Test suite

[HeetVekariya]

• I am getting me familiarise by reading the test suite docs.
• While going through the test suite docs, i run below command which gives 4 errors:

pytest  --disable-pytest-warnings

Errors:

1. test_align.py

_____________________________________ ERROR collecting MDAnalysisTests/analysis/test_align.py _____________________________________
ImportError while importing test module '/home/heet/Work/Development/mdanalysis/testsuite/MDAnalysisTests/analysis/test_align.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
/home/heet/Work/Development/mdanalysis/testsuite/MDAnalysisTests/analysis/test_align.py:27: in <module>
    from MDAnalysis.analysis.align import HAS_BIOPYTHON
E   ImportError: cannot import name 'HAS_BIOPYTHON' from 'MDAnalysis.analysis.align' (/home/heet/anaconda3/envs/mdanalysis-dev/lib/python3.10/site-packages/MDAnalysis/analysis/align.py)

2. test_leaflet.py

____________________________________ ERROR collecting MDAnalysisTests/analysis/test_leaflet.py ____________________________________
ImportError while importing test module '/home/heet/Work/Development/mdanalysis/testsuite/MDAnalysisTests/analysis/test_leaflet.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
/home/heet/Work/Development/mdanalysis/testsuite/MDAnalysisTests/analysis/test_leaflet.py:29: in <module>
    from MDAnalysis.analysis.leaflet import LeafletFinder, optimize_cutoff, HAS_NX
E   ImportError: cannot import name 'HAS_NX' from 'MDAnalysis.analysis.leaflet' (/home/heet/anaconda3/envs/mdanalysis-dev/lib/python3.10/site-packages/MDAnalysis/analysis/leaflet.py)

3. test_nucleicacids.py

_________________________________ ERROR collecting MDAnalysisTests/analysis/test_nucleicacids.py __________________________________
ImportError while importing test module '/home/heet/Work/Development/mdanalysis/testsuite/MDAnalysisTests/analysis/test_nucleicacids.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
/home/heet/Work/Development/mdanalysis/testsuite/MDAnalysisTests/analysis/test_nucleicacids.py:30: in <module>
    from MDAnalysis.analysis.nucleicacids import (NucPairDist, WatsonCrickDist,
E   ImportError: cannot import name 'MajorPairDist' from 'MDAnalysis.analysis.nucleicacids' (/home/heet/anaconda3/envs/mdanalysis-dev/lib/python3.10/site-packages/MDAnalysis/analysis/nucleicacids.py)

4. test_residugroup.py

___________________________________ ERROR collecting MDAnalysisTests/core/test_residuegroup.py ____________________________________
ImportError while importing test module '/home/heet/Work/Development/mdanalysis/testsuite/MDAnalysisTests/core/test_residuegroup.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
/home/heet/Work/Development/mdanalysis/testsuite/MDAnalysisTests/core/test_residuegroup.py:29: in <module>
    from MDAnalysis.core.topologyattrs import HAS_BIOPYTHON
E   ImportError: cannot import name 'HAS_BIOPYTHON' from 'MDAnalysis.core.topologyattrs' (/home/heet/anaconda3/envs/mdanalysis-dev/lib/python3.10/site-packages/MDAnalysis/core/topologyattrs.py)

Overall summery:

============================================================ short test summary info =============================================================
ERROR analysis/test_align.py
ERROR analysis/test_leaflet.py
ERROR analysis/test_nucleicacids.py
ERROR core/test_residuegroup.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
==================================================== 3 skipped, 6 warnings, 4 errors in 9.43s ====================================================

• Does this allowed to persist or needed to be solved in another issue?

[HeetVekariya]

• @IAlibay can you give me information about what/how development environment should be initialised ?
• I am doing contributions to MDAnalysis, so am i in the development environment or not ?

[IAlibay]

@HeetVekariya please see here for more information on how to set up a development environment: https://userguide.mdanalysis.org/stable/contributing_code.html#creating-a-development-environment

[HeetVekariya]

• I have already performed the steps of the docs you have referred me for setting up the development environment.
• The errors i have shown above is also observed in that environment only.

[IAlibay]

@HeetVekariya I can confirm that these tests failures are not happening locally or on our CI suite. This seems like an installation mishap.

Could you run python -Ic "import MDAnalysisTests; print(MDAnalysisTests.__version__)" in your development environment? If so, what value do you get?

[HeetVekariya]

Output:

(mdanalysis-dev) heet@heet:~/Work/Development/mdanalysis/testsuite/MDAnalysisTests$ python -Ic "import MDAnalysisTests; print(MDAnalysisTests.__ve
rsion__)"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/heet/anaconda3/envs/mdanalysis-dev/lib/python3.10/site-packages/MDAnalysisTests/__init__.py", line 95, in <module>
    import pytest
  File "/home/heet/anaconda3/envs/mdanalysis-dev/lib/python3.10/site-packages/pytest/__init__.py", line 5, in <module>
    from _pytest._code import ExceptionInfo
  File "/home/heet/anaconda3/envs/mdanalysis-dev/lib/python3.10/site-packages/_pytest/_code/__init__.py", line 2, in <module>
    from .code import Code
  File "/home/heet/anaconda3/envs/mdanalysis-dev/lib/python3.10/site-packages/_pytest/_code/code.py", line 59, in <module>
    from exceptiongroup import BaseExceptionGroup
ModuleNotFoundError: No module named 'exceptiongroup'

[IAlibay]

How odd, what happens if you run python -Ic "import MDAnalysis; print(MDAnalysis.__version__)"?