🤖 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 <[email protected]> Co-authored-by: Christopher Kuenneth <[email protected]> * 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 <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Christopher Kuenneth <[email protected]> Co-authored-by: Chris Kuenneth <[email protected]>
kuelumbus · Dec 29, 2024 · 54f333a · 54f333a
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -51,7 +51,7 @@ workflows:
       - linux-arm64-wheels:
           matrix:
             parameters:
-              python-version: ["39", "310", "311", "312"]
+              python-version: ["39", "310", "311", "312", "313"]
       # - osx-wheels:
       #     matrix:
       #       parameters:

diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -42,10 +42,10 @@ jobs:
             python: 312
             bitness: 64
             platform_id: win_amd64
-          # - os: windows-2019
-          #   python: 313
-          #   bitness: 64
-          #   platform_id: win_amd64
+          - os: windows-2019
+            python: 313
+            bitness: 64
+            platform_id: win_amd64
 
           # Linux 64 bit Intel: x86_64
           - os: ubuntu-latest
@@ -64,10 +64,10 @@ jobs:
             python: 312
             bitness: 64
             platform_id: manylinux_x86_64
-          # - os: ubuntu-latest
-          #   python: 313
-          #   bitness: 64
-          #   platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 313
+            bitness: 64
+            platform_id: manylinux_x86_64
 
           # Linux 64 bit ARM: aarch64 (on Circle CI)
 
@@ -88,10 +88,10 @@ jobs:
             bitness: 64
             python: 312
             platform_id: macosx_arm64
-          # - os: macos-14
-          #   bitness: 64
-          #   python: 313
-          #   platform_id: macosx_arm64
+          - os: macos-14
+            bitness: 64
+            python: 313
+            platform_id: macosx_arm64
 
           # MacOS 64 bit Intel: x86_64
           - os: macos-12
@@ -110,10 +110,10 @@ jobs:
             bitness: 64
             python: 312
             platform_id: macosx_x86_64
-          # - os: macos-12
-          #   bitness: 64
-          #   python: 313
-          #   platform_id: macosx_x86_64
+          - os: macos-12
+            bitness: 64
+            python: 313
+            platform_id: macosx_x86_64
 
     steps:
       - uses: actions/checkout@v4
@@ -126,7 +126,7 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.11'
+          python-version: '3.13'
 
       - name: Export GitHub Actions cache environment variables for vcpkg
         if: ${{ runner.os == 'Windows' }}
@@ -152,7 +152,6 @@ jobs:
       - name: Build wheels
         env:
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
-          CIBW_ARCHS: all
 
         run: |
           if [ "$RUNNER_OS" == "Windows" ]; then

diff --git a/README.md b/README.md
@@ -18,13 +18,13 @@ Please open an issue if you find something missing or not working as expected.
 ![GitHub Repo stars](https://img.shields.io/github/stars/kuelumbus/rdkit-pypi?style=for-the-badge&logo=github)
 ## Available Builds
 
-| OS      | Arch    | Bit | Conditions                                          | 3.8            | 3.9 | 3.10 | 3.11 | 3.12 | CI                |
-| ------- | ------- | --- | --------------------------------------------------- | -------------- | --- | ---- | ---- | ---- | ----------------- |
-| Linux   | intel   | 64  | glibc >= 2.28 (e.g., Ubuntu 18.04+, CentOS 6+, ...) | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    | Github Actions    |
-| Linux   | aarch64 | 64  | glibc >= 2.28 (e.g., Raspberry Pi, ...)             | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    | Circle CI         |
-| macOS   | intel   | 64  | >= macOS 10.13                                      | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    | Github Actions    |
-| macOS   | armv8   | 64  | >= macOS 11, M1 hardware                            | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    | Github Actions |
-| Windows | intel   | 64  |                                                     | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    | Github Actions    |
+| OS      | Arch    | Bit | Conditions                                          | 3.8            | 3.9 | 3.10 | 3.11 | 3.12 | 3.13 | CI             |
+| ------- | ------- | --- | --------------------------------------------------- | -------------- | --- | ---- | ---- | ---- | ---- | -------------- |
+| Linux   | intel   | 64  | glibc >= 2.28 (e.g., Ubuntu 18.04+, CentOS 6+, ...) | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    | ✔️    | Github Actions |
+| Linux   | aarch64 | 64  | glibc >= 2.28 (e.g., Raspberry Pi, ...)             | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    | ✔️    | Circle CI      |
+| macOS   | intel   | 64  | >= macOS 10.13                                      | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    | ✔️    | Github Actions |
+| macOS   | armv8   | 64  | >= macOS 11, M1 hardware                            | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    | ✔️    | Github Actions |
+| Windows | intel   | 64  |                                                     | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    | ✔️    | Github Actions |
 
 ## Installation
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -2,7 +2,7 @@
 requires = [
     "setuptools==75.2.0",
     "wheel",
-    "cmake == 3.30.4",
+    "cmake == 3.31.1",
     "numpy",
     "conan == 1.64.0",
     "ninja",

diff --git a/setup.py b/setup.py
@@ -12,7 +12,7 @@
 from setuptools.command.build_ext import build_ext as build_ext_orig
 
 # RDKit version to build (tag from github repository)
-rdkit_tag = "Release_2024_03_6"
+rdkit_tag = "Release_2024_09_1"
 
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
@@ -176,21 +176,6 @@ def replace_all(file, search_exp, replace_exp):
             'target_link_libraries(rdkit_py_base INTERFACE "boost::python${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}" "boost::numpy${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}")',
         )
 
-        # on windows, cmake is not configured to detect the python*.lib dynamic library
-        # 
-        # replace_all(
-        #     "CMakeLists.txt",
-        #     'target_link_libraries(rdkit_py_base INTERFACE ${Python3_LIBRARIES} )',
-        #     'message("HERE")\n message(${Python3_LIBRARIES})\n target_link_libraries(rdkit_py_base INTERFACE ${Python3_LIBRARIES} )',
-        # )
-
-        # on windows; bug in 2024_03_6
-        replace_all(
-            "CMakeLists.txt",
-            'target_link_libraries(rdkit_py_base INTERFACE ${Python3_LIBRARY} )',
-            'target_link_libraries(rdkit_py_base INTERFACE ${Python3_LIBRARIES} )',
-        )
-
         if "macosx" in os.environ["CIBW_BUILD"]:
             # Replace Cairo with cairo because conan uses lower case target names
             # only on MacOS cairo is installed using conan
@@ -205,6 +190,20 @@ def replace_all(file, search_exp, replace_exp):
                 'target_link_libraries(MolDraw2D_static PUBLIC cairo::cairo)',
             )
 
+        # introduced in 2024_09_01 for compiling pubchem shape.
+        replace_all(
+            "External/pubchem_shape/Wrap/CMakeLists.txt",
+            'find_package(Python3 COMPONENTS Interpreter Development NumPy REQUIRED)',
+            'find_package(Python3 COMPONENTS Interpreter Development NumPy)',
+        )
+
+
+
+        print("---- Conf vars", file=sys.stderr)
+        print(sysconfig.get_paths(), file=sys.stderr)
+        print(sysconfig.get_config_vars(), file=sys.stderr)
+        print("---- Conf vars", file=sys.stderr)
+
 
 
         print("---- Conf vars", file=sys.stderr)
@@ -288,10 +287,12 @@ def to_win_path(pt: Path):
             options += [
                 "-DRDK_OPTIMIZE_POPCNT=OFF",
                 # Otherwise, cmake tries to link the system freetype
-                "-DFREETYPE_LIBRARY=/opt/homebrew/lib/libfreetype.dylib",
-                "-DFREETYPE_INCLUDE_DIRS=/opt/homebrew/include",
+                # "-DFREETYPE_LIBRARY=/opt/homebrew/lib/libfreetype.dylib",
+                # "-DFREETYPE_INCLUDE_DIRS=/opt/homebrew/include",
                 # Arm64 build start with development target 11.0
                 f"-DCMAKE_OSX_DEPLOYMENT_TARGET={os.environ.get('MACOSX_DEPLOYMENT_TARGET', '11.0')}",
+                f"-DCMAKE_OSX_ARCHITECTURES=arm64",
+                f"-DCMAKE_VERBOSE_MAKEFILE=ON" # Increase verbosity
             ]
 
         if "linux" in sys.platform: