🤖 Bump RDKit version to Release_2024_03_3 (#101)

* Set RDKit version to Release_2024_03_3

* 🤖 Bump RDKit version to Release_2024_03_1 (#97)

* Set RDKit version to Release_2024_03_1

* Set RDKit version to Release_2024_03_1

* 🤖 Bump RDKit version to Release_2023_09_6 (#93)

* Set RDKit version to Release_2023_09_6

* Add the site-packages path to the PYTHONPATH. The rdkit stubs script tries to find the site-package path.

* Install, then build stubs.

* Build stubs and add to wheel files

* Update

* Update actions

* Chreey-pick font fix and copy stubs to `rdkit-stubs` directory

* Add copy log

* Correct copytree logging

* Bump cibuildwheel

* Pin setuptools version

* Auto search for files to include in the wheels

* Fix artifact upload

* Refactor paths

* Enable ssh

* Switch to arm GH action runners (macos-14).

* Copy dlls to project directory for windows.

* Cahne compile profile and add workaround for unary function

* Reenable UNARY_BINARY_FUNCTION

* try other flags

* Windows: make sure dlls, pyds, and libs are copied.

* Use boost 1.81 for macOS arm64 wheels

* Remove the cross compilation code.

* Enable cirrus builds

* set boost version to 1.82 for mac arm64

* Tyr other windows paths for placing dlls.

* Set boost version to 1.84 for mac arm64

* Try different dylib path

* Decativate copying dylibs for macos

* Use monterey runners

* Set dylib directory to home/lib

* Pass search path to build command

* Fix setting DYLD_LIBRARY_PATH

* Disable arm64 builds on GH Actions. This is too slow

* Remove deprecated code

* Disable cross compilation code

* Add cirrus CI

* Make lib dir before copying.

* Add lib path to delocate

* Change lib path to absolute

* setup ssh only if failure

* Enable win builds on cirrus ci

* Remove cirrus ci  windows builds

* Print stubs errors to comand line

* Correct path

* correct path again

* Add pillow as build requirement. It's required for building the stubs.

* Enable ssh for windows

* Don't include *.pyc files in the wheels

* Fix ignore function

* Run ssh on a workflow_dispatch "manual event"

* Remove event

* add lib dir to path env

* Add more dll search paths

* Search for pyd dll and lib

* Add VCPKG lib path to PATH env variable

* Add vcpkg binary cache

* Speed up builds with ninja

* Fix ninja build

* Remove ninja build flags

* Run tmate terminal only on debug flag

---------

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>

* [skip ci] Install freetype for mac builds

* Add freetype path explicitly [skip ci]

* Overwrite build settings for mac [skip ci]

* Fix settings

* Remove freetype hints [skip ci]

* Fix python 3.8 armv8 macos issue [skip ci]

* Fix syntax [skip ci]

* fix again [skip ci]

* Cleaning

* Bump conan to 1.64.0

* Remove rdkit cherry pick

* Set RDKit version to Release_2024_03_1

* Remove cherry picking code

* Enable ninja builds for linux to speed

* Merge branch 'main' into bump-rdkit-Release_2024_03_1

---------

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>

* Enable tmate on fail

* trigger on push and pull

* Revert GH trigger

* Avoid linking VCRUNTIME140_1 for widnows builds

* 🤖 Bump RDKit version to Release_2024_03_2 (#100)

* Set RDKit version to Release_2024_03_2

* Merge branch 'main' into bump-rdkit-Release_2024_03_2

* Drop the cherry picking code again

* Retire oldest-supported-numpy package

* Update boost version to make compatible with numpy 2

* Fix windows builds

* Enable tmate on fail

* Trigger

* update actions trigger

* Revert changes

* Avoid linking VCRUNTIME140_1

* downgrade boost to 1.78 for windows

* Correct if statement

* set bosot to 1.85   [skip ci]

* tyr boost 1.78 [skip ci]

* Disable tests [skip ci]

* remove

* Skip tests

* Modify names of uploads [skip ci]

* Choose different boost version [skip ci]

* Add numpy 2 patch [skip ci]

* Fix dll search path for windows stubs [skip ci]

* Add Python 3.11 patch back [skip ci]

* Fix patch file format

* Bump cibuildwheel to 2.19.1

* Fix code to append to python path

* Use UV build frontend

* Enable macos builds on circle ci

* Fix config

* Fix xcode

* Compile with  numpy <2.0

* Restrict numpy to smaller 2.0

* Fix

---------

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>
Co-authored-by: Chris Kuenneth <44866753+kuelumbus@users.noreply.github.com>

* Disable osx builds on circle ci

* Allow numpy 2.0

* Fix yum sources

* Fix yum install

* Fix yum commands

* Set boost version for windows to 1.78 [skip ci]

* Upgrade  to new manylinux image 2_28

* Fix Windows compiler errors

* Update Readme [skip ci]

---------

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>

Author: 3 people

.circleci/config.yml

@@ -16,35 +16,33 @@ jobs:
           environment:
             CIBW_BUILD: cp<< parameters.python-version >>-manylinux_aarch64
             CIBW_ARCHS: aarch64
-            CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
-            CIBW_MANYLINUX_I686_IMAGE: manylinux2014
 
           command: |
             python3 -m pip install cibuildwheel==2.17.0
             python3 -m cibuildwheel --output-dir wheelhouse
       - store_artifacts:
           path: wheelhouse/
 
-  osx-wheels:
-    working_directory: ~/osx-wheels
-    macos:
-      xcode: 15.4.0
-    resource_class: macos.m1.medium.gen1
-    parameters:
-      python-version:
-        type: string
-    steps:
-      - checkout
-      - run:
-          name: Build the OS X wheels.
-          environment:
-            CIBW_BUILD: cp<< parameters.python-version >>-macosx_arm64
+  # osx-wheels:
+  #   working_directory: ~/osx-wheels
+  #   macos:
+  #     xcode: 15.4.0
+  #   resource_class: macos.m1.medium.gen1
+  #   parameters:
+  #     python-version:
+  #       type: string
+  #   steps:
+  #     - checkout
+  #     - run:
+  #         name: Build the OS X wheels.
+  #         environment:
+  #           CIBW_BUILD: cp<< parameters.python-version >>-macosx_arm64
 
-          command: |
-            pip3 install cibuildwheel==2.17.0
-            cibuildwheel --output-dir wheelhouse
-      - store_artifacts:
-          path: wheelhouse/
+  #         command: |
+  #           pip3 install cibuildwheel==2.17.0
+  #           cibuildwheel --output-dir wheelhouse
+  #     - store_artifacts:
+  #         path: wheelhouse/
 
 
 workflows:
@@ -54,7 +52,8 @@ workflows:
           matrix:
             parameters:
               python-version: ["38", "39", "310", "311", "312"]
-      - osx-wheels:
-          matrix:
-            parameters:
-              python-version: ["38", "39", "310", "311", "312"]
+      # - osx-wheels:
+      #     matrix:
+      #       parameters:
+      #         python-version: ["38", "39", "310", "311", "312"]
+

.github/workflows/wheels.yml

@@ -53,27 +53,22 @@ jobs:
             python: 38
             bitness: 64
             platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
           - os: ubuntu-latest
             python: 39
             bitness: 64
             platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
           - os: ubuntu-latest
             python: 310
             bitness: 64
             platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
           - os: ubuntu-latest
             python: 311
             bitness: 64
             platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
           - os: ubuntu-latest
             python: 312
             bitness: 64
             platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
 
           # Linux 64 bit ARM: aarch64 (on Circle CI)
 
@@ -137,8 +132,6 @@ jobs:
         env:
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
           CIBW_ARCHS: all
-          CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.manylinux_image }}
-          CIBW_MANYLINUX_I686_IMAGE: ${{ matrix.manylinux_image }}
 
         run: |
           if [ "$RUNNER_OS" == "Windows" ]; then

README.md

@@ -20,8 +20,8 @@ Please open an issue if you find something missing or not working as expected.
 
 | OS      | Arch    | Bit | Conditions                                          | 3.8 | 3.9 | 3.10 | 3.11 | 3.12 | CI             |
 | ------- | ------- | --- | --------------------------------------------------- | --- | --- | ---- | ---- | ---- | -------------- |
-| Linux   | intel   | 64  | glibc >= 2.17 (e.g., Ubuntu 16.04+, CentOS 6+, ...) | ✔️   | ✔️   | ✔️    | ✔️    | ✔️    | Github Actions |
-| Linux   | aarch64 | 64  | glibc >= 2.17 (e.g., Raspberry Pi, ...)             | ✔️   | ✔️   | ✔️    | ✔️    | ✔️    | Circle CI      |
+| Linux   | intel   | 64  | glibc >= 2.28 (e.g., Ubuntu 18.04+, CentOS 6+, ...) | ✔️   | ✔️   | ✔️    | ✔️    | ✔️    | Github Actions |
+| Linux   | aarch64 | 64  | glibc >= 2.28 (e.g., Raspberry Pi, ...)             | ✔️   | ✔️   | ✔️    | ✔️    | ✔️    | Circle CI      |
 | macOS   | intel   | 64  | >= macOS 10.13                                      | ✔️   | ✔️   | ✔️    | ✔️    | ✔️    | Github Actions |
 | macOS   | armv8   | 64  | >= macOS 11, M1 hardware                            | ✔️   | ✔️   | ✔️    | ✔️    | ✔️    | Cirrus CI Actions |
 | Windows | intel   | 64  |                                                     | ✔️   | ✔️   | ✔️    | ✔️    | ✔️    | Github Actions |

pyproject.toml

@@ -3,7 +3,7 @@ requires = [
     "setuptools==69.2.0",
     "wheel",
     "cmake == 3.26.4",
-    "numpy < 2.0",
+    "numpy",
     "conan == 1.64.0",
     "ninja",
     "pybind11-stubgen",
@@ -21,20 +21,14 @@ test-command = "pytest --exitfirst --verbose --failed-first {package}/tests"
 # test-skip = "*-win_amd64"
 
 
+manylinux-x86_64-image = "quay.io/pypa/manylinux_2_28_x86_64:latest"
+manylinux-aarch64-image = "quay.io/pypa/manylinux_2_28_aarch64:latest"
+
+
 [tool.cibuildwheel.linux]
 before-all = [
-    # Has eigen3-devel.aarch64
-    "yum install -y epel-release",
-    # "yum install -y wget freetype-devel libpng12-devel pixman-devel zlib-devel eigen3-devel",
-    "yum install -y wget freetype-devel libpng12-devel pixman-devel zlib-devel",
-    # cairo-devel from the centos repo does not work, build here
-    "wget https://www.cairographics.org/snapshots/cairo-1.15.14.tar.xz --no-check-certificate",
-    "tar xvf cairo-*",
-    "cd cairo-*",
-    "./configure",
-    "make -j 20",
-    "make install",
-    "cd ..",
+    "yum update -y",
+    "yum install freetype-devel libpng-devel pixman-devel zlib-devel eigen3-devel cairo-devel -y"
 ]
 
 repair-wheel-command = [

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_2"
+rdkit_tag = "Release_2024_03_3"
 
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
@@ -188,8 +188,6 @@ def build_rdkit(self, ext):
                 # DRDK_INSTALL_STATIC_LIBS should be fixed in newer RDKit builds. Remove?
                 "-DRDK_INSTALL_STATIC_LIBS=OFF",
                 "-DRDK_INSTALL_DLLS_MSVC=ON",
-                # Avoid linking `VCRUNTIME140_1.dll`. https://github.com/pypa/cibuildwheel/issues/423
-                "-DCMAKE_CXX_FLAGS=-d2FH4-", 
             ]
 
             def to_win_path(pt: Path):