🤖 Bump RDKit version to Release_2024_09_2

.circleci/config.yml

@@ -18,7 +18,7 @@ jobs:
             CIBW_ARCHS: aarch64
 
           command: |
-            python3 -m pip install cibuildwheel==2.21.3
+            python3 -m pip install cibuildwheel==2.22.0
             python3 -m cibuildwheel --output-dir wheelhouse
       - store_artifacts:
           path: wheelhouse/

.github/workflows/wheels.yml

@@ -94,23 +94,23 @@ jobs:
             platform_id: macosx_arm64
 
           # MacOS 64 bit Intel: x86_64
-          - os: macos-12
+          - os: macos-13
             bitness: 64
             python: 39
             platform_id: macosx_x86_64
-          - os: macos-12
+          - os: macos-13
             bitness: 64
             python: 310
             platform_id: macosx_x86_64
-          - os: macos-12
+          - os: macos-13
             bitness: 64
             python: 311
             platform_id: macosx_x86_64
-          - os: macos-12
+          - os: macos-13
             bitness: 64
             python: 312
             platform_id: macosx_x86_64
-          - os: macos-12
+          - os: macos-13
             bitness: 64
             python: 313
             platform_id: macosx_x86_64
@@ -158,7 +158,7 @@ jobs:
             cd C:\\rdkit
             echo "C:\\libs" >> $GITHUB_PATH
           fi
-          python -m pip install cibuildwheel==2.21.3
+          python -m pip install cibuildwheel==2.22.0
           python -m cibuildwheel --output-dir wheelhouse
         shell: bash
 

README.md

@@ -23,7 +23,7 @@ Please open an issue if you find something missing or not working as expected.
 | 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 |
+| macOS   | armv8   | 64  | >= macOS 11, M1 hardware                            | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    |  ✔️   | Github Actions |
 | Windows | intel   | 64  |                                                     | last: 2024.3.5 | ✔️   | ✔️    | ✔️    | ✔️    | ✔️    | Github Actions |
 
 ## Installation

pyproject.toml

@@ -4,7 +4,7 @@ requires = [
     "wheel",
     "cmake == 3.31.1",
     "numpy",
-    "conan == 1.64.0",
+    "conan == 1.66.0",
     "ninja",
     "pybind11-stubgen",
     "Pillow",  # required for building the stubs

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_09_1"
+rdkit_tag = "Release_2024_09_2"
 
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
@@ -196,21 +196,8 @@ def replace_all(file, search_exp, replace_exp):
             '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)
-        print(sysconfig.get_paths(), file=sys.stderr)
-        print(sysconfig.get_config_vars(), file=sys.stderr)
-        print("---- Conf vars", file=sys.stderr)
-
+
 
         # Define CMake options
         options = [
@@ -294,6 +281,14 @@ def to_win_path(pt: Path):
                 f"-DCMAKE_OSX_ARCHITECTURES=arm64",
                 f"-DCMAKE_VERBOSE_MAKEFILE=ON" # Increase verbosity
             ]
+            # for python 3.13 macOS ARM64, 'CFLAGS', 'LDFLAGS', 'LDSHARED', 'BLDSHARED'  contains '-arch x86_64'
+            #  see https://github.com/rdkit/rdkit/blob/498f57a4eb99a67d842cbc3f89f94b302f398a11/CMakeLists.txt#L376C59-L376C95
+            # remove "-arch x86_64" from PYTHON_LDSHARED
+            if "cp313" in os.environ["CIBW_BUILD"]:
+                old =  '${Python3_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var(\'LDSHARED\').lstrip().split(\' \', 1)[1])"'
+                new = '${Python3_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var(\'LDSHARED\').lstrip().split(\' \', 1)[1].replace(\'-arch x86_64\', \'\'))"'
+                replace_all("CMakeLists.txt", old, new)
+
 
         if "linux" in sys.platform:
             # Use ninja for linux builds
@@ -310,7 +305,7 @@ def to_win_path(pt: Path):
             ]
         else:
             cmds = [
-                f"cmake -S . -B build --debug-find-pkg=Python3 {' '.join(options)} ",
+                f"cmake -S . -B build -LAH --debug-find-pkg=Python3 {' '.join(options)} ",
                 "cmake --build build --config Release",
                 "cmake --install build",
             ]
@@ -321,6 +316,13 @@ def to_win_path(pt: Path):
         path_site_packages = rdkit_install_path / "lib" / py_name / "site-packages"
         if sys.platform == "win32":
             path_site_packages = rdkit_install_path / "Lib" / "site-packages"
+
+
+        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("!!! --- CMAKE build command and variables for RDKit", file=sys.stderr)
         print(cmds, file=sys.stderr)