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Fix CI for RDKit and Windows #134

Merged
merged 3 commits into from
Jul 31, 2024
Merged

Fix CI for RDKit and Windows #134

merged 3 commits into from
Jul 31, 2024

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RMeli
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@RMeli RMeli commented Jul 31, 2024

This PR pins RDKit on Windows to rdkit<=2024.03.4.

rdkit/rdkit#7679
conda-forge/rdkit-feedstock#168

Additionally, unused rustworkx-only conda environments are removed.


CI for Windows started failing, while Linux is not affected. macOS is too slow to complete before jobs are cancelled, but locally everything works fine.

The error is the following:

ERROR tests/test_rmsd.py::test_rmsdwrapper_single_molecule[networkx-lambda_max_fast-minimize] - NameError: name 'load' is not defined
ERROR tests/test_rmsd.py::test_rmsdwrapper_single_molecule[networkx-lambda_max_fast-no_minimize] - NameError: name 'load' is not defined
ERROR tests/test_rmsd.py::test_rmsdwrapper_single_molecule[networkx-lambda_max_fallback-minimize] - NameError: name 'load' is not defined
ERROR tests/test_rmsd.py::test_rmsdwrapper_single_molecule[networkx-lambda_max_fallback-no_minimize] - NameError: name 'load' is not defined
===== 44 failed, 128 passed, 34 skipped, 4 warnings, 706 errors in 15.67s =====

and seems to appear only on Windows (and possibly only with RDKit).

@RMeli
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RMeli commented Jul 31, 2024

The import error resulting in __all__ = [] is the following:

ImportError while loading conftest 'D:\a\spyrmsd\spyrmsd\tests\conftest.py'.
tests\conftest.py:16: in <module>
    from spyrmsd import io
spyrmsd\io.py:26: in <module>
    raise e
spyrmsd\io.py:14: in <module>
    from spyrmsd.optional.rdkit import (
spyrmsd\optional\rdkit.py:6: in <module>
    import rdkit.Chem as Chem
C:\Users\runneradmin\miniconda3\envs\spyrmsd\lib\site-packages\rdkit\__init__.py:6: in <module>
    from . import rdBase
E   ImportError: DLL load failed while importing rdBase: The specified module could not be found.

@RMeli
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RMeli commented Jul 31, 2024

Pinning to rdkit<=2024.03.4 in CI (for Windows only) seems to avoid the issue.

@RMeli RMeli self-assigned this Jul 31, 2024
@RMeli RMeli mentioned this pull request Jul 31, 2024
@RMeli RMeli marked this pull request as ready for review July 31, 2024 20:11
@RMeli RMeli merged commit 174c38a into develop Jul 31, 2024
38 checks passed
@RMeli RMeli deleted the win-fix branch July 31, 2024 20:23
@RMeli RMeli mentioned this pull request Aug 5, 2024
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