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commented
1 year ago Codecov Report
Base: 38.00% // Head: 41.50% // Increases project coverage by +3.49% :tada:
Coverage data is based on head (
9d7cf78) compared to base (e087497). Patch coverage: 57.64% of modified lines in pull request are covered.
Additional details and impacted files
```diff @@ Coverage Diff @@ ## main #23 +/- ## ========================================== + Coverage 38.00% 41.50% +3.49% ========================================== Files 18 18 Lines 1392 1412 +20 ========================================== + Hits 529 586 +57 + Misses 863 826 -37 ``` | [Impacted Files](https://codecov.io/gh/compomics/psm_utils/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics) | Coverage Δ | | |---|---|---| | [psm\_utils/io/maxquant.py](https://codecov.io/gh/compomics/psm_utils/pull/23/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL2lvL21heHF1YW50LnB5) | `84.61% <ø> (-0.30%)` | :arrow_down: | | [psm\_utils/io/\_\_init\_\_.py](https://codecov.io/gh/compomics/psm_utils/pull/23/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL2lvL19faW5pdF9fLnB5) | `36.25% <16.66%> (-0.12%)` | :arrow_down: | | [psm\_utils/io/\_base\_classes.py](https://codecov.io/gh/compomics/psm_utils/pull/23/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL2lvL19iYXNlX2NsYXNzZXMucHk=) | `67.85% <50.00%> (-8.34%)` | :arrow_down: | | [psm\_utils/io/tsv.py](https://codecov.io/gh/compomics/psm_utils/pull/23/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL2lvL3Rzdi5weQ==) | `39.08% <50.00%> (-0.25%)` | :arrow_down: | | [psm\_utils/psm\_list.py](https://codecov.io/gh/compomics/psm_utils/pull/23/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL3BzbV9saXN0LnB5) | `59.16% <65.51%> (+33.72%)` | :arrow_up: | | [psm\_utils/io/peptide\_record.py](https://codecov.io/gh/compomics/psm_utils/pull/23/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL2lvL3BlcHRpZGVfcmVjb3JkLnB5) | `47.09% <66.66%> (ø)` | | | [psm\_utils/peptidoform.py](https://codecov.io/gh/compomics/psm_utils/pull/23/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL3BlcHRpZG9mb3JtLnB5) | `28.80% <73.33%> (+3.23%)` | :arrow_up: | | [psm\_utils/\_\_init\_\_.py](https://codecov.io/gh/compomics/psm_utils/pull/23/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL19faW5pdF9fLnB5) | `100.00% <100.00%> (ø)` | | | [psm\_utils/io/msamanda.py](https://codecov.io/gh/compomics/psm_utils/pull/23/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL2lvL21zYW1hbmRhLnB5) | `70.37% <100.00%> (-0.54%)` | :arrow_down: | | [psm\_utils/io/mzid.py](https://codecov.io/gh/compomics/psm_utils/pull/23/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL2lvL216aWQucHk=) | `30.62% <100.00%> (ø)` | | | ... and [6 more](https://codecov.io/gh/compomics/psm_utils/pull/23/diff?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics):umbrella: View full report at Codecov.
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Added
PSM: Addion_mobilityfieldPSMList: Allow slicing with bool arrays (e.g.,psm_df[psm_df["retention_time"] < 2000])rename_modifications: Add support for fixed modificationsPSM.get_usi()methodset_ranksandget_rank1_psmsmethodsChanged
PSMList: Refactorset_ranksandget_rank1_psmsmethods.vscode/settings.json|Fixed
PSMList: Truncate repr to first five entries only, avoiding crashing notebook outputPeptidoform: Minor typing fixadd_fixed_modifications: Allow input as dict as well as list of tuplesio: Fix issue where theNamedTemporaryFilefor_supports_write_psmwas seen as invalid Percolator fileio.convert: passprogressbarargument to class, notwrite_fileio.mzid: Add more supported MS-GF score names, make SpecEValue defaultio.peptide_record:spec_idis now a required column (spectrum_idis also required in PSM)io.peptide_record: Fix parsing of C-terminal modifications from proforma to peprecio.percolator: Fix Percolator peptide notation writing (fixes #18)io.tsv: Fix issue whereTSVReaderwould not use string type for metadataio.xtandem: Fix issue where optional arguments were not accepted byXTandemReaderio.xtandem: Do not split spectrum title on spaceio.xtandem: Fix issue where optional arguments were not accepted byXTandemReader