pixi install fails with "No module named 'numpy.distutils'"

[NickleDave]

Hi all,

I am unable to run pixi install with my package, it fails with the following traceback:

$ pixi install
  × failed to solve the pypi requirements of 'default' 'linux-64'
  ╰─▶ Build backend failed to determine metadata through `prepare_metadata_for_build_wheel` with exit status: 1
      --- stdout:
      
      --- stderr:
      Traceback (most recent call last):
        File "<string>", line 14, in <module>
        File "/home/ildefonso/.cache/rattler/cache/uv-cache/builds-v0/.tmp2zyCIo/lib/python3.12/site-packages/setuptools/build_meta.py", line 373, in
      prepare_metadata_for_build_wheel
          self.run_setup()
        File "/home/ildefonso/.cache/rattler/cache/uv-cache/builds-v0/.tmp2zyCIo/lib/python3.12/site-packages/setuptools/build_meta.py", line 516, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/home/ildefonso/.cache/rattler/cache/uv-cache/builds-v0/.tmp2zyCIo/lib/python3.12/site-packages/setuptools/build_meta.py", line 318, in run_setup
          exec(code, locals())
        File "<string>", line 354, in <module>
        File "<string>", line 87, in get_ext_modules
      ModuleNotFoundError: No module named 'numpy.distutils'
      ---

If I instead do pixi install -vvv I can see that it looks like the install process tries to build a wheel for numpy. A bit surprising since I am pretty sure the wheels exist on pypi.

Click to expand snippet of `-vvv` output

Here's an excerpt from that output:

DEBUG install{num_wheels=1}:install_wheel{wheel=setuptools-75.2.0-py3-none-any.http.whl}: install_wheel_rs::linker: Writing extra metadata name=PackageName("setuptools")
DEBUG install{num_wheels=1}:install_wheel{wheel=setuptools-75.2.0-py3-none-any.http.whl}: install_wheel_rs::linker: Writing record name=PackageName("setuptools")
DEBUG resolve_pypi{group=default platform=linux-64}:get_or_build_wheel_metadata{dist=numba==0.51.2}:build_metadata{dist=numba==0.51.2}:setup_build{version_id="numba==0.51.2" subdirectory=None}: uv_build: Calling `setuptools.build_meta:__legacy__.get_requires_for_build_wheel()`
DEBUG resolve_pypi{group=default platform=linux-64}:get_or_build_wheel_metadata{dist=numba==0.51.2}:build_metadata{dist=numba==0.51.2}:setup_build{version_id="numba==0.51.2" subdirectory=None}: uv_build: Installing extra requirements for build backend
DEBUG solve: uv_resolver::resolver: Solving with installed Python version: 3.12.7
DEBUG solve: uv_resolver::resolver: Adding direct dependency: setuptools>=40.8.0
DEBUG solve: uv_resolver::resolver: Adding direct dependency: numpy>=1.11
 INFO solve: pubgrub::internal::partial_solution: add_decision: root @ 0a0.dev0    
DEBUG solve:choose_version{package=setuptools}: uv_resolver::resolver: Searching for a compatible version of setuptools (>=40.8.0)
DEBUG solve:choose_version{package=setuptools}: uv_resolver::resolver: Selecting: setuptools==75.2.0 [compatible] (setuptools-75.2.0-py3-none-any.whl)
 INFO solve: pubgrub::internal::partial_solution: add_decision: setuptools @ 75.2.0    
DEBUG resolve_pypi{group=default platform=linux-64}:get_or_build_wheel_metadata{dist=numba==0.51.2}:build_metadata{dist=numba==0.51.2}:setup_build{version_id="numba==0.51.2" subdirectory=None}:process_request{request=Versions numpy}:simple_api{package=numpy}:get_cacheable: uv_client::cached_client: Found fresh response for: https://pypi.org/simple/numpy/
DEBUG solve:choose_version{package=numpy}: uv_resolver::resolver: Searching for a compatible version of numpy (>=1.11)
DEBUG solve:choose_version{package=numpy}: uv_resolver::resolver: Selecting: numpy==2.1.2 [compatible] (numpy-2.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl)
DEBUG resolve_pypi{group=default platform=linux-64}:get_or_build_wheel_metadata{dist=numba==0.51.2}:build_metadata{dist=numba==0.51.2}:setup_build{version_id="numba==0.51.2" subdirectory=None}:process_request{request=Prefetch numpy >=1.11}:get_or_build_wheel_metadata{dist=numpy==2.1.2}:wheel_metadata{built_dist=numpy==2.1.2}:get_serde:get_cacheable: uv_client::cached_client: Found fresh response for: https://files.pythonhosted.org/packages/9b/b4/e3c7e6fab0f77fff6194afa173d1f2342073d91b1d3b4b30b17c3fb4407a/numpy-2.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
 INFO solve: pubgrub::internal::partial_solution: add_decision: numpy @ 2.1.2    
DEBUG solve: uv_resolver::resolver::batch_prefetch: Tried 2 versions: numpy 1, setuptools 1
DEBUG solve: uv_resolver::resolver: Split specific environment resolution took 0.007s
DEBUG resolve_pypi{group=default platform=linux-64}:get_or_build_wheel_metadata{dist=numba==0.51.2}:build_metadata{dist=numba==0.51.2}:setup_build{version_id="numba==0.51.2" subdirectory=None}:install{resolution="numpy==2.1.2, setuptools==75.2.0" venv="/home/ildefonso/.cache/rattler/cache/uv-cache/builds-v0/.tmpjSM8c9"}: uv_dispatch: Installing in numpy==2.1.2, setuptools==75.2.0 in /home/ildefonso/.cache/rattler/cache/uv-cache/builds-v0/.tmpjSM8c9
DEBUG resolve_pypi{group=default platform=linux-64}:get_or_build_wheel_metadata{dist=numba==0.51.2}:build_metadata{dist=numba==0.51.2}:setup_build{version_id="numba==0.51.2" subdirectory=None}:install{resolution="numpy==2.1.2, setuptools==75.2.0" venv="/home/ildefonso/.cache/rattler/cache/uv-cache/builds-v0/.tmpjSM8c9"}: uv_installer::plan: Requirement already cached: numpy==2.1.2
DEBUG resolve_pypi{group=default platform=linux-64}:get_or_build_wheel_metadata{dist=numba==0.51.2}:build_metadata{dist=numba==0.51.2}:setup_build{version_id="numba==0.51.2" subdirectory=None}:install{resolution="numpy==2.1.2, setuptools==75.2.0" venv="/home/ildefonso/.cache/rattler/cache/uv-cache/builds-v0/.tmpjSM8c9"}: uv_installer::plan: Requirement already installed: setuptools==75.2.0
DEBUG resolve_pypi{group=default platform=linux-64}:get_or_build_wheel_metadata{dist=numba==0.51.2}:build_metadata{dist=numba==0.51.2}:setup_build{version_id="numba==0.51.2" subdirectory=None}:install{resolution="numpy==2.1.2, setuptools==75.2.0" venv="/home/ildefonso/.cache/rattler/cache/uv-cache/builds-v0/.tmpjSM8c9"}: uv_dispatch: Installing build requirement: numpy==2.1.2
DEBUG install{num_wheels=1}:install_wheel{wheel=numpy-2.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.http.whl}: install_wheel_rs::linker: Extracting file name=PackageName("numpy")
DEBUG install{num_wheels=1}:install_wheel{wheel=numpy-2.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.http.whl}: install_wheel_rs::linker: Extracted 819 files name=PackageName("numpy")
DEBUG install{num_wheels=1}:install_wheel{wheel=numpy-2.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.http.whl}: install_wheel_rs::linker: Writing entrypoints name=PackageName("numpy")
DEBUG install{num_wheels=1}:install_wheel{wheel=numpy-2.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.http.whl}: install_wheel_rs::linker: No data name=PackageName("numpy")
DEBUG install{num_wheels=1}:install_wheel{wheel=numpy-2.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.http.whl}: install_wheel_rs::linker: Writing extra metadata name=PackageName("numpy")
DEBUG install{num_wheels=1}:install_wheel{wheel=numpy-2.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.http.whl}: install_wheel_rs::linker: Writing record name=PackageName("numpy")
DEBUG resolve_pypi{group=default platform=linux-64}:get_or_build_wheel_metadata{dist=numba==0.51.2}:build_metadata{dist=numba==0.51.2}: uv_build: Calling `setuptools.build_meta:__legacy__.prepare_metadata_for_build_wheel()`
DEBUG resolve_conda{group=default platform=linux-64}:Connection{peer=Client}: h2::codec::framed_write: send frame=GoAway { error_code: NO_ERROR, last_stream_id: StreamId(0) }
DEBUG resolve_conda{group=default platform=linux-64}:get_or_create_subdir{channel=Channel { platforms: None, base_url: Url { scheme: "https", cannot_be_a_base: false, username: "", password: None, host: Some(Domain("conda.anaconda.org")), port: None, path: "/conda-forge/", query: None, fragment: None }, name: Some("conda-forge") } platform=NoArch}:fetch_repo_data{cache_path=/home/ildefonso/.cache/rattler/cache/repodata}:Connection{peer=Client}: h2::codec::framed_write: send frame=GoAway { error_code: NO_ERROR, last_stream_id: StreamId(0) }
DEBUG resolve_conda{group=default platform=linux-64}:Connection{peer=Client}: h2::proto::connection: Connection::poll; connection error error=GoAway(b"", NO_ERROR, Library)
DEBUG resolve_conda{group=default platform=linux-64}:get_or_create_subdir{channel=Channel { platforms: None, base_url: Url { scheme: "https", cannot_be_a_base: false, username: "", password: None, host: Some(Domain("conda.anaconda.org")), port: None, path: "/conda-forge/", query: None, fragment: None }, name: Some("conda-forge") } platform=NoArch}:fetch_repo_data{cache_path=/home/ildefonso/.cache/rattler/cache/repodata}:Connection{peer=Client}: h2::proto::connection: Connection::poll; connection error error=GoAway(b"", NO_ERROR, Library)
  × failed to solve the pypi requirements of 'default' 'linux-64'
  ╰─▶ Build backend failed to determine metadata through `prepare_metadata_for_build_wheel` with exit status: 1
      --- stdout:
      
      --- stderr:
      Traceback (most recent call last):
        File "<string>", line 14, in <module>
        File "/home/ildefonso/.cache/rattler/cache/uv-cache/builds-v0/.tmpjSM8c9/lib/python3.12/site-packages/setuptools/build_meta.py", line 373, in
      prepare_metadata_for_build_wheel
          self.run_setup()
        File "/home/ildefonso/.cache/rattler/cache/uv-cache/builds-v0/.tmpjSM8c9/lib/python3.12/site-packages/setuptools/build_meta.py", line 516, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/home/ildefonso/.cache/rattler/cache/uv-cache/builds-v0/.tmpjSM8c9/lib/python3.12/site-packages/setuptools/build_meta.py", line 318, in run_setup
          exec(code, locals())
        File "<string>", line 354, in <module>
        File "<string>", line 87, in get_ext_modules
      ModuleNotFoundError: No module named 'numpy.distutils'
      ---

I'm really not sure what else to do to troubleshoot this.
Please find my pyproject.toml manifest here, if it helps:
https://github.com/vocalpy/vocalpy/tree/test-pixi-install
Doing git clone followed by pixi install on a linux system should reproduce the issue.

For context, I am trying to switch to pixi so that I can generate oracle test data for this library from another package -- I want to do this in an env with a lockfile so I can avoid dealing with docker, thinking this will be "good enough" replicability.
So all the commented out stuff in the pyproject.toml is from me trying to do that with a pixi feature, and then going through a process of elimination where I finally realized the source of this error is my actual project, and not the pixi feature I was adding.