local wheel failures

log.txt

$ git diff | cat && cibuildwheel                                                                       15:13:06  ☁  1.10.0 ☂
diff --git a/basesetup.py b/basesetup.py
index a4535a9d..add89a4a 100644
--- a/basesetup.py
+++ b/basesetup.py
@@ -60,9 +60,7 @@ class CompilerDetection:
             self.compiler_args_sse2 = []
         self.compiler_args_sse3 = ["-mssse3"] if (self.sse3_enabled and not self.msvc) else []
         self.compiler_args_neon = []
-        self.compiler_args_warn = (
-            ["-Wno-unused-function", "-Wno-unreachable-code", "-Wno-sign-compare"] if not self.msvc else []
-        )
+        self.compiler_args_warn = ['-Wno-unused-function', '-Wno-unreachable-code', '-Wno-sign-compare', '-Wno-error=incompatible-function-pointer-types'] if not self.msvc else []

         if self.neon_enabled:
             self.compiler_args_sse2 = []
diff --git a/pyproject.toml b/pyproject.toml
index 8521747b..fe2a401f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,3 +28,7 @@ select = [
 "mdtraj/geometry/__init__.py" = ["F403", "F405"]
 "mdtraj/core/trajectory.py" = ["F401"]
 "mdtraj/utils/unit/**" = ["F403", "F405"]
+
+[tool.cibuildwheel]
+before-all = "uname -a"
+
diff --git a/setup.py b/setup.py
index 5fbec04e..f37f8df1 100644
--- a/setup.py
+++ b/setup.py
@@ -33,8 +33,8 @@ except ValueError:


 ##########################
-VERSION = "1.9.10.dev0"
-ISRELEASED = False
+VERSION = "1.10.0"
+ISRELEASED = True
 __version__ = VERSION
 ##########################


     _ _       _ _   _       _           _
 ___|_| |_ _ _|_| |_| |_ _ _| |_ ___ ___| |
|  _| | . | | | | | . | | | |   | -_| -_| |
|___|_|___|___|_|_|___|_____|_|_|___|___|_|

cibuildwheel version 2.18.1

Build options:
  platform: macos
  architectures: arm64
  build_selector:
    build_config: *
    skip_config:
    requires_python: None
    prerelease_pythons: False
    free_threaded_support: False
  output_dir: /Users/mattthompson/software/mdtraj/wheelhouse
  package_dir: /Users/mattthompson/software/mdtraj
  test_selector:
    skip_config:
  before_all:
  before_build:
  before_test:
  build_frontend: None
  build_verbosity: 0
  config_settings:
  container_engine: docker
  dependency_constraints: pinned
  environment:
  manylinux_images: None
  musllinux_images: None
  repair_command: delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}
  test_command:
  test_extras:
  test_requires:

Cache folder: /Users/mattthompson/Library/Caches/cibuildwheel

Here we go!


Building cp38-macosx_arm64 wheel
CPython 3.8 macOS arm64 - Apple Silicon

Installing Python cp38...

+ pkgutil --pkgs

                                                              ✓ 0.03s
Setting up build environment...

+ /Users/mattthompson/micromamba/envs/mdtraj-dev/bin/python3.11 -sS /Users/mattthompson/Library/Caches/cibuildwheel/virtualenv-20.26.2.pyz --activators= --no-periodic-update --pip=24.0 --no-setuptools --no-wheel --symlink-app-data --python /Library/Frameworks/Python.framework/Versions/3.8/bin/python3 /private/var/folders/p1/176rcfkn6zlbbjq4bdjmv2pr0000gn/T/cibw-run-ps7i_e4q/cp38-macosx_arm64/build/venv
created virtual environment CPython3.8.10.final.0-64 in 34ms
  creator CPython3Posix(dest=/private/var/folders/p1/176rcfkn6zlbbjq4bdjmv2pr0000gn/T/cibw-run-ps7i_e4q/cp38-macosx_arm64/build/venv, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=24.0, via=symlink, app_data_dir=/Users/mattthompson/Library/Application Support/virtualenv)
    added seed packages: pip==24.0
+ python -m pip install --upgrade pip -c /Users/mattthompson/micromamba/envs/mdtraj-dev/lib/python3.11/site-packages/cibuildwheel/resources/constraints-python38.txt
Requirement already satisfied: pip in ./lib/python3.8/site-packages (24.0)
+ which pip
/private/var/folders/p1/176rcfkn6zlbbjq4bdjmv2pr0000gn/T/cibw-run-ps7i_e4q/cp38-macosx_arm64/build/venv/bin/pip
+ pip --version
pip 24.0 from /private/var/folders/p1/176rcfkn6zlbbjq4bdjmv2pr0000gn/T/cibw-run-ps7i_e4q/cp38-macosx_arm64/build/venv/lib/python3.8/site-packages/pip (python 3.8)
+ which pip
+ which python
/private/var/folders/p1/176rcfkn6zlbbjq4bdjmv2pr0000gn/T/cibw-run-ps7i_e4q/cp38-macosx_arm64/build/venv/bin/python
+ python --version
Python 3.8.10
+ which python

                                                              ✓ 1.54s
Installing build tools...

+ pip install --upgrade delocate -c /Users/mattthompson/micromamba/envs/mdtraj-dev/lib/python3.11/site-packages/cibuildwheel/resources/constraints-python38.txt
Collecting delocate
  Using cached delocate-0.11.0-py3-none-any.whl.metadata (14 kB)
Collecting packaging>=20.9 (from delocate)
  Using cached packaging-24.0-py3-none-any.whl.metadata (3.2 kB)
Collecting typing-extensions (from delocate)
  Using cached typing_extensions-4.11.0-py3-none-any.whl.metadata (3.0 kB)
Collecting macholib (from delocate)
  Using cached macholib-1.16.3-py2.py3-none-any.whl.metadata (11 kB)
Collecting altgraph>=0.17 (from macholib->delocate)
  Using cached altgraph-0.17.4-py2.py3-none-any.whl.metadata (7.3 kB)
Using cached delocate-0.11.0-py3-none-any.whl (228 kB)
Using cached packaging-24.0-py3-none-any.whl (53 kB)
Using cached macholib-1.16.3-py2.py3-none-any.whl (38 kB)
Using cached typing_extensions-4.11.0-py3-none-any.whl (34 kB)
Using cached altgraph-0.17.4-py2.py3-none-any.whl (21 kB)
Installing collected packages: altgraph, typing-extensions, packaging, macholib, delocate
Successfully installed altgraph-0.17.4 delocate-0.11.0 macholib-1.16.3 packaging-24.0 typing-extensions-4.11.0

                                                              ✓ 0.92s
Building wheel...

+ python -m pip freeze --all
+ python -m pip wheel /Users/mattthompson/software/mdtraj --wheel-dir=/private/var/folders/p1/176rcfkn6zlbbjq4bdjmv2pr0000gn/T/cibw-run-ps7i_e4q/cp38-macosx_arm64/built_wheel --no-deps
Processing /Users/mattthompson/software/mdtraj
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: mdtraj
  Building wheel for mdtraj (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for mdtraj (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [111 lines of output]
      C compiler:
      Attempting to autodetect OpenMP support... Did not detect OpenMP support
      Attempting to autodetect SSE2   support... Did not detect SSE2 support
      Attempting to autodetect SSE3   support... Did not detect SSE3 support
      Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
      Attempting to autodetect NEON   support... Did not detect NEON support

      [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx
      [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx
      [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx
      [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx
      [ 5/10] Cythonizing mdtraj/geometry/drid.pyx
      [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx
      [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx
      [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx
      [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx
      [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx
      running bdist_wheel
      running build
      running build_py
      copying mdtraj/version.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj
      copying mdtraj/io.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj
      copying mdtraj/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj
      copying mdtraj/core/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/core
      copying mdtraj/core/trajectory.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/core
      copying mdtraj/core/element.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/core
      copying mdtraj/core/topology.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/core
      copying mdtraj/core/selection.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/core
      copying mdtraj/core/residue_names.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/core
      copying mdtraj/formats/gro.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/xyzfile.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/lammpstrj.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/hoomdxml.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/prmtop.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/openmmxml.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/lh5.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/registry.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/mol2.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/psf.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/hdf5.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/gsd.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/amberrst.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/netcdf.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/arc.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/pdbx.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/formats/mdcrd.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats
      copying mdtraj/utils/delay_import.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils
      copying mdtraj/utils/zipped.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils
      copying mdtraj/utils/contextmanagers.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils
      copying mdtraj/utils/unitcell.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils
      copying mdtraj/utils/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils
      copying mdtraj/utils/singleton.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils
      copying mdtraj/utils/rotation.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils
      copying mdtraj/utils/validation.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils
      copying mdtraj/testing/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/testing
      copying mdtraj/testing/docstrings.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/testing
      copying mdtraj/testing/docscrape.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/testing
      copying mdtraj/testing/testing.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/testing
      copying mdtraj/scripts/mdinspect.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/scripts
      copying mdtraj/scripts/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/scripts
      copying mdtraj/scripts/mdconvert.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/scripts
      copying mdtraj/geometry/internal.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/dssp.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/sasa.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/rg.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/alignment.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/angle.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/order.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/dihedral.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/distance.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/rdf.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/shape.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/hbond.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/geometry/contact.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/geometry
      copying mdtraj/reporters/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/reporters
      copying mdtraj/reporters/netcdfreporter.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/reporters
      copying mdtraj/reporters/xtcreporter.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/reporters
      copying mdtraj/reporters/dcdreporter.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/reporters
      copying mdtraj/reporters/basereporter.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/reporters
      copying mdtraj/reporters/hdf5reporter.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/reporters
      copying mdtraj/nmr/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/nmr
      copying mdtraj/nmr/scalar_couplings.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/nmr
      copying mdtraj/nmr/shift_wrappers.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/nmr
      copying mdtraj/formats/pdb/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats/pdb
      copying mdtraj/formats/pdb/pdbfile.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats/pdb
      copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats/pdb
      copying mdtraj/utils/unit/doctests.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/prefix.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/unit_definitions.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/constants.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/__init__.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/mymatrix.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/unit_math.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/unit.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/baseunit.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/unit_operators.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/quantity.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/utils/unit/basedimension.py -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/utils/unit
      copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats/pdb/data
      copying mdtraj/formats/pdb/data/residues.xml -> build/lib.macosx-11.0-arm64-cpython-38/mdtraj/formats/pdb/data
      running build_ext
      building 'mdtraj.formats.xtc' extension
      arm64-apple-darwin20.0.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -g -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/mattthompson/micromamba/envs/openff-interchange-dev/include -D_FORTIFY_SOURCE=2 -isystem /Users/mattthompson/micromamba/envs/openff-interchange-dev/include -arch arm64 -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/private/var/folders/p1/176rcfkn6zlbbjq4bdjmv2pr0000gn/T/pip-build-env-a_y4h01g/overlay/lib/python3.8/site-packages/numpy/core/include -I/private/var/folders/p1/176rcfkn6zlbbjq4bdjmv2pr0000gn/T/cibw-run-ps7i_e4q/cp38-macosx_arm64/build/venv/include -I/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.macosx-11.0-arm64-cpython-38/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare -Wno-error=incompatible-function-pointer-types
      warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      error: command 'arm64-apple-darwin20.0.0-clang' failed: No such file or directory
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for mdtraj
Failed to build mdtraj
ERROR: Failed to build one or more wheels

                                                             ✕ 40.71s
Error: Command ['python', '-m', 'pip', 'wheel', '/Users/mattthompson/software/mdtraj', '--wheel-dir=/private/var/folders/p1/176rcfkn6zlbbjq4bdjmv2pr0000gn/T/cibw-run-ps7i_e4q/cp38-macosx_arm64/built_wheel', '--no-deps'] failed with code 1. None