Merge pull request #1 from asiomchen/whl-fix

Whl fix

Author: asiomchen

.github/workflows/publish.yml

@@ -58,25 +58,24 @@ jobs:
           name: cibw-sdist
           path: dist/*.tar.gz
 
-  # upload_pypi:
-  #   needs: [build_wheels, build_sdist]
-  #   runs-on: ubuntu-latest
-  #   environment: pypi
-  #   permissions:
-  #     id-token: write
-  #   if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
-  #   steps:
-  #     - uses: actions/download-artifact@v5
-  #       with:
-  #         # unpacks all CIBW artifacts into dist/
-  #         pattern: cibw-*
-  #         path: dist
-  #         merge-multiple: true
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
 
-  #     - uses: pypa/gh-action-pypi-publish@release/v1
-  #       # To test uploads to TestPyPI, uncomment the following:
-  #       with:
-  #         repository-url: https://test.pypi.org/legacy/
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        # To test uploads to TestPyPI, uncomment the following:
+        # with:
+        #   repository-url: https://test.pypi.org/legacy/
 
 
   github-release:
@@ -94,7 +93,7 @@ jobs:
       - name: Download all the dists
         uses: actions/download-artifact@v6
         with:
-          name: cibw-sdist
+          pattern: cibw-*
           path: dist/
           merge-multiple: true
       - name: Sign the dists with Sigstore🔏
@@ -103,14 +102,16 @@ jobs:
           inputs: >-
             ./dist/*.tar.gz
             ./dist/*.whl
-      - name: Create GitHub Release
-        env:
-          GITHUB_TOKEN: ${{ github.token }}
-        run: >-
-          gh release create
-          "$GITHUB_REF_NAME"
-          --repo "$GITHUB_REPOSITORY"
-          --generate-notes --draft
+      # this is broken for now, need to crreate the release first
+      # see https://github.com/orgs/community/discussions/180369
+      # - name: Create GitHub Release
+      #   env:
+      #     GITHUB_TOKEN: ${{ github.token }}
+      #   run: >-
+      #     gh release create
+      #     "$GITHUB_REF_NAME"
+      #     --repo "$GITHUB_REPOSITORY"
+      #     --generate-notes --draft
       - name: Upload artifact signatures to GitHub Release
         env:
           GITHUB_TOKEN: ${{ github.token }}

README.rst

@@ -1,6 +1,10 @@
 CGRTools
 ========
 
+**Fork Notice: This is a maintained fork of the original CGRtools project with updates for modern Python versions (3.10-3.14) and automated wheel builds for Linux (x86_64, ARM64) and macOS (Intel, Apple Silicon).
+It fixes the issue with newer Cython versions, makes package PEP517-complient and provides precompiled wheels for easier installation.**
+
+**[WIP] to fix your broken builds replace `cgrtools` with `cgrtools-plus` in your dependencies.**
 
 .. image:: https://zenodo.org/badge/14690494.svg
    :target: https://zenodo.org/badge/latestdoi/14690494
@@ -78,20 +82,18 @@ General part
 
 * **stable version available through PyPI**::
 
-    pip install CGRTools
+    pip install cgrtools-plus
 
 * Install CGRtools with MRV files parsing support::
 
-    pip install CGRTools[mrv]
-
+    pip install cgrtools-plus[mrv]
 * Install CGRtools with structures `clean2d` support (Note: install NodeJS into system, see `details <https://github.com/sqreen/PyMiniRacer>`_)::
 
-    pip install CGRtools[clean2d]
+    pip install cgrtools-plus[clean2d]
 
 * Install CGRtools with optimized XYZ parser::
 
-    pip install CGRtools[jit]
-
+    pip install cgrtools-plus[jit]
 
 **If you still have questions, please open issue within github.**
 
@@ -100,7 +102,7 @@ PACKAGING
 
 For wheel generation just type next command in source root::
 
-    python setup.py bdist_wheel
+    python -m build
 
 COPYRIGHT
 =========

pyproject.toml

@@ -3,9 +3,9 @@ requires = ["setuptools>=64", "wheel", "cython>=0.29,<3.2"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "CGRtools"
+name = "cgrtools-plus"
 version = "4.1.35"
-description = "Tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach"
+description = "Tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach - Enhanced fork with modern Python support"
 readme = "README.rst"
 requires-python = ">=3.8"
 license = "LGPL-3.0-or-later"
@@ -15,9 +15,9 @@ authors = [
     {name = "Valentina Afonina"}
 ]
 maintainers = [
-    {name = "Dr. Timur Madzhidov", email = "tmadzhidov@gmail.com"}
+    {name = "Anton Siomchen", email = "anton.siomchen+cgrtools@gmail.com"}
 ]
-keywords = ["chemistry", "chemoinformatics", "CGR", "reaction", "molecule"]
+keywords = ["chemistry", "chemoinformatics", "reaction", "molecule"]
 classifiers = [
     "Environment :: Plugins",
     "Intended Audience :: Science/Research",
@@ -54,10 +54,10 @@ dev = [
 ]
 
 [project.urls]
-Homepage = "https://github.com/cimm-kzn/CGRtools"
+Homepage = "https://github.com/asiomchen/CGRtools"
 Documentation = "https://cgrtools.readthedocs.io"
-Repository = "https://github.com/cimm-kzn/CGRtools"
-Issues = "https://github.com/cimm-kzn/CGRtools/issues"
+Repository = "https://github.com/asiomchen/CGRtools"
+Issues = "https://github.com/asiomchen/CGRtools/issues"
 
 [tool.setuptools]
 zip-safe = false
@@ -71,5 +71,5 @@ include = ["CGRtools*"]
 
 [tool.cibuildwheel]
 build = ["cp310-*", "cp311-*", "cp312-*", "cp313-*", "cp314-*"]
-skip = ["*-musllinux_*", "pp*"]
+skip = ["*-musllinux_*"]
 build-frontend = "build"

setup.py

@@ -70,6 +70,7 @@ def get_data_files():
         so_path = Path('INCHI/libinchi.so')
         if so_path.exists():
             data_files.append(('lib', ['INCHI/libinchi.so']))
+    #TODO for MacOS InChI library should be built from source 
 
     return data_files