BUILD: Cython.Compiler.Errors: 'free_threading_config.pxi' not found

[yohplala]

Installation check

• I have read the installation guide.

Platform

Ubuntu 24.04.2 LTS

Installation Method

Built from source

pandas Version

Build from main

Python Version

py310

Installation Logs

Doing

git clone https://github.com/pandas-dev/pandas
cd pandas
python setup.py build_ext -j 4

Results in

Cython.Compiler.Errors.InternalError: Internal compiler error: 'free_threading_config.pxi' not found

File "/home/runner/work/fastparquet/fastparquet/pandas/setup.py", line 684, in ext_modules=maybe_cythonize(extensions, compiler_directives=directives), File "/home/runner/work/fastparquet/fastparquet/pandas/setup.py", line 424, in maybe_cythonize return cythonize(extensions, *args, **kwargs) File "/usr/share/miniconda/envs/test/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1010, in cythonize module_list, module_metadata = create_extension_list( File "/usr/share/miniconda/envs/test/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line [85](https://github.com/dask/fastparquet/actions/runs/13975910111/job/39129502656?pr=951#step:6:86)9, in create_extension_list kwds = deps.distutils_info(file, aliases, base).values File "/usr/share/miniconda/envs/test/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 707, in distutils_info return (self.transitive_merge(filename, self.distutils_info0, DistutilsInfo.merge) File "/usr/share/miniconda/envs/test/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 716, in transitive_merge return self.transitive_merge_helper( File "/usr/share/miniconda/envs/test/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 722, in transitive_merge_helper deps = extract(node) File "/usr/share/miniconda/envs/test/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 6[87](https://github.com/dask/fastparquet/actions/runs/13975910111/job/39129502656?pr=951#step:6:88), in distutils_info0 cimports, externs, incdirs = self.cimports_externs_incdirs(filename) File "Cython/Utils.py", line 129, in Cython.Utils.cached_method.wrapper File "/usr/share/miniconda/envs/test/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 574, in cimports_externs_incdirs for include in self.included_files(filename): File "Cython/Utils.py", line 129, in Cython.Utils.cached_method.wrapper File "/usr/share/miniconda/envs/test/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 556, in included_files include_path = self.context.find_include_file(include, source_file_path=filename) File "/usr/share/miniconda/envs/test/lib/python3.10/site-packages/Cython/Compiler/Main.py", line 299, in find_include_file error(pos, "'%s' not found" % filename) File "/usr/share/miniconda/envs/test/lib/python3.10/site-packages/Cython/Compiler/Errors.py", line 178, in error raise InternalError(message) Cython.Compiler.Errors.InternalError: Internal compiler error: 'free_threading_config.pxi' not found

I am trying to solve this trouble which has raised in this fastparquet CI workflow while working on some other stuffs.

Environment file is populated this way:

name: test_env
channels:
  - conda-forge
dependencies:
  - python=3.10
  - bson
  - lz4
  - lzo
  - pytest
  - pandas
  - dask
  - pytest-cov
  - thrift
  - numpy
  - cramjam
  - pyspark=3.3
  - packaging
  - orjson
  - ujson
  - python-rapidjson
  - meson-python
  - pyarrow

Workflow is as follows.

  pandas:
    name: pandas
    runs-on: ubuntu-latest
    steps:
      - name: APT
        run: sudo apt-get install liblzo2-dev

      - name: Checkout
        uses: actions/checkout@v2
        with:
          fetch-depth: 0

      - name: Fetch upstream tags
        run: |
          git remote add upstream https://github.com/dask/fastparquet.git
          git fetch upstream --tags

      - name: Setup conda
        uses: conda-incubator/setup-miniconda@v3
        with:
          environment-file: ci/environment-py310.yml

      - name: pip-install
        shell: bash -l {0}
        run: |
          pip install Cython
          pip install hypothesis
          pip install pytest-localserver pytest-xdist pytest-asyncio
          pip install -e . --no-deps # Install fastparquet
          pip install versioneer # Needed for pandas build
          git clone https://github.com/pandas-dev/pandas
          cd pandas
          python setup.py build_ext -j 4
          pip install -e . --no-build-isolation

      - name: Run Tests
        shell: bash -l {0}
        run: |
          pytest -v  fastparquet/ # fastparquet test suite against dev pandas
          pytest --verbose pandas/pandas/tests/io/test_parquet.py
          # Test parquet with different filesystems
          pytest --verbose pandas/pandas/tests/io/test_gcs.py pandas/pandas/tests/io/test_fsspec.py -k "parquet"

Thanks for any help!

[WuYff]

I also got this error. How to solve it?