Fix merge conflict

.github/workflows/tests.yml

@@ -17,31 +17,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
         os: [ubuntu-latest, windows-latest, macos-latest]
         experimental: [false,]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov wheel
-        pip install -e .
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      run: uv sync --all-extras --dev
+
     - name: Run unit and system tests
       run: |
-        pytest -v --cov=mokapot tests/
+        uv run pytest -v --cov=mokapot tests/
+
     - name: Upload coverage to codecov
       uses: codecov/codecov-action@v3
       with:

.gitignore

@@ -111,4 +111,5 @@ venv.bak/
 .idea/
 
 tests/integration_tests/run*
-
+/temp/
+/.run/

.gitlab-ci.yml

@@ -40,11 +40,17 @@ publish:
     - python -m build --sdist --wheel .
     - TWINE_PASSWORD=${CI_JOB_TOKEN} TWINE_USERNAME=gitlab-ci-token python -m twine upload --repository-url https://gitlab.com/api/v4/projects/${CI_PROJECT_ID}/packages/pypi dist/*
 
+check_formatting:
+  extends: .with_twine
+  stage: test
+  script:
+    - pip install .[dev]
+    - ruff check . --exclude docs/
+
 unit_test:
   extends: .with_twine
   stage: test
   script:
     - pip install .[dev]
     - pip install pytest
     - pytest tests/
-

data/percolator-noSplit-extended-201-bad.tab

@@ -1,4 +1,4 @@
-SpecId	Label	ScanNr	ExpMass	Mass	MS8_feature_5	missedCleavages	MS8_feature_7	MS8_feature_13	MS8_feature_20	MS8_feature_21	MS8_feature_22	MS8_feature_24	MS8_feature_29	MS8_feature_30	MS8_feature_32	MS8_feature_33	MS8_feature_34	MS8_feature_35	MS8_feature_37	MS8_feature_38	MS8_feature_39	MS8_feature_40	MS8_feature_41	MS8_feature_42	MS8_feature_43	MS8_feature_44	MS8_feature_45	MS8_feature_47	MS8_feature_52	MS8_feature_53	MS8_feature_55	MS8_feature_56	MS8_feature_57	MS8_feature_58	MS8_feature_60	MS8_feature_61	MS8_feature_62	MS8_feature_63	MS8_feature_64	MS8_feature_65	MS8_feature_66	MS8_feature_67	MS8_feature_68	MS8_feature_70	MS8_feature_75	MS8_feature_76	MS8_feature_78	MS8_feature_79	MS8_feature_80	MS8_feature_81	MS8_feature_83	MS8_feature_84	MS8_feature_85	MS8_feature_86	MS8_feature_87	MS8_feature_88	MS8_feature_89	MS8_feature_90	MS8_feature_91	MS8_feature_93	MS8_feature_98	MS8_feature_99	MS8_feature_101	MS8_feature_102	MS8_feature_103	MS8_feature_104	MS8_feature_106	MS8_feature_107	MS8_feature_108	MS8_feature_109	MS8_feature_110	MS8_feature_111	MS8_feature_116	MS8_feature_118	MS8_feature_119	MS8_feature_124	MS8_feature_126	MS8_feature_127	MS8_feature_132	MS8_feature_134	MS8_feature_135	MS8_feature_140	MS8_feature_142	MS8_feature_143	MS8_feature_144	MS8_feature_146	MS8_feature_147	MS8_feature_148	MS8_feature_149	MS8_feature_150	MS8_feature_151	MS8_feature_152	MS8_feature_153	MS8_feature_154	MS8_feature_155	MS8_feature_156	MS8_feature_157	MS8_feature_158	Peptide	Proteins	ModifiedPeptide	PCM	PeptideGroup
+SpecId	Label	ScanNr	ExpMass	Mass	MS8_feature_5	missedCleavages	MS8_feature_7	MS8_feature_13	MS8_feature_20	MS8_feature_21	MS8_feature_22	MS8_feature_24	MS8_feature_29	MS8_feature_30	MS8_feature_32	MS8_feature_33	MS8_feature_34	MS8_feature_35	MS8_feature_37	MS8_feature_38	MS8_feature_39	MS8_feature_40	MS8_feature_41	MS8_feature_42	MS8_feature_43	MS8_feature_44	MS8_feature_45	MS8_feature_47	MS8_feature_52	MS8_feature_53	MS8_feature_55	MS8_feature_56	MS8_feature_57	MS8_feature_58	MS8_feature_60	MS8_feature_61	MS8_feature_62	MS8_feature_63	MS8_feature_64	MS8_feature_65	MS8_feature_66	MS8_feature_67	MS8_feature_68	MS8_feature_70	MS8_feature_75	MS8_feature_76	MS8_feature_78	MS8_feature_79	MS8_feature_80	MS8_feature_81	MS8_feature_83	MS8_feature_84	MS8_feature_85	MS8_feature_86	MS8_feature_87	MS8_feature_88	MS8_feature_89	MS8_feature_90	MS8_feature_91	MS8_feature_93	MS8_feature_98	MS8_feature_99	MS8_feature_101	MS8_feature_102	MS8_feature_103	MS8_feature_104	MS8_feature_106	MS8_feature_107	MS8_feature_108	MS8_feature_109	MS8_feature_110	MS8_feature_111	MS8_feature_116	MS8_feature_118	MS8_feature_119	MS8_feature_124	MS8_feature_126	MS8_feature_127	MS8_feature_132	MS8_feature_134	MS8_feature_135	MS8_feature_140	MS8_feature_142	MS8_feature_143	MS8_feature_144	MS8_feature_146	MS8_feature_147	MS8_feature_148	MS8_feature_149	MS8_feature_150	MS8_feature_151	MS8_feature_152	MS8_feature_153	MS8_feature_154	MS8_feature_155	MS8_feature_156	MS8_feature_157	MS8_feature_158	Peptide	Proteins	ModifiedPeptide	Precursor	PeptideGroup
 390120	1	52505	2984.374317675	2984.374317675	27	1	4.39773287346864	1.05600619360352	0.185185185185185	1.11111111111111	2.81481481481481	35	4.99716807635322	0.174402239166153	0.111111111111111	0.00529100552753166	0.0804232844599971	0.0317460320614002	-1.20775864924016	0.00317460326132951	0.600000023841858	0.000922763211442017	0.00055365791724004	0.104641347657766	0.0740740740740741	0.444444444444444	2.55555555555556	14	4.56519603562033	0.358209911483048	0.037037037037037	0.00529100552753166	0.182539674970839	0.0317460320614002	-1.51853827336966	0.00264550276376583	0.5	0.00189529062167343	0.000947645310836716	0.179104955741524	0.0740740740740741	0.592592592592593	2.55555555555556	18	4.56519603562033	0.355785448846456	0.037037037037037	0.00411522636810939	0.141975305698536	0.0329218109448751	-1.51853827336966	0.00205761318405469	0.5	0.00146413766048257	0.000732068830241284	0.177892724423228	0.185185185185185	1.11111111111111	2.55555555555556	35	4.92084022385512	0.15368946169618	0.111111111111111	0.00529100552753166	0.0730158708713673	0.0317460320614002	-1.1792680662246	0.00317460326132951	0.600000023841858	0.000813171791357855	0.000487903066332671	0.0922136806819505	0.0740740740740741	0.148148148148148	0.839147686958313	0	0.0740740740740741	0.596351504325867	0	0.0740740740740741	0.596351504325867	0.0740740740740741	0.148148148148148	0.839147686958313	4	14.0633640289307	14.0633640289307	7.51776170730591	7.18997812271118	0	0	0	0	0	0	0	0	-1.05600619360352	262211	_.dummy._	5133041	513304104	3746459
 167618	-1	35142	1598.79490536	1598.79490536	13	1	5.2123265552766	0.0782731870117175	0.615384615384615	1.38461538461538	29.6153846153846	26	6.23419631596735	0.68169286154319	0.461538461538462	0.02366863993498	1.139053271367	0.0532544392805833	-1.23618708000169	0.0177514793781134	0.75	0.0161347428861119	0.012101056773891	0.511269646157393	0.153846153846154	1.07692307692308	26.9230769230769	16	4.21731303051421	0.509927000412204	0.0769230769230769	0.00961538461538462	1.68269230769231	0.0673076923076923	-3.04056367951856	0.00480769230769231	0.5	0.00490314423473273	0.00245157211736636	0.254963500206102	0.230769230769231	1.46153846153846	26.9230769230769	22	4.39931826509783	0.475203076933652	0.0769230769230769	0.0104895108021223	1.22377623044527	0.0664335672671978	-2.85876431935613	0.00349650360070742	0.333333343267441	0.00498464780869727	0.00166154926956576	0.158401030365269	0.384615384615385	1.61538461538462	26.9230769230769	26	5.167312164545	0.786869767626696	0.230769230769231	0.0147928996728017	1.0355029472938	0.0621301761040321	-2.0936832299775	0.00887573968905669	0.600000023841858	0.0116400855280625	0.00698405122664308	0.472121879336455	0.384615384615385	0.538461538461538	3.06590270996094	0.0769230769230769	0.0769230769230769	4.209068775177	0.0769230769230769	0.0769230769230769	7.7958083152771	0.230769230769231	0.230769230769231	3.89074325561523	3	14.6776256561279	8.77441215515137	4.29312372207642	5.5558910369873	0	0	0	0	0	0	0	0	0.0782731870117175	2286595	_.dummy._	2178398	217839803	1788327
 47826	1	38693	1483.782350015	1483.782350015	12	1	5.33775257770524	0.744991249755863	0.666666666666667	1.91666666666667	25.5	31	5.87355472778032	0.534035432491101	0.416666666666667	0.0215053757031759	0.822580655415853	0.0618279576301575	-1.43610371273436	0.0134408598144849	0.625	0.0114846326145291	0.00717789538408071	0.333772145306938	0.166666666666667	0.916666666666667	22.8333333333333	13	4.66878509363779	0.754139716754149	0.166666666666667	0.0128205132981141	1.75641028086344	0.0705128212769826	-2.33735102703985	0.0128205132981141	1	0.0096684582672826	0.0096684582672826	0.754139716754149	0.25	1.58333333333333	22.8333333333333	22	4.77529467454582	0.658024571737302	0.166666666666667	0.0113636367022991	1.03787875175476	0.0719696978727977	-2.23139621492402	0.00757575780153275	0.666666686534882	0.00747755217440866	0.00498503478293911	0.438683060898641	0.583333333333333	2	22.8333333333333	31	5.52196035496777	0.335201948098924	0.416666666666667	0.0188172037402789	0.736559152603149	0.0645161271095276	-1.49625222801692	0.0134408598144849	0.714285731315613	0.00630756335151585	0.00450540239393989	0.239429968636258	0.416666666666667	0.416666666666667	2.52091455459595	0.166666666666667	0.166666666666667	3.12026619911194	0.166666666666667	0.166666666666667	3.1865119934082	0.416666666666667	0.416666666666667	3.1865119934082	3	16.0624752044678	13.8793077468872	5.27713108062744	6.50826787948608	0	0	0	0	0	0	0	0	-0.744991249755863	1213451	_.dummy._	1880410	188041003	1559331

mokapot/__init__.py

@@ -22,5 +22,4 @@
 from .parsers.pin import read_pin, read_percolator
 from .parsers.pepxml import read_pepxml
 from .parsers.fasta import read_fasta, make_decoys, digest
-from .writers import to_flashlfq, to_txt
-from .confidence import LinearConfidence, plot_qvalues, assign_confidence
+from .confidence import Confidence, assign_confidence