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Feature/confidence streaming #127

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merged 15 commits into from
Dec 4, 2024

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codecov bot commented Oct 4, 2024

Codecov Report

Attention: Patch coverage is 82.89567% with 241 lines in your changes missing coverage. Please review.

Project coverage is 83.39%. Comparing base (6b8fbfd) to head (7f58137).

Files with missing lines Patch % Lines
mokapot/tdmodel.py 0.00% 128 Missing ⚠️
mokapot/tabular_data/base.py 84.44% 28 Missing ⚠️
mokapot/tabular_data/streaming.py 82.02% 16 Missing ⚠️
mokapot/dataset.py 91.58% 9 Missing ⚠️
mokapot/peps.py 93.12% 9 Missing ⚠️
mokapot/confidence.py 94.66% 8 Missing ⚠️
mokapot/tabular_data/target_decoy_writer.py 78.94% 8 Missing ⚠️
mokapot/statistics.py 92.70% 7 Missing ⚠️
mokapot/rollup.py 94.94% 5 Missing ⚠️
mokapot/tabular_data/format_chooser.py 85.71% 5 Missing ⚠️
... and 6 more
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #127      +/-   ##
==========================================
- Coverage   84.60%   83.39%   -1.21%     
==========================================
  Files          26       33       +7     
  Lines        2949     3108     +159     
==========================================
+ Hits         2495     2592      +97     
- Misses        454      516      +62     

☔ View full report in Codecov by Sentry.
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* ✨ log more infos
* ✨ uses uv for env setup; fix dependencies
@wfondrie wfondrie self-requested a review December 4, 2024 21:17
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We will fix CI/CD and do some cleanup in a later PR. Thanks!

@wfondrie wfondrie merged commit 9fb32cb into wfondrie:main Dec 4, 2024
1 of 10 checks passed
jspaezp pushed a commit to jspaezp/mokapot that referenced this pull request Dec 5, 2024
* ✨ 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 (wfondrie#48)

* ✨ log more infos
* ✨ uses uv for env setup; fix dependencies

---------

Co-authored-by: Elmar Zander <elmar.zander@googlemail.com>
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3 participants