libsbml build fails with miniconda for macos-14/python3.8

[FFroehlich]

File "<string>", line 2, in <module>
          File "<pip-setuptools-caller>", line 34, in <module>
          File "/private/var/folders/05/lw6x4b813x3_l5mvmn51kvlc0000gn/T/pip-install-cm3_4oij/python-libsbml_ddab1a3054d84d1dba9c41c93e0a4cc1/setup.py", line 347, in <module>
            setup(name             = package_name,
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/__init__.py", line 116, in setup
            _install_setup_requires(attrs)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/__init__.py", line 89, in _install_setup_requires
            _fetch_build_eggs(dist)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/__init__.py", line 94, in _fetch_build_eggs
            dist.fetch_build_eggs(dist.setup_requires)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/dist.py", line 664, in fetch_build_eggs
            return _fetch_build_eggs(self, requires)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/installer.py", line 40, in _fetch_build_eggs
            resolved_dists = pkg_resources.working_set.resolve(
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/pkg_resources/__init__.py", line 897, in resolve
            dist = self._resolve_dist(
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/pkg_resources/__init__.py", line 933, in _resolve_dist
            dist = best[req.key] = env.best_match(
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1271, in best_match
            return self.obtain(req, installer)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1307, in obtain
            return installer(requirement) if installer else None
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/installer.py", line 108, in _fetch_build_egg_no_warn
            wheel.install_as_egg(dist_location)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/wheel.py", line 122, in install_as_egg
            self._install_as_egg(destination_eggdir, zf)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/wheel.py", line 130, in _install_as_egg
            self._convert_metadata(zf, destination_eggdir, dist_info, egg_info)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/wheel.py", line 175, in _convert_metadata
            os.rename(dist_info, egg_info)
        OSError: [Errno 66] Directory not empty: '/private/var/folders/05/lw6x4b813x3_l5mvmn51kvlc0000gn/T/pip-install-cm3_4oij/python-libsbml_ddab1a3054d84d1dba9c41c93e0a4cc1/.eggs/swig-4.4.1-py3.8-macosx-11.0-arm64.egg/swig-4.4.1.dist-info' -> '/private/var/folders/05/lw6x4b813x3_l5mvmn51kvlc0000gn/T/pip-install-cm3_4oij/python-libsbml_ddab1a3054d84d1dba9c41c93e0a4cc1/.eggs/swig-4.4.1-py3.8-macosx-11.0-arm64.egg/EGG-INFO'
        [end of output]
    
    note: This error originates from a subprocess, and is likely not a problem with pip.
    ERROR: Failed building wheel for python-libsbml
    error: subprocess-exited-with-error
    
    × python setup.py clean did not run successfully.
    │ exit code: 1
    ╰─> [48 lines of output]
        Using libSBML from: /private/var/folders/05/lw6x4b813x3_l5mvmn51kvlc0000gn/T/pip-install-cm3_4oij/python-libsbml_ddab1a3054d84d1dba9c41c93e0a4cc1/libsbml_source
        Using VERSION.txt: /private/var/folders/05/lw6x4b813x3_l5mvmn51kvlc0000gn/T/pip-install-cm3_4oij/python-libsbml_ddab1a3054d84d1dba9c41c93e0a4cc1/libsbml_source/VERSION.txt
        Creating: python-libsbml
        Version is: 5.21.0
        building for python: 3.8.20 | packaged by conda-forge | (default, Sep 30 2024, 17:48:42)
        [Clang 17.0.6 ]
        /Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
        !!
        
                ********************************************************************************
                Requirements should be satisfied by a PEP 517 installer.
                If you are using pip, you can try `pip install --use-pep517`.
                ********************************************************************************
        
        !!
          dist.fetch_build_eggs(dist.setup_requires)
        Traceback (most recent call last):
          File "<string>", line 2, in <module>
          File "<pip-setuptools-caller>", line 34, in <module>
          File "/private/var/folders/05/lw6x4b813x3_l5mvmn51kvlc0000gn/T/pip-install-cm3_4oij/python-libsbml_ddab1a3054d84d1dba9c41c93e0a4cc1/setup.py", line 347, in <module>
            setup(name             = package_name,
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/__init__.py", line 116, in setup
            _install_setup_requires(attrs)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/__init__.py", line 89, in _install_setup_requires
            _fetch_build_eggs(dist)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/__init__.py", line 94, in _fetch_build_eggs
            dist.fetch_build_eggs(dist.setup_requires)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/dist.py", line 664, in fetch_build_eggs
            return _fetch_build_eggs(self, requires)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/installer.py", line 40, in _fetch_build_eggs
            resolved_dists = pkg_resources.working_set.resolve(
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/pkg_resources/__init__.py", line 897, in resolve
            dist = self._resolve_dist(
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/pkg_resources/__init__.py", line 933, in _resolve_dist
            dist = best[req.key] = env.best_match(
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1271, in best_match
            return self.obtain(req, installer)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1307, in obtain
            return installer(requirement) if installer else None
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/installer.py", line 108, in _fetch_build_egg_no_warn
            wheel.install_as_egg(dist_location)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/wheel.py", line 122, in install_as_egg
            self._install_as_egg(destination_eggdir, zf)
  Warning:    File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/wheel.py", line 130, in _install_as_egg
            self._convert_metadata(zf, destination_eggdir, dist_info, egg_info)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/wheel.py", line 175, in _convert_metadata
            os.rename(dist_info, egg_info)
        OSError: [Errno 66] Directory not empty: '/private/var/folders/05/lw6x4b813x3_l5mvmn51kvlc0000gn/T/pip-install-cm3_4oij/python-libsbml_ddab1a3054d84d1dba9c41c93e0a4cc1/.eggs/swig-4.4.1-py3.8-macosx-11.0-arm64.egg/swig-4.4.1.dist-info' -> '/private/var/folders/05/lw6x4b813x3_l5mvmn51kvlc0000gn/T/pip-install-cm3_4oij/python-libsbml_ddab1a3054d84d1dba9c41c93e0a4cc1/.eggs/swig-4.4.1-py3.8-macosx-11.0-arm64.egg/EGG-INFO'
        [end of output]
    
    note: This error originates from a subprocess, and is likely not a problem with pip.
    ERROR: Failed cleaning build dir for python-libsbml
  ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (python-libsbml)
  
  
     File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/wheel.py", line 130, in _install_as_egg
            self._convert_metadata(zf, destination_eggdir, dist_info, egg_info)
          File "/Users/runner/miniconda3/envs/pysb/lib/python3.8/site-packages/setuptools/wheel.py", line 175, in _convert_metadata
            os.rename(dist_info, egg_info)
        OSError: [Errno 66] Directory not empty: '/private/var/folders/05/lw6x4b813x3_l5mvmn51kvlc0000gn/T/pip-install-cm3_4oij/python-libsbml_ddab1a3054d84d1dba9c41c93e0a4cc1/.eggs/swig-4.4.1-py3.8-macosx-11.0-arm64.egg/swig-4.4.1.dist-info' -> '/private/var/folders/05/lw6x4b813x3_l5mvmn51kvlc0000gn/T/pip-install-cm3_4oij/python-libsbml_ddab1a3054d84d1dba9c41c93e0a4cc1/.eggs/swig-4.4.1-py3.8-macosx-11.0-arm64.egg/EGG-INFO'
        [end of output]
    
    note: This error originates from a subprocess, and is likely not a problem with pip.
    ERROR: Failed cleaning build dir for python-libsbml
  ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (python-libsbml)

see https://github.com/pysb/pysb/actions/runs/21901633658/job/63231144772?pr=608 for details

I suspect this may have been broken by setuptools82, python 3.9-12 appear to be fine.

[fbergmann]

since python 3.8 was out of support, we did not create wheels for it ... i could add them if they are really needed

[FFroehlich]

since python 3.8 was out of support, we did not create wheels for it ... i could add them if they are really needed

They are not needed. I might help to require some minimum python version to ensure more informative error messages, but could also understand if you don't want to give too much help to people using python versions that have been end-of-life for a long time.