init a branch to convert to uv settings (using .toml).

Author: jajupmochi

.idea/graphkit-learn.iml

@@ -0,0 +1,21 @@
+cmake_minimum_required(VERSION 3.18)
+project(graphkit_learn LANGUAGES CXX)
+
+# Set Python version requirements
+find_package(Python REQUIRED COMPONENTS Interpreter Development)
+
+# Add the gedlib subdirectory if it exists
+if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/gklearn/gedlib/CMakeLists.txt")
+    add_subdirectory(gklearn/gedlib)
+endif()
+
+# Install Python packages
+install(DIRECTORY gklearn 
+        DESTINATION ${SKBUILD_PLATLIB_DIR}
+        PATTERN "*.egg-info" EXCLUDE
+        PATTERN "*.git*" EXCLUDE
+        PATTERN "__pycache__" EXCLUDE
+        PATTERN "*.cpp" EXCLUDE
+        PATTERN "*.o" EXCLUDE
+        PATTERN "*.so" EXCLUDE
+        PATTERN "*.pyc" EXCLUDE)

.idea/misc.xml

@@ -11,10 +11,12 @@
 """
 
 # info
-__version__ = "0.1"
-__author__  = "Benoit Gaüzère"
-__date__    = "November 2017"
- 
+import datetime
+
+__version__ = '0.2.1.post' + datetime.now().strftime('%Y%m%d%H%M%S')
+__author__ = 'Linlin Jia, Benoit Gaüzère, Paul Honeine'
+__date__ = 'November 2017'
+
 # import sub modules
 # from gklearn import c_ext
 # from gklearn import ged

CMakeLists.txt

@@ -0,0 +1,55 @@
+cmake_minimum_required(VERSION 3.18)
+project(gedlibpy LANGUAGES CXX)
+
+# Find Python and dependencies
+find_package(Python REQUIRED COMPONENTS Interpreter Development NumPy)
+find_package(Cython REQUIRED)
+include(UseCython)
+
+# Set Cython language level
+set(CYTHON_LANGUAGE_LEVEL "3")
+
+# Include directories
+set(GEDLIB_INCLUDE_DIRS
+    "${CMAKE_CURRENT_SOURCE_DIR}/src"
+    "${CMAKE_CURRENT_SOURCE_DIR}/include"
+    "${CMAKE_CURRENT_SOURCE_DIR}/include/lsape.5/include"
+    "${CMAKE_CURRENT_SOURCE_DIR}/include/eigen.3.3.4/Eigen"
+    "${CMAKE_CURRENT_SOURCE_DIR}/include/nomad.3.8.1/src"
+    "${CMAKE_CURRENT_SOURCE_DIR}/include/nomad.3.8.1/ext/sgtelib/src"
+    "${CMAKE_CURRENT_SOURCE_DIR}/include/libsvm.3.22"
+    "${CMAKE_CURRENT_SOURCE_DIR}/include/fann.2.2.0/include"
+    "${CMAKE_CURRENT_SOURCE_DIR}/include/boost.1.69.0"
+    ${Python_NumPy_INCLUDE_DIRS}
+)
+
+# Library directories
+set(GEDLIB_LIBRARY_DIRS
+    "${CMAKE_CURRENT_SOURCE_DIR}/lib/fann.2.2.0"
+    "${CMAKE_CURRENT_SOURCE_DIR}/lib/libsvm.3.22"
+    "${CMAKE_CURRENT_SOURCE_DIR}/lib/nomad.3.8.1"
+)
+
+# Libraries to link
+set(GEDLIB_LIBRARIES doublefann sgtelib svm nomad)
+
+# Create the Cython extension module
+add_cython_target(gedlibpy CXX)
+add_library(gedlibpy MODULE ${gedlibpy})
+
+# Set include directories for the module
+target_include_directories(gedlibpy PUBLIC ${GEDLIB_INCLUDE_DIRS})
+
+# Set library directories for the module
+target_link_directories(gedlibpy PUBLIC ${GEDLIB_LIBRARY_DIRS})
+
+# Link libraries
+target_link_libraries(gedlibpy PUBLIC ${GEDLIB_LIBRARIES} Python::Python)
+
+# Set C++ standard
+target_compile_features(gedlibpy PRIVATE cxx_std_11)
+
+# Install the Cython extension
+install(TARGETS gedlibpy
+        LIBRARY DESTINATION ${SKBUILD_PLATLIB_DIR}/gklearn/gedlib
+        RUNTIME DESTINATION ${SKBUILD_PLATLIB_DIR}/gklearn/gedlib)

gklearn/__init__.py

@@ -0,0 +1,31 @@
+[build-system]
+requires = ["scikit-build-core>=0.5.0", "wheel", "setuptools>=42", "cmake>=3.18", "cython>=0.29.0", "numpy"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "gedlibpy"
+version = "0.1.0"
+authors = [
+    {name = "Lambert Natacha and Linlin Jia", email = "linlin.jia@unibe.ch"},
+]
+description = "A Python wrapper library for C++ library GEDLIB of graph edit distances"
+readme = "README.rst"
+license = {text = "GNU General Public License v3 (GPLv3)"}
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+]
+requires-python = ">=3.11"
+
+[project.urls]
+Source = "https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/gedlib"
+Tracker = "https://github.com/jajupmochi/graphkit-learn/issues"
+
+[tool.scikit-build]
+wheel.expand-macos-universal-tags = true
+cmake.minimum-version = "3.18"
+build-dir = "build/{wheel_tag}"
+cmake.verbose = true

gklearn/gedlib/CMakeLists.txt

@@ -0,0 +1,61 @@
+[build-system]
+requires = ["scikit-build-core>=0.8.0", "wheel", "setuptools>=42", "dynamic-metadata"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "graphkit-learn"
+dynamic = ["version"]
+authors = [
+    { name = "Linlin Jia", email = "jajupmochi@gmail.com" },
+]
+description = "A Python library for machine learning on graphs."
+readme = "README.md"
+license = { text = "GNU General Public License v3 (GPLv3)" }
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+]
+requires-python = ">=3.11"
+dependencies = [
+    "control>=0.10.1",
+    "cvxopt>=1.3.2",
+    "cvxpy>=1.6.5",
+    "cython>=3.1.0",
+    "matplotlib>=3.10.3",
+    "mosek>=11.0.20",
+    "networkx>=3.4.2",
+    "numpy>=2.2.5",
+    "scikit-learn>=1.6.1",
+    "scipy>=1.15.3",
+    "slycot>=0.6.0",
+    "tabulate>=0.9.0",
+    "tqdm>=4.67.1",
+]
+
+[project.urls]
+Documentation = "https://graphkit-learn.readthedocs.io"
+Source = "https://github.com/jajupmochi/graphkit-learn"
+Tracker = "https://github.com/jajupmochi/graphkit-learn/issues"
+
+[tool.scikit-build]
+wheel.expand-macos-universal-tags = true
+cmake.version = ">=3.18"
+build-dir = "build/{wheel_tag}"
+build.verbose = true
+wheel.packages = ["gklearn"]
+
+[tool.scikit-build.sdist]
+include = ["gklearn/**/*", "CMakeLists.txt"]
+exclude = ["gklearn/gedlib/gedlib-master", "*.cpp", "*.so", "**/*.pyc"]
+
+[tool.scikit-build.cmake.define]
+BUILD_SHARED_LIBS = "ON"
+
+[tool.dynamic-metadata.version]
+provider = "dynamic_metadata.plugins.regex"
+input = "gklearn/__init__.py"
+regex = "(?i)^(__version__|VERSION) *= *(['\"])v?(?P<value>.+?)\\2"
+