Sync upstream after confidence streaming merge #51
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* ✨ cherry picks internal fixes from !68 and !70 * Cherry pick feature/confidence_streaming branch * ✨ adds filelock dependency for tests * 💄 linting * 💄 reformat to satisfy linter k * ✨ imports type annotations from future for python 3.9 * ✨ make pytest and cli behave with type annotations in Python 3.9 * ✨ test dropping Python 3.9 support - inspired by https://github.com/wfondrie/mokapot/pull/126/files#diff-1db27d93186e46d3b441ece35801b244db8ee144ff1405ca27a163bfe878957fL20 * Set scale_to_one to false in *all* cases * Fixed path problems probably causing errors under windows * Fix more possible path issues * Fix warning about bitwise not in python 3.12 * Fix problem with numpy 2.x's different str rep of floats * Make hashing of rows for splitting independent of numpy version and spectra columns * Feature/streaming fix windows (#48) * ✨ log more infos * ✨ uses uv for env setup; fix dependencies --------- Co-authored-by: Elmar Zander <[email protected]>
Fixed retention time division by 60. Time is required in minutes for FlashLFQ, it's already in minutues Co-authored-by: William Fondrie <[email protected]>
* (feat) added auto handling of traditional pin and testing * (fix) added handling of default direction * (fix) changed intermediate files pin->tsv and fixed tests accordingly * (chore) formatting on docs and removed T20 from them * (chore) upgraded to upstream actions * (chore) removed unused dependency in docs * (chore) reformatted tests * Feature/confidence streaming (#127) * ✨ cherry picks internal fixes from !68 and !70 * Cherry pick feature/confidence_streaming branch * ✨ adds filelock dependency for tests * 💄 linting * 💄 reformat to satisfy linter k * ✨ imports type annotations from future for python 3.9 * ✨ make pytest and cli behave with type annotations in Python 3.9 * ✨ test dropping Python 3.9 support - inspired by https://github.com/wfondrie/mokapot/pull/126/files#diff-1db27d93186e46d3b441ece35801b244db8ee144ff1405ca27a163bfe878957fL20 * Set scale_to_one to false in *all* cases * Fixed path problems probably causing errors under windows * Fix more possible path issues * Fix warning about bitwise not in python 3.12 * Fix problem with numpy 2.x's different str rep of floats * Make hashing of rows for splitting independent of numpy version and spectra columns * Feature/streaming fix windows (#48) * ✨ log more infos * ✨ uses uv for env setup; fix dependencies --------- Co-authored-by: Elmar Zander <[email protected]> * Small changes for FlashLFQ writer (#131) Fixed retention time division by 60. Time is required in minutes for FlashLFQ, it's already in minutues Co-authored-by: William Fondrie <[email protected]> * wip: formatting and rebasing fixes * chore: ruff format * wip,chore: re-adding flashlfq support * ci,fix: fixed confidence out and ci migration * format: eof newline * wip,fix: progress to re-add flashlfq output * chore: uv lock and formatting * chore: added pr template * wip: make brew generic again * wip,fix: added deleter to on psm dataset * feat: re-added flashlfq support * chore: linting + formatting * fix: fixtures and progess in definition of cols * test, fix: annotated/commented new fixtures * lint: formatting * ci: removed fail on codecov fail * ci: test speedup replacing RF with dtree * ci: attempt to fix test docker build * refactor: change stats to dataclass * refactor: extracted output writer factory * refactor: extracted level manager in confidence * refactor: extracted level writer group * refactor: extracted more writer builder work to class * feat: score propagation and unscored confidence * feat(confidence): add data reading api * feat,experiment: Experimental qvalue-fdr estimation * chore,docs: updated basic docs to curr api and updated typing * chore: updated basic n joint model docs code (md in progress) * chore: updated notebook * chore,confidence: update docstrings * chore,qvalue: removed commented out code * chore: fixed line length lints in docstrings * fix,sqlite: fixed path for sqlite writer * feat, wip: compound key on spectrum * refactor,wip: centralized column group logic * refactor,dataset: broke module into files and changed tdc implementation to remove numba * fix: fixed string to bool target col conversion and added notes on tests * ci: enabled lint and test on all PRs * chore: updated triqler and np versions * feat,doc: fixed empty cols in proteins and better column descriptions in docstrings * test: added content testing to cli testing + csv -> tsv * fix: flashlfq and misc fixes * ci: added extra xml to test makefile * chore: unify naming schemas * chore: self-review cleanup * fix,chore: updated makefile and fixed iterator * chore: self-review cleanup --------- Co-authored-by: Siegfried Gessulat <[email protected]> Co-authored-by: Elmar Zander <[email protected]> Co-authored-by: Ivan Chudinov <[email protected]> Co-authored-by: William Fondrie <[email protected]>
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