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Apply automated docs & notebooks freshness + normalization checks#3231

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C-Achard wants to merge 5 commits intocy/automated-docs&nb-reportfrom
cy/automated-docs&nb-report-apply
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Apply automated docs & notebooks freshness + normalization checks#3231
C-Achard wants to merge 5 commits intocy/automated-docs&nb-reportfrom
cy/automated-docs&nb-report-apply

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@C-Achard C-Achard commented Mar 6, 2026 •
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Applies the --write option of the scripts added in #3228.

⚠️ NOTE: do NOT rerun the script with --write in this PR, as adding metadata considers them (correctly) to have been changed recently - make sure to keep correct timestamps before merging. CI checks will not perform as expected otherwise.

Checks

  • .md files only show frontmatter edits
  • .ipnyb files are functional
    • nbformatted notebooks render correctly/are not broken
    • Non-nbformatted notebooks only show metadata field edits

@C-Achard C-Achard added this to the CI Overhaul milestone Mar 6, 2026
@C-Achard C-Achard self-assigned this Mar 6, 2026
@C-Achard C-Achard added enhancement New feature or request COLAB Jupyter related to jupyter notebooks documentation documentation updates/comments CI Related to CI/CD jobs and automated testing labels Mar 6, 2026
@C-Achard C-Achard requested a review from Copilot March 6, 2026 10:51
Copilot AI reviewed Mar 6, 2026
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Pull request overview

Applies automated “freshness + normalization” tooling across docs and notebooks by writing standardized deeplabcut metadata (and, in a couple notebooks, normalizing notebook JSON structure).

Changes:

  • Adds deeplabcut.last_git_updated + deeplabcut.ignore frontmatter to many .md docs pages.
  • Adds metadata.deeplabcut blocks to multiple .ipynb notebooks.
  • Normalizes formatting/structure in some notebooks and updates the docs/notebooks tool README formatting.

Reviewed changes

Copilot reviewed 63 out of 65 changed files in this pull request and generated no comments.

Show a summary per file
File Description
tools/docs_and_notebooks_tool_README.md Adjusts CI integration command formatting in docs tool README.
examples/JUPYTER/Docker_TrainNetwork_VideoAnalysis.ipynb Adds metadata.deeplabcut freshness metadata.
examples/JUPYTER/Demo_yourowndata.ipynb Adds metadata.deeplabcut freshness metadata.
examples/JUPYTER/Demo_napari.ipynb Adds metadata.deeplabcut freshness metadata.
examples/JUPYTER/Demo_labeledexample_Openfield.ipynb Adds metadata.deeplabcut freshness metadata.
examples/JUPYTER/Demo_labeledexample_MouseReaching.ipynb Adds metadata.deeplabcut freshness metadata.
examples/JUPYTER/Demo_3D_DeepLabCut.ipynb Adds metadata.deeplabcut freshness metadata.
examples/COLAB/COLAB_transformer_reID.ipynb Normalizes notebook JSON and adds metadata.deeplabcut freshness metadata.
examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis.ipynb Adds metadata.deeplabcut freshness metadata.
examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis.ipynb Adds metadata.deeplabcut freshness metadata.
examples/COLAB/COLAB_YOURDATA_SuperAnimal.ipynb Adds metadata.deeplabcut freshness metadata.
examples/COLAB/COLAB_DLC_ModelZoo.ipynb Normalizes notebook JSON and adds metadata.deeplabcut freshness metadata.
examples/COLAB/COLAB_DEMO_mouse_openfield.ipynb Adds metadata.deeplabcut freshness metadata.
examples/COLAB/COLAB_DEMO_SuperAnimal.ipynb Adds metadata.deeplabcut freshness metadata.
examples/COLAB/COLAB_BUCTD_and_CTD_tracking.ipynb Adds metadata.deeplabcut freshness metadata.
examples/COLAB/COLAB_3miceDemo.ipynb Adds metadata.deeplabcut freshness metadata.
docs/standardDeepLabCut_UserGuide.md Adds docs frontmatter for freshness tracking.
docs/roadmap.md Adds docs frontmatter for freshness tracking.
docs/recipes/publishing_notebooks_into_the_DLC_main_cookbook.md Adds docs frontmatter for freshness tracking.
docs/recipes/post.md Adds docs frontmatter for freshness tracking.
docs/recipes/pose_cfg_file_breakdown.md Adds docs frontmatter for freshness tracking.
docs/recipes/nn.md Adds docs frontmatter for freshness tracking.
docs/recipes/io.md Adds docs frontmatter for freshness tracking.
docs/recipes/installTips.md Adds docs frontmatter for freshness tracking.
docs/recipes/fmpose3d.ipynb Adds metadata.deeplabcut freshness metadata.
docs/recipes/flip_and_rotate.ipynb Adds metadata.deeplabcut freshness metadata.
docs/recipes/UsingModelZooPupil.md Adds docs frontmatter for freshness tracking.
docs/recipes/TechHardware.md Adds docs frontmatter for freshness tracking.
docs/recipes/OtherData.md Adds docs frontmatter for freshness tracking.
docs/recipes/OpenVINO.md Adds docs frontmatter for freshness tracking.
docs/recipes/MegaDetectorDLCLive.md Adds docs frontmatter for freshness tracking.
docs/recipes/DLCMethods.md Adds docs frontmatter for freshness tracking.
docs/recipes/ClusteringNapari.md Adds docs frontmatter for freshness tracking.
docs/recipes/BatchProcessing.md Adds docs frontmatter for freshness tracking.
docs/quick-start/tutorial_maDLC.md Adds docs frontmatter for freshness tracking.
docs/quick-start/single_animal_quick_guide.md Adds docs frontmatter for freshness tracking.
docs/pytorch_dlc.md Adds docs frontmatter for freshness tracking.
docs/pytorch/user_guide.md Adds docs frontmatter for freshness tracking.
docs/pytorch/pytorch_config.md Adds docs frontmatter for freshness tracking.
docs/pytorch/architectures.md Adds docs frontmatter for freshness tracking.
docs/pytorch/Benchmarking_shuffle_guide.md Adds docs frontmatter for freshness tracking.
docs/maDLC_UserGuide.md Adds docs frontmatter for freshness tracking.
docs/intro.md Adds docs frontmatter for freshness tracking.
docs/installation.md Adds docs frontmatter for freshness tracking.
docs/gui/napari_GUI.md Adds docs frontmatter for freshness tracking.
docs/gui/PROJECT_GUI.md Adds docs frontmatter for freshness tracking.
docs/docker.md Adds docs frontmatter for freshness tracking.
docs/deeplabcutlive.md Adds docs frontmatter for freshness tracking.
docs/course.md Adds docs frontmatter for freshness tracking.
docs/convert_maDLC.md Adds docs frontmatter for freshness tracking.
docs/citation.md Adds docs frontmatter for freshness tracking.
docs/benchmark.md Adds docs frontmatter for freshness tracking.
docs/beginner-guides/video-analysis.md Adds docs frontmatter for freshness tracking.
docs/beginner-guides/manage-project.md Adds docs frontmatter for freshness tracking.
docs/beginner-guides/labeling.md Adds docs frontmatter for freshness tracking.
docs/beginner-guides/beginners-guide.md Adds docs frontmatter for freshness tracking.
docs/beginner-guides/Training-Evaluation.md Adds docs frontmatter for freshness tracking.
docs/UseOverviewGuide.md Adds docs frontmatter for freshness tracking.
docs/README.md Adds docs frontmatter for freshness tracking.
docs/Overviewof3D.md Adds docs frontmatter for freshness tracking.
docs/ModelZoo.md Adds docs frontmatter for freshness tracking.
docs/MISSION_AND_VALUES.md Adds docs frontmatter for freshness tracking.
docs/HelperFunctions.md Adds docs frontmatter for freshness tracking.
docs/Governance.md Adds docs frontmatter for freshness tracking.
Comments suppressed due to low confidence (4)

examples/COLAB/COLAB_transformer_reID.ipynb:1

  • This notebook now includes non-null execution_count values and captured cell outputs, which tends to create noisy diffs and frequent churn for example notebooks. If the repo convention is to keep notebooks source-controlled in a clean state, clear all outputs and reset execution counts to null (and, if needed, enforce via a formatter/stripper in tooling or pre-commit).
    examples/COLAB/COLAB_transformer_reID.ipynb:1
  • This notebook now includes non-null execution_count values and captured cell outputs, which tends to create noisy diffs and frequent churn for example notebooks. If the repo convention is to keep notebooks source-controlled in a clean state, clear all outputs and reset execution counts to null (and, if needed, enforce via a formatter/stripper in tooling or pre-commit).
    examples/COLAB/COLAB_transformer_reID.ipynb:1
  • This notebook now includes non-null execution_count values and captured cell outputs, which tends to create noisy diffs and frequent churn for example notebooks. If the repo convention is to keep notebooks source-controlled in a clean state, clear all outputs and reset execution counts to null (and, if needed, enforce via a formatter/stripper in tooling or pre-commit).
    examples/COLAB/COLAB_transformer_reID.ipynb:1
  • This notebook now includes non-null execution_count values and captured cell outputs, which tends to create noisy diffs and frequent churn for example notebooks. If the repo convention is to keep notebooks source-controlled in a clean state, clear all outputs and reset execution counts to null (and, if needed, enforce via a formatter/stripper in tooling or pre-commit).

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C-Achard commented Mar 6, 2026

Closing for now, a small tweak is needed to prevent the loophole mentioned above.

@C-Achard C-Achard closed this Mar 6, 2026
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CI Related to CI/CD jobs and automated testing COLAB documentation documentation updates/comments enhancement New feature or request Jupyter related to jupyter notebooks

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