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@desilinguist
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After banging my head against this for a whole day, I finally figured out that adding a pyproject.toml disables the measurement of test coverage in subprocesses for some inexplicable reason. This means that we lose coverage of the code in all the entry point scripts under the main() function. I tried lots of solutions but in the end I had to end up deleting pyproject.toml and just rely on other configuration files.

Here are the actual changes in this PR:

  • Delete pyproject.toml.
  • Add .isort.cfg to control isort during development.
  • Update .pre-commit-config.yaml to include all of the flags that we need all the tools to have.
  • Update the CI configuration files to no longer use the defaults channel or the nose-cov PyPI package since they are no longer needed.
  • Replace coveralls with codecov in requirements.txt.
  • Add new tests for convert_feature_json.py.

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codecov bot commented Jan 14, 2023

Codecov Report

Base: 89.60% // Head: 93.20% // Increases project coverage by +3.60% 🎉

Coverage data is based on head (07ecf72) compared to base (e55a0a3).
Patch has no changes to coverable lines.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #589      +/-   ##
==========================================
+ Coverage   89.60%   93.20%   +3.60%     
==========================================
  Files          31       31              
  Lines        4549     4549              
==========================================
+ Hits         4076     4240     +164     
+ Misses        473      309     -164     
Impacted Files Coverage Δ
rsmtool/utils/commandline.py 97.13% <0.00%> (+0.40%) ⬆️
rsmtool/utils/cross_validation.py 95.34% <0.00%> (+5.81%) ⬆️
rsmtool/convert_feature_json.py 73.33% <0.00%> (+13.33%) ⬆️
rsmtool/rsmtool.py 99.13% <0.00%> (+20.00%) ⬆️
rsmtool/rsmxval.py 98.09% <0.00%> (+20.95%) ⬆️
rsmtool/rsmpredict.py 99.14% <0.00%> (+21.36%) ⬆️
rsmtool/utils/logging.py 89.79% <0.00%> (+24.48%) ⬆️
rsmtool/rsmeval.py 97.80% <0.00%> (+27.47%) ⬆️
rsmtool/rsmsummarize.py 97.75% <0.00%> (+28.08%) ⬆️
rsmtool/rsmcompare.py 94.80% <0.00%> (+28.57%) ⬆️

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@mulhod
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mulhod commented Jan 14, 2023

Well, it's unfortunate that it's interacting in this way.

@desilinguist
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Well, it's unfortunate that it's interacting in this way.

Yeah it's very strange. I tried lots of things like moving the coverage configuration from .coveragerc into pyproject.toml, keeping both around, etc. and nothing worked. Very strange.

@desilinguist desilinguist merged commit c6ffc74 into main Jan 17, 2023
@delete-merged-branch delete-merged-branch bot deleted the 588-increase-test-coverage branch January 17, 2023 13:37
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4 participants