Feature/api multi rawfile support - Githubissues

wilhelm-lab / oktoberfest

Rescoring and spectral library generation pipeline for proteomics.

MIT License

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Feature/api multi rawfile support #212

Closed picciama closed 2 months ago

picciama commented 2 months ago

PR Checklist

[x] This comment contains a description of changes (with reason)
[ ] Referenced issue is linked
[ ] If you've fixed a bug or added code that should be tested, add tests!
[x] Documentation in docs is updated

Description of changes

updated spectrum-io to remove tables dependency causing issues on MacOS (not needed anyways)
allow forwarding multiple mzml files to the load spectrum function in spectrum-io
allow calibration of all rawfiles at once

Technical details

group by rawfile when creating the alignment dataframe for ce calibration
extend type checking and conversion of all filenames to path objects or creation of singleton list in case of only one provided filename
bumped version of spectrum-io to 0.4.3 in pyproject.toml

Additional context