Bump to 2024_03_4

.github/workflows/wheels.yml

@@ -72,6 +72,28 @@ jobs:
 
           # Linux 64 bit ARM: aarch64 (on Circle CI)
 
+          # MacOS 64 bit Intel: x86_64
+          - os: macos-14
+            bitness: 64
+            python: 38
+            platform_id: macosx_arm64
+          - os: macos-14
+            bitness: 64
+            python: 39
+            platform_id: macosx_arm64
+          - os: macos-14
+            bitness: 64
+            python: 310
+            platform_id: macosx_arm64
+          - os: macos-14
+            bitness: 64
+            python: 311
+            platform_id: macosx_arm64
+          - os: macos-14
+            bitness: 64
+            python: 312
+            platform_id: macosx_arm64
+
           # MacOS 64 bit Intel: x86_64
           - os: macos-12
             bitness: 64
@@ -109,7 +131,7 @@ jobs:
 
       - name: Export GitHub Actions cache environment variables for vcpkg
         if: ${{ runner.os == 'Windows' }}
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || '');

pyproject.toml

@@ -44,7 +44,7 @@ environment-pass = ["CIBW_BUILD"]
 before-all = ["brew install gnu-sed eigen cairo freetype"]
 
 repair-wheel-command = [
-    "export DYLD_LIBRARY_PATH='/usr/local/lib:/usr/lib:/Users/admin/lib'",
+    "export DYLD_LIBRARY_PATH='/usr/local/lib:/usr/lib:/Users/admin/lib:/Users/runner/work/lib'",
     "source conan/conanrun.sh",
     "delocate-listdeps {wheel}",
     "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel}",

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_3"
+rdkit_tag = "Release_2024_03_4"
 
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
@@ -103,6 +103,10 @@ def conan_install(self, boost_version, conan_toolchain_path):
         if "linux" in sys.platform:
             cmd += ["--build=b2", "-pr:b", "default"]
 
+        if "cp38-macosx_arm64" in os.environ["CIBW_BUILD"]:
+            # only in this case, conan detects x68_64 instead of armv8
+            cmd += ["-s", "arch=armv8", "-s", "arch_build=armv8"]
+
         check_call(cmd)
 
     def build_rdkit(self, ext):
@@ -145,6 +149,24 @@ def build_rdkit(self, ext):
         # Start build process
         os.chdir(str("rdkit"))
 
+        # Fix a bug in conan or rdkit: target name for numpy is boost::numpy{pyversion} with small 'b'
+        # and not Boost::numpy{pyversion}
+        # Line 345 in 2024_03_04 in CMakeLists.txt
+        # target_link_libraries(rdkit_py_base INTERFACE Boost::${Boost_Python_Lib} "Boost::numpy${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")
+        import fileinput
+
+        def replace_all(file, search_exp, replace_exp):
+            with fileinput.input(file, inplace=True) as f:
+                for line in f:
+                    if search_exp in line:
+                        line = line.replace(search_exp, replace_exp)
+                    print(line, end='')
+
+        replace_all(
+            "CMakeLists.txt",
+            'target_link_libraries(rdkit_py_base INTERFACE Boost::${Boost_Python_Lib} "Boost::numpy${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")',
+            'target_link_libraries(rdkit_py_base INTERFACE Boost::${Boost_Python_Lib} "boost::numpy${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")'
+        )
 
         # Define CMake options
         options = [
@@ -217,8 +239,11 @@ def to_win_path(pt: Path):
         if "macosx_arm64" in os.environ["CIBW_BUILD"]:
             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",
             ]
-            
+
         if "linux" in sys.platform:
             # Use ninja for linux builds
             cmds = [
@@ -283,23 +308,25 @@ def to_win_path(pt: Path):
                 [copy_file(i, str(to_path)) for i in boost_lib_path.rglob("*.lib")]
                 [copy_file(i, str(to_path)) for i in boost_lib_path_bin_windows_only.rglob("*.dll")]
 
-
                 variables["PATH"] = os.environ["PATH"] + os.pathsep + str(to_path)
 
             # VCPKG libs
             variables["PATH"] = os.environ["PATH"] + os.pathsep + str(vcpkg_lib)
 
-
-
-        elif "darwin" in sys.platform:
-            # on Github Actions
-            to_path = Path('/usr/local/lib')
-            if "macosx_arm64" in os.environ["CIBW_BUILD"]:
+        elif "darwin" in sys.platform: 
+            # Github actions
+            to_path = Path("/Users/runner/work/lib")
+            if 'CIRRUS_CI' in os.environ:
                 # on cirrus CI
-                to_path = Path('/Users/admin/lib')
-                to_path.mkdir(parents=True, exist_ok=True)
-                variables["DYLD_LIBRARY_PATH"] = str(to_path)
+                to_path = Path("/Users/admin/lib")
+
+            # Make sure path exists?
+            to_path.mkdir(parents=True, exist_ok=True)
 
+            # Add path to DYLD_LIBRARY_PATH for generating stubs
+            variables["DYLD_LIBRARY_PATH"] = str(to_path)
+
+            # copy all boost and rdkit libs to one path
             [copy_file(i, str(to_path)) for i in rdkit_lib_path.rglob("*dylib")]
             [copy_file(i, str(to_path)) for i in boost_lib_path.rglob("*dylib")]
 
@@ -329,8 +356,11 @@ def to_win_path(pt: Path):
         ]
 
         # Print the stubs error file to rdkit-stubs/gen_rdkit_stubs.err
-        stubs_error_file = build_path / 'rdkit' / "build" /"rdkit-stubs" / "gen_rdkit_stubs.err"
-        with open(stubs_error_file, 'r') as fin: print(fin.read(), file=sys.stderr)
+        stubs_error_file = (
+            build_path / "rdkit" / "build" / "rdkit-stubs" / "gen_rdkit_stubs.err"
+        )
+        with open(stubs_error_file, "r") as fin:
+            print(fin.read(), file=sys.stderr)
 
         os.chdir(str(cwd))
 
@@ -359,13 +389,11 @@ def to_win_path(pt: Path):
         wheel_path = Path(self.get_ext_fullpath(ext.name)).absolute().parent
         wheel_path.mkdir(exist_ok=True)
 
-
-
         # Copy RDMKit files to .../rdkit directory
         def _logpath(path, names):
             ignore_patterns
             print(f"In directory {path} copy files: {names}", file=sys.stderr)
-            return ignore_patterns('*.pyc')(path, names)
+            return ignore_patterns("*.pyc")(path, names)
 
         # Copy the RDKit stubs files to the rdkit-stubs wheels path
         copytree(dir_rdkit_stubs, wheel_path / "rdkit-stubs", ignore=_logpath)
@@ -408,7 +436,7 @@ def _logpath(path, names):
     long_description=long_description,
     long_description_content_type="text/markdown",
     install_requires=[
-        "numpy < 2.0",
+        "numpy",
         "Pillow",
     ],
     ext_modules=[