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Update documentation links, section anchors, and MyST markup so references resolve correctly across the README, guides, and recipes. This also replaces a few embedded API include blocks with direct links, adds a missing GenTL backend reference target, and fixes a stale notebook docs link.
…solve) See e.g. pose_cfg_file_breakdown
Add Jupyter Book `tableofcontents` directives to the notebook, PyTorch, and recipes landing pages so these section indexes render navigable child-page listings in the docs.
C-Achard
added this pull request to stack #3539
September 30, 2026 13:08
C-Achard
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Copilot review overview
🟡 Changes recommended
Three numbered citations now link to the general bibliography instead of their corresponding references.
Review effort: Balanced
Findings: 1
Open (1)
What changed in this PR
Updates documentation links, anchors, directives, and landing pages to reduce build warnings.
Changes:
- Retargets obsolete user-guide and API links.
- Fixes MyST references, directive options, and heading anchors.
- Adds child-page tables of contents to landing pages.
| File | Description |
|---|---|
README.md |
Updates the examples link. |
examples/JUPYTER/Demo_yourowndata.ipynb |
Retargets the user guide. |
examples/JUPYTER/Demo_labeledexample_Openfield.ipynb |
Retargets the user guide. |
examples/JUPYTER/Demo_labeledexample_MouseReaching.ipynb |
Retargets the user guide. |
examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis.ipynb |
Updates workflow links. |
examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis.ipynb |
Updates multi-animal workflow links. |
examples/COLAB/COLAB_transformer_reID.ipynb |
Retargets the multi-animal guide. |
examples/COLAB/COLAB_DEMO_mouse_openfield.ipynb |
Updates workflow links. |
examples/COLAB/COLAB_BUCTD_and_CTD_tracking.ipynb |
Fixes guide and architecture anchors. |
examples/COLAB/COLAB_3miceDemo.ipynb |
Retargets the multi-animal guide. |
docs/UseOverviewGuide.md |
Fixes references and examples links. |
docs/recipes/UsingModelZooPupil.md |
Fixes the installation reference. |
docs/recipes/TechHardware.md |
Removes obsolete installation guidance. |
docs/recipes/pose_cfg_file_breakdown.md |
Retargets internal anchors and citations. |
docs/recipes/nn.md |
Fixes the training-dataset reference. |
docs/recipes/index.md |
Adds the recipe table of contents. |
docs/pytorch/user_guide.md |
Fixes anchors and guide references. |
docs/pytorch/index.md |
Adds the PyTorch table of contents. |
docs/notebooks/your_data.md |
Adds child-page navigation. |
docs/notebooks/main_demos.md |
Adds child-page navigation. |
docs/notebooks/extra.md |
Adds child-page navigation. |
docs/main-workflows/user-guide.md |
Fixes directive options and comments. |
docs/main-workflows/multi-animal-tracking.md |
Replaces broken API includes and links. |
docs/installation.md |
Removes obsolete installation links. |
docs/gui/napari/tracking/basic_usage.md |
Removes an invalid figure option. |
docs/dlc-live/dlc-live-gui/user_guide/cameras_backends/gentl_backend.md |
Adds the missing reference label. |
deeplabcut/gui/tabs/docs.py |
Updates the GUI documentation URL. |
_config.yml |
Enables MyST heading anchors. |
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| ### 2.1.E `pafwidth` | ||
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| The default value is `20`. PAF stands for part affinity fields. It is a method of learning associations between pairs of bodyparts by preserving the location and orientation of the limb (the connection between two keypoints). This learned part affinity helps in proper animal assembly, making the model less prone to associating bodyparts of one individual with those of another. [1](#ref1) | ||
| The default value is `20`. PAF stands for part affinity fields. It is a method of learning associations between pairs of bodyparts by preserving the location and orientation of the limb (the connection between two keypoints). This learned part affinity helps in proper animal assembly, making the model less prone to associating bodyparts of one individual with those of another. [1](#references) |
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Fixes roughly 53 docs build warnings.
Retargets links to pages that are no longer published, and fixes cross-references, anchors and directive options warnings.
Main changes
URL_MA_CONFIGUREindeeplabcut/gui/tabs/docs.py) now points tomain-workflows/user-guide.html#b-configure-the-project.UseOverviewGuide,pytorch/user_guide,recipes/nnand 9 notebooks now point to the matching sections ofmain-workflows/user-guide.installTipsare removed frominstallation.mdandTechHardware.md; the linked content (Ubuntu 18.04/20.04 CUDA setup, TF 1.15 DirectML) no longer applies to DLC 3.myst_heading_anchors: 3in_config.ymlmakes in-pagetext](#heading-slug)links resolve; all such links indocs/target H1–H3.eval-rstAPI includes inmulti-animal-tracking.mdresolved to a non-existent path; they are replaced by links to the dev-docs API reference, as inuser-guide.md.sec:important-info-regd-usage,file:how-to-install, a newfile:dlclivegui-gentl-backendlabel, and stale anchors inpose_cfg_file_breakdown.md,pytorch/user_guide.mdand the BUCTD notebook.figure :caption:,admonition :class-container:(now:class:), and an unknown{comment}directive (now an HTML comment).pytorch/index,recipes/index, threenotebooks/*) now render their child pages with{tableofcontents}.