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Docs audit [April 2026]: update multi-animal guide#3335

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Docs audit [April 2026]: update multi-animal guide#3335
deruyter92 wants to merge 22 commits into
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in line with the main single animal guide, this PR updates the formatting of the multi-animal guide

@C-Achard C-Achard added the documentation documentation updates/comments label May 20, 2026
@C-Achard C-Achard added this to the Docs audit: April 2026 milestone May 21, 2026
@C-Achard C-Achard changed the title docs audit [April 2026] update ma guide Docs audit [April 2026]: update multi-animal guide May 21, 2026
@deruyter92 deruyter92 force-pushed the jaap/docs-audit-2026-update-ma-guide branch from c4dc4dd to 101ffa1 Compare May 26, 2026 14:53
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deruyter92 commented May 26, 2026

@C-Achard, maybe it is ready for a first round of review.

Changes:
After first editing the single and multi-animal guides separately, I decided (after our discussion) that it would be worthwile to try to merge them. Thanks to your custom CSS dropdowns and admonitions, I think the user can easily skip and hide the information that is not relevant.

In summary the docs now look like this:

  • 1 merged 'DeepLabCut user guide` with a shared workflow.
  • The workflow is separated in phases (similar to the original maDLC docs), which are subdivided in steps.
  • All multi-animal or single-animal-specific information is put inside a custom dropdown, to easily hide irrelevant info. (@C-Achard thanks for the custom CSS!)
  • A special case is made for the multi-animal tracking:
    • Since the default video_analysis step uses auto_track=True in version 3.0 onward, the standard user does not have to worry about tracking by default. This is now made very explicit in the documentation.
    • More information on the tracking steps and how to run them manually is contained in a separate doc page: multi-animal tracking.

I think the multi-animal tracking docs still need quite some (formatting and correction) work, but the merged user guide is getting there.

Since all multi-animal-specific info is tagged in dedicated admonitions/dropdowns, we can easily go back to the old situation, in case we prefer to have two separate (largely duplicated) doc pages.

@deruyter92 deruyter92 requested a review from C-Achard May 26, 2026 15:07
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C-Achard commented May 27, 2026

@deruyter92 I had a few issues in the user_guide file, the frontmatter metadata was a bit malformed, and the dropdowns did not render correctly. Is it okay if I push a fixed version?
(My CSS example was also not fully correct, which is now fixed)

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C-Achard commented May 27, 2026

Very important question: what is the font in the workflow chart actually?
image

Comment thread docs/main-workflows/user-guide.md
Comment thread docs/main-workflows/user-guide.md Outdated
@C-Achard C-Achard force-pushed the cy/docs-audit-2026-update-single-animal branch from 69a1ca3 to 1b2a42b Compare May 27, 2026 14:28
Replace markdown-style links with Sphinx {ref} cross-reference roles in docs/UseOverviewGuide.md and docs/maDLC_UserGuide.md to ensure proper Sphinx rendering. Also fix a malformed bracket/URL in docs/pytorch/architectures.md for the Ye et al. citation link.
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@C-Achard thanks for the review!

Very important question: what is the font in the workflow chart actually?
I used Courier 10 Pitch, which an online font search tool found most similar to the one in the logo

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@deruyter92 This is suffering from the outdated squashed commits mismatch as well, happy to fix it if needed!

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Cutoff should be ba8e985^

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I'm not working on it a the moment, so feel free to rebase as you wish! Thanks for taking care of it!

C-Achard and others added 11 commits May 29, 2026 13:34
* Update custom.css

* Refine workflow dropdown styles and colors

Update docs/_static/custom.css to adjust dark-theme variables and overhaul workflow dropdown styling. Changed single/multi-animal background variables, replaced old title-prefix approach with CSS-generated emoji titles, and hid sphinx-design's no-title icon. Apply consistent header/body color variables for sd-card dropdowns, keep text/chevron colors stable, and disable pydata's hover darken/lighten effect to prevent color shifts on focus/hover. These changes ensure consistent appearance and correct application of border/background styles overridden by pydata.
deruyter92 and others added 7 commits June 1, 2026 11:10
Update documentation to use MyST's :class-container for dropdown directives (previous :class usages updated in docs/_static/custom.css and docs/main-workflows/user-guide.md). Also correct the YAML frontmatter formatting in user-guide.md (expand inline metadata into a proper YAML block). These changes align docs with current MyST/Sphinx directive syntax and fix frontmatter parsing.
Adjust multi-animal CSS variables in light and dark themes to be more distinct from hint/tip boxes. Updated --multi-animal-border to #57c4be, --multi-animal-bg to #e8f8f7, --multi-animal-title-bg to #21a197, and --multi-animal-title-text to #000000 in both themes.
Editorial and formatting updates to the main user guide and added an updated multi-animal figure. Changes include: clarified multi-animal workflow wording, strengthened guidance (emphasis on recommended options), reworked admonitions (hint/danger/tip), improved paragraph flow and bullet structure, clarified frame selection methods and recommendations, updated examples and GUI notes, refined training/evaluation/tracking explanations, and replaced the multi-animal figure reference with docs/images/box1-multi-rec.png (recolored for new CSS). Miscellaneous typography and markup fixes (code blocks, YAML/file references, and symbol styling) to improve readability.
Improve rendering and correctness in docs/main-workflows/user-guide.md: change admonition key to `class-container`, update dropdown/admonition syntax, fix code block languages (python -> yaml/text), correct example function parameter (`config` -> `config_path`), adjust heading capitalization and list formatting. These changes ensure examples render correctly and the docs reflect the actual API usage.
Add single- and multi-animal quick-start pages to the Main workflows overview in _toc.yml and substantially rewrite both quick-start docs. single_animal_quick_guide.md was reorganized into a clear step-by-step workflow (create project, configure, extract/label frames, create dataset, train/evaluate, analyze/filter/plot/create videos) with concrete Python examples, notes, and tips (use absolute paths, no spaces in body-part names). tutorial_maDLC.md was refactored into a multi-animal overview with GUI and Python workflows, clearer config guidance for multi-animal fields, extraction/annotation/checking steps, separate training engine examples (PyTorch/TensorFlow), and explicit tracking steps (analyze, convert detections, stitch tracklets, create labeled videos) plus helpful notes. Overall improvements focus on clarity, concrete examples, and actionable tips for users.
@C-Achard C-Achard force-pushed the jaap/docs-audit-2026-update-ma-guide branch from dcf941a to 01f907e Compare June 1, 2026 09:10
C-Achard added 3 commits June 1, 2026 11:25
Relocate the important guidance about selecting diverse training frames to the section near frame extraction/functionality, making it more contextually relevant. Clean up manual frame-selection wording, normalize the selection-method bullets, and adjust figure/code-fence markup (wrap figure in a comment) to prevent rendering issues. Minor formatting fixes for clarity.
Remove the parenthetical reference to www.deeplabcut.org and merge the broken sentence in the TensorFlow Engine augmentation section to improve readability and flow. No functional changes; content about available loaders remains the same.
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