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choderalab / openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
http://openmmtools.readthedocs.io
MIT License
244 stars 76 forks source link

Work with upstream to update to work with new SciPy Versions #743

Open mikemhenry opened 3 weeks ago

mikemhenry commented 3 weeks ago

Hitting this issue in CI:

FAILED openmmtools/tests/test_testsystems.py::test_properties_all_testsystems - TypeError: Could not parse Amber ASCII restart file /home/runner/micromamba/envs/openmmtools-test/lib/python3.10/site-packages/openmmtools/data/dhfr/JAC.inpcrd

But the actual issue is from openmm:

    def __init__(self, filename, asNumpy=False):
        try:
>           from scipy.io import NetCDFFile
E           ImportError: cannot import name 'NetCDFFile' from 'scipy.io' (/home/runner/micromamba/envs/openmmtools-test/lib/python3.10/site-packages/scipy/io/__init__.py)

../../../micromamba/envs/openmmtools-test/lib/python3.10/site-packages/openmm/app/internal/amber_file_parser.py:1440: ImportError

It has been fixed: https://github.com/openmm/openmm/issues/4601

But the conda-forge recipe needs to be updated

ijpulidos commented 3 weeks ago

Thanks for the issue. Tbh, I don't like the way this was solved in openmm, since netcdf_file is a class and it doesn't seem to be "pythonic" to use it that way. That said, are there any guidelines from the scipy team on this that we know of?

ijpulidos commented 3 weeks ago

Oh, but I see it's on the openmm side to be fixed, we are not using it directly here in openmmtools. Got it!