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.

[matthewfeickert]

👋 @NickleDave Whatever issue you were having seems to have been transitory, as I was able to build and install vocalpy with no issues on my

$ uname -ms
Linux x86_64

machine:

$ pixi --version
pixi 0.44.0
$ git clone --recursive [email protected]:vocalpy/vocalpy.git
$ cd vocalpy
$ git checkout origin/test-pixi-install -b test-pixi-install
$ pixi install
✔ The default environment has been installed.
$ pixi list vocalpy
Package  Version  Build  Size  Kind  Source
vocalpy  0.9.5                 pypi   (editable)
$ pixi run python -c 'import vocalpy; print(vocalpy)'
<module 'vocalpy' from '/tmp/vocalpy/src/vocalpy/__init__.py'>

[NickleDave]

Excellent, thank you @matthewfeickert!
Guess I have no reason not to switch now 🙂

[matthewfeickert]

Yeah, I've been very much enjoying the support that's been added by enabling this for some of my libraries. It is great to not have to long sections in the dev docs on how to get setup now and to get to replace it with a single Pixi command. :)