9A-Fa-f]+));", fixup, text) def literal_destringizer(rep): @@ -109,8 +108,6 @@ def literal_destringizer(rep): ValueError If `rep` is not a Python literal. """ - msg = "literal_destringizer is deprecated and will be removed in 3.0." - warnings.warn(msg, DeprecationWarning) if isinstance(rep, str): orig_rep = rep try: @@ -122,26 +119,26 @@ def literal_destringizer(rep): class Pattern(Enum): - """encodes the index of each token-matching pattern in `tokenize`.""" + """encodes the index of each token-matching pattern in `tokenize`.""" - KEYS = 0 - REALS = 1 - INTS = 2 - STRINGS = 3 - DICT_START = 4 - DICT_END = 5 - COMMENT_WHITESPACE = 6 + KEYS = 0 + REALS = 1 + INTS = 2 + STRINGS = 3 + DICT_START = 4 + DICT_END = 5 + COMMENT_WHITESPACE = 6 class Token(NamedTuple): - category: Pattern - value: Any - line: int - position: int + category: Pattern + value: Any + line: int + position: int def parse_gml(lines, label="label", destringizer=None): - """Parse GML graph from a string or iterable. + """Parse GML graph from a string or iterable. Parameters ---------- @@ -189,224 +186,224 @@ def parse_gml(lines, label="label", destringizer=None): See the module docstring :mod:`easygraph.readwrite.gml` for more details. """ - def decode_line(line): - if isinstance(line, bytes): - try: - line.decode("ascii") - except UnicodeDecodeError as err: - raise EasyGraphError("input is not ASCII-encoded") from err - if not isinstance(line, str): - line = str(line) - return line - - def filter_lines(lines): - if isinstance(lines, str): - lines = decode_line(lines) - lines = lines.splitlines() - yield from lines - else: - for line in lines: - line = decode_line(line) - if line and line[-1] == "\n": - line = line[:-1] - if line.find("\n") != -1: - raise EasyGraphError("input line contains newline") - yield line - - G = parse_gml_lines(filter_lines(lines), label, destringizer) - return G + def decode_line(line): + if isinstance(line, bytes): + try: + line.decode("ascii") + except UnicodeDecodeError as err: + raise EasyGraphError("input is not ASCII-encoded") from err + if not isinstance(line, str): + line = str(line) + return line + + def filter_lines(lines): + if isinstance(lines, str): + lines = decode_line(lines) + lines = lines.splitlines() + yield from lines + else: + for line in lines: + line = decode_line(line) + if line and line[-1] == "\n": + line = line[:-1] + if line.find("\n") != -1: + raise EasyGraphError("input line contains newline") + yield line + + G = parse_gml_lines(filter_lines(lines), label, destringizer) + return G def parse_gml_lines(lines, label, destringizer): - """Parse GML `lines` into a graph.""" - - def tokenize(): - patterns = [ - r"[A-Za-z][0-9A-Za-z_]*\b", # keys - # reals - r"[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*|INF)(?:[Ee][+-]?[0-9]+)?", - r"[+-]?[0-9]+", # ints - r'".*?"', # strings - r"\[", # dict start - r"\]", # dict end - r"#.*$|\s+", # comments and whitespaces - ] - tokens = re.compile("|".join(f"({pattern})" for pattern in patterns)) - lineno = 0 - for line in lines: - length = len(line) - pos = 0 - while pos < length: - match = tokens.match(line, pos) - if match is None: - m = f"cannot tokenize {line[pos:]} at ({lineno + 1}, {pos + 1})" - raise EasyGraphError(m) - for i in range(len(patterns)): - group = match.group(i + 1) - if group is not None: - if i == 0: # keys - value = group.rstrip() - elif i == 1: # reals - value = float(group) - elif i == 2: # ints - value = int(group) - else: - value = group - if i != 6: # comments and whitespaces - yield Token(Pattern(i), value, lineno + 1, pos + 1) - pos += len(group) - break - lineno += 1 - yield Token(None, None, lineno + 1, 1) # EOF - - def unexpected(curr_token, expected): - category, value, lineno, pos = curr_token - value = repr(value) if value is not None else "EOF" - raise EasyGraphError(f"expected {expected}, found {value} at ({lineno}, {pos})") - - def consume(curr_token, category, expected): - if curr_token.category == category: - return next(tokens) - unexpected(curr_token, expected) - - def parse_dict(curr_token): - # dict start - curr_token = consume(curr_token, Pattern.DICT_START, "'['") - # dict contents - curr_token, dct = parse_kv(curr_token) - # dict end - curr_token = consume(curr_token, Pattern.DICT_END, "']'") - return curr_token, dct - - def parse_kv(curr_token): - dct = defaultdict(list) - while curr_token.category == Pattern.KEYS: - key = curr_token.value - curr_token = next(tokens) - category = curr_token.category - if category == Pattern.REALS or category == Pattern.INTS: - value = curr_token.value - curr_token = next(tokens) - elif category == Pattern.STRINGS: - value = unescape(curr_token.value[1:-1]) - if destringizer: - try: - value = destringizer(value) - except ValueError: - pass - curr_token = next(tokens) - elif category == Pattern.DICT_START: - curr_token, value = parse_dict(curr_token) - else: - if key in ("id", "label", "source", "target"): - try: - # String convert the token value - value = unescape(str(curr_token.value)) - if destringizer: - try: - value = destringizer(value) - except ValueError: - pass - curr_token = next(tokens) - except Exception: - msg = ( - "an int, float, string, '[' or string" - + " convertable ASCII value for node id or label" - ) - unexpected(curr_token, msg) - elif curr_token.value in {"NAN", "INF"}: - value = float(curr_token.value) - curr_token = next(tokens) - else: # Otherwise error out - unexpected(curr_token, "an int, float, string or '['") - dct[key].append(value) - - def clean_dict_value(value): - if not isinstance(value, list): - return value - if len(value) == 1: - return value[0] - if value[0] == LIST_START_VALUE: - return value[1:] - return value - - dct = {key: clean_dict_value(value) for key, value in dct.items()} - return curr_token, dct - - def parse_graph(): - curr_token, dct = parse_kv(next(tokens)) - if curr_token.category is not None: # EOF - unexpected(curr_token, "EOF") - if "graph" not in dct: - raise EasyGraphError("input contains no graph") - graph = dct["graph"] - if isinstance(graph, list): - raise EasyGraphError("input contains more than one graph") - return graph - - tokens = tokenize() - graph = parse_graph() - directed = graph.pop("directed", False) - multigraph = graph.pop("multigraph", False) - if not multigraph: - G = eg.DiGraph() if directed else eg.Graph() - else: - G = eg.MultiDiGraph() if directed else eg.MultiGraph() - graph_attr = {k: v for k, v in graph.items() if k not in ("node", "edge")} - G.graph.update(graph_attr) - - def pop_attr(dct, category, attr, i): - try: - return dct.pop(attr) - except KeyError as err: - raise EasyGraphError(f"{category} #{i} has no {attr!r} attribute") from err - - nodes = graph.get("node", []) - mapping = {} - node_labels = set() - for i, node in enumerate(nodes if isinstance(nodes, list) else [nodes]): - id = pop_attr(node, "node", "id", i) - if id in G: - raise EasyGraphError(f"node id {id!r} is duplicated") - if label is not None and label != "id": - node_label = pop_attr(node, "node", label, i) - if node_label in node_labels: - raise EasyGraphError(f"node label {node_label!r} is duplicated") - node_labels.add(node_label) - mapping[id] = node_label - G.add_node(id, **node) - - edges = graph.get("edge", []) - for i, edge in enumerate(edges if isinstance(edges, list) else [edges]): - source = pop_attr(edge, "edge", "source", i) - target = pop_attr(edge, "edge", "target", i) - if source not in G: - raise EasyGraphError(f"edge #{i} has undefined source {source!r}") - if target not in G: - raise EasyGraphError(f"edge #{i} has undefined target {target!r}") - if not multigraph: - if not G.has_edge(source, target): - G.add_edge(source, target, **edge) - else: - arrow = "->" if directed else "--" - msg = f"edge #{i} ({source!r}{arrow}{target!r}) is duplicated" - raise EasyGraphError(msg) - else: - key = edge.pop("key", None) - if key is not None and G.has_edge(source, target, key): - arrow = "->" if directed else "--" - msg = f"edge #{i} ({source!r}{arrow}{target!r}, {key!r})" - msg2 = 'Hint: If multigraph add "multigraph 1" to file header.' - raise EasyGraphError(msg + " is duplicated\n" + msg2) - G.add_edge(source, target, key, **edge) - - if label is not None and label != "id": - G = eg.relabel_nodes(G, mapping) - return G + """Parse GML `lines` into a graph.""" + + def tokenize(): + patterns = [ + r"[A-Za-z][0-9A-Za-z_]*\b", # keys + # reals + r"[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*|INF)(?:[Ee][+-]?[0-9]+)?", + r"[+-]?[0-9]+", # ints + r'".*?"', # strings + r"\[", # dict start + r"\]", # dict end + r"#.*$|\s+", # comments and whitespaces + ] + tokens = re.compile("|".join(f"({pattern})" for pattern in patterns)) + lineno = 0 + for line in lines: + length = len(line) + pos = 0 + while pos < length: + match = tokens.match(line, pos) + if match is None: + m = f"cannot tokenize {line[pos:]} at ({lineno + 1}, {pos + 1})" + raise EasyGraphError(m) + for i in range(len(patterns)): + group = match.group(i + 1) + if group is not None: + if i == 0: # keys + value = group.rstrip() + elif i == 1: # reals + value = float(group) + elif i == 2: # ints + value = int(group) + else: + value = group + if i != 6: # comments and whitespaces + yield Token(Pattern(i), value, lineno + 1, pos + 1) + pos += len(group) + break + lineno += 1 + yield Token(None, None, lineno + 1, 1) # EOF + + def unexpected(curr_token, expected): + category, value, lineno, pos = curr_token + value = repr(value) if value is not None else "EOF" + raise EasyGraphError(f"expected {expected}, found {value} at ({lineno}, {pos})") + + def consume(curr_token, category, expected): + if curr_token.category == category: + return next(tokens) + unexpected(curr_token, expected) + + def parse_dict(curr_token): + # dict start + curr_token = consume(curr_token, Pattern.DICT_START, "'['") + # dict contents + curr_token, dct = parse_kv(curr_token) + # dict end + curr_token = consume(curr_token, Pattern.DICT_END, "']'") + return curr_token, dct + + def parse_kv(curr_token): + dct = defaultdict(list) + while curr_token.category == Pattern.KEYS: + key = curr_token.value + curr_token = next(tokens) + category = curr_token.category + if category == Pattern.REALS or category == Pattern.INTS: + value = curr_token.value + curr_token = next(tokens) + elif category == Pattern.STRINGS: + value = unescape(curr_token.value[1:-1]) + if destringizer: + try: + value = destringizer(value) + except ValueError: + pass + curr_token = next(tokens) + elif category == Pattern.DICT_START: + curr_token, value = parse_dict(curr_token) + else: + if key in ("id", "label", "source", "target"): + try: + # String convert the token value + value = unescape(str(curr_token.value)) + if destringizer: + try: + value = destringizer(value) + except ValueError: + pass + curr_token = next(tokens) + except Exception: + msg = ( + "an int, float, string, '[' or string" + + " convertable ASCII value for node id or label" + ) + unexpected(curr_token, msg) + elif curr_token.value in {"NAN", "INF"}: + value = float(curr_token.value) + curr_token = next(tokens) + else: # Otherwise error out + unexpected(curr_token, "an int, float, string or '['") + dct[key].append(value) + + def clean_dict_value(value): + if not isinstance(value, list): + return value + if len(value) == 1: + return value[0] + if value[0] == LIST_START_VALUE: + return value[1:] + return value + + dct = {key: clean_dict_value(value) for key, value in dct.items()} + return curr_token, dct + + def parse_graph(): + curr_token, dct = parse_kv(next(tokens)) + if curr_token.category is not None: # EOF + unexpected(curr_token, "EOF") + if "graph" not in dct: + raise EasyGraphError("input contains no graph") + graph = dct["graph"] + if isinstance(graph, list): + raise EasyGraphError("input contains more than one graph") + return graph + + tokens = tokenize() + graph = parse_graph() + directed = graph.pop("directed", False) + multigraph = graph.pop("multigraph", False) + if not multigraph: + G = eg.DiGraph() if directed else eg.Graph() + else: + G = eg.MultiDiGraph() if directed else eg.MultiGraph() + graph_attr = {k: v for k, v in graph.items() if k not in ("node", "edge")} + G.graph.update(graph_attr) + + def pop_attr(dct, category, attr, i): + try: + return dct.pop(attr) + except KeyError as err: + raise EasyGraphError(f"{category} #{i} has no {attr!r} attribute") from err + + nodes = graph.get("node", []) + mapping = {} + node_labels = set() + for i, node in enumerate(nodes if isinstance(nodes, list) else [nodes]): + id = pop_attr(node, "node", "id", i) + if id in G: + raise EasyGraphError(f"node id {id!r} is duplicated") + if label is not None and label != "id": + node_label = pop_attr(node, "node", label, i) + if node_label in node_labels: + raise EasyGraphError(f"node label {node_label!r} is duplicated") + node_labels.add(node_label) + mapping[id] = node_label + G.add_node(id, **node) + + edges = graph.get("edge", []) + for i, edge in enumerate(edges if isinstance(edges, list) else [edges]): + source = pop_attr(edge, "edge", "source", i) + target = pop_attr(edge, "edge", "target", i) + if source not in G: + raise EasyGraphError(f"edge #{i} has undefined source {source!r}") + if target not in G: + raise EasyGraphError(f"edge #{i} has undefined target {target!r}") + if not multigraph: + if not G.has_edge(source, target): + G.add_edge(source, target, **edge) + else: + arrow = "->" if directed else "--" + msg = f"edge #{i} ({source!r}{arrow}{target!r}) is duplicated" + raise EasyGraphError(msg) + else: + key = edge.pop("key", None) + if key is not None and G.has_edge(source, target, key): + arrow = "->" if directed else "--" + msg = f"edge #{i} ({source!r}{arrow}{target!r}, {key!r})" + msg2 = 'Hint: If multigraph add "multigraph 1" to file header.' + raise EasyGraphError(msg + " is duplicated\n" + msg2) + G.add_edge(source, target, key, **edge) + + if label is not None and label != "id": + G = eg.relabel_nodes(G, mapping) + return G def generate_gml(G, stringizer=None): - r"""Generate a single entry of the graph `G` in GML format. + r"""Generate a single entry of the graph `G` in GML format. Parameters ---------- @@ -465,118 +462,118 @@ def generate_gml(G, stringizer=None): ] ] """ - valid_keys = re.compile("^[A-Za-z][0-9A-Za-z_]*$") - - def stringize(key, value, ignored_keys, indent, in_list=False): - if not isinstance(key, str): - raise EasyGraphError(f"{key!r} is not a string") - if not valid_keys.match(key): - raise EasyGraphError(f"{key!r} is not a valid key") - if not isinstance(key, str): - key = str(key) - if key not in ignored_keys: - if isinstance(value, (int, bool)): - if key == "label": - yield indent + key + ' "' + str(value) + '"' - elif value is True: - # python bool is an instance of int - yield indent + key + " 1" - elif value is False: - yield indent + key + " 0" - # GML only supports signed 32-bit integers - elif value < -(2**31) or value >= 2**31: - yield indent + key + ' "' + str(value) + '"' - else: - yield indent + key + " " + str(value) - elif isinstance(value, float): - text = repr(value).upper() - # GML matches INF to keys, so prepend + to INF. Use repr(float(*)) - # instead of string literal to future proof against changes to repr. - if text == repr(float("inf")).upper(): - text = "+" + text - else: - # GML requires that a real literal contain a decimal point, but - # repr may not output a decimal point when the mantissa is - # integral and hence needs fixing. - epos = text.rfind("E") - if epos != -1 and text.find(".", 0, epos) == -1: - text = text[:epos] + "." + text[epos:] - if key == "label": - yield indent + key + ' "' + text + '"' - else: - yield indent + key + " " + text - elif isinstance(value, dict): - yield indent + key + " [" - next_indent = indent + " " - for key, value in value.items(): - yield from stringize(key, value, (), next_indent) - yield indent + "]" - elif ( - isinstance(value, (list, tuple)) - and key != "label" - and value - and not in_list - ): - if len(value) == 1: - yield indent + key + " " + f'"{LIST_START_VALUE}"' - for val in value: - yield from stringize(key, val, (), indent, True) - else: - if stringizer: - try: - value = stringizer(value) - except ValueError as err: - raise EasyGraphError( - f"{value!r} cannot be converted into a string" - ) from err - if not isinstance(value, str): - raise EasyGraphError(f"{value!r} is not a string") - yield indent + key + ' "' + escape(value) + '"' - - yield "graph [" - - # Output graph attributes - multigraph = G.is_multigraph() - if G.is_directed(): - yield " directed 1" - if multigraph: - yield " multigraph 1" - ignored_keys = {"directed", "multigraph", "node", "edge"} - for attr, value in G.graph.items(): - yield from stringize(attr, value, ignored_keys, " ") - - # Output node data - node_id = dict(zip(G, range(len(G)))) - ignored_keys = {"id", "label"} - for node, attrs in G.nodes.items(): - yield " node [" - yield " id " + str(node_id[node]) - yield from stringize("label", node, (), " ") - for attr, value in attrs.items(): - yield from stringize(attr, value, ignored_keys, " ") - yield " ]" - - # Output edge data - ignored_keys = {"source", "target"} - kwargs = {"data": True} - if multigraph: - ignored_keys.add("key") - kwargs["keys"] = True - for e in G.edges: - yield " edge [" - yield " source " + str(node_id[e[0]]) - yield " target " + str(node_id[e[1]]) - if multigraph: - yield from stringize("key", e[2], (), " ") - for attr, value in e[-1].items(): - yield from stringize(attr, value, ignored_keys, " ") - yield " ]" - yield "]" + valid_keys = re.compile("^[A-Za-z][0-9A-Za-z_]*$") + + def stringize(key, value, ignored_keys, indent, in_list=False): + if not isinstance(key, str): + raise EasyGraphError(f"{key!r} is not a string") + if not valid_keys.match(key): + raise EasyGraphError(f"{key!r} is not a valid key") + if not isinstance(key, str): + key = str(key) + if key not in ignored_keys: + if isinstance(value, (int, bool)): + if key == "label": + yield indent + key + ' "' + str(value) + '"' + elif value is True: + # python bool is an instance of int + yield indent + key + " 1" + elif value is False: + yield indent + key + " 0" + # GML only supports signed 32-bit integers + elif value < -(2**31) or value >= 2**31: + yield indent + key + ' "' + str(value) + '"' + else: + yield indent + key + " " + str(value) + elif isinstance(value, float): + text = repr(value).upper() + # GML matches INF to keys, so prepend + to INF. Use repr(float(*)) + # instead of string literal to future proof against changes to repr. + if text == repr(float("inf")).upper(): + text = "+" + text + else: + # GML requires that a real literal contain a decimal point, but + # repr may not output a decimal point when the mantissa is + # integral and hence needs fixing. + epos = text.rfind("E") + if epos != -1 and text.find(".", 0, epos) == -1: + text = text[:epos] + "." + text[epos:] + if key == "label": + yield indent + key + ' "' + text + '"' + else: + yield indent + key + " " + text + elif isinstance(value, dict): + yield indent + key + " [" + next_indent = indent + " " + for key, value in value.items(): + yield from stringize(key, value, (), next_indent) + yield indent + "]" + elif ( + isinstance(value, (list, tuple)) + and key != "label" + and value + and not in_list + ): + if len(value) == 1: + yield indent + key + " " + f'"{LIST_START_VALUE}"' + for val in value: + yield from stringize(key, val, (), indent, True) + else: + if stringizer: + try: + value = stringizer(value) + except ValueError as err: + raise EasyGraphError( + f"{value!r} cannot be converted into a string" + ) from err + if not isinstance(value, str): + raise EasyGraphError(f"{value!r} is not a string") + yield indent + key + ' "' + escape(value) + '"' + + yield "graph [" + + # Output graph attributes + multigraph = G.is_multigraph() + if G.is_directed(): + yield " directed 1" + if multigraph: + yield " multigraph 1" + ignored_keys = {"directed", "multigraph", "node", "edge"} + for attr, value in G.graph.items(): + yield from stringize(attr, value, ignored_keys, " ") + + # Output node data + node_id = dict(zip(G, range(len(G)))) + ignored_keys = {"id", "label"} + for node, attrs in G.nodes.items(): + yield " node [" + yield " id " + str(node_id[node]) + yield from stringize("label", node, (), " ") + for attr, value in attrs.items(): + yield from stringize(attr, value, ignored_keys, " ") + yield " ]" + + # Output edge data + ignored_keys = {"source", "target"} + kwargs = {"data": True} + if multigraph: + ignored_keys.add("key") + kwargs["keys"] = True + for e in G.edges: + yield " edge [" + yield " source " + str(node_id[e[0]]) + yield " target " + str(node_id[e[1]]) + if multigraph: + yield from stringize("key", e[2], (), " ") + for attr, value in e[-1].items(): + yield from stringize(attr, value, ignored_keys, " ") + yield " ]" + yield "]" @open_file(0, mode="rb") def read_gml(path, label="label", destringizer=None): - """Read graph in GML format from `path`. + """Read graph in GML format from `path`. Parameters ---------- @@ -641,25 +638,25 @@ def read_gml(path, label="label", destringizer=None): """ - def filter_lines(lines): - for line in lines: - try: - line = line.decode("ascii") - except UnicodeDecodeError as err: - raise EasyGraphError("input is not ASCII-encoded") from err - if not isinstance(line, str): - lines = str(lines) - if line and line[-1] == "\n": - line = line[:-1] - yield line + def filter_lines(lines): + for line in lines: + try: + line = line.decode("ascii") + except UnicodeDecodeError as err: + raise EasyGraphError("input is not ASCII-encoded") from err + if not isinstance(line, str): + lines = str(lines) + if line and line[-1] == "\n": + line = line[:-1] + yield line - G = parse_gml_lines(filter_lines(path), label, destringizer) - return G + G = parse_gml_lines(filter_lines(path), label, destringizer) + return G @open_file(1, mode="wb") def write_gml(G, path, stringizer=None): - """Write a graph `G` in GML format to the file or file handle `path`. + """Write a graph `G` in GML format to the file or file handle `path`. Parameters ---------- @@ -718,13 +715,11 @@ def write_gml(G, path, stringizer=None): >>> eg.write_gml(G, "test.gml.gz") """ - for line in generate_gml(G, stringizer): - path.write((line + "\n").encode("ascii")) + for line in generate_gml(G, stringizer): + path.write((line + "\n").encode("ascii")) def literal_stringizer(value): - msg = "literal_stringizer is deprecated and will be removed in 3.0." - warnings.warn(msg, DeprecationWarning) def stringize(value): if isinstance(value, (int, bool)) or value is None: diff --git a/easygraph/readwrite/graphml.py b/easygraph/readwrite/graphml.py index 61e39070..34569f5b 100644 --- a/easygraph/readwrite/graphml.py +++ b/easygraph/readwrite/graphml.py @@ -987,7 +987,7 @@ def decode_data_elements(self, graphml_keys, obj_xml): node_label = None # set GenericNode's configuration as shape type gn = data_element.find(f"{{{self.NS_Y}}}GenericNode") - if gn: + if gn is not None: data["shape_type"] = gn.get("configuration") for node_type in ["GenericNode", "ShapeNode", "SVGNode", "ImageNode"]: pref = f"{{{self.NS_Y}}}{node_type}/{{{self.NS_Y}}}" diff --git a/pyproject.toml b/pyproject.toml index 57037543..48e8ffd1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -60,7 +60,7 @@ dev = [ [tool.pytest.ini_options] python_files = "**/tests/test_*.py" -addopts = "-ra --disable-warnings" +addopts = "-ra" # pyproject.toml From 0b346ee18b1a08fe7ef030fa05a9332cd6279827 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 17:07:35 +0800 Subject: [PATCH 16/17] refactor(graph): standardize string formatting and import usage - Updated all single-quoted strings in `directed_graph.py` to double-quoted strings for consistency. - Replaced `.format` with f-strings for improved readability and performance. - Simplified import statements by removing redundant imports and adhering to PEP 8 guidelines. - Used type hints with native `list` and `dict` instead of `List` and `Dict` from `typing`. These changes align the codebase with modern Python conventions and enhance readability. Signed-off-by: acture --- easygraph/__init__.py | 1 - easygraph/classes/__init__.py | 3 +- easygraph/classes/directed_graph.py | 147 ++-- easygraph/classes/directed_multigraph.py | 2 - easygraph/classes/graph.py | 133 ++- easygraph/classes/graphviews.py | 1 - easygraph/classes/multigraph.py | 3 +- easygraph/classes/operation.py | 2 - easygraph/classes/tests/test_multigraph.py | 3 +- easygraph/classes/tests/test_operation.py | 2 +- easygraph/convert.py | 6 +- easygraph/datasets/get_sample_graph.py | 4 +- easygraph/functions/centrality/betweenness.py | 5 +- easygraph/functions/centrality/clossness.py | 2 - easygraph/functions/centrality/degree.py | 1 - .../functions/centrality/flowbetweenness.py | 1 - easygraph/functions/community/LPA.py | 28 +- easygraph/functions/community/modularity.py | 1 - .../community/modularity_max_detection.py | 1 - easygraph/functions/community/motif.py | 2 - easygraph/functions/components/biconnected.py | 1 - easygraph/functions/components/connected.py | 3 +- .../functions/components/ego_betweenness.py | 2 +- easygraph/functions/drawing/drawing.py | 2 +- easygraph/functions/drawing/plot.py | 3 +- easygraph/functions/drawing/positioning.py | 3 +- easygraph/functions/graph_embedding/NOBE.py | 9 +- .../functions/graph_embedding/deepwalk.py | 25 +- easygraph/functions/graph_embedding/line.py | 15 +- .../functions/graph_embedding/node2vec.py | 36 +- easygraph/functions/graph_embedding/sdne.py | 12 +- .../graph_generator/RandomNetwork.py | 24 +- .../functions/graph_generator/classic.py | 4 +- easygraph/functions/not_sorted/bridges.py | 2 - easygraph/functions/not_sorted/cluster.py | 1 - easygraph/functions/not_sorted/laplacian.py | 2 - easygraph/functions/not_sorted/mst.py | 4 +- easygraph/functions/not_sorted/pagerank.py | 2 - .../not_sorted/tests/test_cluster.py | 3 +- .../not_sorted/tests/test_pagerank.py | 2 +- easygraph/functions/path/path.py | 11 +- .../functions/structural_holes/AP_Greedy.py | 22 +- easygraph/functions/structural_holes/HAM.py | 24 +- easygraph/functions/structural_holes/HIS.py | 18 +- easygraph/functions/structural_holes/ICC.py | 20 +- easygraph/functions/structural_holes/MaxD.py | 16 +- easygraph/functions/structural_holes/NOBE.py | 7 +- .../functions/structural_holes/SHII_metric.py | 13 +- .../functions/structural_holes/evaluation.py | 50 +- .../functions/structural_holes/maxBlock.py | 17 +- .../functions/structural_holes/metrics.py | 21 +- .../strong_connected_component.py | 4 +- .../functions/structural_holes/weakTie.py | 2 - easygraph/readwrite/edgelist.py | 1 - easygraph/readwrite/gexf.py | 15 +- easygraph/readwrite/gml.py | 762 +++++++++--------- easygraph/readwrite/graphml.py | 6 +- easygraph/readwrite/graphviz.py | 1 - easygraph/readwrite/pajek.py | 1 - easygraph/readwrite/tests/test_gexf.py | 7 +- easygraph/readwrite/tests/test_gml.py | 10 +- easygraph/readwrite/tests/test_graphml.py | 5 +- easygraph/readwrite/tests/test_graphviz.py | 5 +- easygraph/readwrite/tests/test_pajek.py | 6 +- easygraph/readwrite/tests/test_pickle.py | 1 - easygraph/readwrite/tests/test_ucinet.py | 1 - easygraph/readwrite/ucinet.py | 30 +- easygraph/tests/test_convert.py | 2 - easygraph/utils/convert_to_matrix.py | 1 - easygraph/utils/decorators.py | 51 +- easygraph/utils/exception.py | 1 - easygraph/utils/mapped_queue.py | 2 - easygraph/utils/misc.py | 142 ++-- .../utils/tests/test_convert_to_matrix.py | 3 +- easygraph/utils/type_change.py | 1 - pyproject.toml | 16 +- scripts/archive/check_installation.py | 1 - 77 files changed, 829 insertions(+), 970 deletions(-) diff --git a/easygraph/__init__.py b/easygraph/__init__.py index c7fd4998..fd312f29 100644 --- a/easygraph/__init__.py +++ b/easygraph/__init__.py @@ -3,7 +3,6 @@ import easygraph.functions import easygraph.readwrite import easygraph.utils - from easygraph.classes import * from easygraph.datasets import * from easygraph.functions import * diff --git a/easygraph/classes/__init__.py b/easygraph/classes/__init__.py index 7d0d57fa..88a0da96 100644 --- a/easygraph/classes/__init__.py +++ b/easygraph/classes/__init__.py @@ -1,7 +1,6 @@ from .directed_graph import DiGraph from .directed_multigraph import MultiDiGraph -from .graph import Graph -from .graph import GraphC +from .graph import Graph, GraphC from .graphviews import * from .multigraph import MultiGraph from .operation import * diff --git a/easygraph/classes/directed_graph.py b/easygraph/classes/directed_graph.py index 98f97178..c877bbe9 100644 --- a/easygraph/classes/directed_graph.py +++ b/easygraph/classes/directed_graph.py @@ -1,8 +1,4 @@ -from typing import Dict -from typing import List - import easygraph.convert as convert - from easygraph.classes.graph import Graph from easygraph.utils.exception import EasyGraphError @@ -35,7 +31,7 @@ class DiGraph(Graph): Create an graph with attributes. - >>> G = eg.Graph(name='Karate Club', date='2020.08.21') + >>> G = eg.Graph(name="Karate Club", date="2020.08.21") **Attributes:** @@ -142,7 +138,7 @@ def out_degree(self, weight="weight"): Examples -------- - >>> G.out_degree(weight='weight') + >>> G.out_degree(weight="weight") """ degree = dict() @@ -184,7 +180,7 @@ def in_degree(self, weight="weight"): Examples -------- - >>> G.in_degree(weight='weight') + >>> G.in_degree(weight="weight") """ degree = dict() @@ -228,11 +224,11 @@ def degree(self, weight="weight"): -------- >>> G.degree() - >>> G.degree(weight='weight') + >>> G.degree(weight="weight") or you can customize the weight key - >>> G.degree(weight='weight_1') + >>> G.degree(weight="weight_1") """ degree = dict() @@ -265,7 +261,7 @@ def size(self, weight=None): Returns the total of all edge weights in G: - >>> G.size(weight='weight') + >>> G.size(weight="weight") """ s = sum(d for v, d in self.out_degree(weight=weight).items()) @@ -407,7 +403,7 @@ def neighbors(self, node): Examples -------- >>> G = eg.Graph() - >>> G.add_edges([(1,2), (2,3), (2,4)]) + >>> G.add_edges([(1, 2), (2, 3), (2, 4)]) >>> for neighbor in G.neighbors(node=2): ... print(neighbor) @@ -416,7 +412,7 @@ def neighbors(self, node): try: return iter(self._adj[node]) except KeyError: - print("No node {}".format(node)) + print(f"No node {node}") successors = neighbors @@ -436,7 +432,7 @@ def predecessors(self, node): Examples -------- >>> G = eg.Graph() - >>> G.add_edges([(1,2), (2,3), (2,4)]) + >>> G.add_edges([(1, 2), (2, 3), (2, 4)]) >>> for predecessor in G.predecessors(node=2): ... print(predecessor) @@ -445,7 +441,7 @@ def predecessors(self, node): try: return iter(self._pred[node]) except KeyError: - print("No node {}".format(node)) + print(f"No node {node}") def all_neighbors(self, node): """Returns an iterator of a node's neighbors, including both successors and predecessors. @@ -463,7 +459,7 @@ def all_neighbors(self, node): Examples -------- >>> G = eg.Graph() - >>> G.add_edges([(1,2), (2,3), (2,4)]) + >>> G.add_edges([(1, 2), (2, 3), (2, 4)]) >>> for neighbor in G.all_neighbors(node=2): ... print(neighbor) @@ -474,7 +470,7 @@ def all_neighbors(self, node): neighbors.extend(self._pred[node]) return iter(neighbors) except KeyError: - print("No node {}".format(node)) + print(f"No node {node}") def add_node(self, node_for_adding, **node_attr): """Add one node @@ -497,19 +493,16 @@ def add_node(self, node_for_adding, **node_attr): Examples -------- - >>> G.add_node('a') - >>> G.add_node('hello world') - >>> G.add_node('Jack', age=10) + >>> G.add_node("a") + >>> G.add_node("hello world") + >>> G.add_node("Jack", age=10) - >>> G.add_node('Jack', **{ - ... 'age': 10, - ... 'gender': 'M' - ... }) + >>> G.add_node("Jack", **{"age": 10, "gender": "M"}) """ self._add_one_node(node_for_adding, node_attr) - def add_nodes(self, nodes_for_adding: list, nodes_attr: List[Dict] = []): + def add_nodes(self, nodes_for_adding: list, nodes_attr: list[dict] = []): """Add nodes with a list of nodes. Parameters @@ -529,31 +522,25 @@ def add_nodes(self, nodes_for_adding: list, nodes_attr: List[Dict] = []): You can add with node attributes using a list of Python dict type, each of which is the attribute of each node, respectively. - >>> G.add_nodes([1, 2, 'a', 'b']) + >>> G.add_nodes([1, 2, "a", "b"]) >>> G.add_nodes(range(1, 200)) - >>> G.add_nodes(['Jack', 'Tom', 'Lily'], nodes_attr=[ - ... { - ... 'age': 10, - ... 'gender': 'M' - ... }, - ... { - ... 'age': 11, - ... 'gender': 'M' - ... }, - ... { - ... 'age': 10, - ... 'gender': 'F' - ... } - ... ]) + >>> G.add_nodes( + ... ["Jack", "Tom", "Lily"], + ... nodes_attr=[ + ... {"age": 10, "gender": "M"}, + ... {"age": 11, "gender": "M"}, + ... {"age": 10, "gender": "F"}, + ... ], + ... ) """ if nodes_attr is None: nodes_attr = [] if not len(nodes_attr) == 0: # Nodes attributes included in input - assert len(nodes_for_adding) == len( - nodes_attr - ), "Nodes and Attributes lists must have same length." + assert len(nodes_for_adding) == len(nodes_attr), ( + "Nodes and Attributes lists must have same length." + ) else: # Set empty attribute for each node nodes_attr = [dict() for i in range(len(nodes_for_adding))] @@ -661,14 +648,12 @@ def add_edge(self, u_of_edge, v_of_edge, **edge_attr): Examples -------- - >>> G.add_edge(1,2) - >>> G.add_edge('Jack', 'Tom', weight=10) + >>> G.add_edge(1, 2) + >>> G.add_edge("Jack", "Tom", weight=10) Add edge with attributes, edge weight, for example, - >>> G.add_edge(1, 2, **{ - ... 'weight': 20 - ... }) + >>> G.add_edge(1, 2, **{"weight": 20}) """ self._add_one_edge(u_of_edge, v_of_edge, edge_attr) @@ -676,7 +661,7 @@ def add_edge(self, u_of_edge, v_of_edge, **edge_attr): def add_weighted_edge(self, u_of_edge, v_of_edge, weight): self._add_one_edge(u_of_edge, v_of_edge, edge_attr={"weight": weight}) - def add_edges(self, edges_for_adding, edges_attr: List[Dict] = []): + def add_edges(self, edges_for_adding, edges_attr: list[dict] = []): """Add a list of edges. Parameters @@ -692,30 +677,19 @@ def add_edges(self, edges_for_adding, edges_attr: List[Dict] = []): -------- Add a list of edges into *G* - >>> G.add_edges([ - ... (1, 2), - ... (3, 4), - ... ('Jack', 'Tom') - ... ]) + >>> G.add_edges([(1, 2), (3, 4), ("Jack", "Tom")]) Add edge with attributes, for example, edge weight, - >>> G.add_edges([(1,2), (2, 3)], edges_attr=[ - ... { - ... 'weight': 20 - ... }, - ... { - ... 'weight': 15 - ... } - ... ]) + >>> G.add_edges([(1, 2), (2, 3)], edges_attr=[{"weight": 20}, {"weight": 15}]) """ if edges_attr is None: edges_attr = [] if not len(edges_attr) == 0: # Edges attributes included in input - assert len(edges_for_adding) == len( - edges_attr - ), "Edges and Attributes lists must have same length." + assert len(edges_for_adding) == len(edges_attr), ( + "Edges and Attributes lists must have same length." + ) else: # Set empty attribute for each edge edges_attr = [dict() for i in range(len(edges_for_adding))] @@ -723,7 +697,7 @@ def add_edges(self, edges_for_adding, edges_attr: List[Dict] = []): try: edge = edges_for_adding[i] attr = edges_attr[i] - assert len(edge) == 2, "Edge tuple {} must be 2-tuple.".format(edge) + assert len(edge) == 2, f"Edge tuple {edge} must be 2-tuple." self._add_one_edge(edge[0], edge[1], attr) except Exception as err: print(err) @@ -823,13 +797,13 @@ def add_edges_from_file(self, file, weighted=False): Then add them to *G* - >>> G.add_edges_from_file(file='./club_network.txt', weighted=True) + >>> G.add_edges_from_file(file="./club_network.txt", weighted=True) """ import re - with open(file, "r") as fp: + with open(file) as fp: edges = fp.readlines() if weighted: for edge in edges: @@ -877,7 +851,7 @@ def remove_node(self, node_to_remove): -------- Remove node *Jack* from *G* - >>> G.remove_node('Jack') + >>> G.remove_node("Jack") """ try: @@ -885,7 +859,7 @@ def remove_node(self, node_to_remove): preds = list(self._pred[node_to_remove]) del self._node[node_to_remove] except KeyError: # Node not exists in self - raise KeyError("No node {} in graph.".format(node_to_remove)) + raise KeyError(f"No node {node_to_remove} in graph.") for succ in succs: # Remove edges start with node_to_remove del self._pred[succ][node_to_remove] for pred in preds: # Remove edges end with node_to_remove @@ -911,15 +885,13 @@ def remove_nodes(self, nodes_to_remove: list): -------- Remove node *[1, 2, 'a', 'b']* from *G* - >>> G.remove_nodes([1, 2, 'a', 'b']) + >>> G.remove_nodes([1, 2, "a", "b"]) """ - for ( - node - ) in ( + for node in ( nodes_to_remove ): # If not all nodes included in graph, give up removing other nodes - assert node in self._node, "Remove Error: No node {} in graph".format(node) + assert node in self._node, f"Remove Error: No node {node} in graph" for node in nodes_to_remove: self.remove_node(node) @@ -942,14 +914,14 @@ def remove_edge(self, u, v): -------- Remove edge (1,2) from *G* - >>> G.remove_edge(1,2) + >>> G.remove_edge(1, 2) """ try: del self._adj[u][v] del self._pred[v][u] except KeyError: - raise KeyError("No edge {}-{} in graph.".format(u, v)) + raise KeyError(f"No edge {u}-{v} in graph.") def remove_edges(self, edges_to_remove: [tuple]): """Remove a list of edges from your graph. @@ -969,10 +941,7 @@ def remove_edges(self, edges_to_remove: [tuple]): -------- Remove the edges *('Jack', 'Mary')* amd *('Mary', 'Tom')* from *G* - >>> G.remove_edge([ - ... ('Jack', 'Mary'), - ... ('Mary', 'Tom') - ... ]) + >>> G.remove_edge([("Jack", "Mary"), ("Mary", "Tom")]) """ for edge in edges_to_remove: @@ -1079,8 +1048,8 @@ def nodes_subgraph(self, from_nodes: list): -------- >>> G = eg.Graph() - >>> G.add_edges([(1,2), (2,3), (2,4), (4,5)]) - >>> G_sub = G.nodes_subgraph(from_nodes= [1,2,3]) + >>> G.add_edges([(1, 2), (2, 3), (2, 4), (4, 5)]) + >>> G_sub = G.nodes_subgraph(from_nodes=[1, 2, 3]) """ G = self.__class__() @@ -1115,12 +1084,8 @@ def ego_subgraph(self, center): Examples -------- >>> G = eg.Graph() - >>> G.add_edges([ - ... ('Jack', 'Maria'), - ... ('Maria', 'Andy'), - ... ('Jack', 'Tom') - ... ]) - >>> G.ego_subgraph(center='Jack') + >>> G.add_edges([("Jack", "Maria"), ("Maria", "Andy"), ("Jack", "Tom")]) + >>> G.ego_subgraph(center="Jack") """ neighbors_of_center = list(self.all_neighbors(center)) neighbors_of_center.append(center) @@ -1154,11 +1119,7 @@ def to_index_node_graph(self, begin_index=0): as well as node-to-index dictionary. >>> G = eg.Graph() - >>> G.add_edges([ - ... ('Jack', 'Maria'), - ... ('Maria', 'Andy'), - ... ('Jack', 'Tom') - ... ]) + >>> G.add_edges([("Jack", "Maria"), ("Maria", "Andy"), ("Jack", "Tom")]) >>> G_index_graph, index_of_node, node_of_index = G.to_index_node_graph() """ diff --git a/easygraph/classes/directed_multigraph.py b/easygraph/classes/directed_multigraph.py index 9ca78519..66a6dfd5 100644 --- a/easygraph/classes/directed_multigraph.py +++ b/easygraph/classes/directed_multigraph.py @@ -2,12 +2,10 @@ import easygraph as eg import easygraph.convert as convert - from easygraph.classes.directed_graph import DiGraph from easygraph.classes.multigraph import MultiGraph from easygraph.utils.exception import EasyGraphError - __all__ = ["MultiDiGraph"] diff --git a/easygraph/classes/graph.py b/easygraph/classes/graph.py index b5ac5166..598835de 100644 --- a/easygraph/classes/graph.py +++ b/easygraph/classes/graph.py @@ -1,8 +1,4 @@ -from typing import Dict -from typing import List - import easygraph.convert as convert - from easygraph.utils.exception import EasyGraphError @@ -34,7 +30,7 @@ class Graph: Create an graph with attributes. - >>> G = eg.Graph(name='Karate Club', date='2020.08.21') + >>> G = eg.Graph(name="Karate Club", date="2020.08.21") **Attributes:** @@ -145,7 +141,7 @@ def degree(self, weight="weight"): if you have customized weight key 'weight_1'. - >>> G.degree(weight='weight_1') + >>> G.degree(weight="weight_1") """ degree = dict() @@ -210,7 +206,7 @@ def size(self, weight=None): Returns the total of all edge weights in G: - >>> G.size(weight='weight') + >>> G.size(weight="weight") """ s = sum(d for v, d in self.degree(weight=weight).items()) @@ -352,7 +348,7 @@ def neighbors(self, node): Examples -------- >>> G = eg.Graph() - >>> G.add_edges([(1,2), (2,3), (2,4)]) + >>> G.add_edges([(1, 2), (2, 3), (2, 4)]) >>> for neighbor in G.neighbors(node=2): ... print(neighbor) @@ -360,7 +356,7 @@ def neighbors(self, node): try: return iter(self._adj[node]) except KeyError: - print("No node {}".format(node)) + print(f"No node {node}") all_neighbors = neighbors @@ -385,19 +381,16 @@ def add_node(self, node_for_adding, **node_attr): Examples -------- - >>> G.add_node('a') - >>> G.add_node('hello world') - >>> G.add_node('Jack', age=10) + >>> G.add_node("a") + >>> G.add_node("hello world") + >>> G.add_node("Jack", age=10) - >>> G.add_node('Jack', **{ - ... 'age': 10, - ... 'gender': 'M' - ... }) + >>> G.add_node("Jack", **{"age": 10, "gender": "M"}) """ self._add_one_node(node_for_adding, node_attr) - def add_nodes(self, nodes_for_adding: list, nodes_attr: List[Dict] = []): + def add_nodes(self, nodes_for_adding: list, nodes_attr: list[dict] = []): """Add nodes with a list of nodes. Parameters @@ -417,29 +410,23 @@ def add_nodes(self, nodes_for_adding: list, nodes_attr: List[Dict] = []): You can add with node attributes using a list of Python dict type, each of which is the attribute of each node, respectively. - >>> G.add_nodes([1, 2, 'a', 'b']) + >>> G.add_nodes([1, 2, "a", "b"]) >>> G.add_nodes(range(1, 200)) - >>> G.add_nodes(['Jack', 'Tom', 'Lily'], nodes_attr=[ - ... { - ... 'age': 10, - ... 'gender': 'M' - ... }, - ... { - ... 'age': 11, - ... 'gender': 'M' - ... }, - ... { - ... 'age': 10, - ... 'gender': 'F' - ... } - ... ]) + >>> G.add_nodes( + ... ["Jack", "Tom", "Lily"], + ... nodes_attr=[ + ... {"age": 10, "gender": "M"}, + ... {"age": 11, "gender": "M"}, + ... {"age": 10, "gender": "F"}, + ... ], + ... ) """ if not len(nodes_attr) == 0: # Nodes attributes included in input - assert len(nodes_for_adding) == len( - nodes_attr - ), "Nodes and Attributes lists must have same length." + assert len(nodes_for_adding) == len(nodes_attr), ( + "Nodes and Attributes lists must have same length." + ) else: # Set empty attribute for each node nodes_attr = [dict() for i in range(len(nodes_for_adding))] @@ -544,14 +531,12 @@ def add_edge(self, u_of_edge, v_of_edge, **edge_attr): Examples -------- - >>> G.add_edge(1,2) - >>> G.add_edge('Jack', 'Tom', weight=10) + >>> G.add_edge(1, 2) + >>> G.add_edge("Jack", "Tom", weight=10) Add edge with attributes, edge weight, for example, - >>> G.add_edge(1, 2, **{ - ... 'weight': 20 - ... }) + >>> G.add_edge(1, 2, **{"weight": 20}) """ self._add_one_edge(u_of_edge, v_of_edge, edge_attr) @@ -559,7 +544,7 @@ def add_edge(self, u_of_edge, v_of_edge, **edge_attr): def add_weighted_edge(self, u_of_edge, v_of_edge, weight): self._add_one_edge(u_of_edge, v_of_edge, edge_attr={"weight": weight}) - def add_edges(self, edges_for_adding, edges_attr: List[Dict] = []): + def add_edges(self, edges_for_adding, edges_attr: list[dict] = []): """Add a list of edges. Parameters @@ -575,30 +560,19 @@ def add_edges(self, edges_for_adding, edges_attr: List[Dict] = []): -------- Add a list of edges into *G* - >>> G.add_edges([ - ... (1, 2), - ... (3, 4), - ... ('Jack', 'Tom') - ... ]) + >>> G.add_edges([(1, 2), (3, 4), ("Jack", "Tom")]) Add edge with attributes, for example, edge weight, - >>> G.add_edges([(1,2), (2, 3)], edges_attr=[ - ... { - ... 'weight': 20 - ... }, - ... { - ... 'weight': 15 - ... } - ... ]) + >>> G.add_edges([(1, 2), (2, 3)], edges_attr=[{"weight": 20}, {"weight": 15}]) """ if edges_attr is None: edges_attr = [] if not len(edges_attr) == 0: # Edges attributes included in input - assert len(edges_for_adding) == len( - edges_attr - ), "Edges and Attributes lists must have same length." + assert len(edges_for_adding) == len(edges_attr), ( + "Edges and Attributes lists must have same length." + ) else: # Set empty attribute for each edge edges_attr = [dict() for i in range(len(edges_for_adding))] @@ -606,7 +580,7 @@ def add_edges(self, edges_for_adding, edges_attr: List[Dict] = []): try: edge = edges_for_adding[i] attr = edges_attr[i] - assert len(edge) == 2, "Edge tuple {} must be 2-tuple.".format(edge) + assert len(edge) == 2, f"Edge tuple {edge} must be 2-tuple." self._add_one_edge(edge[0], edge[1], attr) except Exception as err: print(err) @@ -704,13 +678,13 @@ def add_edges_from_file(self, file, weighted=False): Then add them to *G* - >>> G.add_edges_from_file(file='./club_network.txt', weighted=True) + >>> G.add_edges_from_file(file="./club_network.txt", weighted=True) """ import re - with open(file, "r") as fp: + with open(file) as fp: edges = fp.readlines() if weighted: for edge in edges: @@ -758,14 +732,14 @@ def remove_node(self, node_to_remove): -------- Remove node *Jack* from *G* - >>> G.remove_node('Jack') + >>> G.remove_node("Jack") """ try: neighbors = list(self._adj[node_to_remove]) del self._node[node_to_remove] except KeyError: # Node not exists in self - raise EasyGraphError("No node {} in graph.".format(node_to_remove)) + raise EasyGraphError(f"No node {node_to_remove} in graph.") for neighbor in neighbors: # Remove edges with other nodes del self._adj[neighbor][node_to_remove] del self._adj[node_to_remove] # Remove this node @@ -786,15 +760,13 @@ def remove_nodes(self, nodes_to_remove: list): -------- Remove node *[1, 2, 'a', 'b']* from *G* - >>> G.remove_nodes([1, 2, 'a', 'b']) + >>> G.remove_nodes([1, 2, "a", "b"]) """ - for ( - node - ) in ( + for node in ( nodes_to_remove ): # If not all nodes included in graph, give up removing other nodes - assert node in self._node, "Remove Error: No node {} in graph".format(node) + assert node in self._node, f"Remove Error: No node {node} in graph" for node in nodes_to_remove: self.remove_node(node) @@ -817,7 +789,7 @@ def remove_edge(self, u, v): -------- Remove edge (1,2) from *G* - >>> G.remove_edge(1,2) + >>> G.remove_edge(1, 2) """ try: @@ -825,7 +797,7 @@ def remove_edge(self, u, v): if u != v: # self-loop needs only one entry removed del self._adj[v][u] except KeyError: - raise KeyError("No edge {}-{} in graph.".format(u, v)) + raise KeyError(f"No edge {u}-{v} in graph.") def remove_edges(self, edges_to_remove: [tuple]): """Remove a list of edges from your graph. @@ -844,10 +816,7 @@ def remove_edges(self, edges_to_remove: [tuple]): -------- Remove the edges *('Jack', 'Mary')* amd *('Mary', 'Tom')* from *G* - >>> G.remove_edge([ - ... ('Jack', 'Mary'), - ... ('Mary', 'Tom') - ... ]) + >>> G.remove_edge([("Jack", "Mary"), ("Mary", "Tom")]) """ for edge in edges_to_remove: @@ -922,8 +891,8 @@ def nodes_subgraph(self, from_nodes: list): -------- >>> G = eg.Graph() - >>> G.add_edges([(1,2), (2,3), (2,4), (4,5)]) - >>> G_sub = G.nodes_subgraph(from_nodes= [1,2,3]) + >>> G.add_edges([(1, 2), (2, 3), (2, 4), (4, 5)]) + >>> G_sub = G.nodes_subgraph(from_nodes=[1, 2, 3]) """ G = self.__class__() @@ -958,12 +927,8 @@ def ego_subgraph(self, center): Examples -------- >>> G = eg.Graph() - >>> G.add_edges([ - ... ('Jack', 'Maria'), - ... ('Maria', 'Andy'), - ... ('Jack', 'Tom') - ... ]) - >>> G.ego_subgraph(center='Jack') + >>> G.add_edges([("Jack", "Maria"), ("Maria", "Andy"), ("Jack", "Tom")]) + >>> G.ego_subgraph(center="Jack") """ neighbors_of_center = list(self.all_neighbors(center)) neighbors_of_center.append(center) @@ -997,11 +962,7 @@ def to_index_node_graph(self, begin_index=0): as well as node-to-index dictionary. >>> G = eg.Graph() - >>> G.add_edges([ - ... ('Jack', 'Maria'), - ... ('Maria', 'Andy'), - ... ('Jack', 'Tom') - ... ]) + >>> G.add_edges([("Jack", "Maria"), ("Maria", "Andy"), ("Jack", "Tom")]) >>> G_index_graph, index_of_node, node_of_index = G.to_index_node_graph() """ diff --git a/easygraph/classes/graphviews.py b/easygraph/classes/graphviews.py index bbb2a3d8..d68c9ef4 100644 --- a/easygraph/classes/graphviews.py +++ b/easygraph/classes/graphviews.py @@ -1,6 +1,5 @@ from easygraph.utils import only_implemented_for_Directed_graph - __all__ = ["reverse_view"] diff --git a/easygraph/classes/multigraph.py b/easygraph/classes/multigraph.py index a2522ea9..86fcc56f 100644 --- a/easygraph/classes/multigraph.py +++ b/easygraph/classes/multigraph.py @@ -1,13 +1,12 @@ """Base class for MultiGraph.""" + from copy import deepcopy import easygraph as eg import easygraph.convert as convert - from easygraph.classes.graph import Graph from easygraph.utils.exception import EasyGraphError - __all__ = ["MultiGraph"] diff --git a/easygraph/classes/operation.py b/easygraph/classes/operation.py index 03e05bae..95529417 100644 --- a/easygraph/classes/operation.py +++ b/easygraph/classes/operation.py @@ -1,10 +1,8 @@ from itertools import chain import easygraph as eg - from easygraph.utils import * - __all__ = [ "set_edge_attributes", "add_path", diff --git a/easygraph/classes/tests/test_multigraph.py b/easygraph/classes/tests/test_multigraph.py index 28c36210..3e30d4d2 100644 --- a/easygraph/classes/tests/test_multigraph.py +++ b/easygraph/classes/tests/test_multigraph.py @@ -1,6 +1,7 @@ -import easygraph as eg import pytest +import easygraph as eg + class TestMultiGraph: def setup_method(self): diff --git a/easygraph/classes/tests/test_operation.py b/easygraph/classes/tests/test_operation.py index 6245656a..b07c050c 100644 --- a/easygraph/classes/tests/test_operation.py +++ b/easygraph/classes/tests/test_operation.py @@ -1,6 +1,6 @@ -import easygraph as eg import pytest +import easygraph as eg from easygraph.utils import edges_equal diff --git a/easygraph/convert.py b/easygraph/convert.py index d60a9f16..8f3abd36 100644 --- a/easygraph/convert.py +++ b/easygraph/convert.py @@ -1,12 +1,8 @@ import warnings - -from collections.abc import Collection -from collections.abc import Generator -from collections.abc import Iterator +from collections.abc import Collection, Generator, Iterator import easygraph as eg - __all__ = [ "from_dict_of_dicts", "to_easygraph_graph", diff --git a/easygraph/datasets/get_sample_graph.py b/easygraph/datasets/get_sample_graph.py index bfd6ab3f..169ddd4f 100644 --- a/easygraph/datasets/get_sample_graph.py +++ b/easygraph/datasets/get_sample_graph.py @@ -1,6 +1,6 @@ -import easygraph as eg import progressbar +import easygraph as eg __all__ = [ "get_graph_karateclub", @@ -132,7 +132,6 @@ def get_graph_youtube(): """ import gzip - from urllib import request url = "http://socialnetworks.mpi-sws.mpg.de/data/youtube-links.txt.gz" @@ -169,7 +168,6 @@ def get_graph_flickr(): """ import gzip - from urllib import request url = "http://socialnetworks.mpi-sws.mpg.de/data/flickr-links.txt.gz" diff --git a/easygraph/functions/centrality/betweenness.py b/easygraph/functions/centrality/betweenness.py index 8b71caa4..5a5304c3 100644 --- a/easygraph/functions/centrality/betweenness.py +++ b/easygraph/functions/centrality/betweenness.py @@ -1,7 +1,6 @@ from easygraph.utils import * from easygraph.utils.decorators import * - __all__ = [ "betweenness_centrality", ] @@ -83,7 +82,6 @@ def betweenness_centrality( if n_workers is not None: # use the parallel version for large graph import random - from functools import partial from multiprocessing import Pool @@ -169,8 +167,7 @@ def _single_source_bfs_path(G, source): def _single_source_dijkstra_path(G, source, weight="weight"): - from heapq import heappop - from heapq import heappush + from heapq import heappop, heappush push = heappush pop = heappop diff --git a/easygraph/functions/centrality/clossness.py b/easygraph/functions/centrality/clossness.py index 45f79bcc..16f6757a 100644 --- a/easygraph/functions/centrality/clossness.py +++ b/easygraph/functions/centrality/clossness.py @@ -1,7 +1,6 @@ from easygraph.functions.path import * from easygraph.utils import * - __all__ = [ "closeness_centrality", ] @@ -61,7 +60,6 @@ def closeness_centrality(G, weight=None, n_workers=None): if n_workers is not None: # use parallel version for large graph import random - from functools import partial from multiprocessing import Pool diff --git a/easygraph/functions/centrality/degree.py b/easygraph/functions/centrality/degree.py index 844be16c..001d859f 100644 --- a/easygraph/functions/centrality/degree.py +++ b/easygraph/functions/centrality/degree.py @@ -1,6 +1,5 @@ from easygraph.utils.decorators import * - __all__ = ["degree_centrality", "in_degree_centrality", "out_degree_centrality"] diff --git a/easygraph/functions/centrality/flowbetweenness.py b/easygraph/functions/centrality/flowbetweenness.py index cb866da8..6311adaa 100644 --- a/easygraph/functions/centrality/flowbetweenness.py +++ b/easygraph/functions/centrality/flowbetweenness.py @@ -3,7 +3,6 @@ from easygraph.utils.decorators import * - __all__ = [ "flowbetweenness_centrality", ] diff --git a/easygraph/functions/community/LPA.py b/easygraph/functions/community/LPA.py index 3fb8dd75..5c250d1f 100644 --- a/easygraph/functions/community/LPA.py +++ b/easygraph/functions/community/LPA.py @@ -1,15 +1,13 @@ import copy import random - from collections import defaultdict from queue import Queue -import easygraph as eg import numpy as np +import easygraph as eg from easygraph.utils import * - __all__ = [ "LPA", "SLPA", @@ -74,7 +72,7 @@ def LPA(G): break for node in label_dict.keys(): label = label_dict[node] - if label not in cluster_community.keys(): + if label not in cluster_community: cluster_community[label] = [node] else: cluster_community[label].append(node) @@ -104,10 +102,7 @@ def SLPA(G, T, r): Examples ---------- - >>> SLPA(G, - ... T = 20, - ... r = 0.05 - ... ) + >>> SLPA(G, T=20, r=0.05) References ---------- @@ -209,13 +204,7 @@ def HANP(G, m, delta, threshod=1, hier_open=0, combine_open=0): Examples ---------- - >>> HANP(G, - ... m = 0.1, - ... delta = 0.05, - ... threshod = 1, - ... hier_open = 0, - ... combine_open = 0 - ... ) + >>> HANP(G, m=0.1, delta=0.05, threshod=1, hier_open=0, combine_open=0) References ---------- @@ -312,7 +301,7 @@ def HANP(G, m, delta, threshod=1, hier_open=0, combine_open=0): print("After %d iterations, HANP complete." % loop_count) for node in label_dict.keys(): label = label_dict[node] - if label not in cluster_community.keys(): + if label not in cluster_community: cluster_community[label] = [node] else: cluster_community[label].append(node) @@ -349,9 +338,10 @@ def BMLPA(G, p): Examples ---------- - >>> BMLPA(G, - ... p = 0.1, - ... ) + >>> BMLPA( + ... G, + ... p=0.1, + ... ) References ---------- diff --git a/easygraph/functions/community/modularity.py b/easygraph/functions/community/modularity.py index aac3dfda..44dfc7fc 100644 --- a/easygraph/functions/community/modularity.py +++ b/easygraph/functions/community/modularity.py @@ -2,7 +2,6 @@ from easygraph.utils import * - __all__ = ["modularity"] diff --git a/easygraph/functions/community/modularity_max_detection.py b/easygraph/functions/community/modularity_max_detection.py index addb8456..518d170f 100644 --- a/easygraph/functions/community/modularity_max_detection.py +++ b/easygraph/functions/community/modularity_max_detection.py @@ -2,7 +2,6 @@ from easygraph.utils import * from easygraph.utils.mapped_queue import MappedQueue - __all__ = ["greedy_modularity_communities"] diff --git a/easygraph/functions/community/motif.py b/easygraph/functions/community/motif.py index 24ad59a0..0016c75a 100644 --- a/easygraph/functions/community/motif.py +++ b/easygraph/functions/community/motif.py @@ -1,10 +1,8 @@ import random import easygraph as eg - from easygraph.utils import * - __all__ = ["enumerate_subgraph", "random_enumerate_subgraph"] diff --git a/easygraph/functions/components/biconnected.py b/easygraph/functions/components/biconnected.py index 11af37d9..7a1b6a56 100644 --- a/easygraph/functions/components/biconnected.py +++ b/easygraph/functions/components/biconnected.py @@ -2,7 +2,6 @@ from easygraph.utils import * - try: from cpp_easygraph import cpp_biconnected_dfs_record_edges except ImportError: diff --git a/easygraph/functions/components/connected.py b/easygraph/functions/components/connected.py index 41e8d7cf..91e8ef09 100644 --- a/easygraph/functions/components/connected.py +++ b/easygraph/functions/components/connected.py @@ -1,6 +1,5 @@ from easygraph.utils.decorators import * - __all__ = [ "is_connected", "number_connected_components", @@ -111,7 +110,7 @@ def connected_component_of_node(G, node): -------- Returns the connected component of one node `Jack`. - >>> connected_component_of_node(G, node='Jack') + >>> connected_component_of_node(G, node="Jack") """ return set(_plain_bfs(G, node)) diff --git a/easygraph/functions/components/ego_betweenness.py b/easygraph/functions/components/ego_betweenness.py index c53c1e4f..ebf5e6ea 100644 --- a/easygraph/functions/components/ego_betweenness.py +++ b/easygraph/functions/components/ego_betweenness.py @@ -25,7 +25,7 @@ def ego_betweenness(G, node): -------- Returns the betwenness centrality of node 1. - >>> ego_betweenness(G,node=1) + >>> ego_betweenness(G, node=1) Reference --------- diff --git a/easygraph/functions/drawing/drawing.py b/easygraph/functions/drawing/drawing.py index bee494fe..0b141967 100644 --- a/easygraph/functions/drawing/drawing.py +++ b/easygraph/functions/drawing/drawing.py @@ -1,9 +1,9 @@ import random -import easygraph as eg import matplotlib.pyplot as plt import numpy as np +import easygraph as eg __all__ = ["draw_SHS_center", "draw_SHS_center_kk", "draw_kamada_kawai"] diff --git a/easygraph/functions/drawing/plot.py b/easygraph/functions/drawing/plot.py index 82ae2709..738a29aa 100644 --- a/easygraph/functions/drawing/plot.py +++ b/easygraph/functions/drawing/plot.py @@ -1,9 +1,8 @@ -import easygraph as eg import numpy as np import statsmodels.api as sm - from matplotlib import pyplot as plt +import easygraph as eg __all__ = [ "plot_Followers", diff --git a/easygraph/functions/drawing/positioning.py b/easygraph/functions/drawing/positioning.py index 03ac1082..c1e80c75 100644 --- a/easygraph/functions/drawing/positioning.py +++ b/easygraph/functions/drawing/positioning.py @@ -1,6 +1,6 @@ -import easygraph as eg import numpy as np +import easygraph as eg __all__ = [ "random_position", @@ -285,7 +285,6 @@ def _kamada_kawai_solve(dist_mtx, pos_arr, dim): # and starting locations. import numpy as np - from scipy.optimize import minimize meanwt = 1e-3 diff --git a/easygraph/functions/graph_embedding/NOBE.py b/easygraph/functions/graph_embedding/NOBE.py index 820ebcf3..9ff87ea7 100644 --- a/easygraph/functions/graph_embedding/NOBE.py +++ b/easygraph/functions/graph_embedding/NOBE.py @@ -1,9 +1,8 @@ -import easygraph as eg import numpy as np - -from easygraph.utils import * from scipy.sparse.linalg import eigs +import easygraph as eg +from easygraph.utils import * __all__ = ["NOBE", "NOBE_GA"] @@ -27,7 +26,7 @@ def NOBE(G, K): Examples -------- - >>> NOBE(G,K=15) + >>> NOBE(G, K=15) References ---------- @@ -66,7 +65,7 @@ def NOBE_GA(G, K): Examples -------- - >>> NOBE_GA(G,K=15) + >>> NOBE_GA(G, K=15) References ---------- diff --git a/easygraph/functions/graph_embedding/deepwalk.py b/easygraph/functions/graph_embedding/deepwalk.py index 68421740..ec065d3f 100644 --- a/easygraph/functions/graph_embedding/deepwalk.py +++ b/easygraph/functions/graph_embedding/deepwalk.py @@ -1,12 +1,12 @@ import random +from tqdm import tqdm + from easygraph.functions.graph_embedding.node2vec import ( _get_embedding_result_from_gensim_skipgram_model, + learn_embeddings, ) -from easygraph.functions.graph_embedding.node2vec import learn_embeddings from easygraph.utils import * -from tqdm import tqdm - __all__ = ["deepwalk"] @@ -42,16 +42,15 @@ def deepwalk(G, dimensions=128, walk_length=80, num_walks=10, **skip_gram_params Examples -------- - >>> deepwalk(G, - ... dimensions=128, # The graph embedding dimensions. - ... walk_length=80, # Walk length of each random walks. - ... num_walks=10, # Number of random walks. - ... skip_gram_params = dict( # The skip_gram parameters in Python package gensim. - ... window=10, - ... min_count=1, - ... batch_words=4, - ... iter=15 - ... )) + >>> deepwalk( + ... G, + ... dimensions=128, # The graph embedding dimensions. + ... walk_length=80, # Walk length of each random walks. + ... num_walks=10, # Number of random walks. + ... skip_gram_params=dict( # The skip_gram parameters in Python package gensim. + ... window=10, min_count=1, batch_words=4, iter=15 + ... ), + ... ) References ---------- diff --git a/easygraph/functions/graph_embedding/line.py b/easygraph/functions/graph_embedding/line.py index 3cd8d21d..814f0efd 100644 --- a/easygraph/functions/graph_embedding/line.py +++ b/easygraph/functions/graph_embedding/line.py @@ -4,8 +4,7 @@ import numpy as np from easygraph.utils import * -from easygraph.utils.alias import alias_sample -from easygraph.utils.alias import create_alias_table +from easygraph.utils.alias import alias_sample, create_alias_table from easygraph.utils.index_of_node import get_relation_of_index_and_node @@ -28,9 +27,7 @@ def create_model(numNodes, embedding_size, order="second"): except ImportWarning: print("tensorflow not found, please install") pass - from tensorflow.python.keras.layers import Embedding - from tensorflow.python.keras.layers import Input - from tensorflow.python.keras.layers import Lambda + from tensorflow.python.keras.layers import Embedding, Input, Lambda from tensorflow.python.keras.models import Model v_i = Input(shape=(1,)) @@ -92,11 +89,11 @@ def __init__( Examples -------- - >>> model = LINE(G, - ... embedding_size=16, - ... order='all') # The order of model LINE. 'first'，'second' or 'all'. + >>> model = LINE( + ... G, embedding_size=16, order="all" + ... ) # The order of model LINE. 'first'，'second' or 'all'. >>> model.train(batch_size=1024, epochs=1, verbose=2) - >>> embeddings = model.get_embeddings() # Returns the graph embedding results. + >>> embeddings = model.get_embeddings() # Returns the graph embedding results. References ---------- diff --git a/easygraph/functions/graph_embedding/node2vec.py b/easygraph/functions/graph_embedding/node2vec.py index 808bc02d..9b324dd2 100644 --- a/easygraph/functions/graph_embedding/node2vec.py +++ b/easygraph/functions/graph_embedding/node2vec.py @@ -1,10 +1,9 @@ import random import numpy as np - -from easygraph.utils import * from tqdm import tqdm +from easygraph.utils import * __all__ = ["node2vec"] @@ -62,18 +61,18 @@ def node2vec( Examples -------- - >>> node2vec(G, - ... dimensions=128, # The graph embedding dimensions. - ... walk_length=80, # Walk length of each random walks. - ... num_walks=10, # Number of random walks. - ... p=1.0, # The `p` possibility in random walk in [1]_ - ... q=1.0, # The `q` possibility in random walk in [1]_ - ... weight_key='weight', - ... skip_gram_params=dict( # The skip_gram parameters in Python package gensim. - ... window=10, - ... min_count=1, - ... batch_words=4 - ... )) + >>> node2vec( + ... G, + ... dimensions=128, # The graph embedding dimensions. + ... walk_length=80, # Walk length of each random walks. + ... num_walks=10, # Number of random walks. + ... p=1.0, # The `p` possibility in random walk in [1]_ + ... q=1.0, # The `q` possibility in random walk in [1]_ + ... weight_key="weight", + ... skip_gram_params=dict( # The skip_gram parameters in Python package gensim. + ... window=10, min_count=1, batch_words=4 + ... ), + ... ) References ---------- @@ -92,8 +91,7 @@ def node2vec( weight_key=weight_key, ) else: - from joblib import Parallel - from joblib import delayed + from joblib import Parallel, delayed num_walks_lists = np.array_split(range(num_walks), workers) walks = Parallel(n_jobs=workers)( @@ -139,9 +137,9 @@ def change_string_to_node_from_gensim_return_value(value_including_str): embedding_vector[node] = model.wv[str(index_of_node[node])] most_similar_nodes = model.wv.most_similar(str(index_of_node[node])) - most_similar_nodes_of_node[ - node - ] = change_string_to_node_from_gensim_return_value(most_similar_nodes) + most_similar_nodes_of_node[node] = ( + change_string_to_node_from_gensim_return_value(most_similar_nodes) + ) return embedding_vector, most_similar_nodes_of_node diff --git a/easygraph/functions/graph_embedding/sdne.py b/easygraph/functions/graph_embedding/sdne.py index f684fd14..f53e271e 100644 --- a/easygraph/functions/graph_embedding/sdne.py +++ b/easygraph/functions/graph_embedding/sdne.py @@ -64,8 +64,7 @@ def create_model(node_size, hidden_size=[256, 128], l1=1e-5, l2=1e-4): pass except ImportWarning: print("tensorflow not found, please install") - from tensorflow.python.keras.layers import Dense - from tensorflow.python.keras.layers import Input + from tensorflow.python.keras.layers import Dense, Input from tensorflow.python.keras.models import Model from tensorflow.python.keras.regularizers import l1_l2 @@ -133,7 +132,7 @@ def __init__( >>> model = SDNE(G, ... hidden_size=[256, 128]) # The hidden size in SDNE. >>> model.train(batch_size=3000, epochs=40, verbose=2) - >>> embeddings = model.get_embeddings() # Returns the graph embedding results. + >>> embeddings = model.get_embeddings() # Returns the graph embedding results. References ---------- @@ -191,9 +190,7 @@ def train(self, batch_size=1024, epochs=2, initial_epoch=0, verbose=1): if batch_size >= self.node_size: if batch_size > self.node_size: print( - "batch_size({0}) > node_size({1}),set batch_size = {1}".format( - batch_size, self.node_size - ) + f"batch_size({batch_size}) > node_size({self.node_size}),set batch_size = {self.node_size}" ) batch_size = self.node_size return self.model.fit( @@ -233,8 +230,7 @@ def train(self, batch_size=1024, epochs=2, initial_epoch=0, verbose=1): if verbose > 0: print(f"Epoch {epoch + 1}/{epochs}") print( - "{}s - loss: {: .4f} - 2nd_loss: {: .4f} - 1st_loss: {: .4f}" - .format(epoch_time, losses[0], losses[1], losses[2]) + f"{epoch_time}s - loss: {losses[0]: .4f} - 2nd_loss: {losses[1]: .4f} - 1st_loss: {losses[2]: .4f}" ) return hist diff --git a/easygraph/functions/graph_generator/RandomNetwork.py b/easygraph/functions/graph_generator/RandomNetwork.py index 2b6f71cf..4d25709a 100644 --- a/easygraph/functions/graph_generator/RandomNetwork.py +++ b/easygraph/functions/graph_generator/RandomNetwork.py @@ -3,7 +3,6 @@ import easygraph as eg - __all__ = [ "erdos_renyi_M", "erdos_renyi_P", @@ -35,7 +34,12 @@ def erdos_renyi_M(n, edge, directed=False, FilePath=None): -------- Returns an Erdős-Rényi random graph G. - >>> erdos_renyi_M(100,180,directed=False,FilePath="/users/fudanmsn/downloads/RandomNetwork.txt") + >>> erdos_renyi_M( + ... 100, + ... 180, + ... directed=False, + ... FilePath="/users/fudanmsn/downloads/RandomNetwork.txt", + ... ) References ---------- @@ -138,7 +142,12 @@ def erdos_renyi_P(n, p, directed=False, FilePath=None): -------- Returns an Erdős-Rényi random graph G - >>> erdos_renyi_P(100,0.5,directed=False,FilePath="/users/fudanmsn/downloads/RandomNetwork.txt") + >>> erdos_renyi_P( + ... 100, + ... 0.5, + ... directed=False, + ... FilePath="/users/fudanmsn/downloads/RandomNetwork.txt", + ... ) References ---------- @@ -206,7 +215,12 @@ def fast_erdos_renyi_P(n, p, directed=False, FilePath=None): -------- Returns an Erdős-Rényi random graph G - >>> erdos_renyi_P(100,0.5,directed=False,FilePath="/users/fudanmsn/downloads/RandomNetwork.txt") + >>> erdos_renyi_P( + ... 100, + ... 0.5, + ... directed=False, + ... FilePath="/users/fudanmsn/downloads/RandomNetwork.txt", + ... ) References ---------- @@ -289,7 +303,7 @@ def WS_Random(n, k, p, FilePath=None): -------- Returns a small-world graph G - >>> WS_Random(100,10,0.3,"/users/fudanmsn/downloads/RandomNetwork.txt") + >>> WS_Random(100, 10, 0.3, "/users/fudanmsn/downloads/RandomNetwork.txt") """ if k >= n: diff --git a/easygraph/functions/graph_generator/classic.py b/easygraph/functions/graph_generator/classic.py index 6b407d52..fbededba 100644 --- a/easygraph/functions/graph_generator/classic.py +++ b/easygraph/functions/graph_generator/classic.py @@ -1,9 +1,7 @@ import itertools from easygraph.classes import Graph -from easygraph.utils import nodes_or_number -from easygraph.utils import pairwise - +from easygraph.utils import nodes_or_number, pairwise __all__ = ["empty_graph", "path_graph", "complete_graph"] diff --git a/easygraph/functions/not_sorted/bridges.py b/easygraph/functions/not_sorted/bridges.py index b5ef42fa..c52701a7 100644 --- a/easygraph/functions/not_sorted/bridges.py +++ b/easygraph/functions/not_sorted/bridges.py @@ -1,10 +1,8 @@ from itertools import chain import easygraph as eg - from easygraph.utils.decorators import * - __all__ = ["bridges", "has_bridges"] diff --git a/easygraph/functions/not_sorted/cluster.py b/easygraph/functions/not_sorted/cluster.py index 5777ffc6..1d76fd4b 100644 --- a/easygraph/functions/not_sorted/cluster.py +++ b/easygraph/functions/not_sorted/cluster.py @@ -3,7 +3,6 @@ from easygraph.utils.decorators import not_implemented_for - try: from cpp_easygraph import cpp_clustering except ImportError: diff --git a/easygraph/functions/not_sorted/laplacian.py b/easygraph/functions/not_sorted/laplacian.py index 914afd39..b0f2a2b9 100644 --- a/easygraph/functions/not_sorted/laplacian.py +++ b/easygraph/functions/not_sorted/laplacian.py @@ -1,6 +1,5 @@ from easygraph.utils import * - __all__ = ["laplacian"] @@ -41,7 +40,6 @@ def laplacian(G, n_workers=None): if n_workers is not None: # use the parallel version for large graph import random - from functools import partial from multiprocessing import Pool diff --git a/easygraph/functions/not_sorted/mst.py b/easygraph/functions/not_sorted/mst.py index e3ac216e..ae56e1d4 100644 --- a/easygraph/functions/not_sorted/mst.py +++ b/easygraph/functions/not_sorted/mst.py @@ -1,12 +1,10 @@ -from heapq import heappop -from heapq import heappush +from heapq import heappop, heappush from itertools import count from math import isnan from operator import itemgetter from easygraph.utils.decorators import * - __all__ = [ "minimum_spanning_edges", "maximum_spanning_edges", diff --git a/easygraph/functions/not_sorted/pagerank.py b/easygraph/functions/not_sorted/pagerank.py index 3e349bc7..ccb70673 100644 --- a/easygraph/functions/not_sorted/pagerank.py +++ b/easygraph/functions/not_sorted/pagerank.py @@ -1,8 +1,6 @@ import easygraph as eg - from easygraph.utils import * - __all__ = ["pagerank"] diff --git a/easygraph/functions/not_sorted/tests/test_cluster.py b/easygraph/functions/not_sorted/tests/test_cluster.py index 2e7384ec..95feb280 100644 --- a/easygraph/functions/not_sorted/tests/test_cluster.py +++ b/easygraph/functions/not_sorted/tests/test_cluster.py @@ -1,6 +1,7 @@ -import easygraph as eg import pytest +import easygraph as eg + class TestClustering: @classmethod diff --git a/easygraph/functions/not_sorted/tests/test_pagerank.py b/easygraph/functions/not_sorted/tests/test_pagerank.py index 456eba5e..797cc830 100644 --- a/easygraph/functions/not_sorted/tests/test_pagerank.py +++ b/easygraph/functions/not_sorted/tests/test_pagerank.py @@ -1,6 +1,6 @@ -import easygraph as eg import pytest +import easygraph as eg np = pytest.importorskip("numpy") diff --git a/easygraph/functions/path/path.py b/easygraph/functions/path/path.py index 072ccaef..fe40ae6f 100644 --- a/easygraph/functions/path/path.py +++ b/easygraph/functions/path/path.py @@ -1,6 +1,5 @@ from easygraph.utils.decorators import * - __all__ = [ "Dijkstra", "Floyd", @@ -12,10 +11,7 @@ ] try: - from cpp_easygraph import cpp_dijkstra_multisource - from cpp_easygraph import cpp_Floyd - from cpp_easygraph import cpp_Kruskal - from cpp_easygraph import cpp_Prim + from cpp_easygraph import cpp_dijkstra_multisource, cpp_Floyd, cpp_Kruskal, cpp_Prim except ImportError: pass @@ -39,7 +35,7 @@ def Dijkstra(G, node): -------- Returns the length of paths from node 1 to remaining nodes - >>> Dijkstra(G,node=1) + >>> Dijkstra(G, node=1) """ return single_source_dijkstra(G, node) @@ -231,8 +227,7 @@ def multi_source_dijkstra(G, sources, weight="weight", target=None): def _dijkstra_multisource(G, sources, weight="weight", target=None): if G.cflag == 1: return cpp_dijkstra_multisource(G, sources, weight, target) - from heapq import heappop - from heapq import heappush + from heapq import heappop, heappush push = heappush pop = heappop diff --git a/easygraph/functions/structural_holes/AP_Greedy.py b/easygraph/functions/structural_holes/AP_Greedy.py index 9a81725a..ab1147c6 100644 --- a/easygraph/functions/structural_holes/AP_Greedy.py +++ b/easygraph/functions/structural_holes/AP_Greedy.py @@ -2,12 +2,10 @@ import random import easygraph as eg - from easygraph.functions.components.biconnected import generator_articulation_points from easygraph.functions.components.connected import connected_components from easygraph.utils.decorators import * - __all__ = ["common_greedy", "AP_Greedy"] @@ -49,10 +47,12 @@ def common_greedy(G, k, c=1.0, weight="weight"): -------- Returns the top k nodes as structural hole spanners, using **common_greedy**. - >>> common_greedy(G, - ... k = 3, # To find top three structural holes spanners. - ... c = 1.0, # To define zeta: zeta = c * (n*n*n), and zeta is the large value assigned as the shortest distance of two unreachable vertices. - ... weight = 'weight') + >>> common_greedy( + ... G, + ... k=3, # To find top three structural holes spanners. + ... c=1.0, # To define zeta: zeta = c * (n*n*n), and zeta is the large value assigned as the shortest distance of two unreachable vertices. + ... weight="weight", + ... ) References ---------- @@ -265,10 +265,12 @@ def AP_Greedy(G, k, c=1.0, weight="weight"): -------- Returns the top k nodes as structural hole spanners, using **AP_greedy**. - >>> AP_greedy(G, - ... k = 3, # To find top three structural holes spanners. - ... c = 1.0, # To define zeta: zeta = c * (n*n*n), and zeta is the large value assigned as the shortest distance of two unreachable vertices. - ... weight = 'weight') + >>> AP_greedy( + ... G, + ... k=3, # To find top three structural holes spanners. + ... c=1.0, # To define zeta: zeta = c * (n*n*n), and zeta is the large value assigned as the shortest distance of two unreachable vertices. + ... weight="weight", + ... ) References ---------- diff --git a/easygraph/functions/structural_holes/HAM.py b/easygraph/functions/structural_holes/HAM.py index e668df32..1f08f2b1 100644 --- a/easygraph/functions/structural_holes/HAM.py +++ b/easygraph/functions/structural_holes/HAM.py @@ -1,18 +1,15 @@ import scipy.stats as stat - __all__ = ["get_structural_holes_HAM"] from collections import Counter import numpy as np import scipy.linalg as spl import scipy.sparse as sps - -from easygraph.utils import * -from scipy.cluster.vq import kmeans -from scipy.cluster.vq import vq +from scipy.cluster.vq import kmeans, vq from sklearn import metrics +from easygraph.utils import * eps = 2.220446049250313e-16 @@ -184,11 +181,18 @@ def get_structural_holes_HAM(G, k, c, ground_truth_labels): Examples -------- - >>> get_structural_holes_HAM(G, - ... k = 2, # To find top two structural holes spanners. - ... c = 2, - ... ground_truth_labels = [[0], [0], [1], [0], [1]] # The ground truth labels for each node - community detection result, for example. - ... ) + >>> get_structural_holes_HAM( + ... G, + ... k=2, # To find top two structural holes spanners. + ... c=2, + ... ground_truth_labels=[ + ... [0], + ... [0], + ... [1], + ... [0], + ... [1], + ... ], # The ground truth labels for each node - community detection result, for example. + ... ) References ---------- diff --git a/easygraph/functions/structural_holes/HIS.py b/easygraph/functions/structural_holes/HIS.py index 44eda18d..5edf2d5d 100644 --- a/easygraph/functions/structural_holes/HIS.py +++ b/easygraph/functions/structural_holes/HIS.py @@ -1,16 +1,13 @@ import math - from itertools import combinations -from typing import List from easygraph.utils import * - __all__ = ["get_structural_holes_HIS"] @not_implemented_for("multigraph") -def get_structural_holes_HIS(G, C: List[frozenset], epsilon=1e-4, weight="weight"): +def get_structural_holes_HIS(G, C: list[frozenset], epsilon=1e-4, weight="weight"): """Structural hole spanners detection via HIS method. Both **HIS** and **MaxD** are methods in [1]_. @@ -50,11 +47,12 @@ def get_structural_holes_HIS(G, C: List[frozenset], epsilon=1e-4, weight="weight Examples -------- - >>> get_structural_holes_HIS(G, - ... C = [frozenset([1,2,3]), frozenset([4,5,6])], # Two communities - ... epsilon = 0.01, - ... weight = 'weight' - ... ) + >>> get_structural_holes_HIS( + ... G, + ... C=[frozenset([1, 2, 3]), frozenset([4, 5, 6])], # Two communities + ... epsilon=0.01, + ... weight="weight", + ... ) References @@ -83,7 +81,7 @@ def get_structural_holes_HIS(G, C: List[frozenset], epsilon=1e-4, weight="weight return S, I, H -def initialize(G, C: List[frozenset], S: [tuple], weight="weight"): +def initialize(G, C: list[frozenset], S: [tuple], weight="weight"): I, H = dict(), dict() for node in G.nodes: I[node] = dict() diff --git a/easygraph/functions/structural_holes/ICC.py b/easygraph/functions/structural_holes/ICC.py index 6a3c24ed..9361b6e8 100644 --- a/easygraph/functions/structural_holes/ICC.py +++ b/easygraph/functions/structural_holes/ICC.py @@ -1,8 +1,6 @@ import easygraph as eg - from easygraph.utils import * - __all__ = ["ICC", "BICC", "AP_BICC"] @@ -101,7 +99,7 @@ def ICC(G, k): -------- Returns the top k nodes as structural hole spanners, using **ICC**. - >>> ICC(G,k=3) + >>> ICC(G, k=3) References ---------- @@ -118,7 +116,7 @@ def ICC(G, k): MAX = 0 t = v for i in Q: - if MAX < i[1]: + if i[1] > MAX: MAX = i[1] t = i[0] if i_c < MAX: @@ -159,7 +157,7 @@ def BICC(G, k, K, l): -------- Returns the top k nodes as structural hole spanners, using **BICC**. - >>> BICC(G,k=3,K=5,l=4) + >>> BICC(G, k=3, K=5, l=4) References ---------- @@ -176,7 +174,7 @@ def BICC(G, k, K, l): MIN = 10000000 t = v for i in H: - if MIN > i[1]: + if i[1] < MIN: MIN = i[1] t = i[0] if b_i_c > MIN: @@ -191,7 +189,7 @@ def BICC(G, k, K, l): MAX = 0 t = v for i in V: - if MAX < i[1]: + if i[1] > MAX: MAX = i[1] t = i[0] if i_c < MAX: @@ -233,7 +231,7 @@ def AP_BICC(G, k, K, l): -------- Returns the top k nodes as structural hole spanners, using **AP_BICC**. - >>> AP_BICC(G,k=3,K=5,l=4) + >>> AP_BICC(G, k=3, K=5, l=4) References ---------- @@ -251,7 +249,7 @@ def AP_BICC(G, k, K, l): MIN = 10000000 t = v for i in T: - if MIN > i[1]: + if i[1] < MIN: MIN = i[1] t = i[0] if A[v]["c"] > MIN: @@ -272,7 +270,7 @@ def AP_BICC(G, k, K, l): MIN = 10000000 t = v for i in Q: - if MIN > i[1]: + if i[1] < MIN: MIN = i[1] t = i[0] if b_i_c > MIN: @@ -282,7 +280,7 @@ def AP_BICC(G, k, K, l): MAX = 0 t = None for i in Q: - if MAX < i[1]: + if i[1] > MAX: MAX = i[1] t = i[0] T.append([t, A[t]["c"]]) diff --git a/easygraph/functions/structural_holes/MaxD.py b/easygraph/functions/structural_holes/MaxD.py index 1cc29cab..68428174 100644 --- a/easygraph/functions/structural_holes/MaxD.py +++ b/easygraph/functions/structural_holes/MaxD.py @@ -1,13 +1,10 @@ -from typing import List - from easygraph.utils import * - __all__ = ["get_structural_holes_MaxD"] @not_implemented_for("multigraph") -def get_community_kernel(G, C: List[frozenset], weight="weight"): +def get_community_kernel(G, C: list[frozenset], weight="weight"): """ To get community kernels with most degrees. Parameters @@ -53,7 +50,7 @@ def get_community_kernel(G, C: List[frozenset], weight="weight"): return kernels -def get_structural_holes_MaxD(G, k, C: List[frozenset]): +def get_structural_holes_MaxD(G, k, C: list[frozenset]): """Structural hole spanners detection via MaxD method. Both **HIS** and **MaxD** are methods in [1]_. @@ -77,10 +74,11 @@ def get_structural_holes_MaxD(G, k, C: List[frozenset]): Examples -------- - >>> get_structural_holes_MaxD(G, - ... k = 5, # To find top five structural holes spanners. - ... C = [frozenset([1,2,3]), frozenset([4,5,6])] # Two communities - ... ) + >>> get_structural_holes_MaxD( + ... G, + ... k=5, # To find top five structural holes spanners. + ... C=[frozenset([1, 2, 3]), frozenset([4, 5, 6])], # Two communities + ... ) References diff --git a/easygraph/functions/structural_holes/NOBE.py b/easygraph/functions/structural_holes/NOBE.py index 0485900e..cec8eec0 100644 --- a/easygraph/functions/structural_holes/NOBE.py +++ b/easygraph/functions/structural_holes/NOBE.py @@ -1,9 +1,8 @@ -import easygraph as eg import numpy as np +import easygraph as eg from easygraph.utils import * - __all__ = ["NOBE_SH", "NOBE_GA_SH"] from sklearn.cluster import KMeans @@ -31,7 +30,7 @@ def NOBE_SH(G, K, topk): Examples -------- - >>> NOBE_SH(G,K=8,topk=5) + >>> NOBE_SH(G, K=8, topk=5) References ---------- @@ -94,7 +93,7 @@ def NOBE_GA_SH(G, K, topk): Examples -------- - >>> NOBE_GA_SH(G,K=8,topk=5) + >>> NOBE_GA_SH(G, K=8, topk=5) References ---------- diff --git a/easygraph/functions/structural_holes/SHII_metric.py b/easygraph/functions/structural_holes/SHII_metric.py index 5961c8c0..c3ad75d8 100644 --- a/easygraph/functions/structural_holes/SHII_metric.py +++ b/easygraph/functions/structural_holes/SHII_metric.py @@ -1,9 +1,10 @@ import math import random -import easygraph as eg import numpy as np +import easygraph as eg + class NodeParams: def __init__(self, active, inWeight, threshold): @@ -87,7 +88,7 @@ def structural_hole_influence_index( for community_label in range(len(C)): nodesInCommunity = [] seedSetInCommunity = [] - for node in node_label_pair.keys(): + for node in node_label_pair: if node_label_pair[node] == community_label: nodesInCommunity.append(node) if node in S: @@ -176,7 +177,9 @@ def _independent_cascade(G, S, community_label, countIterations, node_label_pair N = G.number_of_nodes() for b in range(countIterations): # print(b, " in ", countIterations) - p_vw = np.zeros((N, N)) # 节点被激活时，激活其它节点的概率,a对b的影响等于b对a的影响 + p_vw = np.zeros( + (N, N) + ) # 节点被激活时，激活其它节点的概率,a对b的影响等于b对a的影响 for random_i in range(N): for random_j in range(random_i + 1, N): num = random.random() @@ -232,7 +235,7 @@ def _linear_threshold(G, S, community_label, countIterations, node_label_pair): for neighbor in G.neighbors(node=v): if neighbor not in S: weight_degree = 1.0 / float(G.in_degree()[neighbor]) - if neighbor not in Q.keys(): + if neighbor not in Q: np = NodeParams(False, weight_degree, random.random()) Q[neighbor] = np T.append(neighbor) @@ -248,7 +251,7 @@ def _linear_threshold(G, S, community_label, countIterations, node_label_pair): if neighbor in S: continue weight_degree = 1.0 / float(G.in_degree()[neighbor]) - if neighbor not in Q.keys(): + if neighbor not in Q: np = NodeParams(False, weight_degree, random.random()) Q[neighbor] = np T.append(neighbor) diff --git a/easygraph/functions/structural_holes/evaluation.py b/easygraph/functions/structural_holes/evaluation.py index 07bd3dfe..a5417866 100644 --- a/easygraph/functions/structural_holes/evaluation.py +++ b/easygraph/functions/structural_holes/evaluation.py @@ -2,11 +2,8 @@ from easygraph.utils import * - try: - from cpp_easygraph import cpp_constraint - from cpp_easygraph import cpp_effective_size - from cpp_easygraph import cpp_hierarchy + from cpp_easygraph import cpp_constraint, cpp_effective_size, cpp_hierarchy except ImportError: pass @@ -103,10 +100,15 @@ def effective_size(G, nodes=None, weight=None, n_workers=None): The Effective Size of node in `nodes`. Examples -------- - >>> effective_size(G, - ... nodes=[1,2,3], # Compute the Effective Size of some nodes. The default is None for all nodes in G. - ... weight='weight' # The weight key of the graph. The default is None for unweighted graph. - ... ) + >>> effective_size( + ... G, + ... nodes=[ + ... 1, + ... 2, + ... 3, + ... ], # Compute the Effective Size of some nodes. The default is None for all nodes in G. + ... weight="weight", # The weight key of the graph. The default is None for unweighted graph. + ... ) References ---------- .. [1] Burt R S. Structural holes: The social structure of competition[M]. @@ -123,7 +125,6 @@ def effective_size(G, nodes=None, weight=None, n_workers=None): if not G.is_directed() and weight is None: if n_workers is not None: import random - from functools import partial from multiprocessing import Pool @@ -154,7 +155,6 @@ def effective_size(G, nodes=None, weight=None, n_workers=None): else: if n_workers is not None: import random - from functools import partial from multiprocessing import Pool @@ -197,10 +197,15 @@ def efficiency(G, nodes=None, weight=None): The Efficiency of node in `nodes`. Examples -------- - >>> efficiency(G, - ... nodes=[1,2,3], # Compute the Efficiency of some nodes. The default is None for all nodes in G. - ... weight='weight' # The weight key of the graph. The default is None for unweighted graph. - ... ) + >>> efficiency( + ... G, + ... nodes=[ + ... 1, + ... 2, + ... 3, + ... ], # Compute the Efficiency of some nodes. The default is None for all nodes in G. + ... weight="weight", # The weight key of the graph. The default is None for unweighted graph. + ... ) References ---------- .. [1] Burt R S. Structural holes: The social structure of competition[M]. @@ -247,11 +252,16 @@ def constraint(G, nodes=None, weight=None, n_workers=None): The Constraint of node in `nodes`. Examples -------- - >>> constraint(G, - ... nodes=[1,2,3], # Compute the Constraint of some nodes. The default is None for all nodes in G. - ... weight='weight', # The weight key of the graph. The default is None for unweighted graph. - ... n_workers=4 # Parallel computing on four workers. The default is None for serial computing. - ... ) + >>> constraint( + ... G, + ... nodes=[ + ... 1, + ... 2, + ... 3, + ... ], # Compute the Constraint of some nodes. The default is None for all nodes in G. + ... weight="weight", # The weight key of the graph. The default is None for unweighted graph. + ... n_workers=4, # Parallel computing on four workers. The default is None for serial computing. + ... ) References ---------- .. [1] Burt R S. Structural holes: The social structure of competition[M]. @@ -278,7 +288,6 @@ def compute_constraint_of_v(v): if n_workers is not None: import random - from functools import partial from multiprocessing import Pool @@ -376,7 +385,6 @@ def hierarchy(G, nodes=None, weight=None, n_workers=None): hierarchy = {} if n_workers is not None: import random - from functools import partial from multiprocessing import Pool diff --git a/easygraph/functions/structural_holes/maxBlock.py b/easygraph/functions/structural_holes/maxBlock.py index a7e8bb66..678f3720 100644 --- a/easygraph/functions/structural_holes/maxBlock.py +++ b/easygraph/functions/structural_holes/maxBlock.py @@ -2,12 +2,13 @@ import random import sys -import easygraph as eg +from strong_connected_component import ( + condensation, + number_strongly_connected_components, +) +import easygraph as eg from easygraph.utils import * -from strong_connected_component import condensation -from strong_connected_component import number_strongly_connected_components - __all__ = [ "maxBlock", @@ -190,10 +191,10 @@ def _get_idom(G, G_tr, node_s, ans_real, desc_set_real): desc_set[node_map[node]] = set() _dfs(node_map[node_s], tr, ans, desc_set) - for key in ans.keys(): + for key in ans: ans[key] -= 1 ans_real[index_map[key]] = ans[key] - for key in desc_set.keys(): + for key in desc_set: desc_set_real[index_map[key]] = set() for value in desc_set[key]: desc_set_real[index_map[key]].add(index_map[value]) @@ -540,7 +541,7 @@ def maxBlockFast(G, k, f_set=None, L=None, flag_weight=False): for node_u in G_tr.nodes: D_u = 0 for desc in desc_set[node_u]: - if desc not in d_dict.keys(): + if desc not in d_dict: print( "Error: desc:", desc, @@ -582,7 +583,7 @@ def maxBlockFast(G, k, f_set=None, L=None, flag_weight=False): for node_u in G_tr.nodes: D_u = 0 for desc in desc_set[node_u]: - if desc not in d_dict.keys(): + if desc not in d_dict: print( "Error: desc:", desc, diff --git a/easygraph/functions/structural_holes/metrics.py b/easygraph/functions/structural_holes/metrics.py index 5ba5491a..9df5b430 100644 --- a/easygraph/functions/structural_holes/metrics.py +++ b/easygraph/functions/structural_holes/metrics.py @@ -1,12 +1,11 @@ import math import random -import easygraph as eg import numpy as np +import easygraph as eg from easygraph.utils import * - __all__ = [ "sum_of_shortest_paths", "nodes_of_max_cc_without_shs", @@ -34,8 +33,8 @@ def sum_of_shortest_paths(G, S): Examples -------- - >>> G_t=eg.datasets.get_graph_blogcatalog() - >>> S_t=eg.AP_Greedy(G_t, 10000) + >>> G_t = eg.datasets.get_graph_blogcatalog() + >>> S_t = eg.AP_Greedy(G_t, 10000) >>> diff = sum_of_shortest_paths(G_t, S_t) >>> print(diff) @@ -84,8 +83,8 @@ def nodes_of_max_cc_without_shs(G, S): Examples -------- - >>> G_t=eg.datasets.get_graph_blogcatalog() - >>> S_t=eg.AP_Greedy(G_t, 10000) + >>> G_t = eg.datasets.get_graph_blogcatalog() + >>> S_t = eg.AP_Greedy(G_t, 10000) >>> maxx = nodes_of_max_cc_without_shs(G_t, S_t) >>> print(maxx) @@ -187,7 +186,7 @@ def structural_hole_influence_index( for community_label in range(len(C)): nodesInCommunity = [] seedSetInCommunity = [] - for node in node_label_pair.keys(): + for node in node_label_pair: if node_label_pair[node] == community_label: nodesInCommunity.append(node) if node in S: @@ -276,7 +275,9 @@ def _independent_cascade(G, S, community_label, countIterations, node_label_pair N = G.number_of_nodes() for b in range(countIterations): # print(b, " in ", countIterations) - p_vw = np.zeros((N, N)) # 节点被激活时，激活其它节点的概率,a对b的影响等于b对a的影响 + p_vw = np.zeros( + (N, N) + ) # 节点被激活时，激活其它节点的概率,a对b的影响等于b对a的影响 for random_i in range(N): for random_j in range(random_i + 1, N): num = random.random() @@ -332,7 +333,7 @@ def _linear_threshold(G, S, community_label, countIterations, node_label_pair): for neighbor in G.neighbors(node=v): if neighbor not in S: weight_degree = 1.0 / float(G.in_degree()[neighbor]) - if neighbor not in Q.keys(): + if neighbor not in Q: np = NodeParams(False, weight_degree, random.random()) Q[neighbor] = np T.append(neighbor) @@ -348,7 +349,7 @@ def _linear_threshold(G, S, community_label, countIterations, node_label_pair): if neighbor in S: continue weight_degree = 1.0 / float(G.in_degree()[neighbor]) - if neighbor not in Q.keys(): + if neighbor not in Q: np = NodeParams(False, weight_degree, random.random()) Q[neighbor] = np T.append(neighbor) diff --git a/easygraph/functions/structural_holes/strong_connected_component.py b/easygraph/functions/structural_holes/strong_connected_component.py index aa9c7a1c..dc499d2b 100644 --- a/easygraph/functions/structural_holes/strong_connected_component.py +++ b/easygraph/functions/structural_holes/strong_connected_component.py @@ -1,8 +1,6 @@ import easygraph as eg - from easygraph.utils.decorators import * - __all__ = [ "number_strongly_connected_components", "strongly_connected_components", @@ -173,7 +171,7 @@ def condensation(G, scc=None): for edge in G.edges: if mapping[edge[0]] != mapping[edge[1]]: C.add_edge(mapping[edge[0]], mapping[edge[1]]) - if edge[1] not in incoming_info.keys(): + if edge[1] not in incoming_info: incoming_info[edge[1]] = set() incoming_info[edge[1]].add(edge[0]) C.graph["incoming_info"] = incoming_info diff --git a/easygraph/functions/structural_holes/weakTie.py b/easygraph/functions/structural_holes/weakTie.py index f19a2298..33e5016e 100644 --- a/easygraph/functions/structural_holes/weakTie.py +++ b/easygraph/functions/structural_holes/weakTie.py @@ -1,8 +1,6 @@ import easygraph as eg - from easygraph.utils import * - __all__ = [ "weakTie", "weakTieLocal", diff --git a/easygraph/readwrite/edgelist.py b/easygraph/readwrite/edgelist.py index f8b5a18b..814c46ab 100644 --- a/easygraph/readwrite/edgelist.py +++ b/easygraph/readwrite/edgelist.py @@ -1,6 +1,5 @@ import easygraph as eg - __all__ = [ "parse_edgelist", ] diff --git a/easygraph/readwrite/gexf.py b/easygraph/readwrite/gexf.py index e86f1350..60c14fea 100644 --- a/easygraph/readwrite/gexf.py +++ b/easygraph/readwrite/gexf.py @@ -1,17 +1,16 @@ import itertools import time - -from xml.etree.ElementTree import Element -from xml.etree.ElementTree import ElementTree -from xml.etree.ElementTree import SubElement -from xml.etree.ElementTree import register_namespace -from xml.etree.ElementTree import tostring +from xml.etree.ElementTree import ( + Element, + ElementTree, + SubElement, + register_namespace, + tostring, +) import easygraph as eg - from easygraph.utils import * - __all__ = ["write_gexf", "relabel_gexf_graph", "generate_gexf", "read_gexf"] diff --git a/easygraph/readwrite/gml.py b/easygraph/readwrite/gml.py index a6d3acb6..a50acff0 100644 --- a/easygraph/readwrite/gml.py +++ b/easygraph/readwrite/gml.py @@ -28,66 +28,61 @@ `Network data page `_. """ - import html.entities as htmlentitydefs import re - from ast import literal_eval from collections import defaultdict from enum import Enum from io import StringIO -from typing import Any -from typing import NamedTuple +from typing import Any, NamedTuple import easygraph as eg - from easygraph.utils import open_file from easygraph.utils.exception import EasyGraphError - __all__ = ["read_gml", "parse_gml", "generate_gml", "write_gml"] LIST_START_VALUE = "_easygraph_list_start" def escape(text): - """Use XML character references to escape characters. + """Use XML character references to escape characters. Use XML character references for unprintable or non-ASCII characters, double quotes and ampersands in a string """ - def fixup(m): - ch = m.group(0) - return "&#" + str(ord(ch)) + ";" + def fixup(m): + ch = m.group(0) + return "&#" + str(ord(ch)) + ";" - text = re.sub('[^ -~]|[&"]', fixup, text) - return text if isinstance(text, str) else str(text) + text = re.sub('[^ -~]|[&"]', fixup, text) + return text if isinstance(text, str) else str(text) def unescape(text): - """Replace XML character references with the referenced characters""" - - def fixup(m): - text = m.group(0) - if text[1] == "#": - # Character reference - if text[2] == "x": - code = int(text[3:-1], 16) - else: - code = int(text[2:-1]) - else: - # Named entity - try: - code = htmlentitydefs.name2codepoint[text[1:-1]] - except KeyError: - return text # leave unchanged - try: - return chr(code) - except (ValueError, OverflowError): - return text # leave unchanged - - return re.sub("&(?:[0-9A-Za-z]+|#(?:[0-9]+|x[0-9A-Fa-f]+));", fixup, text) + """Replace XML character references with the referenced characters""" + + def fixup(m): + text = m.group(0) + if text[1] == "#": + # Character reference + if text[2] == "x": + code = int(text[3:-1], 16) + else: + code = int(text[2:-1]) + else: + # Named entity + try: + code = htmlentitydefs.name2codepoint[text[1:-1]] + except KeyError: + return text # leave unchanged + try: + return chr(code) + except (ValueError, OverflowError): + return text # leave unchanged + + return re.sub("&(?:[0-9A-Za-z]+|#(?:[0-9]+|x[0-9A-Fa-f]+));", fixup, text) def literal_destringizer(rep): @@ -119,26 +114,26 @@ def literal_destringizer(rep): class Pattern(Enum): - """encodes the index of each token-matching pattern in `tokenize`.""" + """encodes the index of each token-matching pattern in `tokenize`.""" - KEYS = 0 - REALS = 1 - INTS = 2 - STRINGS = 3 - DICT_START = 4 - DICT_END = 5 - COMMENT_WHITESPACE = 6 + KEYS = 0 + REALS = 1 + INTS = 2 + STRINGS = 3 + DICT_START = 4 + DICT_END = 5 + COMMENT_WHITESPACE = 6 class Token(NamedTuple): - category: Pattern - value: Any - line: int - position: int + category: Pattern + value: Any + line: int + position: int def parse_gml(lines, label="label", destringizer=None): - """Parse GML graph from a string or iterable. + """Parse GML graph from a string or iterable. Parameters ---------- @@ -186,224 +181,224 @@ def parse_gml(lines, label="label", destringizer=None): See the module docstring :mod:`easygraph.readwrite.gml` for more details. """ - def decode_line(line): - if isinstance(line, bytes): - try: - line.decode("ascii") - except UnicodeDecodeError as err: - raise EasyGraphError("input is not ASCII-encoded") from err - if not isinstance(line, str): - line = str(line) - return line - - def filter_lines(lines): - if isinstance(lines, str): - lines = decode_line(lines) - lines = lines.splitlines() - yield from lines - else: - for line in lines: - line = decode_line(line) - if line and line[-1] == "\n": - line = line[:-1] - if line.find("\n") != -1: - raise EasyGraphError("input line contains newline") - yield line - - G = parse_gml_lines(filter_lines(lines), label, destringizer) - return G + def decode_line(line): + if isinstance(line, bytes): + try: + line.decode("ascii") + except UnicodeDecodeError as err: + raise EasyGraphError("input is not ASCII-encoded") from err + if not isinstance(line, str): + line = str(line) + return line + + def filter_lines(lines): + if isinstance(lines, str): + lines = decode_line(lines) + lines = lines.splitlines() + yield from lines + else: + for line in lines: + line = decode_line(line) + if line and line[-1] == "\n": + line = line[:-1] + if line.find("\n") != -1: + raise EasyGraphError("input line contains newline") + yield line + + G = parse_gml_lines(filter_lines(lines), label, destringizer) + return G def parse_gml_lines(lines, label, destringizer): - """Parse GML `lines` into a graph.""" - - def tokenize(): - patterns = [ - r"[A-Za-z][0-9A-Za-z_]*\b", # keys - # reals - r"[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*|INF)(?:[Ee][+-]?[0-9]+)?", - r"[+-]?[0-9]+", # ints - r'".*?"', # strings - r"\[", # dict start - r"\]", # dict end - r"#.*$|\s+", # comments and whitespaces - ] - tokens = re.compile("|".join(f"({pattern})" for pattern in patterns)) - lineno = 0 - for line in lines: - length = len(line) - pos = 0 - while pos < length: - match = tokens.match(line, pos) - if match is None: - m = f"cannot tokenize {line[pos:]} at ({lineno + 1}, {pos + 1})" - raise EasyGraphError(m) - for i in range(len(patterns)): - group = match.group(i + 1) - if group is not None: - if i == 0: # keys - value = group.rstrip() - elif i == 1: # reals - value = float(group) - elif i == 2: # ints - value = int(group) - else: - value = group - if i != 6: # comments and whitespaces - yield Token(Pattern(i), value, lineno + 1, pos + 1) - pos += len(group) - break - lineno += 1 - yield Token(None, None, lineno + 1, 1) # EOF - - def unexpected(curr_token, expected): - category, value, lineno, pos = curr_token - value = repr(value) if value is not None else "EOF" - raise EasyGraphError(f"expected {expected}, found {value} at ({lineno}, {pos})") - - def consume(curr_token, category, expected): - if curr_token.category == category: - return next(tokens) - unexpected(curr_token, expected) - - def parse_dict(curr_token): - # dict start - curr_token = consume(curr_token, Pattern.DICT_START, "'['") - # dict contents - curr_token, dct = parse_kv(curr_token) - # dict end - curr_token = consume(curr_token, Pattern.DICT_END, "']'") - return curr_token, dct - - def parse_kv(curr_token): - dct = defaultdict(list) - while curr_token.category == Pattern.KEYS: - key = curr_token.value - curr_token = next(tokens) - category = curr_token.category - if category == Pattern.REALS or category == Pattern.INTS: - value = curr_token.value - curr_token = next(tokens) - elif category == Pattern.STRINGS: - value = unescape(curr_token.value[1:-1]) - if destringizer: - try: - value = destringizer(value) - except ValueError: - pass - curr_token = next(tokens) - elif category == Pattern.DICT_START: - curr_token, value = parse_dict(curr_token) - else: - if key in ("id", "label", "source", "target"): - try: - # String convert the token value - value = unescape(str(curr_token.value)) - if destringizer: - try: - value = destringizer(value) - except ValueError: - pass - curr_token = next(tokens) - except Exception: - msg = ( - "an int, float, string, '[' or string" - + " convertable ASCII value for node id or label" - ) - unexpected(curr_token, msg) - elif curr_token.value in {"NAN", "INF"}: - value = float(curr_token.value) - curr_token = next(tokens) - else: # Otherwise error out - unexpected(curr_token, "an int, float, string or '['") - dct[key].append(value) - - def clean_dict_value(value): - if not isinstance(value, list): - return value - if len(value) == 1: - return value[0] - if value[0] == LIST_START_VALUE: - return value[1:] - return value - - dct = {key: clean_dict_value(value) for key, value in dct.items()} - return curr_token, dct - - def parse_graph(): - curr_token, dct = parse_kv(next(tokens)) - if curr_token.category is not None: # EOF - unexpected(curr_token, "EOF") - if "graph" not in dct: - raise EasyGraphError("input contains no graph") - graph = dct["graph"] - if isinstance(graph, list): - raise EasyGraphError("input contains more than one graph") - return graph - - tokens = tokenize() - graph = parse_graph() - directed = graph.pop("directed", False) - multigraph = graph.pop("multigraph", False) - if not multigraph: - G = eg.DiGraph() if directed else eg.Graph() - else: - G = eg.MultiDiGraph() if directed else eg.MultiGraph() - graph_attr = {k: v for k, v in graph.items() if k not in ("node", "edge")} - G.graph.update(graph_attr) - - def pop_attr(dct, category, attr, i): - try: - return dct.pop(attr) - except KeyError as err: - raise EasyGraphError(f"{category} #{i} has no {attr!r} attribute") from err - - nodes = graph.get("node", []) - mapping = {} - node_labels = set() - for i, node in enumerate(nodes if isinstance(nodes, list) else [nodes]): - id = pop_attr(node, "node", "id", i) - if id in G: - raise EasyGraphError(f"node id {id!r} is duplicated") - if label is not None and label != "id": - node_label = pop_attr(node, "node", label, i) - if node_label in node_labels: - raise EasyGraphError(f"node label {node_label!r} is duplicated") - node_labels.add(node_label) - mapping[id] = node_label - G.add_node(id, **node) - - edges = graph.get("edge", []) - for i, edge in enumerate(edges if isinstance(edges, list) else [edges]): - source = pop_attr(edge, "edge", "source", i) - target = pop_attr(edge, "edge", "target", i) - if source not in G: - raise EasyGraphError(f"edge #{i} has undefined source {source!r}") - if target not in G: - raise EasyGraphError(f"edge #{i} has undefined target {target!r}") - if not multigraph: - if not G.has_edge(source, target): - G.add_edge(source, target, **edge) - else: - arrow = "->" if directed else "--" - msg = f"edge #{i} ({source!r}{arrow}{target!r}) is duplicated" - raise EasyGraphError(msg) - else: - key = edge.pop("key", None) - if key is not None and G.has_edge(source, target, key): - arrow = "->" if directed else "--" - msg = f"edge #{i} ({source!r}{arrow}{target!r}, {key!r})" - msg2 = 'Hint: If multigraph add "multigraph 1" to file header.' - raise EasyGraphError(msg + " is duplicated\n" + msg2) - G.add_edge(source, target, key, **edge) - - if label is not None and label != "id": - G = eg.relabel_nodes(G, mapping) - return G + """Parse GML `lines` into a graph.""" + + def tokenize(): + patterns = [ + r"[A-Za-z][0-9A-Za-z_]*\b", # keys + # reals + r"[+-]?(?:[0-9]*\.[0-9]+|[0-9]+\.[0-9]*|INF)(?:[Ee][+-]?[0-9]+)?", + r"[+-]?[0-9]+", # ints + r'".*?"', # strings + r"\[", # dict start + r"\]", # dict end + r"#.*$|\s+", # comments and whitespaces + ] + tokens = re.compile("|".join(f"({pattern})" for pattern in patterns)) + lineno = 0 + for line in lines: + length = len(line) + pos = 0 + while pos < length: + match = tokens.match(line, pos) + if match is None: + m = f"cannot tokenize {line[pos:]} at ({lineno + 1}, {pos + 1})" + raise EasyGraphError(m) + for i in range(len(patterns)): + group = match.group(i + 1) + if group is not None: + if i == 0: # keys + value = group.rstrip() + elif i == 1: # reals + value = float(group) + elif i == 2: # ints + value = int(group) + else: + value = group + if i != 6: # comments and whitespaces + yield Token(Pattern(i), value, lineno + 1, pos + 1) + pos += len(group) + break + lineno += 1 + yield Token(None, None, lineno + 1, 1) # EOF + + def unexpected(curr_token, expected): + category, value, lineno, pos = curr_token + value = repr(value) if value is not None else "EOF" + raise EasyGraphError(f"expected {expected}, found {value} at ({lineno}, {pos})") + + def consume(curr_token, category, expected): + if curr_token.category == category: + return next(tokens) + unexpected(curr_token, expected) + + def parse_dict(curr_token): + # dict start + curr_token = consume(curr_token, Pattern.DICT_START, "'['") + # dict contents + curr_token, dct = parse_kv(curr_token) + # dict end + curr_token = consume(curr_token, Pattern.DICT_END, "']'") + return curr_token, dct + + def parse_kv(curr_token): + dct = defaultdict(list) + while curr_token.category == Pattern.KEYS: + key = curr_token.value + curr_token = next(tokens) + category = curr_token.category + if category == Pattern.REALS or category == Pattern.INTS: + value = curr_token.value + curr_token = next(tokens) + elif category == Pattern.STRINGS: + value = unescape(curr_token.value[1:-1]) + if destringizer: + try: + value = destringizer(value) + except ValueError: + pass + curr_token = next(tokens) + elif category == Pattern.DICT_START: + curr_token, value = parse_dict(curr_token) + else: + if key in ("id", "label", "source", "target"): + try: + # String convert the token value + value = unescape(str(curr_token.value)) + if destringizer: + try: + value = destringizer(value) + except ValueError: + pass + curr_token = next(tokens) + except Exception: + msg = ( + "an int, float, string, '[' or string" + + " convertable ASCII value for node id or label" + ) + unexpected(curr_token, msg) + elif curr_token.value in {"NAN", "INF"}: + value = float(curr_token.value) + curr_token = next(tokens) + else: # Otherwise error out + unexpected(curr_token, "an int, float, string or '['") + dct[key].append(value) + + def clean_dict_value(value): + if not isinstance(value, list): + return value + if len(value) == 1: + return value[0] + if value[0] == LIST_START_VALUE: + return value[1:] + return value + + dct = {key: clean_dict_value(value) for key, value in dct.items()} + return curr_token, dct + + def parse_graph(): + curr_token, dct = parse_kv(next(tokens)) + if curr_token.category is not None: # EOF + unexpected(curr_token, "EOF") + if "graph" not in dct: + raise EasyGraphError("input contains no graph") + graph = dct["graph"] + if isinstance(graph, list): + raise EasyGraphError("input contains more than one graph") + return graph + + tokens = tokenize() + graph = parse_graph() + directed = graph.pop("directed", False) + multigraph = graph.pop("multigraph", False) + if not multigraph: + G = eg.DiGraph() if directed else eg.Graph() + else: + G = eg.MultiDiGraph() if directed else eg.MultiGraph() + graph_attr = {k: v for k, v in graph.items() if k not in ("node", "edge")} + G.graph.update(graph_attr) + + def pop_attr(dct, category, attr, i): + try: + return dct.pop(attr) + except KeyError as err: + raise EasyGraphError(f"{category} #{i} has no {attr!r} attribute") from err + + nodes = graph.get("node", []) + mapping = {} + node_labels = set() + for i, node in enumerate(nodes if isinstance(nodes, list) else [nodes]): + id = pop_attr(node, "node", "id", i) + if id in G: + raise EasyGraphError(f"node id {id!r} is duplicated") + if label is not None and label != "id": + node_label = pop_attr(node, "node", label, i) + if node_label in node_labels: + raise EasyGraphError(f"node label {node_label!r} is duplicated") + node_labels.add(node_label) + mapping[id] = node_label + G.add_node(id, **node) + + edges = graph.get("edge", []) + for i, edge in enumerate(edges if isinstance(edges, list) else [edges]): + source = pop_attr(edge, "edge", "source", i) + target = pop_attr(edge, "edge", "target", i) + if source not in G: + raise EasyGraphError(f"edge #{i} has undefined source {source!r}") + if target not in G: + raise EasyGraphError(f"edge #{i} has undefined target {target!r}") + if not multigraph: + if not G.has_edge(source, target): + G.add_edge(source, target, **edge) + else: + arrow = "->" if directed else "--" + msg = f"edge #{i} ({source!r}{arrow}{target!r}) is duplicated" + raise EasyGraphError(msg) + else: + key = edge.pop("key", None) + if key is not None and G.has_edge(source, target, key): + arrow = "->" if directed else "--" + msg = f"edge #{i} ({source!r}{arrow}{target!r}, {key!r})" + msg2 = 'Hint: If multigraph add "multigraph 1" to file header.' + raise EasyGraphError(msg + " is duplicated\n" + msg2) + G.add_edge(source, target, key, **edge) + + if label is not None and label != "id": + G = eg.relabel_nodes(G, mapping) + return G def generate_gml(G, stringizer=None): - r"""Generate a single entry of the graph `G` in GML format. + r"""Generate a single entry of the graph `G` in GML format. Parameters ---------- @@ -462,118 +457,118 @@ def generate_gml(G, stringizer=None): ] ] """ - valid_keys = re.compile("^[A-Za-z][0-9A-Za-z_]*$") - - def stringize(key, value, ignored_keys, indent, in_list=False): - if not isinstance(key, str): - raise EasyGraphError(f"{key!r} is not a string") - if not valid_keys.match(key): - raise EasyGraphError(f"{key!r} is not a valid key") - if not isinstance(key, str): - key = str(key) - if key not in ignored_keys: - if isinstance(value, (int, bool)): - if key == "label": - yield indent + key + ' "' + str(value) + '"' - elif value is True: - # python bool is an instance of int - yield indent + key + " 1" - elif value is False: - yield indent + key + " 0" - # GML only supports signed 32-bit integers - elif value < -(2**31) or value >= 2**31: - yield indent + key + ' "' + str(value) + '"' - else: - yield indent + key + " " + str(value) - elif isinstance(value, float): - text = repr(value).upper() - # GML matches INF to keys, so prepend + to INF. Use repr(float(*)) - # instead of string literal to future proof against changes to repr. - if text == repr(float("inf")).upper(): - text = "+" + text - else: - # GML requires that a real literal contain a decimal point, but - # repr may not output a decimal point when the mantissa is - # integral and hence needs fixing. - epos = text.rfind("E") - if epos != -1 and text.find(".", 0, epos) == -1: - text = text[:epos] + "." + text[epos:] - if key == "label": - yield indent + key + ' "' + text + '"' - else: - yield indent + key + " " + text - elif isinstance(value, dict): - yield indent + key + " [" - next_indent = indent + " " - for key, value in value.items(): - yield from stringize(key, value, (), next_indent) - yield indent + "]" - elif ( - isinstance(value, (list, tuple)) - and key != "label" - and value - and not in_list - ): - if len(value) == 1: - yield indent + key + " " + f'"{LIST_START_VALUE}"' - for val in value: - yield from stringize(key, val, (), indent, True) - else: - if stringizer: - try: - value = stringizer(value) - except ValueError as err: - raise EasyGraphError( - f"{value!r} cannot be converted into a string" - ) from err - if not isinstance(value, str): - raise EasyGraphError(f"{value!r} is not a string") - yield indent + key + ' "' + escape(value) + '"' - - yield "graph [" - - # Output graph attributes - multigraph = G.is_multigraph() - if G.is_directed(): - yield " directed 1" - if multigraph: - yield " multigraph 1" - ignored_keys = {"directed", "multigraph", "node", "edge"} - for attr, value in G.graph.items(): - yield from stringize(attr, value, ignored_keys, " ") - - # Output node data - node_id = dict(zip(G, range(len(G)))) - ignored_keys = {"id", "label"} - for node, attrs in G.nodes.items(): - yield " node [" - yield " id " + str(node_id[node]) - yield from stringize("label", node, (), " ") - for attr, value in attrs.items(): - yield from stringize(attr, value, ignored_keys, " ") - yield " ]" - - # Output edge data - ignored_keys = {"source", "target"} - kwargs = {"data": True} - if multigraph: - ignored_keys.add("key") - kwargs["keys"] = True - for e in G.edges: - yield " edge [" - yield " source " + str(node_id[e[0]]) - yield " target " + str(node_id[e[1]]) - if multigraph: - yield from stringize("key", e[2], (), " ") - for attr, value in e[-1].items(): - yield from stringize(attr, value, ignored_keys, " ") - yield " ]" - yield "]" + valid_keys = re.compile("^[A-Za-z][0-9A-Za-z_]*$") + + def stringize(key, value, ignored_keys, indent, in_list=False): + if not isinstance(key, str): + raise EasyGraphError(f"{key!r} is not a string") + if not valid_keys.match(key): + raise EasyGraphError(f"{key!r} is not a valid key") + if not isinstance(key, str): + key = str(key) + if key not in ignored_keys: + if isinstance(value, (int, bool)): + if key == "label": + yield indent + key + ' "' + str(value) + '"' + elif value is True: + # python bool is an instance of int + yield indent + key + " 1" + elif value is False: + yield indent + key + " 0" + # GML only supports signed 32-bit integers + elif value < -(2**31) or value >= 2**31: + yield indent + key + ' "' + str(value) + '"' + else: + yield indent + key + " " + str(value) + elif isinstance(value, float): + text = repr(value).upper() + # GML matches INF to keys, so prepend + to INF. Use repr(float(*)) + # instead of string literal to future proof against changes to repr. + if text == repr(float("inf")).upper(): + text = "+" + text + else: + # GML requires that a real literal contain a decimal point, but + # repr may not output a decimal point when the mantissa is + # integral and hence needs fixing. + epos = text.rfind("E") + if epos != -1 and text.find(".", 0, epos) == -1: + text = text[:epos] + "." + text[epos:] + if key == "label": + yield indent + key + ' "' + text + '"' + else: + yield indent + key + " " + text + elif isinstance(value, dict): + yield indent + key + " [" + next_indent = indent + " " + for key, value in value.items(): + yield from stringize(key, value, (), next_indent) + yield indent + "]" + elif ( + isinstance(value, (list, tuple)) + and key != "label" + and value + and not in_list + ): + if len(value) == 1: + yield indent + key + " " + f'"{LIST_START_VALUE}"' + for val in value: + yield from stringize(key, val, (), indent, True) + else: + if stringizer: + try: + value = stringizer(value) + except ValueError as err: + raise EasyGraphError( + f"{value!r} cannot be converted into a string" + ) from err + if not isinstance(value, str): + raise EasyGraphError(f"{value!r} is not a string") + yield indent + key + ' "' + escape(value) + '"' + + yield "graph [" + + # Output graph attributes + multigraph = G.is_multigraph() + if G.is_directed(): + yield " directed 1" + if multigraph: + yield " multigraph 1" + ignored_keys = {"directed", "multigraph", "node", "edge"} + for attr, value in G.graph.items(): + yield from stringize(attr, value, ignored_keys, " ") + + # Output node data + node_id = dict(zip(G, range(len(G)))) + ignored_keys = {"id", "label"} + for node, attrs in G.nodes.items(): + yield " node [" + yield " id " + str(node_id[node]) + yield from stringize("label", node, (), " ") + for attr, value in attrs.items(): + yield from stringize(attr, value, ignored_keys, " ") + yield " ]" + + # Output edge data + ignored_keys = {"source", "target"} + kwargs = {"data": True} + if multigraph: + ignored_keys.add("key") + kwargs["keys"] = True + for e in G.edges: + yield " edge [" + yield " source " + str(node_id[e[0]]) + yield " target " + str(node_id[e[1]]) + if multigraph: + yield from stringize("key", e[2], (), " ") + for attr, value in e[-1].items(): + yield from stringize(attr, value, ignored_keys, " ") + yield " ]" + yield "]" @open_file(0, mode="rb") def read_gml(path, label="label", destringizer=None): - """Read graph in GML format from `path`. + """Read graph in GML format from `path`. Parameters ---------- @@ -638,25 +633,25 @@ def read_gml(path, label="label", destringizer=None): """ - def filter_lines(lines): - for line in lines: - try: - line = line.decode("ascii") - except UnicodeDecodeError as err: - raise EasyGraphError("input is not ASCII-encoded") from err - if not isinstance(line, str): - lines = str(lines) - if line and line[-1] == "\n": - line = line[:-1] - yield line + def filter_lines(lines): + for line in lines: + try: + line = line.decode("ascii") + except UnicodeDecodeError as err: + raise EasyGraphError("input is not ASCII-encoded") from err + if not isinstance(line, str): + lines = str(lines) + if line and line[-1] == "\n": + line = line[:-1] + yield line - G = parse_gml_lines(filter_lines(path), label, destringizer) - return G + G = parse_gml_lines(filter_lines(path), label, destringizer) + return G @open_file(1, mode="wb") def write_gml(G, path, stringizer=None): - """Write a graph `G` in GML format to the file or file handle `path`. + """Write a graph `G` in GML format to the file or file handle `path`. Parameters ---------- @@ -715,12 +710,11 @@ def write_gml(G, path, stringizer=None): >>> eg.write_gml(G, "test.gml.gz") """ - for line in generate_gml(G, stringizer): - path.write((line + "\n").encode("ascii")) + for line in generate_gml(G, stringizer): + path.write((line + "\n").encode("ascii")) def literal_stringizer(value): - def stringize(value): if isinstance(value, (int, bool)) or value is None: if value is True: # GML uses 1/0 for boolean values. diff --git a/easygraph/readwrite/graphml.py b/easygraph/readwrite/graphml.py index 34569f5b..98edd0d5 100644 --- a/easygraph/readwrite/graphml.py +++ b/easygraph/readwrite/graphml.py @@ -42,15 +42,12 @@ """ import warnings - from collections import defaultdict import easygraph as eg - from easygraph.utils import open_file from easygraph.utils.exception import EasyGraphError - __all__ = [ "write_graphml", "read_graphml", @@ -850,8 +847,7 @@ def __init__(self, node_type=str, edge_key_type=int, force_multigraph=False): self.edge_ids = {} # dict mapping (u,v) tuples to edge id attributes def __call__(self, path=None, string=None): - from xml.etree.ElementTree import ElementTree - from xml.etree.ElementTree import fromstring + from xml.etree.ElementTree import ElementTree, fromstring if path is not None: self.xml = ElementTree(file=path) diff --git a/easygraph/readwrite/graphviz.py b/easygraph/readwrite/graphviz.py index cc03ceaf..e3771b20 100644 --- a/easygraph/readwrite/graphviz.py +++ b/easygraph/readwrite/graphviz.py @@ -1,6 +1,5 @@ import easygraph as eg - __all__ = ["write_dot", "read_dot", "from_agraph", "to_agraph"] diff --git a/easygraph/readwrite/pajek.py b/easygraph/readwrite/pajek.py index f90ab827..493231a9 100644 --- a/easygraph/readwrite/pajek.py +++ b/easygraph/readwrite/pajek.py @@ -60,7 +60,6 @@ # import networkx as nx from easygraph.utils import open_file - __all__ = ["read_pajek", "parse_pajek", "generate_pajek", "write_pajek"] diff --git a/easygraph/readwrite/tests/test_gexf.py b/easygraph/readwrite/tests/test_gexf.py index 896a57a6..dd5eff92 100644 --- a/easygraph/readwrite/tests/test_gexf.py +++ b/easygraph/readwrite/tests/test_gexf.py @@ -2,9 +2,10 @@ import sys import time -import easygraph as eg import pytest +import easygraph as eg + class TestGEXF: @classmethod @@ -275,7 +276,7 @@ def test_edge_id_construct(self): expected = f""" - + EasyGraph @@ -306,7 +307,7 @@ def test_numpy_type(self): xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation\ ="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd"\ version="1.2"> - + EasyGraph diff --git a/easygraph/readwrite/tests/test_gml.py b/easygraph/readwrite/tests/test_gml.py index 45946d1f..6180f015 100644 --- a/easygraph/readwrite/tests/test_gml.py +++ b/easygraph/readwrite/tests/test_gml.py @@ -2,16 +2,14 @@ import io import os import tempfile - from ast import literal_eval from contextlib import contextmanager from textwrap import dedent -import easygraph as eg import pytest -from easygraph.readwrite.gml import literal_destringizer -from easygraph.readwrite.gml import literal_stringizer +import easygraph as eg +from easygraph.readwrite.gml import literal_destringizer, literal_stringizer class TestGraph: @@ -269,9 +267,9 @@ def test_float_label(self): def test_name(self): G = eg.parse_gml('graph [ name "x" node [ id 0 label "x" ] ]') - assert "x" == G.graph["name"] + assert G.graph["name"] == "x" G = eg.parse_gml('graph [ node [ id 0 label "x" ] ]') - assert "" == G.name + assert G.name == "" assert "name" not in G.graph def test_graph_types(self): diff --git a/easygraph/readwrite/tests/test_graphml.py b/easygraph/readwrite/tests/test_graphml.py index a3a58c92..bcb0ef52 100644 --- a/easygraph/readwrite/tests/test_graphml.py +++ b/easygraph/readwrite/tests/test_graphml.py @@ -2,12 +2,11 @@ import os import tempfile -import easygraph as eg import pytest +import easygraph as eg from easygraph.readwrite.graphml import GraphMLWriter -from easygraph.utils import edges_equal -from easygraph.utils import nodes_equal +from easygraph.utils import edges_equal, nodes_equal class BaseGraphML: diff --git a/easygraph/readwrite/tests/test_graphviz.py b/easygraph/readwrite/tests/test_graphviz.py index bac33144..1ed5813b 100644 --- a/easygraph/readwrite/tests/test_graphviz.py +++ b/easygraph/readwrite/tests/test_graphviz.py @@ -3,13 +3,10 @@ import pytest - pygraphviz = pytest.importorskip("pygraphviz") import easygraph as eg - -from easygraph.utils import edges_equal -from easygraph.utils import nodes_equal +from easygraph.utils import edges_equal, nodes_equal class TestAGraph: diff --git a/easygraph/readwrite/tests/test_pajek.py b/easygraph/readwrite/tests/test_pajek.py index b21d4b33..6942b702 100644 --- a/easygraph/readwrite/tests/test_pajek.py +++ b/easygraph/readwrite/tests/test_pajek.py @@ -40,16 +40,14 @@ """ Pajek tests """ -import easygraph as eg +import easygraph as eg print(eg) import os import tempfile -from easygraph.utils import edges_equal -from easygraph.utils import nodes_equal - +from easygraph.utils import edges_equal, nodes_equal # from rich import print diff --git a/easygraph/readwrite/tests/test_pickle.py b/easygraph/readwrite/tests/test_pickle.py index 91165f12..106540aa 100644 --- a/easygraph/readwrite/tests/test_pickle.py +++ b/easygraph/readwrite/tests/test_pickle.py @@ -8,7 +8,6 @@ import tempfile import easygraph as eg - from easygraph.utils import edges_equal diff --git a/easygraph/readwrite/tests/test_ucinet.py b/easygraph/readwrite/tests/test_ucinet.py index cfbf7539..39ff2eda 100644 --- a/easygraph/readwrite/tests/test_ucinet.py +++ b/easygraph/readwrite/tests/test_ucinet.py @@ -7,7 +7,6 @@ import easygraph as eg - def filterEdges(edges): return [e[:3] for e in edges] diff --git a/easygraph/readwrite/ucinet.py b/easygraph/readwrite/ucinet.py index 99b080ae..6fbd6b50 100644 --- a/easygraph/readwrite/ucinet.py +++ b/easygraph/readwrite/ucinet.py @@ -21,16 +21,14 @@ for full format information. Short version on http://www.analytictech.com/networks/dataentry.htm """ - import re import shlex -import easygraph as eg import numpy as np +import easygraph as eg from easygraph.utils import open_file - __all__ = ["generate_ucinet", "read_ucinet", "parse_ucinet", "write_ucinet"] @@ -67,9 +65,13 @@ def generate_ucinet(G): yield "data:" - yield str(np.asmatrix(eg.to_numpy_array(G, nodelist=nodes, dtype=int))).replace( - "[", " " - ).replace("]", " ").lstrip().rstrip() + yield ( + str(np.asmatrix(eg.to_numpy_array(G, nodelist=nodes, dtype=int))) + .replace("[", " ") + .replace("]", " ") + .lstrip() + .rstrip() + ) @open_file(0, mode="rb") @@ -85,11 +87,11 @@ def read_ucinet(path, encoding="UTF-8"): G : EasyGraph MultiGraph or MultiDiGraph. Examples -------- - >>> G=eg.path_graph(4) + >>> G = eg.path_graph(4) >>> eg.write_ucinet(G, "test.dl") - >>> G=eg.read_ucinet("test.dl") + >>> G = eg.read_ucinet("test.dl") To create a Graph instead of a MultiGraph use - >>> G1=eg.Graph(G) + >>> G1 = eg.Graph(G) See Also -------- parse_ucinet() @@ -114,7 +116,7 @@ def write_ucinet(G, path, encoding="UTF-8"): Filenames ending in .gz or .bz2 will be compressed. Examples -------- - >>> G=eg.path_graph(4) + >>> G = eg.path_graph(4) >>> eg.write_ucinet(G, "test.net") References ---------- @@ -144,9 +146,7 @@ def parse_ucinet(lines): See UCINET User Guide or http://www.analytictech.com/ucinet/help/hs5000.htm for full format information. Short version on http://www.analytictech.com/networks/dataentry.htm """ - from numpy import genfromtxt - from numpy import isnan - from numpy import reshape + from numpy import genfromtxt, isnan, reshape G = eg.MultiDiGraph() @@ -206,9 +206,7 @@ def parse_ucinet(lines): ) # TODO : row and columns labels - elif token.startswith("row"): # Row labels - pass - elif token.startswith("column"): # Columns labels + elif token.startswith("row") or token.startswith("column"): # Row labels pass elif token.startswith("labels"): diff --git a/easygraph/tests/test_convert.py b/easygraph/tests/test_convert.py index c237c57d..1443ec5e 100644 --- a/easygraph/tests/test_convert.py +++ b/easygraph/tests/test_convert.py @@ -1,12 +1,10 @@ import pytest - np = pytest.importorskip("numpy") pd = pytest.importorskip("pandas") sp = pytest.importorskip("scipy") import easygraph as eg - from easygraph.utils.misc import * diff --git a/easygraph/utils/convert_to_matrix.py b/easygraph/utils/convert_to_matrix.py index 8e005212..ca9816ad 100644 --- a/easygraph/utils/convert_to_matrix.py +++ b/easygraph/utils/convert_to_matrix.py @@ -2,7 +2,6 @@ import easygraph as eg - __all__ = [ "to_numpy_matrix", "from_numpy_array", diff --git a/easygraph/utils/decorators.py b/easygraph/utils/decorators.py index a685547a..43d522cf 100644 --- a/easygraph/utils/decorators.py +++ b/easygraph/utils/decorators.py @@ -3,16 +3,13 @@ import gzip import inspect import re - from collections import defaultdict from os.path import splitext from pathlib import Path import easygraph as eg - from easygraph.utils.exception import EasyGraphError - __all__ = [ "only_implemented_for_UnDirected_graph", "only_implemented_for_Directed_graph", @@ -63,11 +60,13 @@ def not_implemented_for(*graph_types): def sp_function(G): pass + # rule out MultiDiGraph - @not_implemented_for("directed","multigraph") + @not_implemented_for("directed", "multigraph") def sp_np_function(G): pass + # rule out all except DiGraph @not_implemented_for("undirected") @not_implemented_for("multigraph") @@ -130,22 +129,26 @@ def open_file(path_arg, mode="r"): -------- Decorate functions like this:: - @open_file(0,"r") + @open_file(0, "r") def read_function(pathname): pass - @open_file(1,"w") + + @open_file(1, "w") def write_function(G, pathname): pass - @open_file(1,"w") + + @open_file(1, "w") def write_function(G, pathname="graph.dot"): pass - @open_file("pathname","w") + + @open_file("pathname", "w") def write_function(G, pathname="graph.dot"): pass + @open_file("path", "w+") def another_function(arg, **kwargs): path = kwargs["path"] @@ -161,19 +164,19 @@ def another_function(arg, **kwargs): @open_file("path") def some_function(arg1, arg2, path=None): - if path is None: - fobj = tempfile.NamedTemporaryFile(delete=False) - else: - # `path` could have been a string or file object or something - # similar. In any event, the decorator has given us a file object - # and it will close it for us, if it should. - fobj = path - - try: - fobj.write("blah") - finally: - if path is None: - fobj.close() + if path is None: + fobj = tempfile.NamedTemporaryFile(delete=False) + else: + # `path` could have been a string or file object or something + # similar. In any event, the decorator has given us a file object + # and it will close it for us, if it should. + fobj = path + + try: + fobj.write("blah") + finally: + if path is None: + fobj.close() Normally, we'd want to use "with" to ensure that fobj gets closed. However, the decorator will make `path` a file object for us, @@ -256,6 +259,7 @@ def _convert(amount): if amount.currency != currency: amount = amount.to_currency(currency) return amount + return argmap(_convert, which_arg) Despite this common idiom for argmap, most of the following examples @@ -315,10 +319,12 @@ def foo(a, b, c): def double(a): return 2 * a + @argmap(double, 3) def overflow(a, *args): return a, args + print(overflow(1, 2, 3, 4, 5, 6)) # output is 1, (2, 3, 8, 5, 6) **Try Finally** @@ -368,6 +374,7 @@ def _opener(path): # assume `path` handles the closing fclose = lambda: None return path, fclose + return argmap(_opener, which_arg, try_finally=True) which can then be used as:: @@ -925,7 +932,7 @@ def signature(cls, f): def_sig.append(name) fname = cls._name(f) - def_sig = f'def {fname}({", ".join(def_sig)}):' + def_sig = f"def {fname}({', '.join(def_sig)}):" if inspect.isgeneratorfunction(f): _return = "yield from" diff --git a/easygraph/utils/exception.py b/easygraph/utils/exception.py index de7d5f95..ffa286cb 100644 --- a/easygraph/utils/exception.py +++ b/easygraph/utils/exception.py @@ -6,7 +6,6 @@ Base exceptions and errors for EasyGraph. """ - __all__ = ["EasyGraphException", "EasyGraphError", "EasyGraphNotImplemented"] diff --git a/easygraph/utils/mapped_queue.py b/easygraph/utils/mapped_queue.py index 301e6958..9a76872b 100644 --- a/easygraph/utils/mapped_queue.py +++ b/easygraph/utils/mapped_queue.py @@ -3,10 +3,8 @@ Codes from NetworkX - http://networkx.github.io/ """ - import heapq - __all__ = ["MappedQueue"] diff --git a/easygraph/utils/misc.py b/easygraph/utils/misc.py index 61ecac7e..ea5eabb7 100644 --- a/easygraph/utils/misc.py +++ b/easygraph/utils/misc.py @@ -1,32 +1,30 @@ -from itertools import chain -from itertools import tee - +from itertools import chain, tee __all__ = ["split_len", "split", "nodes_equal", "edges_equal", "pairwise"] def split_len(nodes, step=30000): - ret = [] - length = len(nodes) - for i in range(0, length, step): - ret.append(nodes[i : i + step]) - if len(ret[-1]) * 3 < step: - ret[-2] = ret[-2] + ret[-1] - ret = ret[:-1] - return ret + ret = [] + length = len(nodes) + for i in range(0, length, step): + ret.append(nodes[i : i + step]) + if len(ret[-1]) * 3 < step: + ret[-2] = ret[-2] + ret[-1] + ret = ret[:-1] + return ret def split(nodes, n): - ret = [] - length = len(nodes) # 总长 - step = int(length / n) + 1 # 每份的长度 - for i in range(0, length, step): - ret.append(nodes[i : i + step]) - return ret + ret = [] + length = len(nodes) # 总长 + step = int(length / n) + 1 # 每份的长度 + for i in range(0, length, step): + ret.append(nodes[i : i + step]) + return ret def nodes_equal(nodes1, nodes2): - """Check if nodes are equal. + """Check if nodes are equal. Equality here means equal as Python objects. Node data must match if included. @@ -41,19 +39,19 @@ def nodes_equal(nodes1, nodes2): bool True if nodes are equal, False otherwise. """ - nlist1 = list(nodes1) - nlist2 = list(nodes2) - try: - d1 = dict(nlist1) - d2 = dict(nlist2) - except (ValueError, TypeError): - d1 = dict.fromkeys(nlist1) - d2 = dict.fromkeys(nlist2) - return d1 == d2 + nlist1 = list(nodes1) + nlist2 = list(nodes2) + try: + d1 = dict(nlist1) + d2 = dict(nlist2) + except (ValueError, TypeError): + d1 = dict.fromkeys(nlist1) + d2 = dict.fromkeys(nlist2) + return d1 == d2 def edges_equal(edges1, edges2, need_data=True): - """Check if edges are equal. + """Check if edges are equal. Equality here means equal as Python objects. Edge data must match if included. @@ -71,51 +69,51 @@ def edges_equal(edges1, edges2, need_data=True): bool True if edges are equal, False otherwise. """ - from collections import defaultdict - - d1 = defaultdict(dict) - d2 = defaultdict(dict) - c1 = 0 - for c1, e in enumerate(edges1): - u, v = e[0], e[1] - data = [] - if need_data: - data = [e[2:]] - if v in d1[u]: - data = d1[u][v] + data - d1[u][v] = data - d1[v][u] = data - c2 = 0 - for c2, e in enumerate(edges2): - u, v = e[0], e[1] - data = [] - if need_data: - data = [e[2:]] - if v in d2[u]: - data = d2[u][v] + data - d2[u][v] = data - d2[v][u] = data - if c1 != c2: - return False - # can check one direction because lengths are the same. - for n, nbrdict in d1.items(): - for nbr, datalist in nbrdict.items(): - if n not in d2: - return False - if nbr not in d2[n]: - return False - d2datalist = d2[n][nbr] - for data in datalist: - if datalist.count(data) != d2datalist.count(data): - return False - return True + from collections import defaultdict + + d1 = defaultdict(dict) + d2 = defaultdict(dict) + c1 = 0 + for c1, e in enumerate(edges1): + u, v = e[0], e[1] + data = [] + if need_data: + data = [e[2:]] + if v in d1[u]: + data = d1[u][v] + data + d1[u][v] = data + d1[v][u] = data + c2 = 0 + for c2, e in enumerate(edges2): + u, v = e[0], e[1] + data = [] + if need_data: + data = [e[2:]] + if v in d2[u]: + data = d2[u][v] + data + d2[u][v] = data + d2[v][u] = data + if c1 != c2: + return False + # can check one direction because lengths are the same. + for n, nbrdict in d1.items(): + for nbr, datalist in nbrdict.items(): + if n not in d2: + return False + if nbr not in d2[n]: + return False + d2datalist = d2[n][nbr] + for data in datalist: + if datalist.count(data) != d2datalist.count(data): + return False + return True # Recipe from the itertools documentation. def pairwise(iterable, cyclic=False): - "s -> (s0, s1), (s1, s2), (s2, s3), ..." - a, b = tee(iterable) - first = next(b, None) - if cyclic is True: - return zip(a, chain(b, (first,))) - return zip(a, b) + "s -> (s0, s1), (s1, s2), (s2, s3), ..." + a, b = tee(iterable) + first = next(b, None) + if cyclic is True: + return zip(a, chain(b, (first,))) + return zip(a, b) diff --git a/easygraph/utils/tests/test_convert_to_matrix.py b/easygraph/utils/tests/test_convert_to_matrix.py index 59fc645d..e38a63ab 100644 --- a/easygraph/utils/tests/test_convert_to_matrix.py +++ b/easygraph/utils/tests/test_convert_to_matrix.py @@ -1,8 +1,9 @@ import unittest -import easygraph as eg import numpy as np +import easygraph as eg + class ConvertToMatrix(unittest.TestCase): def test_to_numpy_matrix(self): diff --git a/easygraph/utils/type_change.py b/easygraph/utils/type_change.py index 187b2290..c0564fda 100644 --- a/easygraph/utils/type_change.py +++ b/easygraph/utils/type_change.py @@ -1,6 +1,5 @@ import easygraph as eg - __all__ = [ "from_pyGraphviz_agraph", "to_pyGraphviz_agraph", diff --git a/pyproject.toml b/pyproject.toml index 48e8ffd1..33fe5c0d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -101,6 +101,17 @@ ignore = [ # per-file-ignores = { "tests/**.py" = ["S101"] } # —— 各插件的细化配置 —— # +[tool.ruff.format] +# 字符串引号风格: "double" | "single | "preserve" +quote-style = "double" +# 是否在多行字典/列表/元组的最后一项加逗号 +skip-magic-trailing-comma = false +# 是否格式化 docstring（会重新换行） +docstring-code-format = true +# 是否在文件末尾强制留一个换行符 +line-ending = "auto" # auto | lf | crlf | cr +# 控制格式化时是否保留空行 +indent-style = "space" # 只支持 space（未来可能扩展 tab） [tool.ruff.lint.flake8-quotes] # 原 flake8: inline-quotes = double @@ -117,11 +128,6 @@ ban-relative-imports = "all" # 原: type-checking-exempt-modules = typing, typing-extensions exempt-modules = ["typing", "typing_extensions"] -# eradicate（清理注释死码） -[tool.ruff.lint.flake8-eradicate] -# 原 flake8-eradicate 的 whitelist-extend 在 Ruff 中没有等价项； -# 如果你需要排除某些模式，建议用 per-file-ignores 或者在 ERA 里关闭对应规则。 -# aggressive = true #（可选）更激进清理 [tool.tox] # 定义通用配置 diff --git a/scripts/archive/check_installation.py b/scripts/archive/check_installation.py index db73247a..f43da7bf 100755 --- a/scripts/archive/check_installation.py +++ b/scripts/archive/check_installation.py @@ -3,7 +3,6 @@ import easygraph as eg - G = eg.Graph() G.add_edge(1, 2) From 9f3624985c66966d82a9d92040aba029afc58ac8 Mon Sep 17 00:00:00 2001 From: acture Date: Tue, 21 Oct 2025 17:09:33 +0800 Subject: [PATCH 17/17] refactor(core): replace redundant exception handling with `contextlib.suppress` - Replaced `try-except` blocks catching generic exceptions with `contextlib.suppress` for improved readability and performance. - Modified default mutable arguments (`{}` and `[]`) to `None` with proper initialization to prevent unintended side effects. - Simplified `for` loop variables by prefixing unused ones with an underscore (`_`). - Refactored conditional logic to use explicit boolean checks (`if not ...` for clarity). - Updated `dict.keys()` and `dict.items()` iterations to directly iterate over dictionary views. - Standardized function imports to ensure consistency by eliminating relative imports where applicable. These updates improve readability, reduce potential bugs, and align the codebase with Python best practices. Signed-off-by: acture --- easygraph/classes/__init__.py | 12 ++-- easygraph/classes/directed_graph.py | 39 +++++++------ easygraph/classes/directed_multigraph.py | 2 +- easygraph/classes/graph.py | 35 ++++++----- easygraph/classes/multigraph.py | 5 +- easygraph/classes/operation.py | 31 +++------- easygraph/convert.py | 6 +- easygraph/datasets/get_sample_graph.py | 2 +- easygraph/functions/centrality/__init__.py | 8 +-- easygraph/functions/centrality/betweenness.py | 5 +- .../functions/centrality/flowbetweenness.py | 9 +-- easygraph/functions/community/LPA.py | 58 +++++++++---------- easygraph/functions/community/__init__.py | 8 +-- .../community/modularity_max_detection.py | 10 +--- easygraph/functions/components/__init__.py | 6 +- easygraph/functions/components/biconnected.py | 5 +- .../functions/components/ego_betweenness.py | 2 +- easygraph/functions/drawing/__init__.py | 6 +- easygraph/functions/drawing/drawing.py | 2 +- easygraph/functions/drawing/plot.py | 4 +- easygraph/functions/drawing/positioning.py | 20 +++---- .../drawing/tests/test_positioning.py | 2 +- easygraph/functions/graph_embedding/NOBE.py | 2 +- .../functions/graph_embedding/__init__.py | 10 ++-- .../functions/graph_embedding/deepwalk.py | 2 +- .../functions/graph_embedding/node2vec.py | 3 +- easygraph/functions/graph_embedding/sdne.py | 8 ++- .../graph_generator/RandomNetwork.py | 7 +-- .../functions/graph_generator/__init__.py | 4 +- easygraph/functions/not_sorted/__init__.py | 10 ++-- easygraph/functions/not_sorted/bridges.py | 4 +- easygraph/functions/not_sorted/cluster.py | 5 +- easygraph/functions/not_sorted/laplacian.py | 4 +- easygraph/functions/not_sorted/mst.py | 4 +- easygraph/functions/not_sorted/pagerank.py | 2 +- easygraph/functions/path/__init__.py | 2 +- easygraph/functions/path/path.py | 8 +-- .../functions/structural_holes/AP_Greedy.py | 10 ++-- easygraph/functions/structural_holes/HAM.py | 7 +-- easygraph/functions/structural_holes/ICC.py | 2 +- easygraph/functions/structural_holes/MaxD.py | 13 ++--- .../functions/structural_holes/SHII_metric.py | 23 ++++---- .../functions/structural_holes/__init__.py | 20 +++---- .../functions/structural_holes/evaluation.py | 5 +- .../functions/structural_holes/maxBlock.py | 12 ++-- .../functions/structural_holes/metrics.py | 23 ++++---- .../functions/structural_holes/weakTie.py | 7 +-- easygraph/readwrite/edgelist.py | 7 +-- easygraph/readwrite/gexf.py | 29 +++------- easygraph/readwrite/gml.py | 16 ++--- easygraph/readwrite/graphml.py | 38 +++++------- easygraph/readwrite/graphviz.py | 10 +--- easygraph/readwrite/pajek.py | 16 ++--- easygraph/readwrite/tests/test_gexf.py | 2 +- easygraph/readwrite/tests/test_graphml.py | 17 +++--- easygraph/readwrite/tests/test_graphviz.py | 2 +- easygraph/readwrite/tests/test_pajek.py | 2 +- easygraph/readwrite/tests/test_ucinet.py | 9 --- easygraph/readwrite/ucinet.py | 24 +++----- easygraph/utils/convert_to_matrix.py | 26 ++++----- easygraph/utils/decorators.py | 5 +- easygraph/utils/mapped_queue.py | 4 +- easygraph/utils/misc.py | 4 +- easygraph/utils/relabel.py | 5 +- easygraph/utils/type_change.py | 10 +--- 65 files changed, 297 insertions(+), 403 deletions(-) diff --git a/easygraph/classes/__init__.py b/easygraph/classes/__init__.py index 88a0da96..ec2b4b6a 100644 --- a/easygraph/classes/__init__.py +++ b/easygraph/classes/__init__.py @@ -1,6 +1,6 @@ -from .directed_graph import DiGraph -from .directed_multigraph import MultiDiGraph -from .graph import Graph, GraphC -from .graphviews import * -from .multigraph import MultiGraph -from .operation import * +from easygraph.classes.directed_graph import DiGraph +from easygraph.classes.directed_multigraph import MultiDiGraph +from easygraph.classes.graph import Graph, GraphC +from easygraph.classes.graphviews import * +from easygraph.classes.multigraph import MultiGraph +from easygraph.classes.operation import * diff --git a/easygraph/classes/directed_graph.py b/easygraph/classes/directed_graph.py index c877bbe9..24f80805 100644 --- a/easygraph/classes/directed_graph.py +++ b/easygraph/classes/directed_graph.py @@ -1,3 +1,6 @@ +import builtins +import contextlib + import easygraph.convert as convert from easygraph.classes.graph import Graph from easygraph.utils.exception import EasyGraphError @@ -142,7 +145,7 @@ def out_degree(self, weight="weight"): """ degree = dict() - for u, v, d in self.edges: + for u, _v, d in self.edges: if u in degree: degree[u] += d.get(weight, 1) else: @@ -184,7 +187,7 @@ def in_degree(self, weight="weight"): """ degree = dict() - for u, v, d in self.edges: + for _u, v, d in self.edges: if v in degree: degree[v] += d.get(weight, 1) else: @@ -502,7 +505,7 @@ def add_node(self, node_for_adding, **node_attr): """ self._add_one_node(node_for_adding, node_attr) - def add_nodes(self, nodes_for_adding: list, nodes_attr: list[dict] = []): + def add_nodes(self, nodes_for_adding: list, nodes_attr: list[dict] = None): """Add nodes with a list of nodes. Parameters @@ -537,7 +540,9 @@ def add_nodes(self, nodes_for_adding: list, nodes_attr: list[dict] = []): """ if nodes_attr is None: nodes_attr = [] - if not len(nodes_attr) == 0: # Nodes attributes included in input + if nodes_attr is None: + nodes_attr = [] + if len(nodes_attr) != 0: # Nodes attributes included in input assert len(nodes_for_adding) == len(nodes_attr), ( "Nodes and Attributes lists must have same length." ) @@ -612,7 +617,9 @@ def add_nodes_from(self, nodes_for_adding, **attr): self._node[n] = self.node_attr_dict_factory() self._node[n].update(newdict) - def _add_one_node(self, one_node_for_adding, node_attr: dict = {}): + def _add_one_node(self, one_node_for_adding, node_attr: dict = None): + if node_attr is None: + node_attr = {} node = one_node_for_adding if node not in self._node: self._adj[node] = self.adjlist_inner_dict_factory() @@ -661,7 +668,7 @@ def add_edge(self, u_of_edge, v_of_edge, **edge_attr): def add_weighted_edge(self, u_of_edge, v_of_edge, weight): self._add_one_edge(u_of_edge, v_of_edge, edge_attr={"weight": weight}) - def add_edges(self, edges_for_adding, edges_attr: list[dict] = []): + def add_edges(self, edges_for_adding, edges_attr: list[dict] = None): """Add a list of edges. Parameters @@ -686,7 +693,9 @@ def add_edges(self, edges_for_adding, edges_attr: list[dict] = []): """ if edges_attr is None: edges_attr = [] - if not len(edges_attr) == 0: # Edges attributes included in input + if edges_attr is None: + edges_attr = [] + if len(edges_attr) != 0: # Edges attributes included in input assert len(edges_for_adding) == len(edges_attr), ( "Edges and Attributes lists must have same length." ) @@ -809,20 +818,18 @@ def add_edges_from_file(self, file, weighted=False): for edge in edges: edge = re.sub(",", " ", edge) edge = edge.split() - try: + with contextlib.suppress(builtins.BaseException): self.add_edge(edge[0], edge[1], weight=float(edge[2])) - except: - pass else: for edge in edges: edge = re.sub(",", " ", edge) edge = edge.split() - try: + with contextlib.suppress(builtins.BaseException): self.add_edge(edge[0], edge[1]) - except: - pass - def _add_one_edge(self, u_of_edge, v_of_edge, edge_attr: dict = {}): + def _add_one_edge(self, u_of_edge, v_of_edge, edge_attr: dict = None): + if edge_attr is None: + edge_attr = {} u, v = u_of_edge, v_of_edge # add nodes if u not in self._node: @@ -1055,10 +1062,8 @@ def nodes_subgraph(self, from_nodes: list): G = self.__class__() G.graph.update(self.graph) for node in from_nodes: - try: + with contextlib.suppress(KeyError): G.add_node(node, **self._node[node]) - except KeyError: - pass # Edge from_nodes = set(from_nodes) diff --git a/easygraph/classes/directed_multigraph.py b/easygraph/classes/directed_multigraph.py index 66a6dfd5..76ff6f3e 100644 --- a/easygraph/classes/directed_multigraph.py +++ b/easygraph/classes/directed_multigraph.py @@ -244,7 +244,7 @@ def in_edges(self): edges = list() for n, nbrs in self._adj.items(): for nbr, kd in nbrs.items(): - for k, dd in kd.items(): + for k, _dd in kd.items(): edges.append((nbr, n, k)) return edges diff --git a/easygraph/classes/graph.py b/easygraph/classes/graph.py index 598835de..1f373c49 100644 --- a/easygraph/classes/graph.py +++ b/easygraph/classes/graph.py @@ -1,3 +1,6 @@ +import builtins +import contextlib + import easygraph.convert as convert from easygraph.utils.exception import EasyGraphError @@ -390,7 +393,7 @@ def add_node(self, node_for_adding, **node_attr): """ self._add_one_node(node_for_adding, node_attr) - def add_nodes(self, nodes_for_adding: list, nodes_attr: list[dict] = []): + def add_nodes(self, nodes_for_adding: list, nodes_attr: list[dict] = None): """Add nodes with a list of nodes. Parameters @@ -423,7 +426,9 @@ def add_nodes(self, nodes_for_adding: list, nodes_attr: list[dict] = []): ... ) """ - if not len(nodes_attr) == 0: # Nodes attributes included in input + if nodes_attr is None: + nodes_attr = [] + if len(nodes_attr) != 0: # Nodes attributes included in input assert len(nodes_for_adding) == len(nodes_attr), ( "Nodes and Attributes lists must have same length." ) @@ -497,7 +502,9 @@ def add_nodes_from(self, nodes_for_adding, **attr): self._node[n] = self.node_attr_dict_factory() self._node[n].update(newdict) - def _add_one_node(self, one_node_for_adding, node_attr: dict = {}): + def _add_one_node(self, one_node_for_adding, node_attr: dict = None): + if node_attr is None: + node_attr = {} node = one_node_for_adding if node not in self._node: self._adj[node] = self.adjlist_inner_dict_factory() @@ -544,7 +551,7 @@ def add_edge(self, u_of_edge, v_of_edge, **edge_attr): def add_weighted_edge(self, u_of_edge, v_of_edge, weight): self._add_one_edge(u_of_edge, v_of_edge, edge_attr={"weight": weight}) - def add_edges(self, edges_for_adding, edges_attr: list[dict] = []): + def add_edges(self, edges_for_adding, edges_attr: list[dict] = None): """Add a list of edges. Parameters @@ -569,7 +576,9 @@ def add_edges(self, edges_for_adding, edges_attr: list[dict] = []): """ if edges_attr is None: edges_attr = [] - if not len(edges_attr) == 0: # Edges attributes included in input + if edges_attr is None: + edges_attr = [] + if len(edges_attr) != 0: # Edges attributes included in input assert len(edges_for_adding) == len(edges_attr), ( "Edges and Attributes lists must have same length." ) @@ -690,20 +699,18 @@ def add_edges_from_file(self, file, weighted=False): for edge in edges: edge = re.sub(",", " ", edge) edge = edge.split() - try: + with contextlib.suppress(builtins.BaseException): self.add_edge(edge[0], edge[1], weight=float(edge[2])) - except: - pass else: for edge in edges: edge = re.sub(",", " ", edge) edge = edge.split() - try: + with contextlib.suppress(builtins.BaseException): self.add_edge(edge[0], edge[1]) - except: - pass - def _add_one_edge(self, u_of_edge, v_of_edge, edge_attr: dict = {}): + def _add_one_edge(self, u_of_edge, v_of_edge, edge_attr: dict = None): + if edge_attr is None: + edge_attr = {} u, v = u_of_edge, v_of_edge # add nodes if u not in self._node: @@ -898,10 +905,8 @@ def nodes_subgraph(self, from_nodes: list): G = self.__class__() G.graph.update(self.graph) for node in from_nodes: - try: + with contextlib.suppress(KeyError): G.add_node(node, **self._node[node]) - except KeyError: - pass # Edge from_nodes = set(from_nodes) diff --git a/easygraph/classes/multigraph.py b/easygraph/classes/multigraph.py index 86fcc56f..09549f96 100644 --- a/easygraph/classes/multigraph.py +++ b/easygraph/classes/multigraph.py @@ -1,5 +1,6 @@ """Base class for MultiGraph.""" +import contextlib from copy import deepcopy import easygraph as eg @@ -372,10 +373,8 @@ def remove_edges_from(self, ebunch): [] """ for e in ebunch: - try: + with contextlib.suppress(EasyGraphError): self.remove_edge(*e[:3]) - except EasyGraphError: - pass def has_edge(self, u, v, key=None): """Returns True if the graph has an edge between nodes u and v. diff --git a/easygraph/classes/operation.py b/easygraph/classes/operation.py index 95529417..3508914b 100644 --- a/easygraph/classes/operation.py +++ b/easygraph/classes/operation.py @@ -1,3 +1,4 @@ +import contextlib from itertools import chain import easygraph as eg @@ -12,10 +13,8 @@ "number_of_selfloops", "density", ] -try: +with contextlib.suppress(ImportError): from cpp_easygraph import cpp_density -except ImportError: - pass def set_edge_attributes(G, values, name=None): @@ -97,16 +96,12 @@ def set_edge_attributes(G, values, name=None): # if `values` is a dict using `.items()` => {edge: value} if G.is_multigraph(): for (u, v, key), value in values.items(): - try: + with contextlib.suppress(KeyError): G[u][v][key][name] = value - except KeyError: - pass else: for (u, v), value in values.items(): - try: + with contextlib.suppress(KeyError): G[u][v][name] = value - except KeyError: - pass except AttributeError: # treat `values` as a constant for u, v, data in G.edges: @@ -115,16 +110,12 @@ def set_edge_attributes(G, values, name=None): # `values` consists of doct-of-dict {edge: {attr: value}} shape if G.is_multigraph(): for (u, v, key), d in values.items(): - try: + with contextlib.suppress(KeyError): G[u][v][key].update(d) - except KeyError: - pass else: for (u, v), d in values.items(): - try: + with contextlib.suppress(KeyError): G[u][v].update(d) - except KeyError: - pass def add_path(G_to_add_to, nodes_for_path, **attr): @@ -243,20 +234,16 @@ def set_node_attributes(G, values, name=None): # Set node attributes based on type of `values` if name is not None: # `values` must not be a dict of dict try: # `values` is a dict - for n, v in values.items(): - try: + for n, _v in values.items(): + with contextlib.suppress(KeyError): G.nodes[n][name] = values[n] - except KeyError: - pass except AttributeError: # `values` is a constant for n in G: G.nodes[n][name] = values else: # `values` must be dict of dict for n, d in values.items(): - try: + with contextlib.suppress(KeyError): G.nodes[n].update(d) - except KeyError: - pass def topological_generations(G): diff --git a/easygraph/convert.py b/easygraph/convert.py index 8f3abd36..39a34faf 100644 --- a/easygraph/convert.py +++ b/easygraph/convert.py @@ -115,7 +115,7 @@ def to_easygraph_graph(data, create_using=None, multigraph_input=False): msg = "Input is not a correct Pandas DataFrame adjacency edge-list." raise eg.EasyGraphError(msg) from err except ImportError: - warnings.warn("pandas not found, skipping conversion test.", ImportWarning) + warnings.warn("pandas not found, skipping conversion test.", ImportWarning, stacklevel=2) # numpy matrix or ndarray try: @@ -129,7 +129,7 @@ def to_easygraph_graph(data, create_using=None, multigraph_input=False): "Input is not a correct numpy matrix or array." ) from err except ImportError: - warnings.warn("numpy not found, skipping conversion test.", ImportWarning) + warnings.warn("numpy not found, skipping conversion test.", ImportWarning, stacklevel=2) # scipy sparse matrix - any format try: @@ -141,7 +141,7 @@ def to_easygraph_graph(data, create_using=None, multigraph_input=False): "Input is not a correct scipy sparse matrix type." ) from err except ImportError: - warnings.warn("scipy not found, skipping conversion test.", ImportWarning) + warnings.warn("scipy not found, skipping conversion test.", ImportWarning, stacklevel=2) # Note: most general check - should remain last in order of execution # Includes containers (e.g. list, set, dict, etc.), generators, and diff --git a/easygraph/datasets/get_sample_graph.py b/easygraph/datasets/get_sample_graph.py index 169ddd4f..18f856f8 100644 --- a/easygraph/datasets/get_sample_graph.py +++ b/easygraph/datasets/get_sample_graph.py @@ -101,7 +101,7 @@ def sparse2graph(x): G = defaultdict(lambda: set()) cx = x.tocoo() - for i, j, v in zip(cx.row, cx.col, cx.data): + for i, j, _v in zip(cx.row, cx.col, cx.data, strict=False): G[i].add(j) return {str(k): [str(x) for x in v] for k, v in G.items()} diff --git a/easygraph/functions/centrality/__init__.py b/easygraph/functions/centrality/__init__.py index 4b077965..9458a9ae 100644 --- a/easygraph/functions/centrality/__init__.py +++ b/easygraph/functions/centrality/__init__.py @@ -1,4 +1,4 @@ -from .betweenness import * -from .clossness import * -from .degree import * -from .flowbetweenness import * +from easygraph.functions.centrality.betweenness import * +from easygraph.functions.centrality.clossness import * +from easygraph.functions.centrality.degree import * +from easygraph.functions.centrality.flowbetweenness import * diff --git a/easygraph/functions/centrality/betweenness.py b/easygraph/functions/centrality/betweenness.py index 5a5304c3..8442eb53 100644 --- a/easygraph/functions/centrality/betweenness.py +++ b/easygraph/functions/centrality/betweenness.py @@ -132,10 +132,7 @@ def _rescale(betweenness, n, normalized, directed=False, endpoints=False): else: scale = 1 / ((n - 1) * (n - 2)) else: # rescale by 2 for undirected graphs - if not directed: - scale = 0.5 - else: - scale = None + scale = 0.5 if not directed else None if scale is not None: for v in betweenness: betweenness[v] *= scale diff --git a/easygraph/functions/centrality/flowbetweenness.py b/easygraph/functions/centrality/flowbetweenness.py index 6311adaa..789ddb8d 100644 --- a/easygraph/functions/centrality/flowbetweenness.py +++ b/easygraph/functions/centrality/flowbetweenness.py @@ -44,7 +44,7 @@ def flowbetweenness_centrality(G): ----- A flow network is a directed graph where each edge has a capacity and each edge receives a flow. """ - if G.is_directed() == False: + if not G.is_directed(): print("Please input a directed graph") return flow_dict = NumberOfFlow(G) @@ -115,10 +115,7 @@ def edmonds_karp(G, source, sink): if u not in adj[v]: adj[v][u] = dict() flag = 1 - if flag == 1: - x = 0 - else: - x = adj[v][u].get("weight", 1) + x = 0 if flag == 1 else adj[v][u].get("weight", 1) adj[v][u].update({"weight": x}) adj[v][u]["weight"] += path_flow v = parent[v] @@ -138,7 +135,7 @@ def bfs(G, source, sink, parent, adj): if u not in adj: continue for v, attr in adj[u].items(): - if (visited[v] == False) and (attr.get("weight", 1) > 0): + if (not visited[v]) and (attr.get("weight", 1) > 0): queue.append(v) visited[v] = True parent[v] = u diff --git a/easygraph/functions/community/LPA.py b/easygraph/functions/community/LPA.py index 5c250d1f..2626a4d2 100644 --- a/easygraph/functions/community/LPA.py +++ b/easygraph/functions/community/LPA.py @@ -70,7 +70,7 @@ def LPA(G): label_dict = Next_label_dict if estimate_stop_cond(G, label_dict) is True: break - for node in label_dict.keys(): + for node in label_dict: label = label_dict[node] if label not in cluster_community: cluster_community[label] = [node] @@ -115,7 +115,7 @@ def SLPA(G, T, r): nodes = G.nodes adj = G.adj memory = {i: {i: 1} for i in nodes} - for i in range(0, T): + for _i in range(0, T): listenerslist = list(G.nodes) random.shuffle(listenerslist) for listener in listenerslist: @@ -255,37 +255,33 @@ def HANP(G, m, delta, threshod=1, hier_open=0, combine_open=0): ) score = min(score, score_dict[Next_label_dict[node]]) else: - if old_label == Next_label_dict[node]: - cdelta = 0 - else: - cdelta = delta + cdelta = 0 if old_label == Next_label_dict[node] else delta score_dict[Next_label_dict[node]] = UpdateScore( G, node, label_dict, score_dict, cdelta ) - if hier_open == 1 and combine_open == 1: - if old_score - score > 1 / 3: - old_score = score - ( - records, - G, - label_dict, - score_dict, - node_dict, - Next_label_dict, - nodes, - degrees, - distance_dict, - ) = CombineNodes( - records, - G, - label_dict, - score_dict, - node_dict, - Next_label_dict, - nodes, - degrees, - distance_dict, - ) + if hier_open == 1 and combine_open == 1 and old_score - score > 1 / 3: + old_score = score + ( + records, + G, + label_dict, + score_dict, + node_dict, + Next_label_dict, + nodes, + degrees, + distance_dict, + ) = CombineNodes( + records, + G, + label_dict, + score_dict, + node_dict, + Next_label_dict, + nodes, + degrees, + distance_dict, + ) label_dict = Next_label_dict if ( estimate_stop_cond_HANP(G, label_dict, score_dict, degrees, m, threshod) @@ -299,7 +295,7 @@ def HANP(G, m, delta, threshod=1, hier_open=0, combine_open=0): if loop_count > 20: break print("After %d iterations, HANP complete." % loop_count) - for node in label_dict.keys(): + for node in label_dict: label = label_dict[node] if label not in cluster_community: cluster_community[label] = [node] diff --git a/easygraph/functions/community/__init__.py b/easygraph/functions/community/__init__.py index 7836259a..0aabd0d7 100644 --- a/easygraph/functions/community/__init__.py +++ b/easygraph/functions/community/__init__.py @@ -1,4 +1,4 @@ -from .LPA import * -from .modularity import * -from .modularity_max_detection import * -from .motif import * +from easygraph.functions.community.LPA import * +from easygraph.functions.community.modularity import * +from easygraph.functions.community.modularity_max_detection import * +from easygraph.functions.community.motif import * diff --git a/easygraph/functions/community/modularity_max_detection.py b/easygraph/functions/community/modularity_max_detection.py index 518d170f..e2d988e2 100644 --- a/easygraph/functions/community/modularity_max_detection.py +++ b/easygraph/functions/community/modularity_max_detection.py @@ -137,17 +137,11 @@ def greedy_modularity_communities(G, weight="weight"): # Update rows j and k for row, col in [(j, k), (k, j)]: # Save old value for finding heap index - if k in j_set: - d_old = (-dq_dict[row][col], row, col) - else: - d_old = None + d_old = (-dq_dict[row][col], row, col) if k in j_set else None # Update dict for j,k only (i is removed below) dq_dict[row][col] = dq_jk # Save old max of per-row heap - if len(dq_heap[row]) > 0: - d_oldmax = dq_heap[row].h[0] - else: - d_oldmax = None + d_oldmax = dq_heap[row].h[0] if len(dq_heap[row]) > 0 else None # Add/update heaps d = (-dq_jk, row, col) if d_old is None: diff --git a/easygraph/functions/components/__init__.py b/easygraph/functions/components/__init__.py index d1770498..cb5a89b2 100644 --- a/easygraph/functions/components/__init__.py +++ b/easygraph/functions/components/__init__.py @@ -1,3 +1,3 @@ -from .biconnected import * -from .connected import * -from .ego_betweenness import * +from easygraph.functions.components.biconnected import * +from easygraph.functions.components.connected import * +from easygraph.functions.components.ego_betweenness import * diff --git a/easygraph/functions/components/biconnected.py b/easygraph/functions/components/biconnected.py index 7a1b6a56..7069d5fc 100644 --- a/easygraph/functions/components/biconnected.py +++ b/easygraph/functions/components/biconnected.py @@ -1,11 +1,10 @@ +import contextlib from itertools import chain from easygraph.utils import * -try: +with contextlib.suppress(ImportError): from cpp_easygraph import cpp_biconnected_dfs_record_edges -except ImportError: - pass __all__ = [ "is_biconnected", diff --git a/easygraph/functions/components/ego_betweenness.py b/easygraph/functions/components/ego_betweenness.py index ebf5e6ea..d07b7e3e 100644 --- a/easygraph/functions/components/ego_betweenness.py +++ b/easygraph/functions/components/ego_betweenness.py @@ -47,6 +47,6 @@ def ego_betweenness(G, node): for j in range(n): if i != j and C[i, j] == 1 and B[i, j] != 0: sum += 1.0 / B[i, j] - if flag == False: + if not flag: sum /= 2 return sum diff --git a/easygraph/functions/drawing/__init__.py b/easygraph/functions/drawing/__init__.py index 1d8f9532..af602304 100644 --- a/easygraph/functions/drawing/__init__.py +++ b/easygraph/functions/drawing/__init__.py @@ -1,3 +1,3 @@ -from .drawing import * -from .plot import * -from .positioning import * +from easygraph.functions.drawing.drawing import * +from easygraph.functions.drawing.plot import * +from easygraph.functions.drawing.positioning import * diff --git a/easygraph/functions/drawing/drawing.py b/easygraph/functions/drawing/drawing.py index 0b141967..83ffd7e9 100644 --- a/easygraph/functions/drawing/drawing.py +++ b/easygraph/functions/drawing/drawing.py @@ -353,7 +353,7 @@ def draw_kamada_kawai(G, rate=1, style="side"): """ pos = eg.kamada_kawai_layout(G) node = np.zeros((len(pos), 2), float) - m, n = 0, 0 + m, _n = 0, 0 if rate == 1: for i in pos: node[m][0] = pos[i][0] diff --git a/easygraph/functions/drawing/plot.py b/easygraph/functions/drawing/plot.py index 738a29aa..90a3ae60 100644 --- a/easygraph/functions/drawing/plot.py +++ b/easygraph/functions/drawing/plot.py @@ -37,7 +37,7 @@ def plot_Followers(G, SHS): degree = G.degree() sample1 = [] sample2 = [] - for i in degree.keys(): + for i in degree: if i in OU: sample1.append(degree[i]) elif i in SHS: @@ -141,7 +141,7 @@ def plot_Betweenness_Centrality(G, SHS): bc = eg.betweenness_centrality(G) sample1 = [] sample2 = [] - for i in bc.keys(): + for i in bc: if i in OU: sample1.append(bc[i]) elif i in SHS: diff --git a/easygraph/functions/drawing/positioning.py b/easygraph/functions/drawing/positioning.py index c1e80c75..817dfc4c 100644 --- a/easygraph/functions/drawing/positioning.py +++ b/easygraph/functions/drawing/positioning.py @@ -40,7 +40,7 @@ def random_position(G, center=None, dim=2, random_seed=None): rng = np.random.RandomState(seed=random_seed) pos = rng.rand(len(G), dim) + center pos = pos.astype(np.float32) - pos = dict(zip(G, pos)) + pos = dict(zip(G, pos, strict=False)) return pos @@ -78,7 +78,7 @@ def circular_position(G, center=None, scale=1): theta = theta.astype(np.float32) pos = np.column_stack([np.cos(theta), np.sin(theta)]) pos = rescale_position(pos, scale=scale) + center - pos = dict(zip(G, pos)) + pos = dict(zip(G, pos, strict=False)) return pos @@ -142,7 +142,7 @@ def shell_position(G, nlist=None, scale=1, center=None): pos = rescale_position(pos, scale=scale * radius / len(nlist)) + center else: pos = np.array([(scale * radius + center[0], center[1])]) - npos.update(zip(nodes, pos)) + npos.update(zip(nodes, pos, strict=False)) radius += 1.0 return npos @@ -151,10 +151,7 @@ def shell_position(G, nlist=None, scale=1, center=None): def _get_center(center, dim): import numpy as np - if center is None: - center = np.zeros(dim) - else: - center = np.asarray(center) + center = np.zeros(dim) if center is None else np.asarray(center) if dim < 2: raise ValueError("cannot handle dimensions < 2") @@ -260,23 +257,20 @@ def kamada_kawai_layout( elif dim == 2: pos = eg.circular_position(G) else: - pos = {n: pt for n, pt in zip(G, np.linspace(0, 1, len(G)))} + pos = {n: pt for n, pt in zip(G, np.linspace(0, 1, len(G)), strict=False)} pos_arr = np.array([pos[n] for n in G]) pos = _kamada_kawai_solve(dist_mtx, pos_arr, dim) - if center is None: - center = np.zeros(dim) - else: - center = np.asarray(center) + center = np.zeros(dim) if center is None else np.asarray(center) if len(center) != dim: msg = "length of center coordinates must match dimension of layout" raise ValueError(msg) pos = eg.rescale_position(pos, scale=scale) + center - return dict(zip(G, pos)) + return dict(zip(G, pos, strict=False)) def _kamada_kawai_solve(dist_mtx, pos_arr, dim): diff --git a/easygraph/functions/drawing/tests/test_positioning.py b/easygraph/functions/drawing/tests/test_positioning.py index 709e3333..628c1b56 100644 --- a/easygraph/functions/drawing/tests/test_positioning.py +++ b/easygraph/functions/drawing/tests/test_positioning.py @@ -39,7 +39,7 @@ def test_shell_position(self): self.assertListEqual(list(actual_result_one.keys()), [1, 6, 5, 4, 10]) - for nodes, coordinates in actual_result_one.items(): + for _nodes, coordinates in actual_result_one.items(): self.assertAlmostEqual(coordinates[0], 4, delta=1.0) self.assertAlmostEqual(coordinates[1], 10, delta=1.0) diff --git a/easygraph/functions/graph_embedding/NOBE.py b/easygraph/functions/graph_embedding/NOBE.py index 9ff87ea7..e9e1d98a 100644 --- a/easygraph/functions/graph_embedding/NOBE.py +++ b/easygraph/functions/graph_embedding/NOBE.py @@ -122,7 +122,7 @@ def graph_to_d_atleast2(G): def Transition(LG): - N = len(LG) + len(LG) M = LG.size() LLG = eg.DiGraph() for i in LG.edges: diff --git a/easygraph/functions/graph_embedding/__init__.py b/easygraph/functions/graph_embedding/__init__.py index 6367fea0..7c770b50 100644 --- a/easygraph/functions/graph_embedding/__init__.py +++ b/easygraph/functions/graph_embedding/__init__.py @@ -1,5 +1,5 @@ -from .deepwalk import * -from .line import LINE -from .NOBE import * -from .node2vec import * -from .sdne import SDNE +from easygraph.functions.graph_embedding.deepwalk import * +from easygraph.functions.graph_embedding.line import LINE +from easygraph.functions.graph_embedding.NOBE import * +from easygraph.functions.graph_embedding.node2vec import * +from easygraph.functions.graph_embedding.sdne import SDNE diff --git a/easygraph/functions/graph_embedding/deepwalk.py b/easygraph/functions/graph_embedding/deepwalk.py index ec065d3f..9cd299bd 100644 --- a/easygraph/functions/graph_embedding/deepwalk.py +++ b/easygraph/functions/graph_embedding/deepwalk.py @@ -77,7 +77,7 @@ def simulate_walks(G, walk_length, num_walks): walks = [] nodes = list(G.nodes) print("Walk iteration:") - for walk_iter in tqdm(range(num_walks)): + for _walk_iter in tqdm(range(num_walks)): random.shuffle(nodes) for node in nodes: walks.append(_deepwalk_walk(G, walk_length=walk_length, start_node=node)) diff --git a/easygraph/functions/graph_embedding/node2vec.py b/easygraph/functions/graph_embedding/node2vec.py index 9b324dd2..44de057b 100644 --- a/easygraph/functions/graph_embedding/node2vec.py +++ b/easygraph/functions/graph_embedding/node2vec.py @@ -148,7 +148,7 @@ def simulate_walks(G, walk_length, num_walks, p, q, weight_key=None): alias_nodes, alias_edges = _preprocess_transition_probs(G, p, q, weight_key) walks = [] nodes = list(G.nodes) - for walk_iter in tqdm(range(num_walks)): + for _walk_iter in tqdm(range(num_walks)): random.shuffle(nodes) for node in nodes: walks.append( @@ -180,7 +180,6 @@ def _preprocess_transition_probs(G, p, q, weight_key=None): alias_nodes[node] = _alias_setup(normalized_probs) alias_edges = {} - triads = {} if is_directed: for edge in G.edges: diff --git a/easygraph/functions/graph_embedding/sdne.py b/easygraph/functions/graph_embedding/sdne.py index f53e271e..ee537a79 100644 --- a/easygraph/functions/graph_embedding/sdne.py +++ b/easygraph/functions/graph_embedding/sdne.py @@ -59,7 +59,9 @@ def loss_1st(y_true, y_pred): return loss_1st -def create_model(node_size, hidden_size=[256, 128], l1=1e-5, l2=1e-4): +def create_model(node_size, hidden_size=None, l1=1e-5, l2=1e-4): + if hidden_size is None: + hidden_size = [256, 128] try: pass except ImportWarning: @@ -100,7 +102,7 @@ class SDNE: def __init__( self, graph, - hidden_size=[32, 16], + hidden_size=None, alpha=1e-6, beta=5.0, nu1=1e-5, @@ -141,6 +143,8 @@ def __init__( Knowledge Discovery and Data mining. 2016: 1225-1234. """ + if hidden_size is None: + hidden_size = [32, 16] self.graph = graph self.idx2node, self.node2idx = get_relation_of_index_and_node(self.graph) diff --git a/easygraph/functions/graph_generator/RandomNetwork.py b/easygraph/functions/graph_generator/RandomNetwork.py index 4d25709a..f3ad844a 100644 --- a/easygraph/functions/graph_generator/RandomNetwork.py +++ b/easygraph/functions/graph_generator/RandomNetwork.py @@ -352,7 +352,7 @@ def WS_Random(n, k, p, FilePath=None): if adjacent[e_del] == []: adjacent.pop(e_del) e_add = random.randint(0, NUM2) - while e_add == i or G.has_edge(i, e_add) == True: + while e_add == i or G.has_edge(i, e_add): e_add = random.randint(0, NUM2) G.add_edge(i, e_add) if i not in adjacent: @@ -370,10 +370,7 @@ def WS_Random(n, k, p, FilePath=None): def writeRandomNetworkToFile(n, adjacent, FilePath): - if FilePath != None: - f = open(FilePath, "w+") - else: - f = open("RandomNetwork.txt", "w+") + f = open(FilePath, "w+") if FilePath is not None else open("RandomNetwork.txt", "w+") adjacent = sorted(adjacent.items(), key=lambda d: d[0]) for i in adjacent: i[1].sort() diff --git a/easygraph/functions/graph_generator/__init__.py b/easygraph/functions/graph_generator/__init__.py index 067fcece..e6d8bba3 100644 --- a/easygraph/functions/graph_generator/__init__.py +++ b/easygraph/functions/graph_generator/__init__.py @@ -1,2 +1,2 @@ -from .classic import * -from .RandomNetwork import * +from easygraph.functions.graph_generator.classic import * +from easygraph.functions.graph_generator.RandomNetwork import * diff --git a/easygraph/functions/not_sorted/__init__.py b/easygraph/functions/not_sorted/__init__.py index b652e639..767de842 100644 --- a/easygraph/functions/not_sorted/__init__.py +++ b/easygraph/functions/not_sorted/__init__.py @@ -1,5 +1,5 @@ -from .bridges import * -from .cluster import * -from .laplacian import * -from .mst import * -from .pagerank import * +from easygraph.functions.not_sorted.bridges import * +from easygraph.functions.not_sorted.cluster import * +from easygraph.functions.not_sorted.laplacian import * +from easygraph.functions.not_sorted.mst import * +from easygraph.functions.not_sorted.pagerank import * diff --git a/easygraph/functions/not_sorted/bridges.py b/easygraph/functions/not_sorted/bridges.py index c52701a7..d0c67f46 100644 --- a/easygraph/functions/not_sorted/bridges.py +++ b/easygraph/functions/not_sorted/bridges.py @@ -57,7 +57,7 @@ def bridges(G, root=None): """ chains = chain_decomposition(G, root=root) chain_edges = set(chain.from_iterable(chains)) - for u, v, t in G.edges: + for u, v, _t in G.edges: if (u, v) not in chain_edges and (v, u) not in chain_edges: yield u, v @@ -153,7 +153,7 @@ def _build_chain(G, u, v, visited): # For each nontree edge going out of node u... edges = [] for w, v, d in H.edges: - if w == u and d["nontree"] == True: + if w == u and d["nontree"]: edges.append((w, v)) # edges = ((u, v) for u, v, d in H.out_edges(u, data="nontree") if d) for u, v in edges: diff --git a/easygraph/functions/not_sorted/cluster.py b/easygraph/functions/not_sorted/cluster.py index 1d76fd4b..571d2f27 100644 --- a/easygraph/functions/not_sorted/cluster.py +++ b/easygraph/functions/not_sorted/cluster.py @@ -1,12 +1,11 @@ +import contextlib from collections import Counter from itertools import chain from easygraph.utils.decorators import not_implemented_for -try: +with contextlib.suppress(ImportError): from cpp_easygraph import cpp_clustering -except ImportError: - pass __all__ = ["average_clustering", "clustering"] diff --git a/easygraph/functions/not_sorted/laplacian.py b/easygraph/functions/not_sorted/laplacian.py index b0f2a2b9..b07c3547 100644 --- a/easygraph/functions/not_sorted/laplacian.py +++ b/easygraph/functions/not_sorted/laplacian.py @@ -81,7 +81,7 @@ def laplacian(G, n_workers=None): Xi = copy.deepcopy(X) for j in G: - if j in adj.keys() and i in adj[j].keys(): + if j in adj and i in adj[j]: Xi[j] -= adj[j][i].get("weight", 1) Xi[i] = 0 ELGi = sum(Xi[i] * Xi[i] for i in G) + sum(W[i] for i in G) - 2 * W[i] @@ -110,7 +110,7 @@ def laplacian_parallel(nodes, G, X, W, adj, ELG): Xi = copy.deepcopy(X) for j in G: - if j in adj.keys() and i in adj[j].keys(): + if j in adj and i in adj[j]: Xi[j] -= adj[j][i].get("weight", 1) Xi[i] = 0 ELGi = sum(Xi[i] * Xi[i] for i in G) + sum(W[i] for i in G) - 2 * W[i] diff --git a/easygraph/functions/not_sorted/mst.py b/easygraph/functions/not_sorted/mst.py index ae56e1d4..61bbb975 100644 --- a/easygraph/functions/not_sorted/mst.py +++ b/easygraph/functions/not_sorted/mst.py @@ -143,7 +143,7 @@ def filter_nan_edges(edges=edges, weight=weight): yield wt, u, v, d edges = sorted(filter_nan_edges(), key=itemgetter(0)) - for wt, u, v, d in edges: + for _wt, u, v, d in edges: if subtrees[u] != subtrees[v]: if data: yield (u, v, d) @@ -653,7 +653,7 @@ def to_sets(self): """ # Ensure fully pruned paths - for x in self.parents.keys(): + for x in self.parents: _ = self[x] # Evaluated for side-effect only yield from groups(self.parents).values() diff --git a/easygraph/functions/not_sorted/pagerank.py b/easygraph/functions/not_sorted/pagerank.py index ccb70673..f4078058 100644 --- a/easygraph/functions/not_sorted/pagerank.py +++ b/easygraph/functions/not_sorted/pagerank.py @@ -30,7 +30,7 @@ def pagerank(G, alpha=0.85): # eigenvector of largest eigenvalue is at ind, normalized largest = np.array(eigenvectors[:, ind]).flatten().real norm = float(largest.sum()) - return dict(zip(G, map(float, largest / norm))) + return dict(zip(G, map(float, largest / norm), strict=False)) def google_matrix(G, alpha): diff --git a/easygraph/functions/path/__init__.py b/easygraph/functions/path/__init__.py index 67d731a3..71d2e235 100644 --- a/easygraph/functions/path/__init__.py +++ b/easygraph/functions/path/__init__.py @@ -1 +1 @@ -from .path import * +from easygraph.functions.path.path import * diff --git a/easygraph/functions/path/path.py b/easygraph/functions/path/path.py index fe40ae6f..c1b04e18 100644 --- a/easygraph/functions/path/path.py +++ b/easygraph/functions/path/path.py @@ -1,3 +1,5 @@ +import contextlib + from easygraph.utils.decorators import * __all__ = [ @@ -10,10 +12,8 @@ "multi_source_dijkstra", ] -try: +with contextlib.suppress(ImportError): from cpp_easygraph import cpp_dijkstra_multisource, cpp_Floyd, cpp_Kruskal, cpp_Prim -except ImportError: - pass @not_implemented_for("multigraph") @@ -132,7 +132,7 @@ def Prim(G): start = i end = j min_weight = adj[i][j].get("weight", 1) - if start != None and end != None: + if start is not None and end is not None: result_dict[start][end] = min_weight selected.append(end) candidate.remove(end) diff --git a/easygraph/functions/structural_holes/AP_Greedy.py b/easygraph/functions/structural_holes/AP_Greedy.py index ab1147c6..d9925fb2 100644 --- a/easygraph/functions/structural_holes/AP_Greedy.py +++ b/easygraph/functions/structural_holes/AP_Greedy.py @@ -90,7 +90,7 @@ def common_greedy(G, k, c=1.0, weight="weight"): def sort_nodes_by_degree(G, weight="weight"): sorted_nodes = [] - for node, degree in sorted( + for node, _degree in sorted( G.degree(weight=weight).items(), key=lambda x: x[1], reverse=True ): sorted_nodes.append(node) @@ -122,7 +122,7 @@ def procedure1(G, c=1.0): num_subtree_nodes = _get_num_subtree_nodes(spanning_tree, random_root) N_tree = num_subtree_nodes[random_root] - for node, num in num_subtree_nodes.items(): + for _node, num in num_subtree_nodes.items(): upper_bound += 2 * num * (N_tree - num) del component_subgraph, spanning_tree @@ -141,7 +141,7 @@ def _get_spanning_tree_of_component(G): seen = set() def _plain_dfs(u): - for v, edge_data in G.adj[u].items(): + for v, _edge_data in G.adj[u].items(): if v not in seen: seen.add(v) spanning_tree.add_edge(u, v) @@ -162,7 +162,7 @@ def _get_num_subtree_nodes(G, root): def _plain_dfs(u): num_nodes = 1 - for v, edge_data in G.adj[u].items(): + for v, _edge_data in G.adj[u].items(): if v not in seen: seen.add(v) num_nodes += _plain_dfs(v) @@ -391,7 +391,7 @@ def _get_upper_bound_of_non_ap_nodes(G, ap: list, c=1.0): components = connected_components(G) for component in components: non_articulation_points = component - set(ap) - for node in non_articulation_points: + for _node in non_articulation_points: upper_bound_value = 0 upper_bound_value += sum( (len(temp) * (N_G - len(temp))) for temp in components diff --git a/easygraph/functions/structural_holes/HAM.py b/easygraph/functions/structural_holes/HAM.py index 1f08f2b1..1b0e52ef 100644 --- a/easygraph/functions/structural_holes/HAM.py +++ b/easygraph/functions/structural_holes/HAM.py @@ -53,7 +53,7 @@ def avg_entropy(predicted_labels, actual_labels): for label, items in predicted_labels_dict.items(): N_i = float(len(items)) p_i = [] - for label2, items2 in actual_labels_dict.items(): + for _label2, items2 in actual_labels_dict.items(): common = set(items.tolist()).intersection(set(items2.tolist())) p_ij = float(len(common)) / N_i p_i.append(p_ij) @@ -79,7 +79,7 @@ def load_adj_matrix(G): listE.append(edge[0] - 1) listE.append(edge[1] - 1) adj_tuples = np.array(listE).reshape(-1, 2) - n = len(np.unique(adj_tuples)) + len(np.unique(adj_tuples)) vals = np.array([1] * len(G.edges)) max_id = max(max(adj_tuples[:, 0]), max(adj_tuples[:, 1])) + 1 A = sps.csr_matrix( @@ -129,7 +129,6 @@ def label_by_neighbors(AdjMat, labels): assert AdjMat.shape[0] == len(labels), "dimensions are not equal" unlabeled_idx = labels == 0 num_unlabeled = sum(unlabeled_idx) - count = 0 while num_unlabeled > 0: idxs = np.array(np.nonzero(unlabeled_idx)[0]) next_labels = np.zeros(len(labels)) @@ -220,7 +219,7 @@ def get_structural_holes_HAM(G, k, c, ground_truth_labels): F = sym(np.random.random((n, c))) # Algorithm 1 - for step in range(max_iter): + for _step in range(max_iter): Q = sps.identity(n).tocsr() P = L.dot(F) for i in range(n): diff --git a/easygraph/functions/structural_holes/ICC.py b/easygraph/functions/structural_holes/ICC.py index 9361b6e8..328abd1c 100644 --- a/easygraph/functions/structural_holes/ICC.py +++ b/easygraph/functions/structural_holes/ICC.py @@ -260,7 +260,7 @@ def AP_BICC(G, k, K, l): for i in G.nodes: if i not in A: U.append(i) - kk = k - len(T) + k - len(T) Q = [] for v in U: b_i_c = bounded_inverse_closeness_centrality(G, v, l) diff --git a/easygraph/functions/structural_holes/MaxD.py b/easygraph/functions/structural_holes/MaxD.py index 68428174..773d2aa1 100644 --- a/easygraph/functions/structural_holes/MaxD.py +++ b/easygraph/functions/structural_holes/MaxD.py @@ -111,7 +111,7 @@ def get_structural_holes_MaxD(G, k, C: list[frozenset]): save.append(True) q = [] ans_list = [] - for step in range(k): + for _step in range(k): q.clear() sflow.clear() for i in range(n): @@ -124,7 +124,7 @@ def get_structural_holes_MaxD(G, k, C: list[frozenset]): sflow[i % n] += flow[k_] k_ = nex[k_] for i in range(n): - if save[i] == False: + if not save[i]: q.append((-1, i)) else: q.append((sflow[i] + G_index.degree(weight="weight")[i + 1], i)) @@ -132,7 +132,7 @@ def get_structural_holes_MaxD(G, k, C: list[frozenset]): q.reverse() candidates = [] for i in range(n): - if save[q[i][1]] == True and len(candidates) < k: + if save[q[i][1]] and len(candidates) < k: candidates.append(q[i][1]) ret = pick_candidates(n, candidates, kernels, save) ans_list.append(ret[1] + 1) @@ -246,7 +246,7 @@ def dinic_bfs(): k_ = Q[cl] i = head[k_] while i >= 0: - if flow[i] < capa[i] and dsave[point[i]] == True and dist[point[i]] < 0: + if flow[i] < capa[i] and dsave[point[i]] and dist[point[i]] < 0: dist[point[i]] = dist[k_] + 1 Q.append(point[i]) i = nex[i] @@ -324,7 +324,7 @@ def max_flow(n, kernels, save, prev_flow=None): for i in range(node): dsave.append(True) - if prev_flow != None: + if prev_flow is not None: for i in range(nedge): flow.append(prev_flow[i]) else: @@ -358,9 +358,8 @@ def init_MaxD(_node, _src, _dest): dest = _dest global point, capa, flow, nex, head head.clear() - for i in range(node): + for _i in range(node): head.append(-1) - nedge = 0 point.clear() capa.clear() flow.clear() diff --git a/easygraph/functions/structural_holes/SHII_metric.py b/easygraph/functions/structural_holes/SHII_metric.py index c3ad75d8..d69d8079 100644 --- a/easygraph/functions/structural_holes/SHII_metric.py +++ b/easygraph/functions/structural_holes/SHII_metric.py @@ -115,16 +115,15 @@ def structural_hole_influence_index( if neighbor not in seedNeighborSet: seedNeighborSet.append(neighbor) count_neighbor = count_neighbor + 1 - if count_neighbor > 0: - if ( - len(queue) == 1 - and len(oneSeedSet) + len(seedNeighborSet) < seedSetSize - ): - for node in seedNeighborSet: - if node not in oneSeedSet: - oneSeedSet.append(node) - queue.append(node) - seedNeighborSet.clear() + if count_neighbor > 0 and ( + len(queue) == 1 + and len(oneSeedSet) + len(seedNeighborSet) < seedSetSize + ): + for node in seedNeighborSet: + if node not in oneSeedSet: + oneSeedSet.append(node) + queue.append(node) + seedNeighborSet.clear() queue.pop(0) avg_censor_score_1 = 0.0 @@ -175,7 +174,7 @@ def _independent_cascade(G, S, community_label, countIterations, node_label_pair avg_result_1 = 0 avg_result_2 = 0 N = G.number_of_nodes() - for b in range(countIterations): + for _b in range(countIterations): # print(b, " in ", countIterations) p_vw = np.zeros( (N, N) @@ -225,7 +224,7 @@ def _linear_threshold(G, S, community_label, countIterations, node_label_pair): tol = 0.00001 avg_result_1 = 0 avg_result_2 = 0 - for b in range(countIterations): + for _b in range(countIterations): activeNodes = [] # T is the set of nodes that are to be processed T = [] diff --git a/easygraph/functions/structural_holes/__init__.py b/easygraph/functions/structural_holes/__init__.py index 91b10969..275b5944 100644 --- a/easygraph/functions/structural_holes/__init__.py +++ b/easygraph/functions/structural_holes/__init__.py @@ -1,10 +1,10 @@ -from .AP_Greedy import * -from .evaluation import * -from .HAM import * -from .HIS import * -from .ICC import * -from .MaxD import * -from .metrics import * -from .NOBE import * -from .strong_connected_component import * -from .weakTie import * +from easygraph.functions.structural_holes.AP_Greedy import * +from easygraph.functions.structural_holes.evaluation import * +from easygraph.functions.structural_holes.HAM import * +from easygraph.functions.structural_holes.HIS import * +from easygraph.functions.structural_holes.ICC import * +from easygraph.functions.structural_holes.MaxD import * +from easygraph.functions.structural_holes.metrics import * +from easygraph.functions.structural_holes.NOBE import * +from easygraph.functions.structural_holes.strong_connected_component import * +from easygraph.functions.structural_holes.weakTie import * diff --git a/easygraph/functions/structural_holes/evaluation.py b/easygraph/functions/structural_holes/evaluation.py index a5417866..3fb19b1c 100644 --- a/easygraph/functions/structural_holes/evaluation.py +++ b/easygraph/functions/structural_holes/evaluation.py @@ -1,11 +1,10 @@ +import contextlib import math from easygraph.utils import * -try: +with contextlib.suppress(ImportError): from cpp_easygraph import cpp_constraint, cpp_effective_size, cpp_hierarchy -except ImportError: - pass __all__ = ["effective_size", "efficiency", "constraint", "hierarchy"] diff --git a/easygraph/functions/structural_holes/maxBlock.py b/easygraph/functions/structural_holes/maxBlock.py index 678f3720..f308a45d 100644 --- a/easygraph/functions/structural_holes/maxBlock.py +++ b/easygraph/functions/structural_holes/maxBlock.py @@ -25,9 +25,9 @@ def __init__(self, N, M): self.h = [] self.ne = [] self.to = [] - for i in range(N + 1): + for _i in range(N + 1): self.h.append(0) - for i in range(max(N + 1, M + 1)): + for _i in range(max(N + 1, M + 1)): self.ne.append(0) self.to.append(0) @@ -300,7 +300,7 @@ def _get_estimated_opt(G, f_set, k, c, delta): print("Estimating the optimal value OPT...") n = G.number_of_nodes() opt_ub = 0 - for f_key in f_set.keys(): + for f_key in f_set: opt_ub = opt_ub + f_set[f_key] opt_ub = opt_ub * k * (n - 1) T = math.log((opt_ub / (delta / 2)), 2) @@ -324,7 +324,7 @@ def _find_separation_nodes(G): incoming_info = G_s.graph["incoming_info"] G_s_undirected = eg.Graph() sep_nodes = set() - for node in (G_s.nodes).keys(): + for node in (G_s.nodes): SCC_mapping[node] = G_s.nodes[node]["member"] if len(G_s.nodes[node]["member"]) == 1: sep_nodes.add(node) @@ -566,10 +566,10 @@ def maxBlockFast(G, k, f_set=None, L=None, flag_weight=False): non_considered_nodes.remove(chosen_node) else: V_set = set() - for key in SCC_mapping.keys(): + for key in SCC_mapping: for node in SCC_mapping[key]: if (node in non_considered_nodes) and ( - node not in incoming_info.keys() + node not in incoming_info ): V_set.add(node) if len(V_set) > 0: diff --git a/easygraph/functions/structural_holes/metrics.py b/easygraph/functions/structural_holes/metrics.py index 9df5b430..4bdc5e27 100644 --- a/easygraph/functions/structural_holes/metrics.py +++ b/easygraph/functions/structural_holes/metrics.py @@ -213,16 +213,15 @@ def structural_hole_influence_index( if neighbor not in seedNeighborSet: seedNeighborSet.append(neighbor) count_neighbor = count_neighbor + 1 - if count_neighbor > 0: - if ( - len(queue) == 1 - and len(oneSeedSet) + len(seedNeighborSet) < seedSetSize - ): - for node in seedNeighborSet: - if node not in oneSeedSet: - oneSeedSet.append(node) - queue.append(node) - seedNeighborSet.clear() + if count_neighbor > 0 and ( + len(queue) == 1 + and len(oneSeedSet) + len(seedNeighborSet) < seedSetSize + ): + for node in seedNeighborSet: + if node not in oneSeedSet: + oneSeedSet.append(node) + queue.append(node) + seedNeighborSet.clear() queue.pop(0) avg_censor_score_1 = 0.0 @@ -273,7 +272,7 @@ def _independent_cascade(G, S, community_label, countIterations, node_label_pair avg_result_1 = 0 avg_result_2 = 0 N = G.number_of_nodes() - for b in range(countIterations): + for _b in range(countIterations): # print(b, " in ", countIterations) p_vw = np.zeros( (N, N) @@ -323,7 +322,7 @@ def _linear_threshold(G, S, community_label, countIterations, node_label_pair): tol = 0.00001 avg_result_1 = 0 avg_result_2 = 0 - for b in range(countIterations): + for _b in range(countIterations): activeNodes = [] # T is the set of nodes that are to be processed T = [] diff --git a/easygraph/functions/structural_holes/weakTie.py b/easygraph/functions/structural_holes/weakTie.py index 33e5016e..31aa8a27 100644 --- a/easygraph/functions/structural_holes/weakTie.py +++ b/easygraph/functions/structural_holes/weakTie.py @@ -107,10 +107,9 @@ def _computeCloseness(G, c, u, threshold, length): n = 0 strength_sum_u = 0 for v in c: - if u in G[v] and v != u: - if G[v][u]["strength"] != 0: - n += 1 - strength_sum_u += G[v][u]["strength"] + if u in G[v] and v != u and G[v][u]["strength"] != 0: + n += 1 + strength_sum_u += G[v][u]["strength"] closeness_c_u = (strength_sum_u - n * threshold) / length return closeness_c_u diff --git a/easygraph/readwrite/edgelist.py b/easygraph/readwrite/edgelist.py index 814c46ab..fac2bfdb 100644 --- a/easygraph/readwrite/edgelist.py +++ b/easygraph/readwrite/edgelist.py @@ -99,10 +99,7 @@ def parse_edgelist( elif data is True: # no edge types specified try: # try to evaluate as dictionary - if delimiter == ",": - edgedata_str = ",".join(d) - else: - edgedata_str = " ".join(d) + edgedata_str = ",".join(d) if delimiter == "," else " ".join(d) edgedata = dict(literal_eval(edgedata_str.strip())) except Exception as err: raise TypeError( @@ -115,7 +112,7 @@ def parse_edgelist( f"Edge data {d} and data_keys {data} are not the same length" ) edgedata = {} - for (edge_key, edge_type), edge_value in zip(data, d): + for (edge_key, edge_type), edge_value in zip(data, d, strict=False): try: edge_value = edge_type(edge_value) except Exception as err: diff --git a/easygraph/readwrite/gexf.py b/easygraph/readwrite/gexf.py index 60c14fea..7eca6251 100644 --- a/easygraph/readwrite/gexf.py +++ b/easygraph/readwrite/gexf.py @@ -131,10 +131,7 @@ def read_gexf(path, node_type=None, relabel=False, version="1.2draft"): .. [1] GEXF File Format, http://gexf.net/ """ reader = GEXFReader(node_type=node_type, version=version) - if relabel: - G = relabel_gexf_graph(reader(path)) - else: - G = reader(path) + G = relabel_gexf_graph(reader(path)) if relabel else reader(path) return G @@ -282,20 +279,14 @@ def __str__(self): def add_graph(self, G): # first pass through G collecting edge ids - for u, v, dd in G.edges: + for _u, _v, dd in G.edges: eid = dd.get("id") if eid is not None: self.all_edge_ids.add(str(eid)) # set graph attributes - if G.graph.get("mode") == "dynamic": - mode = "dynamic" - else: - mode = "static" + mode = "dynamic" if G.graph.get("mode") == "dynamic" else "static" # Add a graph element to the XML - if G.is_directed(): - default = "directed" - else: - default = "undirected" + default = "directed" if G.is_directed() else "undirected" name = G.graph.get("name", "") graph_element = Element("graph", defaultedgetype=default, mode=mode, name=name) self.graph_element = graph_element @@ -662,10 +653,7 @@ def __call__(self, stream): def make_graph(self, graph_xml): edgedefault = graph_xml.get("defaultedgetype", None) - if edgedefault == "directed": - G = eg.MultiDiGraph() - else: - G = eg.MultiGraph() + G = eg.MultiDiGraph() if edgedefault == "directed" else eg.MultiGraph() # graph attributes graph_name = graph_xml.get("name", "") @@ -732,10 +720,7 @@ def make_graph(self, graph_xml): # switch to Graph or DiGraph if no parallel edges were found. if self.simple_graph: - if G.is_directed(): - G = eg.DiGraph(G) - else: - G = eg.Graph(G) + G = eg.DiGraph(G) if G.is_directed() else eg.Graph(G) return G def add_node(self, G, node_xml, node_attr, node_pid=None): @@ -997,7 +982,7 @@ def relabel_gexf_graph(G): raise EasyGraphError( "Failed to relabel nodes: missing node labels found. Use relabel=False." ) from err - x, y = zip(*mapping) + x, y = zip(*mapping, strict=False) if len(set(y)) != len(G): raise EasyGraphError( "Failed to relabel nodes: duplicate node labels found. Use relabel=False." diff --git a/easygraph/readwrite/gml.py b/easygraph/readwrite/gml.py index a50acff0..87f07834 100644 --- a/easygraph/readwrite/gml.py +++ b/easygraph/readwrite/gml.py @@ -28,6 +28,7 @@ `Network data page `_. """ +import contextlib import html.entities as htmlentitydefs import re from ast import literal_eval @@ -67,10 +68,7 @@ def fixup(m): text = m.group(0) if text[1] == "#": # Character reference - if text[2] == "x": - code = int(text[3:-1], 16) - else: - code = int(text[2:-1]) + code = int(text[3:-1], 16) if text[2] == "x" else int(text[2:-1]) else: # Named entity try: @@ -282,10 +280,8 @@ def parse_kv(curr_token): elif category == Pattern.STRINGS: value = unescape(curr_token.value[1:-1]) if destringizer: - try: + with contextlib.suppress(ValueError): value = destringizer(value) - except ValueError: - pass curr_token = next(tokens) elif category == Pattern.DICT_START: curr_token, value = parse_dict(curr_token) @@ -295,10 +291,8 @@ def parse_kv(curr_token): # String convert the token value value = unescape(str(curr_token.value)) if destringizer: - try: + with contextlib.suppress(ValueError): value = destringizer(value) - except ValueError: - pass curr_token = next(tokens) except Exception: msg = ( @@ -538,7 +532,7 @@ def stringize(key, value, ignored_keys, indent, in_list=False): yield from stringize(attr, value, ignored_keys, " ") # Output node data - node_id = dict(zip(G, range(len(G)))) + node_id = dict(zip(G, range(len(G)), strict=False)) ignored_keys = {"id", "label"} for node, attrs in G.nodes.items(): yield " node [" diff --git a/easygraph/readwrite/graphml.py b/easygraph/readwrite/graphml.py index 98edd0d5..cebbbc77 100644 --- a/easygraph/readwrite/graphml.py +++ b/easygraph/readwrite/graphml.py @@ -533,10 +533,7 @@ def get_key(self, name, attr_type, scope, default): try: return self.keys[keys_key] except KeyError: - if self.named_key_ids: - new_id = name - else: - new_id = f"d{len(list(self.keys))}" + new_id = name if self.named_key_ids else f"d{len(list(self.keys))}" self.keys[keys_key] = new_id key_kwargs = { @@ -619,10 +616,7 @@ def add_graph_element(self, G): """ Serialize graph G in GraphML to the stream. """ - if G.is_directed(): - default_edge_type = "directed" - else: - default_edge_type = "undirected" + default_edge_type = "directed" if G.is_directed() else "undirected" graphid = G.graph.pop("id", None) if graphid is None: @@ -750,10 +744,7 @@ def add_graph_element(self, G): """ Serialize graph G in GraphML to the stream. """ - if G.is_directed(): - default_edge_type = "directed" - else: - default_edge_type = "undirected" + default_edge_type = "directed" if G.is_directed() else "undirected" graphid = G.graph.pop("id", None) if graphid is None: @@ -780,27 +771,27 @@ def add_graph_element(self, G): element_type = self.get_xml_type(self.attr_type(k, "graph", v)) self.get_key(str(k), element_type, "graph", None) # Nodes and data - for node, d in G.nodes.items(): + for _node, d in G.nodes.items(): for k, v in d.items(): self.attribute_types[(str(k), "node")].add(type(v)) - for node, d in G.nodes.items(): + for _node, d in G.nodes.items(): for k, v in d.items(): T = self.get_xml_type(self.attr_type(k, "node", v)) self.get_key(str(k), T, "node", node_default.get(k)) # Edges and data if G.is_multigraph(): - for u, v, ekey, d in G.edges: + for _u, v, _ekey, d in G.edges: for k, v in d.items(): self.attribute_types[(str(k), "edge")].add(type(v)) - for u, v, ekey, d in G.edges: + for _u, v, _ekey, d in G.edges: for k, v in d.items(): T = self.get_xml_type(self.attr_type(k, "edge", v)) self.get_key(str(k), T, "edge", edge_default.get(k)) else: - for u, v, d in G.edges: + for _u, v, d in G.edges: for k, v in d.items(): self.attribute_types[(str(k), "edge")].add(type(v)) - for u, v, d in G.edges: + for _u, v, d in G.edges: for k, v in d.items(): T = self.get_xml_type(self.attr_type(k, "edge", v)) self.get_key(str(k), T, "edge", edge_default.get(k)) @@ -863,10 +854,7 @@ def make_graph(self, graph_xml, graphml_keys, defaults, G=None): # set default graph type edgedefault = graph_xml.get("edgedefault", None) if G is None: - if edgedefault == "directed": - G = eg.MultiDiGraph() - else: - G = eg.MultiGraph() + G = eg.MultiDiGraph() if edgedefault == "directed" else eg.MultiGraph() # set defaults for graph attributes G.graph["node_default"] = {} G.graph["edge_default"] = {} @@ -906,7 +894,7 @@ def add_node(self, G, node_xml, graphml_keys, defaults): # warn on finding unsupported ports tag ports = node_xml.find(f"{{{self.NS_GRAPHML}}}port") if ports is not None: - warnings.warn("GraphML port tag not supported.") + warnings.warn("GraphML port tag not supported.", stacklevel=2) # find the node by id and cast it to the appropriate type node_id = self.node_type(node_xml.get("id")) # get data/attributes for node @@ -922,7 +910,7 @@ def add_edge(self, G, edge_element, graphml_keys): # warn on finding unsupported ports tag ports = edge_element.find(f"{{{self.NS_GRAPHML}}}port") if ports is not None: - warnings.warn("GraphML port tag not supported.") + warnings.warn("GraphML port tag not supported.", stacklevel=2) # raise error if we find mixed directed and undirected edges directed = edge_element.get("directed") @@ -1030,7 +1018,7 @@ def find_graphml_keys(self, graph_element): attr_type = "yfiles" if attr_type is None: attr_type = "string" - warnings.warn(f"No key type for id {attr_id}. Using string") + warnings.warn(f"No key type for id {attr_id}. Using string", stacklevel=2) if attr_name is None: raise eg.EasyGraphError(f"Unknown key for id {attr_id}.") graphml_keys[attr_id] = { diff --git a/easygraph/readwrite/graphviz.py b/easygraph/readwrite/graphviz.py index e3771b20..83ed4f07 100644 --- a/easygraph/readwrite/graphviz.py +++ b/easygraph/readwrite/graphviz.py @@ -36,15 +36,9 @@ def from_agraph(A, create_using=None): """ if create_using is None: if A.is_directed(): - if A.is_strict(): - create_using = eg.DiGraph - else: - create_using = eg.MultiDiGraph + create_using = eg.DiGraph if A.is_strict() else eg.MultiDiGraph else: - if A.is_strict(): - create_using = eg.Graph - else: - create_using = eg.MultiGraph + create_using = eg.Graph if A.is_strict() else eg.MultiGraph # assign defaults N = eg.empty_graph(0, create_using) diff --git a/easygraph/readwrite/pajek.py b/easygraph/readwrite/pajek.py index 493231a9..1fdef768 100644 --- a/easygraph/readwrite/pajek.py +++ b/easygraph/readwrite/pajek.py @@ -76,10 +76,6 @@ def generate_pajek(G): See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm for format information. """ - if G.name == "": - name = "EasyGraph" - else: - name = G.name # Apparently many Pajek format readers can't process this line # So we'll leave it out for now. # yield '*network %s'%name @@ -88,7 +84,7 @@ def generate_pajek(G): yield f"*vertices {G.order()}" nodes = list(G) # make dictionary mapping nodes to integers - nodenumber = dict(zip(nodes, range(1, len(nodes) + 1))) + nodenumber = dict(zip(nodes, range(1, len(nodes) + 1), strict=False)) for n in nodes: # copy node attributes and pop mandatory attributes # to avoid duplication. @@ -113,7 +109,7 @@ def generate_pajek(G): else: warnings.warn( f"Node attribute {k} is not processed." - f" {('Empty attribute' if isinstance(v, str) else 'Non-string attribute')}." + f" {('Empty attribute' if isinstance(v, str) else 'Non-string attribute')}.", stacklevel=2 ) yield s @@ -140,7 +136,7 @@ def generate_pajek(G): else: warnings.warn( f"Edge attribute {k} is not processed." - f" {('Empty attribute' if isinstance(v, str) else 'Non-string attribute')}." + f" {('Empty attribute' if isinstance(v, str) else 'Non-string attribute')}.", stacklevel=2 ) yield s @@ -258,7 +254,7 @@ def parse_pajek(lines): elif l.lower().startswith("*vertices"): nodelabels = {} l, nnodes = l.split() - for i in range(int(nnodes)): + for _i in range(int(nnodes)): l = next(lines) try: splitline = [x for x in shlex.split(str(l))] @@ -276,7 +272,7 @@ def parse_pajek(lines): ) except: pass - extra_attr = zip(splitline[5::2], splitline[6::2]) + extra_attr = zip(splitline[5::2], splitline[6::2], strict=False) G.nodes[label].update(extra_attr) elif l.lower().startswith("*edges") or l.lower().startswith("*arcs"): if l.lower().startswith("*edge"): @@ -307,7 +303,7 @@ def parse_pajek(lines): pass # if there isn't, just assign a 1 # edge_data.update({'value':1}) - extra_attr = zip(splitline[3::2], splitline[4::2]) + extra_attr = zip(splitline[3::2], splitline[4::2], strict=False) edge_data.update(extra_attr) # if G.has_edge(u,v): # multigraph=True diff --git a/easygraph/readwrite/tests/test_gexf.py b/easygraph/readwrite/tests/test_gexf.py index dd5eff92..565465d7 100644 --- a/easygraph/readwrite/tests/test_gexf.py +++ b/easygraph/readwrite/tests/test_gexf.py @@ -163,7 +163,7 @@ def test_read_attribute_graphml(self): assert sorted(G.nodes) == sorted(H.nodes) ge = sorted(G.edges) he = sorted(H.edges) - for a, b in zip(ge, he): + for a, b in zip(ge, he, strict=False): assert a == b self.attribute_fh.seek(0) diff --git a/easygraph/readwrite/tests/test_graphml.py b/easygraph/readwrite/tests/test_graphml.py index bcb0ef52..012c40af 100644 --- a/easygraph/readwrite/tests/test_graphml.py +++ b/easygraph/readwrite/tests/test_graphml.py @@ -376,7 +376,7 @@ def test_read_attribute_graphml(self): assert nodes_equal(sorted(G.nodes), sorted(H.nodes)) ge = sorted(G.edges) he = sorted(H.edges) - for a, b in zip(ge, he): + for a, b in zip(ge, he, strict=False): assert a == b self.attribute_fh.seek(0) @@ -384,7 +384,7 @@ def test_read_attribute_graphml(self): assert sorted(G.nodes) == sorted(PG.nodes) ge = sorted(G.edges) he = sorted(PG.edges) - for a, b in zip(ge, he): + for a, b in zip(ge, he, strict=False): assert a == b def test_node_default_attribute_graphml(self): @@ -502,11 +502,10 @@ def test_multigraph_keys(self): """ fh = io.BytesIO(s.encode("UTF-8")) - G = eg.read_graphml(fh) - expected = [("n0", "n1", "e0"), ("n0", "n1", "e1")] + eg.read_graphml(fh) # assert sorted(G.edges) == expected fh.seek(0) - H = eg.parse_graphml(s) + eg.parse_graphml(s) # assert sorted(H.edges) == expected def test_preserve_multi_edge_data(self): @@ -1179,8 +1178,8 @@ def test_write_read_attribute_named_key_ids_graphml(self): named_key_ids_behavior_fh.seek(0) J = eg.read_graphml(named_key_ids_behavior_fh) - assert all(n1 == n2 for (n1, n2) in zip(H.nodes, J.nodes)) - assert all(e1 == e2 for (e1, e2) in zip(H.edges, J.edges)) + assert all(n1 == n2 for (n1, n2) in zip(H.nodes, J.nodes, strict=False)) + assert all(e1 == e2 for (e1, e2) in zip(H.edges, J.edges, strict=False)) def test_write_read_attribute_numeric_type_graphml(self): from xml.etree.ElementTree import parse @@ -1379,7 +1378,7 @@ def test_multigraph_write_generate_edge_id_from_attribute(self): assert nodes_equal(G.nodes, H.nodes) # assert edges_equal(G.edges, H.edges)x - x = [data.get("eid") for u, v, _, data in H.edges] + [data.get("eid") for u, v, _, data in H.edges] assert sorted(data.get("eid") for u, v, _, data in H.edges) == sorted( edge_attributes.values() ) @@ -1451,7 +1450,7 @@ def test_numpy_float32(self): os.unlink(fname) def test_numpy_float64_inference(self): - np = pytest.importorskip("numpy") + pytest.importorskip("numpy") G = self.attribute_numeric_type_graph fd, fname = tempfile.mkstemp() self.writer(G, fname, infer_numeric_types=True) diff --git a/easygraph/readwrite/tests/test_graphviz.py b/easygraph/readwrite/tests/test_graphviz.py index 1ed5813b..8266f62e 100644 --- a/easygraph/readwrite/tests/test_graphviz.py +++ b/easygraph/readwrite/tests/test_graphviz.py @@ -48,7 +48,7 @@ def agraph_checks(self, G): def test_from_agraph_name(self): G = eg.Graph(name="test") A = eg.to_agraph(G) - H = eg.from_agraph(A) + eg.from_agraph(A) assert G.name == "test" def test_undirected(self): diff --git a/easygraph/readwrite/tests/test_pajek.py b/easygraph/readwrite/tests/test_pajek.py index 6942b702..a01f3edb 100644 --- a/easygraph/readwrite/tests/test_pajek.py +++ b/easygraph/readwrite/tests/test_pajek.py @@ -282,7 +282,7 @@ def test_noname(self): line = "*network\n" other_lines = self.data.split("\n")[1:] data = line + "\n".join(other_lines) - G = eg.parse_pajek(data) + eg.parse_pajek(data) def test_unicode(self): import io diff --git a/easygraph/readwrite/tests/test_ucinet.py b/easygraph/readwrite/tests/test_ucinet.py index 39ff2eda..a48f524d 100644 --- a/easygraph/readwrite/tests/test_ucinet.py +++ b/easygraph/readwrite/tests/test_ucinet.py @@ -253,15 +253,6 @@ def test_read_ucinet(self): def test_write_ucinet(self): fh = io.BytesIO() - data = """\ -dl n=5 format=fullmatrix -data: -0 1 1 1 1 -1 0 1 0 0 -1 1 0 0 1 -1 0 0 0 0 -1 0 1 0 0 -""" graph = eg.MultiDiGraph() graph.add_nodes_from([0, 1, 2, 3, 4]) graph.add_edges_from( diff --git a/easygraph/readwrite/ucinet.py b/easygraph/readwrite/ucinet.py index 6fbd6b50..588caee6 100644 --- a/easygraph/readwrite/ucinet.py +++ b/easygraph/readwrite/ucinet.py @@ -21,6 +21,7 @@ for full format information. Short version on http://www.analytictech.com/networks/dataentry.htm """ +import contextlib import re import shlex @@ -163,14 +164,12 @@ def parse_ucinet(lines): lexer.whitespace_split = True number_of_nodes = 0 - number_of_matrices = 0 nr = 0 # number of rows (rectangular matrix) nc = 0 # number of columns (rectangular matrix) ucinet_format = "fullmatrix" # Format by default labels = {} # Contains labels of nodes row_labels_embedded = False # Whether labels are embedded in data or not cols_labels_embedded = False - diagonal = True # whether the main diagonal is present or absent KEYWORDS = ("format", "data:", "labels:") # TODO remove ':' in keywords @@ -188,14 +187,14 @@ def parse_ucinet(lines): nc = int(get_param(r"\d+", token, lexer)) number_of_nodes = max(nr, nc) elif token.startswith("nm"): - number_of_matrices = int(get_param(r"\d+", token, lexer)) + int(get_param(r"\d+", token, lexer)) else: number_of_nodes = int(get_param(r"\d+", token, lexer)) nr = number_of_nodes nc = number_of_nodes elif token.startswith("diagonal"): - diagonal = get_param("present|absent", token, lexer) + get_param("present|absent", token, lexer) elif token.startswith("format"): ucinet_format = get_param( @@ -234,7 +233,7 @@ def parse_ucinet(lines): params = {} if cols_labels_embedded: # params['names'] = True - labels = dict(zip(range(0, nc), data_lines.splitlines()[1].split())) + labels = dict(zip(range(0, nc), data_lines.splitlines()[1].split(), strict=False)) # params['skip_header'] = 2 # First character is \n if row_labels_embedded: # Skip first column # TODO rectangular case : labels can differ from rows to columns @@ -243,10 +242,8 @@ def parse_ucinet(lines): if ucinet_format == "fullmatrix": # In Python3 genfromtxt requires bytes string - try: + with contextlib.suppress(TypeError): data_lines = bytes(data_lines, "utf-8") - except TypeError: - pass # Do not use splitlines() because it is not necessarily written as a square matrix data = genfromtxt([data_lines], case_sensitive=False, **params) if cols_labels_embedded or row_labels_embedded: @@ -267,10 +264,7 @@ def parse_ucinet(lines): pass else: for neighbor in row[1:]: - if ucinet_format == "nodelist1": - source = row[0] - else: - source = str(i) + source = row[0] if ucinet_format == "nodelist1" else str(i) s += source + " " + neighbor + "\n" G = eg.parse_edgelist( @@ -280,7 +274,7 @@ def parse_ucinet(lines): ) if not row_labels_embedded or not cols_labels_embedded: - G = eg.relabel_nodes(G, dict(zip(list(G.nodes), [i - 1 for i in G.nodes]))) + G = eg.relabel_nodes(G, dict(zip(list(G.nodes), [i - 1 for i in G.nodes], strict=False))) elif ucinet_format == "edgelist1": G = eg.parse_edgelist( @@ -290,7 +284,7 @@ def parse_ucinet(lines): ) if not row_labels_embedded or not cols_labels_embedded: - G = eg.relabel_nodes(G, dict(zip(list(G.nodes), [i - 1 for i in G.nodes]))) + G = eg.relabel_nodes(G, dict(zip(list(G.nodes), [i - 1 for i in G.nodes], strict=False))) # Relabel nodes if labels: @@ -320,6 +314,6 @@ def get_param(regex, token, lines): try: n = next(lines) except StopIteration: - raise Exception("Parameter %s value not recognized" % token) + raise Exception(f"Parameter {token} value not recognized") query = re.search(regex, n) return query.group() diff --git a/easygraph/utils/convert_to_matrix.py b/easygraph/utils/convert_to_matrix.py index ca9816ad..4b548945 100644 --- a/easygraph/utils/convert_to_matrix.py +++ b/easygraph/utils/convert_to_matrix.py @@ -28,12 +28,12 @@ def to_numpy_matrix(G, edge_sign=1.0, not_edge_sign=0.0): """ import numpy as np - index_of_node = dict(zip(G.nodes, range(len(G)))) + index_of_node = dict(zip(G.nodes, range(len(G)), strict=False)) N = len(G) M = np.full((N, N), not_edge_sign) for u, udict in G.adj.items(): - for v, data in udict.items(): + for v, _data in udict.items(): M[index_of_node[u], index_of_node[v]] = edge_sign M = np.asmatrix(M) @@ -153,7 +153,7 @@ def from_numpy_array(A, parallel_edges=False, create_using=None): G.add_nodes_from(range(n)) # Get a list of all the entries in the array with nonzero entries. These # coordinates become edges in the graph. (convert to int from np.int64) - edges = ((int(e[0]), int(e[1])) for e in zip(*A.nonzero())) + edges = ((int(e[0]), int(e[1])) for e in zip(*A.nonzero(), strict=False)) # handle numpy constructed data type if python_type == "void": # Sort the fields by their offset, then by dtype, then by name. @@ -166,7 +166,7 @@ def from_numpy_array(A, parallel_edges=False, create_using=None): v, { name: kind_to_python_type[dtype.kind](val) - for (_, dtype, name), val in zip(fields, A[u, v]) + for (_, dtype, name), val in zip(fields, A[u, v], strict=False) }, ) for u, v in edges @@ -319,7 +319,7 @@ def to_numpy_array( raise eg.EasyGraphError("nodelist contains duplicates.") undirected = not G.is_directed() - index = dict(zip(nodelist, range(nlen))) + index = dict(zip(nodelist, range(nlen), strict=False)) # Initially, we start with an array of nans. Then we populate the array # using data from the graph. Afterwards, any leftover nans will be @@ -557,7 +557,7 @@ def from_pandas_edgelist( g = eg.empty_graph(0, create_using) if edge_attr is None: - g.add_edges_from(zip(df[source], df[target])) + g.add_edges_from(zip(df[source], df[target], strict=False)) return g reserved_columns = [source, target] @@ -578,7 +578,7 @@ def from_pandas_edgelist( ) try: - attribute_data = zip(*[df[col] for col in attr_col_headings]) + attribute_data = zip(*[df[col] for col in attr_col_headings], strict=False) except (KeyError, TypeError) as err: msg = f"Invalid edge_attr argument: {edge_attr}" raise eg.EasyGraphError(msg) from err @@ -588,23 +588,23 @@ def from_pandas_edgelist( if edge_key is not None: try: multigraph_edge_keys = df[edge_key] - attribute_data = zip(attribute_data, multigraph_edge_keys) + attribute_data = zip(attribute_data, multigraph_edge_keys, strict=False) except (KeyError, TypeError) as err: msg = f"Invalid edge_key argument: {edge_key}" raise eg.EasyGraphError(msg) from err - for s, t, attrs in zip(df[source], df[target], attribute_data): + for s, t, attrs in zip(df[source], df[target], attribute_data, strict=False): if edge_key is not None: attrs, multigraph_edge_key = attrs key = g.add_edge(s, t, key=multigraph_edge_key) else: key = g.add_edge(s, t) - g[s][t][key].update(zip(attr_col_headings, attrs)) + g[s][t][key].update(zip(attr_col_headings, attrs, strict=False)) else: - for s, t, attrs in zip(df[source], df[target], attribute_data): + for s, t, attrs in zip(df[source], df[target], attribute_data, strict=False): g.add_edge(s, t) - g[s][t].update(zip(attr_col_headings, attrs)) + g[s][t].update(zip(attr_col_headings, attrs, strict=False)) return g @@ -773,7 +773,7 @@ def _coo_gen_triples(A): """ row, col, data = A.row, A.col, A.data - return zip(row, col, data) + return zip(row, col, data, strict=False) def _dok_gen_triples(A): diff --git a/easygraph/utils/decorators.py b/easygraph/utils/decorators.py index 43d522cf..91634cee 100644 --- a/easygraph/utils/decorators.py +++ b/easygraph/utils/decorators.py @@ -934,10 +934,7 @@ def signature(cls, f): fname = cls._name(f) def_sig = f"def {fname}({', '.join(def_sig)}):" - if inspect.isgeneratorfunction(f): - _return = "yield from" - else: - _return = "return" + _return = "yield from" if inspect.isgeneratorfunction(f) else "return" call_sig = f"{_return} {{}}({', '.join(call_sig)})" diff --git a/easygraph/utils/mapped_queue.py b/easygraph/utils/mapped_queue.py index 9a76872b..bde8651d 100644 --- a/easygraph/utils/mapped_queue.py +++ b/easygraph/utils/mapped_queue.py @@ -51,8 +51,10 @@ class MappedQueue: Pearson Education. """ - def __init__(self, data=[]): + def __init__(self, data=None): """Priority queue class with updatable priorities.""" + if data is None: + data = [] self.h = list(data) self.d = dict() self._heapify() diff --git a/easygraph/utils/misc.py b/easygraph/utils/misc.py index ea5eabb7..ba5a7d9d 100644 --- a/easygraph/utils/misc.py +++ b/easygraph/utils/misc.py @@ -115,5 +115,5 @@ def pairwise(iterable, cyclic=False): a, b = tee(iterable) first = next(b, None) if cyclic is True: - return zip(a, chain(b, (first,))) - return zip(a, b) + return zip(a, chain(b, (first,)), strict=False) + return zip(a, b, strict=False) diff --git a/easygraph/utils/relabel.py b/easygraph/utils/relabel.py index 0a6cbece..347f20bd 100644 --- a/easygraph/utils/relabel.py +++ b/easygraph/utils/relabel.py @@ -2,10 +2,7 @@ def relabel_nodes(G, mapping): - if not hasattr(mapping, "__getitem__"): - m = {n: mapping(n) for n in G} - else: - m = mapping + m = {n: mapping(n) for n in G} if not hasattr(mapping, "__getitem__") else mapping return _relabel_copy(G, m) diff --git a/easygraph/utils/type_change.py b/easygraph/utils/type_change.py index c0564fda..97bf8456 100644 --- a/easygraph/utils/type_change.py +++ b/easygraph/utils/type_change.py @@ -39,15 +39,9 @@ def from_pyGraphviz_agraph(A, create_using=None): """ if create_using is None: if A.is_directed(): - if A.is_strict(): - create_using = eg.DiGraph - else: - create_using = eg.MultiDiGraph + create_using = eg.DiGraph if A.is_strict() else eg.MultiDiGraph else: - if A.is_strict(): - create_using = eg.Graph - else: - create_using = eg.MultiGraph + create_using = eg.Graph if A.is_strict() else eg.MultiGraph # assign defaults N = eg.empty_graph(0, create_using)