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github-actions[bot]Create or Update Pull Request Actionkuelumbus
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🤖 Bump RDKit version to Release_2024_09_1 (#116)
* Set RDKit version to Release_2024_09_1 * 🤖 Bump RDKit version to Release_2024_03_6 (#113) * Set RDKit version to Release_2024_03_6 * Fix boost detection issue with case-sensetive * Add python3 directory hint to cmake * Improve python root path finding. * Typo * Improve Python version detection for win * Add system lib install path of python * typo * Improve finding python 3 on win * Improve python finding for windows * Bump cmake and setupt tools * Add missing comma * improve lib finding * oops * deactivate tmate action * bump cibuildweehl * print config vars * Fix library path for python on win * Try * enable debug mode * give more search pa * Fix path * path * Get windows paths * oops * Fix * fix * try * test * test * Enable debug * t * Fix * test * Verbose output for compilation * verbose * Try 10 * enable find debug * fix * Fix * Clean up an try ninja for windows * Remove ninja on windows --------- Co-authored-by: Create or Update Pull Request Action <create-or-update-pull-request@users.noreply.github.com> Co-authored-by: Christopher Kuenneth <christopher.kuenneth@gmail.com> * Enable Python 3.13 builds in GH actions and circle cci * fix finding python3.11.lib * Fix python 3.13 builds * enable debug for macos * Remove CIBW_ARCHS keyword * Update GithubAction python version. * Update cmake * Specify arm64 for cmake builds * Fix --------- Co-authored-by: Create or Update Pull Request Action <create-or-update-pull-request@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Christopher Kuenneth <christopher.kuenneth@gmail.com> Co-authored-by: Chris Kuenneth <44866753+kuelumbus@users.noreply.github.com>
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‎.circleci/config.yml

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@@ -51,7 +51,7 @@ workflows:
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- linux-arm64-wheels:
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matrix:
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parameters:
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python-version: ["39", "310", "311", "312"]
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python-version: ["39", "310", "311", "312", "313"]
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# - osx-wheels:
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# matrix:
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# parameters:

‎.github/workflows/wheels.yml

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@@ -42,10 +42,10 @@ jobs:
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python: 312
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bitness: 64
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platform_id: win_amd64
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# - os: windows-2019
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# python: 313
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# bitness: 64
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# platform_id: win_amd64
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- os: windows-2019
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python: 313
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bitness: 64
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platform_id: win_amd64
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# Linux 64 bit Intel: x86_64
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- os: ubuntu-latest
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python: 312
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bitness: 64
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platform_id: manylinux_x86_64
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# - os: ubuntu-latest
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# python: 313
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# bitness: 64
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# platform_id: manylinux_x86_64
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- os: ubuntu-latest
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python: 313
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bitness: 64
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platform_id: manylinux_x86_64
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# Linux 64 bit ARM: aarch64 (on Circle CI)
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bitness: 64
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python: 312
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platform_id: macosx_arm64
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# - os: macos-14
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# bitness: 64
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# python: 313
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# platform_id: macosx_arm64
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- os: macos-14
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bitness: 64
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python: 313
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platform_id: macosx_arm64
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# MacOS 64 bit Intel: x86_64
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- os: macos-12
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bitness: 64
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python: 312
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platform_id: macosx_x86_64
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# - os: macos-12
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# bitness: 64
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# python: 313
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# platform_id: macosx_x86_64
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- os: macos-12
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bitness: 64
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python: 313
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platform_id: macosx_x86_64
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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name: Install Python
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with:
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python-version: '3.11'
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python-version: '3.13'
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- name: Export GitHub Actions cache environment variables for vcpkg
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if: ${{ runner.os == 'Windows' }}
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- name: Build wheels
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env:
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CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
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CIBW_ARCHS: all
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run: |
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if [ "$RUNNER_OS" == "Windows" ]; then

‎README.md

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@@ -18,13 +18,13 @@ Please open an issue if you find something missing or not working as expected.
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![GitHub Repo stars](https://img.shields.io/github/stars/kuelumbus/rdkit-pypi?style=for-the-badge&logo=github)
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## Available Builds
2020

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| OS | Arch | Bit | Conditions | 3.8 | 3.9 | 3.10 | 3.11 | 3.12 | CI |
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| ------- | ------- | --- | --------------------------------------------------- | -------------- | --- | ---- | ---- | ---- | ----------------- |
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| Linux | intel | 64 | glibc >= 2.28 (e.g., Ubuntu 18.04+, CentOS 6+, ...) | last: 2024.3.5 | ✔️ | ✔️ | ✔️ | ✔️ | Github Actions |
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| Linux | aarch64 | 64 | glibc >= 2.28 (e.g., Raspberry Pi, ...) | last: 2024.3.5 | ✔️ | ✔️ | ✔️ | ✔️ | Circle CI |
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| macOS | intel | 64 | >= macOS 10.13 | last: 2024.3.5 | ✔️ | ✔️ | ✔️ | ✔️ | Github Actions |
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| macOS | armv8 | 64 | >= macOS 11, M1 hardware | last: 2024.3.5 | ✔️ | ✔️ | ✔️ | ✔️ | Github Actions |
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| Windows | intel | 64 | | last: 2024.3.5 | ✔️ | ✔️ | ✔️ | ✔️ | Github Actions |
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| OS | Arch | Bit | Conditions | 3.8 | 3.9 | 3.10 | 3.11 | 3.12 | 3.13 | CI |
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| ------- | ------- | --- | --------------------------------------------------- | -------------- | --- | ---- | ---- | ---- | ---- | -------------- |
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| Linux | intel | 64 | glibc >= 2.28 (e.g., Ubuntu 18.04+, CentOS 6+, ...) | last: 2024.3.5 | ✔️ | ✔️ | ✔️ | ✔️ | ✔️ | Github Actions |
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| Linux | aarch64 | 64 | glibc >= 2.28 (e.g., Raspberry Pi, ...) | last: 2024.3.5 | ✔️ | ✔️ | ✔️ | ✔️ | ✔️ | Circle CI |
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| macOS | intel | 64 | >= macOS 10.13 | last: 2024.3.5 | ✔️ | ✔️ | ✔️ | ✔️ | ✔️ | Github Actions |
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| macOS | armv8 | 64 | >= macOS 11, M1 hardware | last: 2024.3.5 | ✔️ | ✔️ | ✔️ | ✔️ | ✔️ | Github Actions |
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| Windows | intel | 64 | | last: 2024.3.5 | ✔️ | ✔️ | ✔️ | ✔️ | ✔️ | Github Actions |
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## Installation
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‎pyproject.toml

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@@ -2,7 +2,7 @@
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requires = [
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"setuptools==75.2.0",
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"wheel",
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"cmake == 3.30.4",
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"cmake == 3.31.1",
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"numpy",
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"conan == 1.64.0",
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"ninja",

‎setup.py

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@@ -12,7 +12,7 @@
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from setuptools.command.build_ext import build_ext as build_ext_orig
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# RDKit version to build (tag from github repository)
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rdkit_tag = "Release_2024_03_6"
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rdkit_tag = "Release_2024_09_1"
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with open("README.md", "r", encoding="utf-8") as fh:
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long_description = fh.read()
@@ -176,21 +176,6 @@ def replace_all(file, search_exp, replace_exp):
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'target_link_libraries(rdkit_py_base INTERFACE "boost::python${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}" "boost::numpy${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}")',
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)
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# on windows, cmake is not configured to detect the python*.lib dynamic library
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#
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# replace_all(
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# "CMakeLists.txt",
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# 'target_link_libraries(rdkit_py_base INTERFACE ${Python3_LIBRARIES} )',
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# 'message("HERE")\n message(${Python3_LIBRARIES})\n target_link_libraries(rdkit_py_base INTERFACE ${Python3_LIBRARIES} )',
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# )
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# on windows; bug in 2024_03_6
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replace_all(
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"CMakeLists.txt",
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'target_link_libraries(rdkit_py_base INTERFACE ${Python3_LIBRARY} )',
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'target_link_libraries(rdkit_py_base INTERFACE ${Python3_LIBRARIES} )',
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)
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if "macosx" in os.environ["CIBW_BUILD"]:
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# Replace Cairo with cairo because conan uses lower case target names
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# only on MacOS cairo is installed using conan
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'target_link_libraries(MolDraw2D_static PUBLIC cairo::cairo)',
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)
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193+
# introduced in 2024_09_01 for compiling pubchem shape.
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replace_all(
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"External/pubchem_shape/Wrap/CMakeLists.txt",
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'find_package(Python3 COMPONENTS Interpreter Development NumPy REQUIRED)',
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'find_package(Python3 COMPONENTS Interpreter Development NumPy)',
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)
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print("---- Conf vars", file=sys.stderr)
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print(sysconfig.get_paths(), file=sys.stderr)
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print(sysconfig.get_config_vars(), file=sys.stderr)
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print("---- Conf vars", file=sys.stderr)
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print("---- Conf vars", file=sys.stderr)
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options += [
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"-DRDK_OPTIMIZE_POPCNT=OFF",
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# Otherwise, cmake tries to link the system freetype
291-
"-DFREETYPE_LIBRARY=/opt/homebrew/lib/libfreetype.dylib",
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"-DFREETYPE_INCLUDE_DIRS=/opt/homebrew/include",
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# "-DFREETYPE_LIBRARY=/opt/homebrew/lib/libfreetype.dylib",
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# "-DFREETYPE_INCLUDE_DIRS=/opt/homebrew/include",
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# Arm64 build start with development target 11.0
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f"-DCMAKE_OSX_DEPLOYMENT_TARGET={os.environ.get('MACOSX_DEPLOYMENT_TARGET', '11.0')}",
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f"-DCMAKE_OSX_ARCHITECTURES=arm64",
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f"-DCMAKE_VERBOSE_MAKEFILE=ON" # Increase verbosity
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]
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if "linux" in sys.platform:

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