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PyProphet / pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
http://www.openswath.org
BSD 3-Clause "New" or "Revised" License
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Issue Module Import py.test #86

Open oliveralka opened 3 years ago

oliveralka commented 3 years ago

I stumbled over an issue that the tests running by py.test, would not be able to import modules - I am actually not sure why. After removing the __init__.py from the tests directory, all modules could be imported without any issues.

I just wanted to report it, if anyone else runs into the same issue.

py.test ./tests

python 3.8 MacOS 15.5.5

before removing:

============================================================================================================================ ERRORS =============================================================================================================================
_________________________________________________________________________________________________________ ERROR collecting tests/test_data_handling.py __________________________________________________________________________________________________________
ImportError while importing test module '/Users/alka/Documents/work/software/pyprophet_test/pyprophet/tests/test_data_handling.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_data_handling.py:4: in <module>
    from pyprophet.data_handling import check_for_unique_blocks
pyprophet/data_handling.py:9: in <module>
    from .optimized import find_top_ranked, rank
pyprophet/optimized.py:1: in <module>
    from ._optimized import *
E   ModuleNotFoundError: No module named 'pyprophet._optimized'
______________________________________________________________________________________________________________ ERROR collecting tests/test_ipf.py _______________________________________________________________________________________________________________
ImportError while importing test module '/Users/alka/Documents/work/software/pyprophet_test/pyprophet/tests/test_ipf.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_ipf.py:4: in <module>
    from pyprophet.ipf import prepare_precursor_bm, prepare_transition_bm, apply_bm, compute_model_fdr
pyprophet/ipf.py:9: in <module>
    from .data_handling import check_sqlite_table
pyprophet/data_handling.py:9: in <module>
    from .optimized import find_top_ranked, rank
pyprophet/optimized.py:1: in <module>
    from ._optimized import *
E   ModuleNotFoundError: No module named 'pyprophet._optimized'
___________________________________________________________________________________________________________ ERROR collecting tests/test_optimized.py ____________________________________________________________________________________________________________
ImportError while importing test module '/Users/alka/Documents/work/software/pyprophet_test/pyprophet/tests/test_optimized.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_optimized.py:2: in <module>
    import pyprophet.optimized as o
pyprophet/optimized.py:1: in <module>
    from ._optimized import *
E   ModuleNotFoundError: No module named 'pyprophet._optimized'
_________________________________________________________________________________________________________ ERROR collecting tests/test_pyprophet_ipf.py __________________________________________________________________________________________________________
ImportError while importing test module '/Users/alka/Documents/work/software/pyprophet_test/pyprophet/tests/test_pyprophet_ipf.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_pyprophet_ipf.py:13: in <module>
    from pyprophet.ipf import read_pyp_peakgroup_precursor
pyprophet/ipf.py:9: in <module>
    from .data_handling import check_sqlite_table
pyprophet/data_handling.py:9: in <module>
    from .optimized import find_top_ranked, rank
pyprophet/optimized.py:1: in <module>
    from ._optimized import *
E   ModuleNotFoundError: No module named 'pyprophet._optimized'
________________________________________________________________________________________________________ ERROR collecting tests/test_pyprophet_score.py _________________________________________________________________________________________________________
ImportError while importing test module '/Users/alka/Documents/work/software/pyprophet_test/pyprophet/tests/test_pyprophet_score.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_pyprophet_score.py:13: in <module>
    from pyprophet.ipf import read_pyp_peakgroup_precursor
pyprophet/ipf.py:9: in <module>
    from .data_handling import check_sqlite_table
pyprophet/data_handling.py:9: in <module>
    from .optimized import find_top_ranked, rank
pyprophet/optimized.py:1: in <module>
    from ._optimized import *
E   ModuleNotFoundError: No module named 'pyprophet._optimized'
_____________________________________________________________________________________________________________ ERROR collecting tests/test_stats.py ______________________________________________________________________________________________________________
ImportError while importing test module '/Users/alka/Documents/work/software/pyprophet_test/pyprophet/tests/test_stats.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_stats.py:4: in <module>
    from pyprophet.stats import to_one_dim_array, pnorm, pemp, pi0est, qvalue, bw_nrd0, lfdr, stat_metrics
pyprophet/stats.py:12: in <module>
    from .optimized import (find_nearest_matches as _find_nearest_matches,
pyprophet/optimized.py:1: in <module>
    from ._optimized import *
E   ModuleNotFoundError: No module named 'pyprophet._optimized'
==================================================================================================================== short test summary info ====================================================================================================================
ERROR tests/test_data_handling.py
ERROR tests/test_ipf.py
ERROR tests/test_optimized.py
ERROR tests/test_pyprophet_ipf.py
ERROR tests/test_pyprophet_score.py
ERROR tests/test_stats.py

after removing:

platform darwin -- Python 3.8.0, pytest-5.4.3, py-1.9.0, pluggy-0.13.1
rootdir: /Users/alka/Documents/work/software/pyprophet_test/pyprophet
plugins: regtest-1.4.4
collected 53 items                                                                                                                                                                                                                                              

tests/test_data_handling.py ..                                                                                                                                                                                                                            [  3%]
tests/test_ipf.py ....                                                                                                                                                                                                                                    [ 11%]
tests/test_optimized.py .....                                                                                                                                                                                                                             [ 20%]
tests/test_pyprophet_export.py ..........                                                                                                                                                                                                                 [ 39%]
tests/test_pyprophet_ipf.py .....                                                                                                                                                                                                                         [ 49%]
tests/test_pyprophet_levels_contexts.py ..                                                                                                                                                                                                                [ 52%]
tests/test_pyprophet_score.py .................                                                                                                                                                                                                           [ 84%]
tests/test_stats.py ........                                                                                                                                                                                                                              [100%]