Error installing from source on ARM Mac

[stenczelt]

I am having trouble installing from source on an M2 Mac.

pip install .                                                                                                                                             sella-issue-1 09:06:50 am
Processing /private/tmp/sella-issue-1/sella
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Collecting numpy>=1.14.0 (from Sella==2.3.2)
  Obtaining dependency information for numpy>=1.14.0 from https://files.pythonhosted.org/packages/35/21/9e150d654da358beb29fe216f339dc17f2b2ac13fff2a89669401a910550/numpy-1.26.0-cp311-cp311-macosx_11_0_arm64.whl.metadata
  Using cached numpy-1.26.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (99 kB)
Collecting scipy>=1.1.0 (from Sella==2.3.2)
  Obtaining dependency information for scipy>=1.1.0 from https://files.pythonhosted.org/packages/50/8b/2057417a07a6fee8ed8be40e37bac4a502cae4cf44468a02962bbe81b8af/scipy-1.11.3-cp311-cp311-macosx_12_0_arm64.whl.metadata
  Using cached scipy-1.11.3-cp311-cp311-macosx_12_0_arm64.whl.metadata (165 kB)
Collecting ase>=3.18.0 (from Sella==2.3.2)
  Using cached ase-3.22.1-py3-none-any.whl (2.2 MB)
Collecting jax>=0.2.3 (from Sella==2.3.2)
  Obtaining dependency information for jax>=0.2.3 from https://files.pythonhosted.org/packages/b5/5b/5131520dd9a384a640399e5efe4324fdee9e8a48685a33d08eb47140ccc3/jax-0.4.18-py3-none-any.whl.metadata
  Using cached jax-0.4.18-py3-none-any.whl.metadata (23 kB)
Collecting jaxlib>=0.1.56 (from Sella==2.3.2)
  Obtaining dependency information for jaxlib>=0.1.56 from https://files.pythonhosted.org/packages/a0/8b/909e428f04212587941841239ffe99806784cd49d0a8ace305f913d88c9b/jaxlib-0.4.18-cp311-cp311-macosx_11_0_arm64.whl.metadata
  Using cached jaxlib-0.4.18-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.0 kB)
Collecting matplotlib>=3.1.0 (from ase>=3.18.0->Sella==2.3.2)
  Obtaining dependency information for matplotlib>=3.1.0 from https://files.pythonhosted.org/packages/af/f3/fb27b3b902fc759bbca3f9d0336c48069c3022e57552c4b0095d997c7ea8/matplotlib-3.8.0-cp311-cp311-macosx_11_0_arm64.whl.metadata
  Using cached matplotlib-3.8.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.8 kB)
Collecting ml-dtypes>=0.2.0 (from jax>=0.2.3->Sella==2.3.2)
  Obtaining dependency information for ml-dtypes>=0.2.0 from https://files.pythonhosted.org/packages/22/54/f50df872e42beffe566e29b6ef6cc9daf3901160c9e5290e254aad54560f/ml_dtypes-0.3.1-cp311-cp311-macosx_10_9_universal2.whl.metadata
  Using cached ml_dtypes-0.3.1-cp311-cp311-macosx_10_9_universal2.whl.metadata (20 kB)
Collecting opt-einsum (from jax>=0.2.3->Sella==2.3.2)
  Using cached opt_einsum-3.3.0-py3-none-any.whl (65 kB)
Collecting contourpy>=1.0.1 (from matplotlib>=3.1.0->ase>=3.18.0->Sella==2.3.2)
  Obtaining dependency information for contourpy>=1.0.1 from https://files.pythonhosted.org/packages/2c/8e/656f8e7cd316aa68d9824744773e90dbd71f847429d10c82001e927480a2/contourpy-1.1.1-cp311-cp311-macosx_11_0_arm64.whl.metadata
  Using cached contourpy-1.1.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.9 kB)
Collecting cycler>=0.10 (from matplotlib>=3.1.0->ase>=3.18.0->Sella==2.3.2)
  Obtaining dependency information for cycler>=0.10 from https://files.pythonhosted.org/packages/e7/05/c19819d5e3d95294a6f5947fb9b9629efb316b96de511b418c53d245aae6/cycler-0.12.1-py3-none-any.whl.metadata
  Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib>=3.1.0->ase>=3.18.0->Sella==2.3.2)
  Obtaining dependency information for fonttools>=4.22.0 from https://files.pythonhosted.org/packages/49/ba/ebe5599acf47371393191091ae95fca08eb6f12fd151b52c8dbebb990d25/fonttools-4.43.1-cp311-cp311-macosx_10_9_universal2.whl.metadata
  Using cached fonttools-4.43.1-cp311-cp311-macosx_10_9_universal2.whl.metadata (152 kB)
Collecting kiwisolver>=1.0.1 (from matplotlib>=3.1.0->ase>=3.18.0->Sella==2.3.2)
  Obtaining dependency information for kiwisolver>=1.0.1 from https://files.pythonhosted.org/packages/4a/fe/23d7fa78f7c66086d196406beb1fb2eaf629dd7adc01c3453033303d17fa/kiwisolver-1.4.5-cp311-cp311-macosx_11_0_arm64.whl.metadata
  Using cached kiwisolver-1.4.5-cp311-cp311-macosx_11_0_arm64.whl.metadata (6.4 kB)
Collecting packaging>=20.0 (from matplotlib>=3.1.0->ase>=3.18.0->Sella==2.3.2)
  Obtaining dependency information for packaging>=20.0 from https://files.pythonhosted.org/packages/ec/1a/610693ac4ee14fcdf2d9bf3c493370e4f2ef7ae2e19217d7a237ff42367d/packaging-23.2-py3-none-any.whl.metadata
  Using cached packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pillow>=6.2.0 (from matplotlib>=3.1.0->ase>=3.18.0->Sella==2.3.2)
  Obtaining dependency information for pillow>=6.2.0 from https://files.pythonhosted.org/packages/e4/93/9226cc667ed8785333969c03deb2a36af2f3757284d3a2cf2ebd70331c32/Pillow-10.0.1-cp311-cp311-macosx_11_0_arm64.whl.metadata
  Using cached Pillow-10.0.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (9.5 kB)
Collecting pyparsing>=2.3.1 (from matplotlib>=3.1.0->ase>=3.18.0->Sella==2.3.2)
  Obtaining dependency information for pyparsing>=2.3.1 from https://files.pythonhosted.org/packages/39/92/8486ede85fcc088f1b3dba4ce92dd29d126fd96b0008ea213167940a2475/pyparsing-3.1.1-py3-none-any.whl.metadata
  Using cached pyparsing-3.1.1-py3-none-any.whl.metadata (5.1 kB)
Collecting python-dateutil>=2.7 (from matplotlib>=3.1.0->ase>=3.18.0->Sella==2.3.2)
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting six>=1.5 (from python-dateutil>=2.7->matplotlib>=3.1.0->ase>=3.18.0->Sella==2.3.2)
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Using cached jax-0.4.18-py3-none-any.whl (1.7 MB)
Using cached jaxlib-0.4.18-cp311-cp311-macosx_11_0_arm64.whl (65.9 MB)
Using cached numpy-1.26.0-cp311-cp311-macosx_11_0_arm64.whl (14.0 MB)
Using cached scipy-1.11.3-cp311-cp311-macosx_12_0_arm64.whl (29.7 MB)
Using cached matplotlib-3.8.0-cp311-cp311-macosx_11_0_arm64.whl (7.5 MB)
Using cached ml_dtypes-0.3.1-cp311-cp311-macosx_10_9_universal2.whl (348 kB)
Using cached contourpy-1.1.1-cp311-cp311-macosx_11_0_arm64.whl (233 kB)
Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Using cached fonttools-4.43.1-cp311-cp311-macosx_10_9_universal2.whl (2.7 MB)
Using cached kiwisolver-1.4.5-cp311-cp311-macosx_11_0_arm64.whl (66 kB)
Using cached packaging-23.2-py3-none-any.whl (53 kB)
Using cached Pillow-10.0.1-cp311-cp311-macosx_11_0_arm64.whl (3.3 MB)
Using cached pyparsing-3.1.1-py3-none-any.whl (103 kB)
Building wheels for collected packages: Sella
  Building wheel for Sella (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for Sella (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [50 lines of output]
      /private/var/folders/83/sdc3psbx0h74nbfnh5hh6rc40000gn/T/pip-build-env-9h9dwvt6/overlay/lib/python3.11/site-packages/setuptools/dist.py:498: SetuptoolsDeprecationWarning: Invalid dash-separated options
      !!

              ********************************************************************************
              Usage of dash-separated 'description-file' will not be supported in future
              versions. Please use the underscore name 'description_file' instead.

              This deprecation is overdue, please update your project and remove deprecated
              calls to avoid build errors in the future.

              See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
              ********************************************************************************

      !!
        opt = self.warn_dash_deprecation(opt, section)
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.macosx-13-arm64-cpython-311
      creating build/lib.macosx-13-arm64-cpython-311/sella
      copying sella/internal.py -> build/lib.macosx-13-arm64-cpython-311/sella
      copying sella/__init__.py -> build/lib.macosx-13-arm64-cpython-311/sella
      copying sella/linalg.py -> build/lib.macosx-13-arm64-cpython-311/sella
      copying sella/hessian_update.py -> build/lib.macosx-13-arm64-cpython-311/sella
      copying sella/samd.py -> build/lib.macosx-13-arm64-cpython-311/sella
      copying sella/peswrapper.py -> build/lib.macosx-13-arm64-cpython-311/sella
      copying sella/eigensolvers.py -> build/lib.macosx-13-arm64-cpython-311/sella
      creating build/lib.macosx-13-arm64-cpython-311/sella/optimize
      copying sella/optimize/optimize.py -> build/lib.macosx-13-arm64-cpython-311/sella/optimize
      copying sella/optimize/stepper.py -> build/lib.macosx-13-arm64-cpython-311/sella/optimize
      copying sella/optimize/irc.py -> build/lib.macosx-13-arm64-cpython-311/sella/optimize
      copying sella/optimize/__init__.py -> build/lib.macosx-13-arm64-cpython-311/sella/optimize
      copying sella/optimize/restricted_step.py -> build/lib.macosx-13-arm64-cpython-311/sella/optimize
      creating build/lib.macosx-13-arm64-cpython-311/sella/utilities
      copying sella/utilities/__init__.py -> build/lib.macosx-13-arm64-cpython-311/sella/utilities
      running build_ext
      building 'sella.force_match' extension
      creating build/temp.macosx-13-arm64-cpython-311
      creating build/temp.macosx-13-arm64-cpython-311/sella
      clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -I/private/var/folders/83/sdc3psbx0h74nbfnh5hh6rc40000gn/T/pip-build-env-9h9dwvt6/overlay/lib/python3.11/site-packages/numpy/core/include -I/private/var/folders/83/sdc3psbx0h74nbfnh5hh6rc40000gn/T/pip-build-env-9h9dwvt6/overlay/lib/python3.11/site-packages/numpy/core/include -I/private/tmp/sella-issue-1/venv/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.11/include/python3.11 -c sella/force_match.c -o build/temp.macosx-13-arm64-cpython-311/sella/force_match.o
      In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/Availability.h:166,
                       from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/stdlib.h:61,
                       from /opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.11/include/python3.11/Python.h:23,
                       from sella/force_match.c:38:
      /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/13/include-fixed/AvailabilityInternal.h:162:10: fatal error: AvailabilityInternalLegacy.h: No such file or directory
        162 | #include <AvailabilityInternalLegacy.h>
            |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      compilation terminated.
      error: command '/opt/homebrew/bin/clang' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for Sella
Failed to build Sella
ERROR: Could not build wheels for Sella, which is required to install pyproject.toml-based projects

Same happens if I am using gcc and if I am using the setup.py directly with python setup.py install (after installing dependencies).

How to get around this, have you seen it on any ARM Mac?

versions of software:

• gcc (Homebrew GCC 13.2.0) 13.2.0
• MacOS 14.0
• Python 3.11.5

Tried on 723756f