wfondrie / mokapot

Fast and flexible semi-supervised learning for peptide detection in Python
https://mokapot.readthedocs.io
Apache License 2.0
40 stars 14 forks source link

[Breaking enhancement] Swap out Pandas for Polars #96

Open wfondrie opened 1 year ago

wfondrie commented 1 year ago

This is a huge, in-progress PR swapping out the Pandas backend for Polars. The goal is to improve the speed and scalability of mokapot.

In addition to this huge change, this PR also:

Notably, this PR may also merge in work done by @sambenfredj.

codecov[bot] commented 8 months ago

Codecov Report

Merging #96 (d9bfc33) into main (ca5a8df) will decrease coverage by 5.45%. The diff coverage is 88.95%.

:exclamation: Current head d9bfc33 differs from pull request most recent head 96de300. Consider uploading reports for the commit 96de300 to get more accurate results

@@            Coverage Diff             @@
##             main      #96      +/-   ##
==========================================
- Coverage   85.36%   79.92%   -5.45%     
==========================================
  Files          19       21       +2     
  Lines        1640     1315     -325     
==========================================
- Hits         1400     1051     -349     
- Misses        240      264      +24     
Files Coverage Δ
mokapot/__init__.py 100.00% <100.00%> (+40.00%) :arrow_up:
mokapot/base.py 100.00% <100.00%> (ø)
mokapot/mixins.py 100.00% <100.00%> (ø)
mokapot/parsers/__init__.py 100.00% <100.00%> (ø)
mokapot/qvalues.py 68.62% <100.00%> (+24.47%) :arrow_up:
mokapot/version.py 100.00% <100.00%> (ø)
mokapot/writers/__init__.py 100.00% <100.00%> (ø)
mokapot/schema.py 98.66% <98.66%> (ø)
mokapot/writers/flashlfq.py 96.66% <95.23%> (-3.34%) :arrow_down:
mokapot/writers/tabular.py 97.29% <97.29%> (ø)
... and 11 more

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