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Prepare migration to pandas 3.0 by deruyter92 · Pull Request #3360 · DeepLabCut/DeepLabCut · GitHub

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Prepare migration to pandas 3.0 - #3360

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MMathisLab merged 12 commits into
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Prepare migration to pandas 3.0#3360
MMathisLab merged 12 commits into
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deruyter92 commented Jun 9, 2026 •
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Pandas released version 3.0 in Jan 2026 which introduces breaking changes for our codebase. It would be useful to address the places where it currently breaks, so we can remove the upperbound version we introduced in #3186. See the full tracking issue #3362, for an overview of related PRs.

Small fixes and flagged patterns:
As exploratory preparation, this PR implements small fixes in preparation to 3.0 migration. Also it flags breaking instances based on a targeted search for these patterns:

  • Chained .loc assignment (copy on write; CoW) -> mutate parent object directly instead of a subset view
  • groupby(..., axis=1) -> groupby on the transposed df
  • Column-level groupby(level=...) -> groupby on the transposed df
  • select_dtypes(include="object") -> string type migration
  • deprecated options like future.no_silent_downcasting

Future mode testing:
Also this PR adds a new tool for CI or local testing, using the pandas 2.3 future options that warns for CoW patterns and detects where str type should be included instead of only object.

C-Achard changed the title migrate to pandas 3.0 Migrate to pandas 3.0 Jun 9, 2026
C-Achard added enhancement New feature or request backwards compatibility issues concerning prior to current versions dependencies Pull requests that update a dependency file labels Jun 9, 2026
deruyter92 mentioned this pull request Jun 10, 2026
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deruyter92 changed the title Migrate to pandas 3.0 Prepare migration to pandas 3.0 Jun 10, 2026

deruyter92 commented Jun 10, 2026 •
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edit: @C-Achard, I have changed the scope of this PR to small preparatory fixes. The whole pandas migration to 3.0 will entail more work than I initially estimated. This PR flags just a few examples and adds a useful tool for CI if we decide to push forward with this.

We might re-consider if the whole migration will be worth it in the first-place. Pandas 3.0 is relatively new and I doubt that users will rely on it soon, so I think we may be save with restricting to 2.x for the time being, until we eventually refactor the keypoint/dataset management in its entirety. See also tracking issue #3362

deruyter92 requested a review from C-Achard June 10, 2026 09:51
deruyter92 marked this pull request as ready for review June 10, 2026 09:52
C-Achard reviewed Jun 10, 2026
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Comment thread deeplabcut/core/inferenceutils.py Outdated
C-Achard approved these changes Jun 10, 2026
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Choose a reason Spam Abuse Off Topic Outdated Duplicate Resolved Low Quality

Very good start, just a few small comments but nothing blocking I think. Thanks for taking care of this!

Comment thread deeplabcut/gui/tracklet_toolbox.py Outdated
Comment thread deeplabcut/pose_estimation_tensorflow/core/evaluate_multianimal.py Outdated
Comment thread deeplabcut/utils/pandas_future_mode.py
Comment thread deeplabcut/utils/make_labeled_video.py
Comment thread examples/testscript_pytorch_multi_animal.py

C-Achard commented Jun 10, 2026

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(Note: trying to fix current CI issues seen here in #3363 )

deruyter92 and others added 5 commits June 11, 2026 09:39
add reference
18fa964 
Co-authored-by: Cyril Achard <cyril.achard@epfl.ch>
add reference
19d3bcd 
Co-authored-by: Cyril Achard <cyril.achard@epfl.ch>
add reference
b87f13c 
Co-authored-by: Cyril Achard <cyril.achard@epfl.ch>
revert transpose on bodypart in 4be0e60. (Following c9d8635)
7037dab
linting: fix line length
667ee53

deruyter92 commented Jun 11, 2026

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@C-Achard Thanks for the review. Good points, I've applied all your suggestions.

MMathisLab merged commit 59a292a into main Jun 25, 2026
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MMathisLab deleted the jaap/migrate-pd-3 branch June 25, 2026 19:51
C-Achard added this to the v3.0.1 milestone Jun 26, 2026
AxelNoun mentioned this pull request Jul 19, 2026
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deruyter92 mentioned this pull request Jul 20, 2026
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AxelNoun mentioned this pull request Aug 13, 2026
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backwards compatibility issues concerning prior to current versions dependencies Pull requests that update a dependency file enhancement New feature or request

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