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github-actions[bot]Create or Update Pull Request Actionkuelumbus
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🤖 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>
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‎.circleci/config.yml

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@@ -18,7 +18,7 @@ jobs:
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CIBW_ARCHS: aarch64
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command: |
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python3 -m pip install cibuildwheel==2.20.0
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python3 -m pip install cibuildwheel==2.21.3
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python3 -m cibuildwheel --output-dir wheelhouse
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- store_artifacts:
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path: wheelhouse/

‎.github/workflows/wheels.yml

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@@ -159,7 +159,7 @@ jobs:
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cd C:\\rdkit
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echo "C:\\libs" >> $GITHUB_PATH
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fi
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python -m pip install cibuildwheel==2.20.0
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python -m pip install cibuildwheel==2.21.3
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python -m cibuildwheel --output-dir wheelhouse
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shell: bash
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‎pyproject.toml

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@@ -1,8 +1,8 @@
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[build-system]
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requires = [
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"setuptools==69.2.0",
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"setuptools==75.2.0",
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"wheel",
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"cmake == 3.26.4",
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"cmake == 3.30.4",
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"numpy",
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"conan == 1.64.0",
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"ninja",

‎setup.py

Lines changed: 42 additions & 16 deletions
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@@ -5,14 +5,14 @@
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from pathlib import Path
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from shutil import copytree, rmtree, ignore_patterns
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from subprocess import call, check_call
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from sysconfig import get_paths
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import sysconfig
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from textwrap import dedent
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from setuptools import Extension, find_packages, setup
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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_5"
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rdkit_tag = "Release_2024_03_6"
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with open("README.md", "r", encoding="utf-8") as fh:
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long_description = fh.read()
@@ -168,14 +168,28 @@ def replace_all(file, search_exp, replace_exp):
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# Fix a bug in conan or rdkit: target name for numpy is boost::numpy{pyversion} with small 'b'
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# and not Boost::numpy{pyversion}
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# Line 345 in 2024_03_04 in CMakeLists.txt
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# target_link_libraries(rdkit_py_base INTERFACE Boost::${Boost_Python_Lib} "Boost::numpy${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")
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# Line 312 in 2024_03_06 in CMakeLists.txt
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# NEW: target_link_libraries(rdkit_py_base INTERFACE "Boost::python${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}" "Boost::numpy${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}")
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replace_all(
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"CMakeLists.txt",
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'target_link_libraries(rdkit_py_base INTERFACE Boost::${Boost_Python_Lib} "Boost::numpy${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")',
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'target_link_libraries(rdkit_py_base INTERFACE Boost::${Boost_Python_Lib} "boost::numpy${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")',
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'target_link_libraries(rdkit_py_base INTERFACE "Boost::python${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}" "Boost::numpy${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}")',
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'target_link_libraries(rdkit_py_base INTERFACE "boost::python${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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)
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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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# Define CMake options
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options = [
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# f"-DCMAKE_FIND_DEBUG_MODE=ON", # Enable debug mode
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f"-DCMAKE_TOOLCHAIN_FILE={conan_toolchain_path / 'conan_toolchain.cmake'}",
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# For the toolchain file this needs to be set
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f"-DCMAKE_POLICY_DEFAULT_CMP0091=NEW",
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# Boost_VERSION_STRING is set but Boost_LIB_VERSION is not set by conan.
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# Boost_LIB_VERSION is required by RDKit => Set manually
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f"-DBoost_LIB_VERSION={boost_lib_version}",
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# Select correct python interpreter
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f"-DPYTHON_EXECUTABLE={sys.executable}",
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f"-DPYTHON_INCLUDE_DIR={get_paths()['include']}",
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# Select correct python 3 version
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f"-DPython3_ROOT_DIR={Path(sys.prefix)}",
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# RDKit build flags
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"-DRDK_BUILD_INCHI_SUPPORT=ON",
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"-DRDK_BUILD_AVALON_SUPPORT=ON",
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"-DRDK_BUILD_PYTHON_WRAPPERS=ON",
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"-DRDK_BOOST_PYTHON3_NAME=python", # Overwrite this. This is the name of the interface in cmake defined by conan.
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"-DRDK_BUILD_YAEHMOP_SUPPORT=ON",
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"-DRDK_BUILD_XYZ2MOL_SUPPORT=ON",
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"-DRDK_INSTALL_INTREE=OFF",
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vcpkg_path = cwd
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vcpkg_inc = vcpkg_path / "vcpkg_installed" / "x64-windows" / "include"
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vcpkg_lib = vcpkg_path / "vcpkg_installed" / "x64-windows" / "lib"
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if sys.platform == "win32":
253+
def to_win_path(pt: Path):
254+
return str(pt).replace("\\", "/")
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options += [
233-
"-Ax64",
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# DRDK_INSTALL_STATIC_LIBS should be fixed in newer RDKit builds. Remove?
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"-DRDK_INSTALL_STATIC_LIBS=OFF",
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"-DRDK_INSTALL_DLLS_MSVC=ON",
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]
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239-
def to_win_path(pt: Path):
240-
return str(pt).replace("\\", "/")
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# Link cairo and freetype
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options += [
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f"-DCAIRO_INCLUDE_DIR={to_win_path(vcpkg_inc)}",
@@ -277,13 +297,19 @@ def to_win_path(pt: Path):
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if "linux" in sys.platform:
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# Use ninja for linux builds
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cmds = [
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f"cmake -S . -B build -G Ninja {' '.join(options)} ",
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f"cmake -S . -B build -G Ninja --debug-find-pkg=Python3 {' '.join(options)} ",
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"cmake --build build --config Release",
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"cmake --install build",
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]
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elif sys.platform == "win32":
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cmds = [
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f"cmake -S . -B build --debug-find-pkg=Python3 {' '.join(options)} ",
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"cmake --build build --config Release -v",
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"cmake --install build",
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]
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else:
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cmds = [
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f"cmake -S . -B build {' '.join(options)} ",
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f"cmake -S . -B build --debug-find-pkg=Python3 {' '.join(options)} ",
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"cmake --build build --config Release",
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"cmake --install build",
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]

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