Installation fails on Python 3.13

[veenstrajelmer]

Minimal, reproducible code sample, a copy-pastable example if possible

pip install numcodecs in a python 3.13 environment (Windows 10 with conda in my case)

Problem description

Results in:

  ERROR: Failed building wheel for numcodecs
Failed to build numcodecs
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (numcodecs)

Traceback from `pip install zarr`

``` (py313_env) c:\DATA>pip install zarr Collecting zarr Using cached zarr-2.18.3-py3-none-any.whl.metadata (5.7 kB) Collecting asciitree (from zarr) Using cached asciitree-0.3.3-py3-none-any.whl Requirement already satisfied: numpy>=1.24 in c:\users\veenstra\appdata\local\miniforge3\envs\py313_env\lib\site-packages (from zarr) (2.1.2) Collecting numcodecs>=0.10.0 (from zarr) Using cached numcodecs-0.13.0.tar.gz (5.9 MB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Collecting fasteners (from zarr) Using cached fasteners-0.19-py3-none-any.whl.metadata (4.9 kB) Using cached zarr-2.18.3-py3-none-any.whl (210 kB) Using cached fasteners-0.19-py3-none-any.whl (18 kB) Building wheels for collected packages: numcodecs Building wheel for numcodecs (pyproject.toml) ... error error: subprocess-exited-with-error

× Building wheel for numcodecs (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [241 lines of output]
[numcodecs] setting up Blosc extension
[numcodecs] compiling Blosc extension with SSE2 support
[numcodecs] compiling Blosc extension with AVX2 support
[numcodecs] setting up Zstandard extension
[numcodecs] setting up LZ4 extension
[numcodecs] setting up compat extension
[numcodecs] setting up shuffle extension
[numcodecs] setting up vlen extension
[numcodecs] setting up fletcher32 extension
[numcodecs] setting up jenkins extension
running bdist_wheel
running build
running build_py
creating build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\abc.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\astype.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\base64.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\bitround.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\bz2.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\categorize.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\checksum32.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\compat.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\delta.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\fixedscaleoffset.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\gzip.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\json.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\lzma.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\msgpacks.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\ndarray_like.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\packbits.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\pcodec.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\pickles.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\quantize.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\registry.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\shuffle.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\version.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\zfpy.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs\zlib.py -> build\lib.win-amd64-cpython-313\numcodecs
copying .\numcodecs_init_.py -> build\lib.win-amd64-cpython-313\numcodecs
creating build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\common.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_astype.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_base64.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_bitround.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_blosc.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_bz2.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_categorize.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_checksum32.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_compat.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_delta.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_entrypoints.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_entrypoints_backport.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_fixedscaleoffset.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_fletcher32.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_gzip.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_jenkins.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_json.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_lz4.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_lzma.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_msgpacks.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_ndarray_like.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_packbits.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_pcodec.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_pickles.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_quantize.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_registry.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_shuffle.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_vlen_array.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_vlen_bytes.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_vlen_utf8.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_zfpy.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_zlib.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests\test_zstd.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
copying .\numcodecs\tests_init_.py -> build\lib.win-amd64-cpython-313\numcodecs\tests
running egg_info
writing numcodecs.egg-info\PKG-INFO
writing dependency_links to numcodecs.egg-info\dependency_links.txt
writing requirements to numcodecs.egg-info\requires.txt
writing top-level names to numcodecs.egg-info\top_level.txt
ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
reading manifest file 'numcodecs.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.txt'
writing manifest file 'numcodecs.egg-info\SOURCES.txt'
C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\command\build_py.py:218: _Warning: Package 'numcodecs.tests.package_with_entrypoint' is absent from the packages configuration.

    # Package would be ignored #
    Python recognizes 'numcodecs.tests.package_with_entrypoint' as an importable package[^1],
    but it is absent from setuptools' `packages` configuration.
    
    This leads to an ambiguous overall configuration. If you want to distribute this
    package, please make sure that 'numcodecs.tests.package_with_entrypoint' is explicitly added
    to the `packages` configuration field.
    
    Alternatively, you can also rely on setuptools' discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).
    
    You can read more about "package discovery" on setuptools documentation page:
    
    - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
    
    If you don't want 'numcodecs.tests.package_with_entrypoint' to be distributed and are
    already explicitly excluding 'numcodecs.tests.package_with_entrypoint' via
    `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
    you can try to use `exclude_package_data`, or `include-package-data=False` in
    combination with a more fine grained `package-data` configuration.
    
    You can read more about "package data files" on setuptools documentation page:
    
    - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
    
    
    [^1]: For Python, any directory (with suitable naming) can be imported,
          even if it does not contain any `.py` files.
          On the other hand, currently there is no concept of package data
          directory, all directories are treated like packages.

    check.warn(importable)
  creating build\lib.win-amd64-cpython-313\numcodecs\tests\package_with_entrypoint
  copying .\numcodecs\tests\package_with_entrypoint\__init__.py -> build\lib.win-amd64-cpython-313\numcodecs\tests\package_with_entrypoint
  creating build\lib.win-amd64-cpython-313\numcodecs\tests\package_with_entrypoint-0.1.dist-info
  copying .\numcodecs\tests\package_with_entrypoint-0.1.dist-info\entry_points.txt -> build\lib.win-amd64-cpython-313\numcodecs\tests\package_with_entrypoint-0.1.dist-info
  running build_ext
  Compiling numcodecs/blosc.pyx because it changed.
  [1/1] Cythonizing numcodecs/blosc.pyx
  building 'numcodecs.blosc' extension
  [numcodecs] Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
  Traceback (most recent call last):
    File "<string>", line 338, in build_extension
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\Cython\Distutils\build_ext.py", line 135, in build_extension
      super(build_ext, self).build_extension(ext)
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\command\build_ext.py", line 557, in build_extension
      objects = self.compiler.compile(
          sources,
      ...<5 lines>...
          depends=ext.depends,
      )
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\_msvccompiler.py", line 379, in compile
      self.initialize()
      ~~~~~~~~~~~~~~~^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\_msvccompiler.py", line 289, in initialize
      vc_env = _get_vc_env(plat_spec)
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\_msvccompiler.py", line 150, in _get_vc_env
      raise DistutilsPlatformError(
      ...<3 lines>...
      )
  distutils.errors.DistutilsPlatformError: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "C:\Users\veenstra\AppData\Local\miniforge3\envs\py313_env\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 353, in <module>
      main()
      ~~~~^^
    File "C:\Users\veenstra\AppData\Local\miniforge3\envs\py313_env\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 335, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
                               ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
    File "C:\Users\veenstra\AppData\Local\miniforge3\envs\py313_env\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 251, in build_wheel
      return _build_backend().build_wheel(wheel_directory, config_settings,
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                                          metadata_directory)
                                          ^^^^^^^^^^^^^^^^^^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\build_meta.py", line 421, in build_wheel
      return self._build_with_temp_dir(
             ~~~~~~~~~~~~~~~~~~~~~~~~~^
          ['bdist_wheel'],
          ^^^^^^^^^^^^^^^^
      ...<3 lines>...
          self._arbitrary_args(config_settings),
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      )
      ^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\build_meta.py", line 403, in _build_with_temp_dir
      self.run_setup()
      ~~~~~~~~~~~~~~^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\build_meta.py", line 318, in run_setup
      exec(code, locals())
      ~~~~^^^^^^^^^^^^^^^^
    File "<string>", line 383, in <module>
    File "<string>", line 374, in run_setup
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\__init__.py", line 117, in setup
      return distutils.core.setup(**attrs)
             ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 183, in setup
      return run_commands(dist)
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 199, in run_commands
      dist.run_commands()
      ~~~~~~~~~~~~~~~~~^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 954, in run_commands
      self.run_command(cmd)
      ~~~~~~~~~~~~~~~~^^^^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\dist.py", line 950, in run_command
      super().run_command(command)
      ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 973, in run_command
      cmd_obj.run()
      ~~~~~~~~~~~^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\command\bdist_wheel.py", line 398, in run
      self.run_command("build")
      ~~~~~~~~~~~~~~~~^^^^^^^^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 316, in run_command
      self.distribution.run_command(command)
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\dist.py", line 950, in run_command
      super().run_command(command)
      ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 973, in run_command
      cmd_obj.run()
      ~~~~~~~~~~~^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\command\build.py", line 135, in run
      self.run_command(cmd_name)
      ~~~~~~~~~~~~~~~~^^^^^^^^^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 316, in run_command
      self.distribution.run_command(command)
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\dist.py", line 950, in run_command
      super().run_command(command)
      ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 973, in run_command
      cmd_obj.run()
      ~~~~~~~~~~~^^
    File "<string>", line 331, in run
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\command\build_ext.py", line 359, in run
      self.build_extensions()
      ~~~~~~~~~~~~~~~~~~~~~^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\command\build_ext.py", line 476, in build_extensions
      self._build_extensions_serial()
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
    File "C:\Users\veenstra\AppData\Local\Temp\pip-build-env-9vdrdn1g\overlay\Lib\site-packages\setuptools\_distutils\command\build_ext.py", line 502, in _build_extensions_serial
      self.build_extension(ext)
      ~~~~~~~~~~~~~~~~~~~~^^^^^
    File "<string>", line 341, in build_extension
  BuildFailed
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for numcodecs
Failed to build numcodecs
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (numcodecs)

</details>

[dstansby]

Thanks for reporting, this is a known issue that is fixed, we just need to do a release.

[veenstrajelmer]

Great, thanks a lot for the quick reply. I could not find a (closed) issue related to it (I guess it might be #553 in hindsight), so assumed it was not yet resolved. Great to hear that it is though.

[dstansby]

Should work now, 0.13.1 is up on PyPi 🚀

[veenstrajelmer]

Great, indeed it works now, thanks a lot!

[jakirkham]

Similar work is being done in conda-forge with PR: conda-forge/numcodecs-feedstock#110

@dstansby could you please review?