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Title: Apply linting to entire codebase & add CI workflow to check linting by deruyter92 · Pull Request #3216 · DeepLabCut/DeepLabCut · GitHub

Open Graph Title: Apply linting to entire codebase & add CI workflow to check linting by deruyter92 · Pull Request #3216 · DeepLabCut/DeepLabCut

X Title: Apply linting to entire codebase & add CI workflow to check linting by deruyter92 · Pull Request #3216 · DeepLabCut/DeepLabCut

Description: Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans - Apply linting to entire codebase & add CI workflow to check linting by deruyter92 · Pull Request #3216 · DeepLabCut/DeepLabCut

Open Graph Description: This PR is part of the task described in issue #3217 Motivation: Linting has not been applied consistently in existing codebase. Following DeepLabCut/DeepLabCut-live#166, it would be great to intro...

X Description: This PR is part of the task described in issue #3217 Motivation: Linting has not been applied consistently in existing codebase. Following DeepLabCut/DeepLabCut-live#166, it would be great to intro...

Opengraph URL: https://github.com/DeepLabCut/DeepLabCut/pull/3216

X: @github

direct link

Domain: github.com

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Commits84 (84)https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits
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Apply linting to entire codebase & add CI workflow to check lintinghttps://github.com/DeepLabCut/DeepLabCut/pull/3216#top
MMathisLabhttps://github.com/MMathisLab
mainhttps://github.com/DeepLabCut/DeepLabCut/tree/main
jaap/reformat_codebasehttps://github.com/DeepLabCut/DeepLabCut/tree/jaap/reformat_codebase
https://github.com/deruyter92
deruyter92https://github.com/deruyter92
Feb 23, 2026https://github.com/DeepLabCut/DeepLabCut/pull/3216#issue-3977871520
Please reload this pagehttps://github.com/DeepLabCut/DeepLabCut/pull/3216
#3217https://github.com/DeepLabCut/DeepLabCut/issues/3217
DeepLabCut/DeepLabCut-live#166https://github.com/DeepLabCut/DeepLabCut-live/pull/166
Install through pyproject.toml (PEP 518/621) #3184https://github.com/DeepLabCut/DeepLabCut/pull/3184
Update pre-commit & linting configuration #3215https://github.com/DeepLabCut/DeepLabCut/pull/3215
DeepLabCut/DeepLabCut-live#166https://github.com/DeepLabCut/DeepLabCut-live/pull/166
@C-Achardhttps://github.com/C-Achard
Please reload this pagehttps://github.com/DeepLabCut/DeepLabCut/pull/3216
Task: Fix linting & and pre-commit-hooks and add to CI workflow #3217 https://github.com/DeepLabCut/DeepLabCut/issues/3217
Update pre-commit & linting configuration #3215 https://github.com/DeepLabCut/DeepLabCut/pull/3215
https://github.com/C-Achard
C-Achardhttps://github.com/C-Achard
Centralize linting updatehttps://github.com/DeepLabCut/DeepLabCut/milestone/3
Feb 23, 2026https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-23005130506
https://github.com/C-Achard
C-Achardhttps://github.com/C-Achard
Feb 23, 2026https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-23005147371
Task: Fix linting & and pre-commit-hooks and add to CI workflow #3217 https://github.com/DeepLabCut/DeepLabCut/issues/3217
https://github.com/deruyter92
deruyter92https://github.com/deruyter92
MMathisLabhttps://github.com/MMathisLab
MMathisLabhttps://github.com/MMathisLab
February 28, 2026 08:05https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-23154336659
https://github.com/deruyter92
deruyter92https://github.com/deruyter92
deruyter92https://github.com/deruyter92
C-Achardhttps://github.com/C-Achard
Feb 28, 2026https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-23154340039
https://github.com/deruyter92
deruyter92https://github.com/deruyter92
enhancement https://github.com/DeepLabCut/DeepLabCut/issues?q=state%3Aopen%20label%3Aenhancement
Feb 28, 2026https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-23154342544
https://github.com/C-Achard
C-Achardhttps://github.com/C-Achard
CI https://github.com/DeepLabCut/DeepLabCut/issues?q=state%3Aopen%20label%3ACI
Mar 3, 2026https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-23222266255
https://github.com/C-Achard
C-Achardhttps://github.com/C-Achard
Mar 5, 2026 https://github.com/DeepLabCut/DeepLabCut/pull/3216#ref-pullrequest-4027496724
Add automated docs & notebooks freshness + normalization checks #3228 https://github.com/DeepLabCut/DeepLabCut/pull/3228
https://github.com/deruyter92
deruyter92https://github.com/deruyter92
Centralize linting updatehttps://github.com/DeepLabCut/DeepLabCut/milestone/3
CI Overhaulhttps://github.com/DeepLabCut/DeepLabCut/milestone/4
Mar 9, 2026https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-23385996775
deruyter92https://github.com/deruyter92
March 16, 2026 10:13https://github.com/DeepLabCut/DeepLabCut/pull/3216#commits-pushed-abd8f9e
https://github.com/deruyter92
Update pre-commit confighttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/abd8f9e008098ccaa2e6d4fb5e930eeffc922434
abd8f9ehttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/abd8f9e008098ccaa2e6d4fb5e930eeffc922434
https://github.com/deruyter92
Update pyproject.toml with new lintinghttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/9d8dfb294a061cc3bfa34dafe803d08eb788662d
9d8dfb2https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/9d8dfb294a061cc3bfa34dafe803d08eb788662d
https://github.com/deruyter92
add linting CI workflowhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/3fcc0706894689dc8e2875a069f8ff8c2a56dcf5
3fcc070https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/3fcc0706894689dc8e2875a069f8ff8c2a56dcf5
https://github.com/deruyter92
Reformat codebase: ruff format . --config pyproject.tomlhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/8e65bd623b1fbdd2038296d3b5d29b03e3019a2e
8e65bd6https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/8e65bd623b1fbdd2038296d3b5d29b03e3019a2e
https://github.com/deruyter92
deruyter92https://github.com/deruyter92
force-pushedhttps://github.com/DeepLabCut/DeepLabCut/compare/88356ec4942c6f621d216b665db59935e3d7f227..8e65bd623b1fbdd2038296d3b5d29b03e3019a2e
88356echttps://github.com/DeepLabCut/DeepLabCut/commit/88356ec4942c6f621d216b665db59935e3d7f227
8e65bd6https://github.com/DeepLabCut/DeepLabCut/commit/8e65bd623b1fbdd2038296d3b5d29b03e3019a2e
Compare https://github.com/DeepLabCut/DeepLabCut/compare/88356ec4942c6f621d216b665db59935e3d7f227..8e65bd623b1fbdd2038296d3b5d29b03e3019a2e
March 16, 2026 09:18https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-23600153758
C-Achardhttps://github.com/C-Achard
March 16, 2026 15:58https://github.com/DeepLabCut/DeepLabCut/pull/3216#commits-pushed-9785d7a
https://github.com/C-Achard
Update pre-commit hooks and add docformatterhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/9785d7af9a519cea54b9888778e09c47946a9ee4
9785d7ahttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/9785d7af9a519cea54b9888778e09c47946a9ee4
https://github.com/C-Achard
Add Ruff JSON to Markdown report toolhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/3362a7c2370b61cb5dd48bbf821915f1ffa6e650
3362a7chttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/3362a7c2370b61cb5dd48bbf821915f1ffa6e650
https://github.com/C-Achard
Add tool to auto-fix E501 line-lengthshttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/6a140e8f6c03c48e9eec211f9c1b9b7d84397813
6a140e8https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/6a140e8f6c03c48e9eec211f9c1b9b7d84397813
https://github.com/C-Achard
Run autopep8 script to fix errors automaticallyhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/67eeb2b665501a0e908b4af1d580e29fd4bacc7b
67eeb2bhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/67eeb2b665501a0e908b4af1d580e29fd4bacc7b
https://github.com/C-Achard
Enforce docstrings length and robustness in zips/warningshttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/e6a4637ade62f0fbe5d2eb83b25e3526165a6a92
e6a4637https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/e6a4637ade62f0fbe5d2eb83b25e3526165a6a92
https://github.com/C-Achard
Remove ruff-report and ignore tool outputhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/6037535387412e701accd43d35aaccbed463deb5
6037535https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/6037535387412e701accd43d35aaccbed463deb5
https://github.com/C-Achard
Refactor __init__: lazy-load optional APIshttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/68c612811c0b355dd65bd5df25c2bf1fcdd2a00d
68c6128https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/68c612811c0b355dd65bd5df25c2bf1fcdd2a00d
https://github.com/C-Achard
Re-run line length fixeshttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/918fdb9d78c9496a08b9793e6d07644d9f30a66d
918fdb9https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/918fdb9d78c9496a08b9793e6d07644d9f30a66d
https://github.com/C-Achard
Fix window.pyhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/f1b715acf5b9a01d27cb21f0e75eab99adb1eeee
f1b715ahttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/f1b715acf5b9a01d27cb21f0e75eab99adb1eeee
https://github.com/C-Achard
Remove unused importshttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/65dc094a5f999033fc4eff813077f78ee38ab885
65dc094https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/65dc094a5f999033fc4eff813077f78ee38ab885
https://github.com/C-Achard
Fix TF train.pyhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/6936d1c3d59431c90603e654570a57e4da60c3ac
6936d1chttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/6936d1c3d59431c90603e654570a57e4da60c3ac
https://github.com/C-Achard
Fix missing importshttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/ea0fa8edff8273bdddd9cb77c2c85f337a0d7488
ea0fa8ehttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/ea0fa8edff8273bdddd9cb77c2c85f337a0d7488
deruyter92https://github.com/deruyter92
March 18, 2026 16:47https://github.com/DeepLabCut/DeepLabCut/pull/3216#commits-pushed-5858257
https://github.com/deruyter92
https://github.com/C-Achard
adjust line length to max 120 for ~75 files (https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/5858257e16a64dbe7ba187f3827223efbc46cd68
#3248https://github.com/DeepLabCut/DeepLabCut/pull/3248
)https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/5858257e16a64dbe7ba187f3827223efbc46cd68
5858257https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/5858257e16a64dbe7ba187f3827223efbc46cd68
https://github.com/C-Achard
Fix E501https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/2c3e98bc230412cab864debe4fb914b57ebc6f91
2c3e98bhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/2c3e98bc230412cab864debe4fb914b57ebc6f91
https://github.com/C-Achard
Merge branch 'main' into jaap/reformat_codebasehttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/0a72d35d443fb0b45e4b133de15f658eed74d5c6
0a72d35https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/0a72d35d443fb0b45e4b133de15f658eed74d5c6
https://github.com/deruyter92
fix direct call of abstract base method in ctd.pyhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/7a06b2719542a0c9fc9c341b4bfd4882733f34ac
7a06b27https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/7a06b2719542a0c9fc9c341b4bfd4882733f34ac
https://github.com/deruyter92
deruyter92https://github.com/deruyter92
March 19, 2026 17:26https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-23726199390
https://github.com/C-Achard
C-Achardhttps://github.com/C-Achard
March 19, 2026 19:20https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-23729932874
https://github.com/C-Achard
C-Achardhttps://github.com/C-Achard
Mar 19, 2026 https://github.com/DeepLabCut/DeepLabCut/pull/3216#pullrequestreview-3977439984
View reviewed changes https://github.com/DeepLabCut/DeepLabCut/pull/3216/files/7a06b2719542a0c9fc9c341b4bfd4882733f34ac
deruyter92https://github.com/deruyter92
Mar 20, 2026 https://github.com/DeepLabCut/DeepLabCut/pull/3216#ref-commit-8916be5
https://github.com/deruyter92
align pre-commit config with PRhttps://github.com/deruyter92/DeepLabCut/commit/8916be58c9c4d54988f00658d00a5b4d66cefbd2
DeepLabCut#3216https://github.com/DeepLabCut/DeepLabCut/pull/3216
8916be5https://github.com/deruyter92/DeepLabCut/commit/8916be58c9c4d54988f00658d00a5b4d66cefbd2
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March 20, 2026 13:05https://github.com/DeepLabCut/DeepLabCut/pull/3216#commits-pushed-87a34d7
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Merge remote-tracking branch 'upstream/main' into jaap/reformat_codebasehttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/87a34d7f45c10910cf6aea0bd4346b1cb59ffae8
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move ruff_cleanup_helpers documentation to separate filehttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/ee65c6c26c024f0ee6fd651cabdac3656bc37ce2
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Apply linting to newest commits (intellligent CI and inference helpers)https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/8807c410f4dd6348be976e935f7f15c360cd911c
8807c41https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/8807c410f4dd6348be976e935f7f15c360cd911c
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Mar 20, 2026 https://github.com/DeepLabCut/DeepLabCut/pull/3216#ref-commit-86f9ba9
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Align pyproject.toml with PRhttps://github.com/deruyter92/DeepLabCut/commit/86f9ba9d13b8c1ae26f3925fbeea025b1b22435c
DeepLabCut#3216https://github.com/DeepLabCut/DeepLabCut/pull/3216
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March 20, 2026 13:45https://github.com/DeepLabCut/DeepLabCut/pull/3216#commits-pushed-4fd852d
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Update pre-commit & linting configuration (https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/4fd852d18d10f43be2f67363a01278cb39d72cbf
#3215https://github.com/DeepLabCut/DeepLabCut/pull/3215
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4fd852dhttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/4fd852d18d10f43be2f67363a01278cb39d72cbf
#3216https://github.com/DeepLabCut/DeepLabCut/pull/3216
#3216https://github.com/DeepLabCut/DeepLabCut/pull/3216
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Merge remote-tracking branch 'origin/main' into jaap/reformat_codebasehttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/a43562aa285c5f263cce473ccf23c875ce9eb704
a43562ahttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/a43562aa285c5f263cce473ccf23c875ce9eb704
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Run pre-commit on latesthttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/5bfdd3930ae179a665b74dd122c7a3cb1cbacb04
5bfdd39https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/5bfdd3930ae179a665b74dd122c7a3cb1cbacb04
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Fix mutable default for config_kwargshttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/8fd910ab354cc44e8d457f8c357a744bb601d386
8fd910ahttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/8fd910ab354cc44e8d457f8c357a744bb601d386
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Refactor fmpose3d inference formattinghttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/b183029aa9337176d989b731e6bb4c1098a63bfb
b183029https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/b183029aa9337176d989b731e6bb4c1098a63bfb
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Remove temporary yapf config from pyprojecthttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/d19eb98bc637d28f247ee7c1d71a20380776d79d
d19eb98https://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/d19eb98bc637d28f247ee7c1d71a20380776d79d
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Mar 23, 2026 https://github.com/DeepLabCut/DeepLabCut/pull/3216#ref-pullrequest-4122805116
Consolidate test workflow infrastructure in CI #3254 https://github.com/DeepLabCut/DeepLabCut/pull/3254
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Merge branch 'main' into jaap/reformat_codebasehttps://github.com/DeepLabCut/DeepLabCut/pull/3216/commits/6e21fe2fb05fbfb3248995ec8f5d310854e65ccb
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Mar 26, 2026https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-23934292363
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Mar 26, 2026https://github.com/DeepLabCut/DeepLabCut/pull/3216#issuecomment-4135014932
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Mar 30, 2026https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-24043422215
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Mar 30, 2026 https://github.com/DeepLabCut/DeepLabCut/pull/3216#ref-issue-4172400659
Maintenance - Apply linting to existing PRs #3263 https://github.com/DeepLabCut/DeepLabCut/issues/3263
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May 21, 2026 https://github.com/DeepLabCut/DeepLabCut/pull/3216#ref-pullrequest-4492645791
Add 3.0 changelog #3340 https://github.com/DeepLabCut/DeepLabCut/pull/3340
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CI Overhaulhttps://github.com/DeepLabCut/DeepLabCut/milestone/4
Centralize linting updatehttps://github.com/DeepLabCut/DeepLabCut/milestone/3
Jun 29, 2026https://github.com/DeepLabCut/DeepLabCut/pull/3216#event-27322427228
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