Refactor: migrate C++ bindings to pybind11; modernize build, packaging & tests#155

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Acture wants to merge 17 commits intoeasy-graph:pybind11from

Acture:refactor-build

Commits on Oct 20, 2025

refactor(packaging): Remove deprecated test configuration from setup.py
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style(packaging): Use SPDX license identifier 'BSD-3-Clause'
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Commits on Oct 21, 2025

refactor(packaging): Migrate from `setup.py` to `pyproject.toml` and restructure project
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feat(env): Add `.envrc` for automated virtual environment management
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refactor(codebase): Remove unused imports and improve variable naming for clarity
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refactor(cpp_binding): Replace Boost.Python with pybind11 for bindings
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refactor(project): modernize project structure and update dependencies
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refactor(graph): migrate from Boost.Python to pybind11
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refactor(project): remove legacy test and config files, enhance project structure
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chore(tests): remove legacy `nose` dependency
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feat(packaging): add optional Graphviz dependency
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fix(graphml,gexf): replace deprecated `np.float_` with `np.float64`
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fix(packaging): update Graphviz optional dependency to `pygraphviz>=1.14`
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fix(tests): replace deprecated `DataFrame.append` with `pd.concat`
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refactor(readwrite): remove warnings, fix indentation, and clean up parsing logic
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refactor(graph): standardize string formatting and import usage
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refactor(core): replace redundant exception handling with `contextlib.suppress`
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