🤖 Bump RDKit version to Release_2025_09_4 (#145) [skip ci]

* Set RDKit version to Release_2025_09_4

* ci: Update macos-13 to macos-14 (runner retired)

* cherry pick fix for macos

* ci: update cibuildwheel version to 3.3.1 for wheel builds

* deprecate  macOS intel

* Eigen3 is now available in the windows runner image.

---------

Co-authored-by: Create or Update Pull Request Action <create-or-update-pull-request@users.noreply.github.com>
Co-authored-by: Chris Kuenneth <christopher.kuenneth@gmail.com>

Author: 3 people

.circleci/config.yml

@@ -18,7 +18,7 @@ jobs:
             CIBW_ARCHS: aarch64
 
           command: |
-            python3 -m pip install cibuildwheel==3.1.1
+            python3 -m pip install cibuildwheel==3.3.1
             python3 -m cibuildwheel --output-dir wheelhouse
       - store_artifacts:
           path: wheelhouse/

.github/workflows/wheels.yml

@@ -94,26 +94,26 @@ jobs:
             platform_id: macosx_arm64
 
           # MacOS 64 bit Intel: x86_64
-          - os: macos-13
-            bitness: 64
-            python: 310
-            platform_id: macosx_x86_64
-          - os: macos-13
-            bitness: 64
-            python: 311
-            platform_id: macosx_x86_64
-          - os: macos-13
-            bitness: 64
-            python: 312
-            platform_id: macosx_x86_64
-          - os: macos-13
-            bitness: 64
-            python: 313
-            platform_id: macosx_x86_64
-          - os: macos-13
-            bitness: 64
-            python: 314
-            platform_id: macosx_x86_64
+          # - os: macos-14
+          #   bitness: 64
+          #   python: 310
+          #   platform_id: macosx_x86_64
+          # - os: macos-14
+          #   bitness: 64
+          #   python: 311
+          #   platform_id: macosx_x86_64
+          # - os: macos-14
+          #   bitness: 64
+          #   python: 312
+          #   platform_id: macosx_x86_64
+          # - os: macos-14
+          #   bitness: 64
+          #   python: 313
+          #   platform_id: macosx_x86_64
+          # - os: macos-14
+          #   bitness: 64
+          #   python: 314
+          #   platform_id: macosx_x86_64
 
     steps:
       - uses: actions/checkout@v4
@@ -158,7 +158,7 @@ jobs:
             cd C:\\rdkit
             echo "C:\\libs" >> $GITHUB_PATH
           fi
-          python -m pip install cibuildwheel==3.1.1
+          python -m pip install cibuildwheel==3.3.1
           python -m cibuildwheel --output-dir wheelhouse
         shell: bash
 

README.md

@@ -22,7 +22,7 @@ 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 | last: 2025.9.2    | ✔️    | ✔️    | ✔️    | ✔️    | ✔️    | Github Actions |
 | Linux   | aarch64 | 64  | glibc >= 2.28 (e.g., Raspberry Pi, ...)             | last: 2024.3.5 | last: 2025.9.2   | ✔️    | ✔️    | ✔️    | ✔️    | ✔️    | Circle CI      |
-| macOS   | intel   | 64  | >= macOS 10.15                                      | last: 2024.3.5 | last: 2025.9.2   | ✔️    | ✔️    | ✔️    | ✔️    | ✔️    | Github Actions |
+| macOS   | intel   | 64  | >= macOS 10.15                                      | last: 2024.3.5 | last: 2025.9.2   | last: 2025.9.4    | last: 2025.9.4    | last: 2025.9.4    | last: 2025.9.4    | last: 2025.9.4    | Github Actions |
 | macOS   | armv8   | 64  | >= macOS 11, M-Hardware                             | last: 2024.3.5 | last: 2025.9.2   | ✔️    | ✔️    | ✔️    | ✔️    | ✔️    | Github Actions | 
 | Windows | intel   | 64  |                                                     | last: 2024.3.5 | last: 2025.9.2   | ✔️    | ✔️    | ✔️    | ✔️    | ✔️    | Github Actions |
 

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_2025_09_3"
+rdkit_tag = "Release_2025_09_4"
 
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
@@ -118,6 +118,22 @@ def build_rdkit(self, ext):
 
         # Start build process
         os.chdir(str("rdkit"))
+        if rdkit_tag == "Release_2025_09_4":
+            # Cherry-pick fix for MolAlign: brace-init BestAlignmentParams in wrapper
+            # https://github.com/rdkit/rdkit/pull/9042/commits/7c15baca9d662506b61d3395a0d5139be2b67640
+            check_call(["git", "config", "--global", "user.email", '"you@example.com"'])
+            check_call(["git", "config", "--global", "user.name", '"Your Name"'])
+            check_call(["git", "fetch", "origin", "pull/9042/head:pr_9042"])
+            check_call(
+                [
+                    "git",
+                    "cherry-pick",
+                    "--strategy=recursive",
+                    "-X",
+                    "theirs",
+                    "7c15baca9d662506b61d3395a0d5139be2b67640",
+                ]
+            )
 
         # if rdkit_tag == "Release_2025_03_3":
         #     # https://github.com/rdkit/rdkit/pull/8399/commits/e5b1e3caf0c362139a5905575b5f995c470b9300

vcpkg.json

@@ -8,10 +8,6 @@
         {
             "name": "freetype",
             "platform": "windows"
-        },
-        {
-            "name": "eigen3",
-            "platform": "windows"
         }
     ]
 }