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[BUG] Python 3.7 Test Failing in CI #7

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kevin931 opened this issue Mar 21, 2024 · 0 comments
Open

[BUG] Python 3.7 Test Failing in CI #7

kevin931 opened this issue Mar 21, 2024 · 0 comments
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@kevin931
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What issues are you experiencing?

Our CI tests are failing for the Python 3.7 workflow. Here are the errors:

==================================== ERRORS ====================================
______________________ ERROR collecting tests/test_dr.py _______________________
ImportError while importing test module '/home/runner/work/CytofDR/CytofDR/tests/test_dr.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/hostedtoolcache/Python/3.7.[17](https://github.com/kevin931/CytofDR/actions/runs/8368312426/job/22912219782#step:5:18)/x64/lib/python3.7/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_dr.py:1: in <module>
    from CytofDR import dr
CytofDR/__init__.py:3: in <module>
    from CytofDR import dr, evaluation
CytofDR/dr.py:7: in <module>
    import umap
/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/umap/__init__.py:36: in <module>
    from importlib.metadata import version, PackageNotFoundError
E   ModuleNotFoundError: No module named 'importlib.metadata'
__________________ ERROR collecting tests/test_evaluation.py ___________________
ImportError while importing test module '/home/runner/work/CytofDR/CytofDR/tests/test_evaluation.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_evaluation.py:1: in <module>
    from CytofDR import evaluation
CytofDR/__init__.py:3: in <module>
    from CytofDR import dr, evaluation
CytofDR/dr.py:7: in <module>
    import umap
/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/umap/__init__.py:36: in <module>
    from importlib.metadata import version, PackageNotFoundError
E   ModuleNotFoundError: No module named 'importlib.metadata'
=============================== warnings summary ===============================
../../../../../opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/tensorflow_core/contrib/learn/python/learn/learn_io/generator_io.py:[26](https://github.com/kevin931/CytofDR/actions/runs/8368312426/job/22912219782#step:5:27)
  /opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/tensorflow_core/contrib/learn/python/learn/learn_io/generator_io.py:26: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working
    from collections import Container

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

---------- coverage: platform linux, python 3.7.17-final-0 -----------
Coverage XML written to file coverage.xml

=========================== short test summary info ============================
ERROR tests/test_dr.py
ERROR tests/test_evaluation.py
!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!
======================== 1 warning, 2 errors in 13.[38](https://github.com/kevin931/CytofDR/actions/runs/8368312426/job/22912219782#step:5:39)s =========================

To Reproduce

See our CI reports here: https://github.com/kevin931/CytofDR/actions/runs/8368312426/job/22912219782.

Additional context

This may be related to #6 here as well. We will need to the update workflows anyways. The problem is that we cannot drop Python 3.7 support because of SAUCIE and Grandprix. While they are optional dependencies, SAUCIE's overall good performance is very related to our paper. We need to maintain compatibility for as long as possible.

@kevin931 kevin931 added the bug Something isn't working label Mar 21, 2024
@kevin931 kevin931 self-assigned this Mar 21, 2024
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