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clin1234 opened this issue Jun 17, 2024 · 6 comments
Closed

Unable to run code tests, both serial and parallel #29280

clin1234 opened this issue Jun 17, 2024 · 6 comments
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@clin1234
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Describe the bug

Building with Python 3.13 and OpenMP-enabled scipy on Ubuntu succeeeds, but I am unable to run tests, parallel mode or not.

Steps/Code to Reproduce

Using GitHub Codespaces:

  1. Add the deadsnakes/ppa, install python3.13-venv and libpython3.13-dev
  2. python3.13 -m venv sklearn-env, then activate it
  3. Install libopenblas-openmp-dev
  4. pip install wheel numpy scipy cython meson-python ninja
  5. make (or make test-code)

Expected Results

Tests to pass.

Actual Results

make test-code:

python setup.py build_ext -i
Partial import of sklearn during the build process.
/workspaces/scikit-learn/sklearn-env/lib/python3.13/site-packages/setuptools/config/_apply_pyprojecttoml.py:83: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
  corresp(dist, value, root_dir)
running build_ext
running build_clib
building 'libsvm-skl' library
building 'liblinear-skl' library
copying build/lib.linux-x86_64-cpython-313/sklearn/__check_build/_check_build.cpython-313-x86_64-linux-gnu.so -> sklearn/__check_build
copying build/lib.linux-x86_64-cpython-313/sklearn/_isotonic.cpython-313-x86_64-linux-gnu.so -> sklearn
copying build/lib.linux-x86_64-cpython-313/sklearn/_loss/_loss.cpython-313-x86_64-linux-gnu.so -> sklearn/_loss
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_dbscan_inner.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_hierarchical_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_k_means_common.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_k_means_lloyd.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_k_means_elkan.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_k_means_minibatch.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_hdbscan/_linkage.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster/_hdbscan
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_hdbscan/_reachability.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster/_hdbscan
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_hdbscan/_tree.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster/_hdbscan
copying build/lib.linux-x86_64-cpython-313/sklearn/datasets/_svmlight_format_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/datasets
copying build/lib.linux-x86_64-cpython-313/sklearn/decomposition/_online_lda_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/decomposition
copying build/lib.linux-x86_64-cpython-313/sklearn/decomposition/_cdnmf_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/decomposition
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_gradient_boosting.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/_gradient_boosting.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/histogram.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/splitting.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/_binning.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/_predictor.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/_bitset.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/common.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/feature_extraction/_hashing_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/feature_extraction
copying build/lib.linux-x86_64-cpython-313/sklearn/linear_model/_cd_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/linear_model
copying build/lib.linux-x86_64-cpython-313/sklearn/linear_model/_sgd_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/linear_model
copying build/lib.linux-x86_64-cpython-313/sklearn/linear_model/_sag_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/linear_model
copying build/lib.linux-x86_64-cpython-313/sklearn/manifold/_utils.cpython-313-x86_64-linux-gnu.so -> sklearn/manifold
copying build/lib.linux-x86_64-cpython-313/sklearn/manifold/_barnes_hut_tsne.cpython-313-x86_64-linux-gnu.so -> sklearn/manifold
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_dist_metrics.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/cluster/_expected_mutual_info_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_datasets_pair.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_base.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_argkmin.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_argkmin_classmode.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors_classmode.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/preprocessing/_csr_polynomial_expansion.cpython-313-x86_64-linux-gnu.so -> sklearn/preprocessing
copying build/lib.linux-x86_64-cpython-313/sklearn/preprocessing/_target_encoder_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/preprocessing
copying build/lib.linux-x86_64-cpython-313/sklearn/neighbors/_ball_tree.cpython-313-x86_64-linux-gnu.so -> sklearn/neighbors
copying build/lib.linux-x86_64-cpython-313/sklearn/neighbors/_kd_tree.cpython-313-x86_64-linux-gnu.so -> sklearn/neighbors
copying build/lib.linux-x86_64-cpython-313/sklearn/neighbors/_partition_nodes.cpython-313-x86_64-linux-gnu.so -> sklearn/neighbors
copying build/lib.linux-x86_64-cpython-313/sklearn/neighbors/_quad_tree.cpython-313-x86_64-linux-gnu.so -> sklearn/neighbors
copying build/lib.linux-x86_64-cpython-313/sklearn/svm/_newrand.cpython-313-x86_64-linux-gnu.so -> sklearn/svm
copying build/lib.linux-x86_64-cpython-313/sklearn/svm/_libsvm.cpython-313-x86_64-linux-gnu.so -> sklearn/svm
copying build/lib.linux-x86_64-cpython-313/sklearn/svm/_liblinear.cpython-313-x86_64-linux-gnu.so -> sklearn/svm
copying build/lib.linux-x86_64-cpython-313/sklearn/svm/_libsvm_sparse.cpython-313-x86_64-linux-gnu.so -> sklearn/svm
copying build/lib.linux-x86_64-cpython-313/sklearn/tree/_tree.cpython-313-x86_64-linux-gnu.so -> sklearn/tree
copying build/lib.linux-x86_64-cpython-313/sklearn/tree/_splitter.cpython-313-x86_64-linux-gnu.so -> sklearn/tree
copying build/lib.linux-x86_64-cpython-313/sklearn/tree/_criterion.cpython-313-x86_64-linux-gnu.so -> sklearn/tree
copying build/lib.linux-x86_64-cpython-313/sklearn/tree/_utils.cpython-313-x86_64-linux-gnu.so -> sklearn/tree
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/sparsefuncs_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_cython_blas.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/arrayfuncs.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/murmurhash.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_fast_dict.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_openmp_helpers.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_seq_dataset.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_weight_vector.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_random.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_typedefs.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_heap.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_sorting.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_vector_sentinel.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_isfinite.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
pytest --showlocals -v sklearn --durations=20
ImportError while loading conftest '/workspaces/scikit-learn/sklearn/conftest.py'.
_pytest.pathlib.ImportPathMismatchError: ('sklearn.conftest', '/workspaces/scikit-learn/sklearn-env/lib/python3.13/site-packages/sklearn/conftest.py', PosixPath('/workspaces/scikit-learn/sklearn/conftest.py'))
make: *** [Makefile:29: test-code] Error 4

make test-code-parallel:

python setup.py build_ext -i
Partial import of sklearn during the build process.
/workspaces/scikit-learn/sklearn-env/lib/python3.13/site-packages/setuptools/config/_apply_pyprojecttoml.py:83: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
  corresp(dist, value, root_dir)
running build_ext
running build_clib
building 'libsvm-skl' library
building 'liblinear-skl' library
copying build/lib.linux-x86_64-cpython-313/sklearn/__check_build/_check_build.cpython-313-x86_64-linux-gnu.so -> sklearn/__check_build
copying build/lib.linux-x86_64-cpython-313/sklearn/_isotonic.cpython-313-x86_64-linux-gnu.so -> sklearn
copying build/lib.linux-x86_64-cpython-313/sklearn/_loss/_loss.cpython-313-x86_64-linux-gnu.so -> sklearn/_loss
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_dbscan_inner.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_hierarchical_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_k_means_common.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_k_means_lloyd.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_k_means_elkan.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_k_means_minibatch.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_hdbscan/_linkage.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster/_hdbscan
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_hdbscan/_reachability.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster/_hdbscan
copying build/lib.linux-x86_64-cpython-313/sklearn/cluster/_hdbscan/_tree.cpython-313-x86_64-linux-gnu.so -> sklearn/cluster/_hdbscan
copying build/lib.linux-x86_64-cpython-313/sklearn/datasets/_svmlight_format_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/datasets
copying build/lib.linux-x86_64-cpython-313/sklearn/decomposition/_online_lda_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/decomposition
copying build/lib.linux-x86_64-cpython-313/sklearn/decomposition/_cdnmf_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/decomposition
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_gradient_boosting.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/_gradient_boosting.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/histogram.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/splitting.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/_binning.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/_predictor.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/_bitset.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/ensemble/_hist_gradient_boosting/common.cpython-313-x86_64-linux-gnu.so -> sklearn/ensemble/_hist_gradient_boosting
copying build/lib.linux-x86_64-cpython-313/sklearn/feature_extraction/_hashing_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/feature_extraction
copying build/lib.linux-x86_64-cpython-313/sklearn/linear_model/_cd_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/linear_model
copying build/lib.linux-x86_64-cpython-313/sklearn/linear_model/_sgd_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/linear_model
copying build/lib.linux-x86_64-cpython-313/sklearn/linear_model/_sag_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/linear_model
copying build/lib.linux-x86_64-cpython-313/sklearn/manifold/_utils.cpython-313-x86_64-linux-gnu.so -> sklearn/manifold
copying build/lib.linux-x86_64-cpython-313/sklearn/manifold/_barnes_hut_tsne.cpython-313-x86_64-linux-gnu.so -> sklearn/manifold
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_dist_metrics.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/cluster/_expected_mutual_info_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/cluster
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_datasets_pair.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_base.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_argkmin.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_argkmin_classmode.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors_classmode.cpython-313-x86_64-linux-gnu.so -> sklearn/metrics/_pairwise_distances_reduction
copying build/lib.linux-x86_64-cpython-313/sklearn/preprocessing/_csr_polynomial_expansion.cpython-313-x86_64-linux-gnu.so -> sklearn/preprocessing
copying build/lib.linux-x86_64-cpython-313/sklearn/preprocessing/_target_encoder_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/preprocessing
copying build/lib.linux-x86_64-cpython-313/sklearn/neighbors/_ball_tree.cpython-313-x86_64-linux-gnu.so -> sklearn/neighbors
copying build/lib.linux-x86_64-cpython-313/sklearn/neighbors/_kd_tree.cpython-313-x86_64-linux-gnu.so -> sklearn/neighbors
copying build/lib.linux-x86_64-cpython-313/sklearn/neighbors/_partition_nodes.cpython-313-x86_64-linux-gnu.so -> sklearn/neighbors
copying build/lib.linux-x86_64-cpython-313/sklearn/neighbors/_quad_tree.cpython-313-x86_64-linux-gnu.so -> sklearn/neighbors
copying build/lib.linux-x86_64-cpython-313/sklearn/svm/_newrand.cpython-313-x86_64-linux-gnu.so -> sklearn/svm
copying build/lib.linux-x86_64-cpython-313/sklearn/svm/_libsvm.cpython-313-x86_64-linux-gnu.so -> sklearn/svm
copying build/lib.linux-x86_64-cpython-313/sklearn/svm/_liblinear.cpython-313-x86_64-linux-gnu.so -> sklearn/svm
copying build/lib.linux-x86_64-cpython-313/sklearn/svm/_libsvm_sparse.cpython-313-x86_64-linux-gnu.so -> sklearn/svm
copying build/lib.linux-x86_64-cpython-313/sklearn/tree/_tree.cpython-313-x86_64-linux-gnu.so -> sklearn/tree
copying build/lib.linux-x86_64-cpython-313/sklearn/tree/_splitter.cpython-313-x86_64-linux-gnu.so -> sklearn/tree
copying build/lib.linux-x86_64-cpython-313/sklearn/tree/_criterion.cpython-313-x86_64-linux-gnu.so -> sklearn/tree
copying build/lib.linux-x86_64-cpython-313/sklearn/tree/_utils.cpython-313-x86_64-linux-gnu.so -> sklearn/tree
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/sparsefuncs_fast.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_cython_blas.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/arrayfuncs.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/murmurhash.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_fast_dict.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_openmp_helpers.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_seq_dataset.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_weight_vector.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_random.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_typedefs.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_heap.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_sorting.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_vector_sentinel.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
copying build/lib.linux-x86_64-cpython-313/sklearn/utils/_isfinite.cpython-313-x86_64-linux-gnu.so -> sklearn/utils
pytest -n auto --showlocals -v sklearn --durations=20
ERROR: usage: pytest [options] [file_or_dir] [file_or_dir] [...]
pytest: error: unrecognized arguments: -n sklearn
  inifile: /workspaces/scikit-learn/setup.cfg
  rootdir: /workspaces/scikit-learn

make: *** [Makefile:37: test-code-parallel] Error 4

Versions

System:
    python: 3.13.0b2 (main, Jun  8 2024, 19:41:53) [GCC 9.4.0]
executable: /workspaces/scikit-learn/sklearn-env/bin/python
   machine: Linux-6.5.0-1021-azure-x86_64-with-glibc2.31

Python dependencies:
      sklearn: 1.6.dev0
          pip: 24.0
   setuptools: 70.0.0
        numpy: 2.0.0
        scipy: 1.13.1
       Cython: 3.0.10
       pandas: None
   matplotlib: None
       joblib: 1.4.2
threadpoolctl: 3.5.0

Built with OpenMP: True

threadpoolctl info:
       user_api: blas
   internal_api: openblas
    num_threads: 4
         prefix: libopenblas
       filepath: /usr/lib/x86_64-linux-gnu/openblas-openmp/libopenblasp-r0.3.8.so
        version: 0.3.8
threading_layer: openmp
   architecture: Barcelona

       user_api: openmp
   internal_api: openmp
    num_threads: 4
         prefix: libgomp
       filepath: /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
        version: None
@clin1234 clin1234 added Bug Needs Triage Issue requires triage labels Jun 17, 2024
@glemaitre
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For the parallel case, you get the following error:

pytest -n auto --showlocals -v sklearn --durations=20
ERROR: usage: pytest [options] [file_or_dir] [file_or_dir] [...]
pytest: error: unrecognized arguments: -n sklearn
  inifile: /workspaces/scikit-learn/setup.cfg
  rootdir: /workspaces/scikit-learn

make: *** [Makefile:37: test-code-parallel] Error 4

Since this is an error by pytest I assume that you did not install pytest-xdist plugin that should recognize the -n option.

@glemaitre
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Regarding the other error:

pytest --showlocals -v sklearn --durations=20
ImportError while loading conftest '/workspaces/scikit-learn/sklearn/conftest.py'.
_pytest.pathlib.ImportPathMismatchError: ('sklearn.conftest', '/workspaces/scikit-learn/sklearn-env/lib/python3.13/site-packages/sklearn/conftest.py', PosixPath('/workspaces/scikit-learn/sklearn/conftest.py'))
make: *** [Makefile:29: test-code] Error 4

We should try to reproduce it.

@clin1234
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For the parallel case, you get the following error:

pytest -n auto --showlocals -v sklearn --durations=20
ERROR: usage: pytest [options] [file_or_dir] [file_or_dir] [...]
pytest: error: unrecognized arguments: -n sklearn
  inifile: /workspaces/scikit-learn/setup.cfg
  rootdir: /workspaces/scikit-learn

make: *** [Makefile:37: test-code-parallel] Error 4

Since this is an error by pytest I assume that you did not install pytest-xdist plugin that should recognize the -n option.

Installed the plugin, now leads to the ImportPathMismatchError

@lesteve
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lesteve commented Jun 19, 2024 •
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Can you try building with Meson which is our main supported build tool, see https://scikit-learn.org/dev/developers/advanced_installation.html#building-from-source.

Then run the tests with pytest sklearn or something equivalent.

Is there a particular reason you were using python setup.py build_ext -i? The reason I am asking is that I am actually planning to remove setup.py in the not so far future.

Edit: hmmm the question actually becomes: is there any particular reason you are using make test-code? I now realised that make test-code depends on inplace which calls python setup.py build_ext -i ... I would have thought nobody uses make test-code anymore and the Makefile should be cleaned-up.

@clin1234
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Can you try building with Meson which is our main supported build tool, see https://scikit-learn.org/dev/developers/advanced_installation.html#building-from-source.

Then run the tests with pytest sklearn or something equivalent.

Is there a particular reason you were using python setup.py build_ext -i? The reason I am asking is that I am actually planning to remove setup.py in the not so far future.

Edit: hmmm the question actually becomes: is there any particular reason you are using make test-code? I now realised that make test-code depends on inplace which calls python setup.py build_ext -i ... I would have thought nobody uses make test-code anymore and the Makefile should be cleaned-up.

Building with Meson succeeeds, running pytest yields:
================= 29643 passed, 5315 skipped, 91 xfailed, 50 xpassed, 3853 warnings in 312.31s (0:05:12) ==================

@clin1234 clin1234 mentioned this issue Jun 19, 2024
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@lesteve
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lesteve commented Jun 19, 2024 •
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OK great, closing!

Still interested if you had a particularly good reason to use make or make test-code since I am thinking about breaking/changing this a bit ...

@lesteve lesteve closed this as completed Jun 19, 2024
@lesteve lesteve mentioned this issue Jun 19, 2024
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@lesteve @glemaitre @clin1234