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test new flow
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‎.github/workflows/publish.yml‎

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name: Build and upload to PyPI
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on:
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push:
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tags: ['v*']
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jobs:
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build_wheels:
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name: Build wheels for ${{ matrix.os }}
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runs-on: ${{ matrix.runs-on }}
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strategy:
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matrix:
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include:
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- os: linux-intel
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runs-on: ubuntu-latest
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- os: linux-arm
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runs-on: ubuntu-24.04-arm
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- os: windows-intel
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runs-on: windows-latest
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- os: windows-arm
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runs-on: windows-11-arm
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- os: macos-intel
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# macos-15-intel is the last x86_64 runner
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runs-on: macos-15-intel
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- os: macos-arm
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# macos-14+ (including latest) are ARM64 runners
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runs-on: macos-latest
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steps:
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- uses: actions/checkout@v5
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- name: Build wheels
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uses: pypa/cibuildwheel@v3.3.0
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env:
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CIBW_PLATFORM: ${{ matrix.platform || 'auto' }}
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CIBW_ARCHS: ${{ matrix.archs || 'auto' }}
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# Can also be configured directly, using `with:`
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# with:
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# package-dir: .
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# output-dir: wheelhouse
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# config-file: "{package}/pyproject.toml"
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- uses: actions/upload-artifact@v4
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with:
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name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
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path: ./wheelhouse/*.whl
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build_sdist:
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name: Build source distribution
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- name: Build sdist
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run: pipx run build --sdist
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- uses: actions/upload-artifact@v4
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with:
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name: cibw-sdist
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path: dist/*.tar.gz
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# upload_pypi:
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# needs: [build_wheels, build_sdist]
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# runs-on: ubuntu-latest
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# environment: pypi
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# permissions:
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# id-token: write
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# if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
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# steps:
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# - uses: actions/download-artifact@v5
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# with:
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# # unpacks all CIBW artifacts into dist/
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# pattern: cibw-*
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# path: dist
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# merge-multiple: true
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# - uses: pypa/gh-action-pypi-publish@release/v1
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# # To test uploads to TestPyPI, uncomment the following:
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# with:
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# repository-url: https://test.pypi.org/legacy/
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github-release:
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needs: [build_wheels, build_sdist]
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name: >-
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Sign the distribution📦 with Sigstore
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and upload them to GitHub Release
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runs-on: ubuntu-latest
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permissions:
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contents: write # IMPORTANT: mandatory for making GitHub Releases
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id-token: write # IMPORTANT: mandatory for sigstore
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v6
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with:
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name: cibw-sdist
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path: dist/
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merge-multiple: true
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- name: Sign the dists with Sigstore🔏
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uses: sigstore/gh-action-sigstore-python@v3.1.0
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with:
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inputs: >-
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./dist/*.tar.gz
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./dist/*.whl
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- name: Create GitHub Release
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env:
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GITHUB_TOKEN: ${{ github.token }}
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run: >-
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gh release create
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"$GITHUB_REF_NAME"
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--repo "$GITHUB_REPOSITORY"
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--generate-notes --draft
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- name: Upload artifact signatures to GitHub Release
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env:
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GITHUB_TOKEN: ${{ github.token }}
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run: >-
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gh release upload
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"$GITHUB_REF_NAME" dist/**
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--repo "$GITHUB_REPOSITORY"
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‎.gitignore‎

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build/*
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*.egg-info/
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CGRtools/containers/_unpack.c

‎MANIFEST.in‎

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# Include documentation and license files
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include README.rst
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include LICENSE
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include readthedocs.yml
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# Include INCHI library files
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include INCHI/libinchi.so
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include INCHI/libinchi.dll
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include INCHI/LICENCE
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include INCHI/readme.txt
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# Include Cython source files
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include CGRtools/containers/_unpack.pyx
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# Include package data files
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include CGRtools/algorithms/calculate2d/clean2d.js
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# Include test files
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recursive-include test *.sdf *.rdf *.xyz *.rxn *.mrv *.txt
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# Include documentation
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recursive-include doc *.rst *.py *.ipynb
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# Include clean2d build files
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recursive-include clean2d *.json *.js README
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# Exclude build artifacts
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global-exclude *.pyc
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global-exclude *.pyo
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global-exclude __pycache__
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global-exclude *.so
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global-exclude *.c
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prune build
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prune dist
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prune CGRtools.egg-info
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prune __pycache__

‎pyproject.toml‎

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[build-system]
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requires = ["setuptools>=64", "wheel", "cython>=0.29,<3.2"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "CGRtools"
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version = "4.1.35"
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description = "Tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach"
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readme = "README.rst"
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requires-python = ">=3.8"
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license = "LGPL-3.0-or-later"
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authors = [
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{name = "Dr. Ramil Nugmanov", email = "nougmanoff@protonmail.com"},
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{name = "Dr. Timur Madzhidov", email = "tmadzhidov@gmail.com"},
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{name = "Valentina Afonina"}
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]
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maintainers = [
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{name = "Dr. Timur Madzhidov", email = "tmadzhidov@gmail.com"}
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]
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keywords = ["chemistry", "chemoinformatics", "CGR", "reaction", "molecule"]
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classifiers = [
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"Environment :: Plugins",
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"Intended Audience :: Science/Research",
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"Operating System :: OS Independent",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3 :: Only",
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"Programming Language :: Python :: 3.7",
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Topic :: Scientific/Engineering",
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"Topic :: Scientific/Engineering :: Chemistry",
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"Topic :: Scientific/Engineering :: Information Analysis",
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"Topic :: Software Development",
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"Topic :: Software Development :: Libraries",
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"Topic :: Software Development :: Libraries :: Python Modules"
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]
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dependencies = [
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"CachedMethods>=0.1.4,<0.2"
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]
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[project.optional-dependencies]
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mrv = ["lxml>=4.1"]
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clean2d = ["py-mini-racer>=0.4.0"]
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jit = ["numpy>=1.18", "numba>=0.50"]
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dev = [
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"wheel",
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"cython",
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"build",
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"pytest",
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"ipython"
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]
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[project.urls]
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Homepage = "https://github.com/cimm-kzn/CGRtools"
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Documentation = "https://cgrtools.readthedocs.io"
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Repository = "https://github.com/cimm-kzn/CGRtools"
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Issues = "https://github.com/cimm-kzn/CGRtools/issues"
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[tool.setuptools]
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zip-safe = false
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[tool.setuptools.packages.find]
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include = ["CGRtools*"]
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[tool.setuptools.package-data]
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"CGRtools.algorithms.calculate2d" = ["clean2d.js"]
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"CGRtools.containers" = ["_unpack.pyx"]
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[tool.cibuildwheel]
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build = ["cp310-*", "cp311-*", "cp312-*", "cp313-*", "cp314-*"]
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skip = ["*-musllinux_*", "pp*"]
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build-frontend = "build"

‎setup.py‎

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# You should have received a copy of the GNU Lesser General Public License
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# along with this program; if not, see <https://www.gnu.org/licenses/>.
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#
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from distutils.command.sdist import sdist
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from distutils.command.build import build
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from distutils.util import get_platform
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from importlib.util import find_spec
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import sys
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from pathlib import Path
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from setuptools import setup, Extension
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from setuptools.command.build_ext import build_ext as _build_ext
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class _sdist(sdist):
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def finalize_options(self):
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super().finalize_options()
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self.distribution.data_files.append(('lib', ['INCHI/libinchi.so', 'INCHI/libinchi.dll']))
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cmd_class = {'sdist': _sdist}
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if find_spec('wheel'):
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from wheel.bdist_wheel import bdist_wheel
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class _bdist_wheel(bdist_wheel):
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def finalize_options(self):
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super().finalize_options()
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self.root_is_pure = False
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platform = get_platform()
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if platform == 'win-amd64':
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self.distribution.data_files.append(('lib', ['INCHI/libinchi.dll']))
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elif platform == 'linux-x86_64':
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self.distribution.data_files.append(('lib', ['INCHI/libinchi.so']))
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class build_ext(_build_ext):
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"""Custom build_ext to handle Cython compilation."""
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def run(self):
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# Import Cython here and compile just before building
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try:
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from Cython.Build import cythonize
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if self.distribution.ext_modules:
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self.distribution.ext_modules = cythonize(
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self.distribution.ext_modules,
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language_level=3,
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compiler_directives={'embedsignature': True}
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)
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except ImportError:
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# If Cython is not available during build, look for pre-generated C files
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print("Cython not found. Looking for pre-generated C files...", file=sys.stderr)
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c_file = Path('CGRtools/containers/_unpack.c')
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if c_file.exists() and self.distribution.ext_modules:
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# Replace .pyx with .c in sources
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for ext in self.distribution.ext_modules:
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ext.sources = [src.replace('.pyx', '.c') for src in ext.sources]
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else:
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print("Warning: Neither Cython nor pre-generated C files found. "
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"Extension modules will not be built.", file=sys.stderr)
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self.distribution.ext_modules = []
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super().run()
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51-
cmd_class['bdist_wheel'] = _bdist_wheel
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56+
def get_data_files():
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"""Get platform-specific INCHI library files for wheel."""
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import platform
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data_files = []
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system = platform.system()
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machine = platform.machine()
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# Include INCHI libraries based on platform
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if system == 'Windows' and machine in ('AMD64', 'x86_64'):
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dll_path = Path('INCHI/libinchi.dll')
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if dll_path.exists():
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data_files.append(('lib', ['INCHI/libinchi.dll']))
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elif system == 'Linux' and machine in ('x86_64',):
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so_path = Path('INCHI/libinchi.so')
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if so_path.exists():
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data_files.append(('lib', ['INCHI/libinchi.so']))
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return data_files
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54-
if find_spec('cython'):
55-
class _build(build):
56-
def finalize_options(self):
57-
super().finalize_options()
58-
from Cython.Build import cythonize
59-
self.distribution.ext_modules = cythonize(self.distribution.ext_modules, language_level=3)
6076

61-
cmd_class['build'] = _build
77+
# Extension modules
78+
ext_modules = [
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Extension(
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'CGRtools.containers._unpack',
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['CGRtools/containers/_unpack.pyx'],
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extra_compile_args=['-O3']
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)
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]
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# For source distributions, include both library files
87+
if 'sdist' in sys.argv:
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data_files = [('lib', ['INCHI/libinchi.so', 'INCHI/libinchi.dll'])]
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else:
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data_files = get_data_files()
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6492
setup(
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name='CGRtools',
66-
version='4.1.35',
67-
packages=['CGRtools', 'CGRtools.algorithms', 'CGRtools.algorithms.calculate2d', 'CGRtools.algorithms.components',
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'CGRtools.algorithms.standardize', 'CGRtools.containers', 'CGRtools.files', 'CGRtools.files._mdl',
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'CGRtools.periodictable', 'CGRtools.periodictable.element', 'CGRtools.reactor', 'CGRtools.utils',
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'CGRtools.attributes'],
71-
url='https://github.com/cimm-kzn/CGRtools',
72-
license='LGPLv3',
73-
author='Dr. Ramil Nugmanov, Dr. Timur Madzhidov, Valentina Afonina',
74-
author_email='tmadzhidov@gmail.com',
75-
python_requires='>=3.6.1',
76-
cmdclass=cmd_class,
77-
ext_modules=[Extension('CGRtools.containers._unpack', ['CGRtools/containers/_unpack.pyx'],
78-
extra_compile_args=['-O3'])],
79-
setup_requires=['wheel', 'cython'],
80-
install_requires=['CachedMethods>=0.1.4,<0.2'],
81-
extras_require={'mrv': ['lxml>=4.1'], 'clean2d': ['py-mini-racer>=0.4.0'], 'jit': ['numpy>=1.18', 'numba>=0.50']},
82-
package_data={'CGRtools.algorithms.calculate2d': ['clean2d.js'], 'CGRtools.containers': ['_unpack.pyx']},
83-
data_files=[],
93+
ext_modules=ext_modules,
94+
data_files=data_files,
95+
cmdclass={'build_ext': build_ext},
8496
zip_safe=False,
85-
long_description=(Path(__file__).parent / 'README.rst').read_text(),
86-
classifiers=['Environment :: Plugins',
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'Intended Audience :: Science/Research',
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'License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)',
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'Operating System :: OS Independent',
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'Programming Language :: Python',
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'Programming Language :: Python :: 3 :: Only',
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'Programming Language :: Python :: 3.7',
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'Programming Language :: Python :: 3.8',
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'Programming Language :: Python :: 3.9',
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'Programming Language :: Python :: 3.10',
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'Topic :: Scientific/Engineering',
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'Topic :: Scientific/Engineering :: Chemistry',
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'Topic :: Scientific/Engineering :: Information Analysis',
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'Topic :: Software Development',
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'Topic :: Software Development :: Libraries',
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'Topic :: Software Development :: Libraries :: Python Modules'],
102-
command_options={'build_sphinx': {'source_dir': ('setup.py', 'doc'),
103-
'build_dir': ('setup.py', 'build/doc'),
104-
'all_files': ('setup.py', True)}}
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)

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