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[Breaking enhancement] Swap out Pandas for Polars #96

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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:

  • Adds type hints
  • Depreciates LinearPsmDataset in favor of just PsmDataset, with an upcoming PeptideDataset for DIA data. Similar API changes will also be made with the Confidence classes.

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

@wfondrie wfondrie changed the title [Breaking enhancement] Swap our Pandas for Polars [Breaking enhancement] Swap out Pandas for Polars Nov 3, 2023
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codecov bot commented Nov 8, 2023

Codecov Report

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

❗ 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%) ⬆️
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%) ⬆️
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%) ⬇️
mokapot/writers/tabular.py 97.29% <97.29%> (ø)
... and 11 more

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@wfondrie wfondrie closed this Sep 6, 2024
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