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PEP 8 compliance, type hints, and Google-style docstrings#13

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aalexmmaldonado wants to merge 13 commits intomainfrom
cleanup
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PEP 8 compliance, type hints, and Google-style docstrings#13
aalexmmaldonado wants to merge 13 commits intomainfrom
cleanup

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@aalexmmaldonado aalexmmaldonado commented Jul 9, 2025

This PR starts to rework the module names, classes, and imports to be PEP 8 compliant. This includes snake_case for modules and functions and CamelCase for classes. Type hints are being added to improve developer experience, but RDKit appears to not have reliable stubs besides this package that does not seem to be well maintained. Docstrings should also be in the Google style.

@aalexmmaldonado aalexmmaldonado changed the title PEP8 compliance, type hints, and Google-style docstrings PEP 8 compliance, type hints, and Google-style docstrings Jul 9, 2025
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Codecov Report

Attention: Patch coverage is 66.12903% with 105 lines in your changes missing coverage. Please review.

Project coverage is 57.22%. Comparing base (e58342a) to head (c867b18).

Files with missing lines Patch % Lines
gypsum_dl/start.py 28.00% 29 Missing and 7 partials ⚠️
gypsum_dl/steps/io/load.py 26.66% 11 Missing ⚠️
gypsum_dl/molecule.py 84.78% 7 Missing ⚠️
gypsum_dl/parallelizer.py 70.00% 5 Missing and 1 partial ⚠️
gypsum_dl/container.py 75.00% 5 Missing ⚠️
gypsum_dl/steps/smiles/prepare.py 61.53% 5 Missing ⚠️
gypsum_dl/chem_utils.py 63.63% 3 Missing and 1 partial ⚠️
gypsum_dl/steps/conf/convert.py 60.00% 2 Missing and 2 partials ⚠️
gypsum_dl/steps/conf/minimize.py 70.00% 2 Missing and 1 partial ⚠️
gypsum_dl/steps/io/output.py 57.14% 1 Missing and 2 partials ⚠️
... and 9 more
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #13      +/-   ##
==========================================
+ Coverage   56.41%   57.22%   +0.81%     
==========================================
  Files          25       25              
  Lines        1980     1924      -56     
  Branches      381      385       +4     
==========================================
- Hits         1117     1101      -16     
+ Misses        716      669      -47     
- Partials      147      154       +7     

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3 participants