From 69a3ee38ddef42d7e011f7bc930b523a78e16cb6 Mon Sep 17 00:00:00 2001 From: C-Achard Date: Fri, 6 Feb 2026 19:48:51 +0100 Subject: [PATCH 1/4] Update docs TOC and Sphinx excludes Add Sphinx exclude_patterns to _config.yml to ignore virtual environments, site-packages, and build directories during doc builds (".venv/**", "venv/**", "**/site-packages/**", "_build/**", "**/_build/**"). Reformat _toc.yml into a proper jb-book "parts:" structure with correctly nested captions and chapters, normalize emoji-bearing captions with quotes, and restore many documentation sections. Also add a placeholder "DLC-Live!" entry with nested chapters/sections for the dlc-live GUI documentation. These changes clean up the table of contents and prevent unrelated files from being included in the documentation build. --- _config.yml | 7 ++ _toc.yml | 206 +++++++++++++++++++++++++++------------------------- 2 files changed, 113 insertions(+), 100 deletions(-) diff --git a/_config.yml b/_config.yml index a24fcaf718..c7582131f1 100644 --- a/_config.yml +++ b/_config.yml @@ -7,6 +7,13 @@ sphinx: config: autodoc_mock_imports: ["wx", "matplotlib", "qtpy", "PySide6", "napari", "shiboken6"] mermaid_output_format: raw + exclude_patterns: + - ".venv/**" + - "venv/**" + - "**/site-packages/**" + - "_build/**" + - "**/_build/**" + extra_extensions: - numpydoc - sphinxcontrib.mermaid diff --git a/_toc.yml b/_toc.yml index 35478006e0..581d098deb 100644 --- a/_toc.yml +++ b/_toc.yml @@ -1,103 +1,109 @@ format: jb-book root: README + parts: -- caption: Getting Started - chapters: - - file: docs/UseOverviewGuide - - file: docs/course -- caption: Installation - chapters: - - file: docs/installation - - file: docs/recipes/installTips - - file: docs/docker - -- caption: Main User Guides - chapters: - - file: docs/standardDeepLabCut_UserGuide - - file: docs/maDLC_UserGuide - - file: docs/Overviewof3D - - file: docs/HelperFunctions - -- caption: Graphical User Interfaces (GUIs) - chapters: - - file: docs/gui/PROJECT_GUI - - file: docs/gui/napari_GUI -- caption: DLC3 PyTorch Specific Docs - chapters: - - file: docs/pytorch/user_guide.md - - file: docs/pytorch/pytorch_config.md - - file: docs/pytorch/architectures.md -- caption: Quick Start Tutorials - chapters: - - file: docs/quick-start/single_animal_quick_guide - - file: docs/quick-start/tutorial_maDLC -- caption: 🚀 Beginner's Guide to DeepLabCut - chapters: - - file: docs/beginner-guides/beginners-guide - - file: docs/beginner-guides/manage-project - - file: docs/beginner-guides/labeling - - file: docs/beginner-guides/Training-Evaluation - - file: docs/beginner-guides/video-analysis -- caption: 🚀 Main Demo Notebooks - chapters: - - file: examples/COLAB/COLAB_DEMO_SuperAnimal - - file: examples/COLAB/COLAB_DEMO_mouse_openfield - - file: examples/COLAB/COLAB_3miceDemo - - file: examples/COLAB/COLAB_HumanPose_with_RTMPose - - - -- caption: 🚀 Notebooks For Your Data - chapters: - - file: examples/COLAB/COLAB_YOURDATA_SuperAnimal - - file: examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis - - file: examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis - -- caption: 🚀 Special Feature Demos - chapters: - - file: examples/COLAB/COLAB_transformer_reID - - file: examples/COLAB/COLAB_BUCTD_and_CTD_tracking - - file: examples/JUPYTER/Demo_3D_DeepLabCut - - file: examples/COLAB/COLAB_DLC_ModelZoo - -- caption: 🧑‍🍳 Cookbook (detailed helper guides) - chapters: - - file: docs/convert_maDLC - - file: docs/recipes/OtherData - - file: docs/recipes/io - - file: docs/recipes/nn - - file: docs/recipes/post - - file: docs/recipes/BatchProcessing - - file: docs/recipes/DLCMethods - - file: docs/recipes/ClusteringNapari - - file: docs/recipes/OpenVINO - - file: docs/recipes/flip_and_rotate - - file: docs/recipes/pose_cfg_file_breakdown - - file: docs/recipes/publishing_notebooks_into_the_DLC_main_cookbook - -- caption: Hardware Tips - chapters: - - file: docs/recipes/TechHardware -- caption: DeepLabCut-Live! - chapters: - - file: docs/deeplabcutlive -- caption: 🦄 DeepLabCut Model Zoo - chapters: - - file: docs/ModelZoo - - file: docs/recipes/UsingModelZooPupil - -- caption: DeepLabCut Benchmarking - chapters: - - file: docs/benchmark - - file: docs/pytorch/Benchmarking_shuffle_guide - -- caption: Mission & Contribute - chapters: - - file: docs/MISSION_AND_VALUES - - file: docs/roadmap - - file: docs/Governance - - file: CONTRIBUTING - -- caption: Citations for DeepLabCut - chapters: - - file: docs/citation + - caption: Getting Started + chapters: + - file: docs/UseOverviewGuide + - file: docs/course + + - caption: Installation + chapters: + - file: docs/installation + - file: docs/recipes/installTips + - file: docs/docker + + - caption: Main User Guides + chapters: + - file: docs/standardDeepLabCut_UserGuide + - file: docs/maDLC_UserGuide + - file: docs/Overviewof3D + - file: docs/HelperFunctions + + - caption: Graphical User Interfaces (GUIs) + chapters: + - file: docs/gui/PROJECT_GUI + - file: docs/gui/napari_GUI + + - caption: DLC3 PyTorch Specific Docs + chapters: + - file: docs/pytorch/user_guide.md + - file: docs/pytorch/pytorch_config.md + - file: docs/pytorch/architectures.md + + - caption: Quick Start Tutorials + chapters: + - file: docs/quick-start/single_animal_quick_guide + - file: docs/quick-start/tutorial_maDLC + + - caption: "🚀 Beginner's Guide to DeepLabCut" + chapters: + - file: docs/beginner-guides/beginners-guide + - file: docs/beginner-guides/manage-project + - file: docs/beginner-guides/labeling + - file: docs/beginner-guides/Training-Evaluation + - file: docs/beginner-guides/video-analysis + + - caption: "🚀 Main Demo Notebooks" + chapters: + - file: examples/COLAB/COLAB_DEMO_SuperAnimal + - file: examples/COLAB/COLAB_DEMO_mouse_openfield + - file: examples/COLAB/COLAB_3miceDemo + - file: examples/COLAB/COLAB_HumanPose_with_RTMPose + + - caption: "🚀 Notebooks For Your Data" + chapters: + - file: examples/COLAB/COLAB_YOURDATA_SuperAnimal + - file: examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis + - file: examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis + + - caption: "🚀 Special Feature Demos" + chapters: + - file: examples/COLAB/COLAB_transformer_reID + - file: examples/COLAB/COLAB_BUCTD_and_CTD_tracking + - file: examples/JUPYTER/Demo_3D_DeepLabCut + - file: examples/COLAB/COLAB_DLC_ModelZoo + + - caption: "🧑‍🍳 Cookbook (detailed helper guides)" + chapters: + - file: docs/convert_maDLC + - file: docs/recipes/OtherData + - file: docs/recipes/io + - file: docs/recipes/nn + - file: docs/recipes/post + - file: docs/recipes/BatchProcessing + - file: docs/recipes/DLCMethods + - file: docs/recipes/ClusteringNapari + - file: docs/recipes/OpenVINO + - file: docs/recipes/flip_and_rotate + - file: docs/recipes/pose_cfg_file_breakdown + - file: docs/recipes/publishing_notebooks_into_the_DLC_main_cookbook + + - caption: Hardware Tips + chapters: + - file: docs/recipes/TechHardware + + - caption: DeepLabCut-Live! + chapters: + - file: docs/deeplabcutlive + + - caption: "🦄 DeepLabCut Model Zoo" + chapters: + - file: docs/ModelZoo + - file: docs/recipes/UsingModelZooPupil + + - caption: DeepLabCut Benchmarking + chapters: + - file: docs/benchmark + - file: docs/pytorch/Benchmarking_shuffle_guide + + - caption: "Mission & Contribute" + chapters: + - file: docs/MISSION_AND_VALUES + - file: docs/roadmap + - file: docs/Governance + - file: CONTRIBUTING + + - caption: Citations for DeepLabCut + chapters: + - file: docs/citation From eee5ad7bac085e15e167236344ae7b398c1cd2b9 Mon Sep 17 00:00:00 2001 From: C-Achard Date: Fri, 6 Feb 2026 20:09:10 +0100 Subject: [PATCH 2/4] Revert indent changes --- _toc.yml | 210 +++++++++++++++++++++++++++---------------------------- 1 file changed, 105 insertions(+), 105 deletions(-) diff --git a/_toc.yml b/_toc.yml index 581d098deb..a0e45450e0 100644 --- a/_toc.yml +++ b/_toc.yml @@ -2,108 +2,108 @@ format: jb-book root: README parts: - - caption: Getting Started - chapters: - - file: docs/UseOverviewGuide - - file: docs/course - - - caption: Installation - chapters: - - file: docs/installation - - file: docs/recipes/installTips - - file: docs/docker - - - caption: Main User Guides - chapters: - - file: docs/standardDeepLabCut_UserGuide - - file: docs/maDLC_UserGuide - - file: docs/Overviewof3D - - file: docs/HelperFunctions - - - caption: Graphical User Interfaces (GUIs) - chapters: - - file: docs/gui/PROJECT_GUI - - file: docs/gui/napari_GUI - - - caption: DLC3 PyTorch Specific Docs - chapters: - - file: docs/pytorch/user_guide.md - - file: docs/pytorch/pytorch_config.md - - file: docs/pytorch/architectures.md - - - caption: Quick Start Tutorials - chapters: - - file: docs/quick-start/single_animal_quick_guide - - file: docs/quick-start/tutorial_maDLC - - - caption: "🚀 Beginner's Guide to DeepLabCut" - chapters: - - file: docs/beginner-guides/beginners-guide - - file: docs/beginner-guides/manage-project - - file: docs/beginner-guides/labeling - - file: docs/beginner-guides/Training-Evaluation - - file: docs/beginner-guides/video-analysis - - - caption: "🚀 Main Demo Notebooks" - chapters: - - file: examples/COLAB/COLAB_DEMO_SuperAnimal - - file: examples/COLAB/COLAB_DEMO_mouse_openfield - - file: examples/COLAB/COLAB_3miceDemo - - file: examples/COLAB/COLAB_HumanPose_with_RTMPose - - - caption: "🚀 Notebooks For Your Data" - chapters: - - file: examples/COLAB/COLAB_YOURDATA_SuperAnimal - - file: examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis - - file: examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis - - - caption: "🚀 Special Feature Demos" - chapters: - - file: examples/COLAB/COLAB_transformer_reID - - file: examples/COLAB/COLAB_BUCTD_and_CTD_tracking - - file: examples/JUPYTER/Demo_3D_DeepLabCut - - file: examples/COLAB/COLAB_DLC_ModelZoo - - - caption: "🧑‍🍳 Cookbook (detailed helper guides)" - chapters: - - file: docs/convert_maDLC - - file: docs/recipes/OtherData - - file: docs/recipes/io - - file: docs/recipes/nn - - file: docs/recipes/post - - file: docs/recipes/BatchProcessing - - file: docs/recipes/DLCMethods - - file: docs/recipes/ClusteringNapari - - file: docs/recipes/OpenVINO - - file: docs/recipes/flip_and_rotate - - file: docs/recipes/pose_cfg_file_breakdown - - file: docs/recipes/publishing_notebooks_into_the_DLC_main_cookbook - - - caption: Hardware Tips - chapters: - - file: docs/recipes/TechHardware - - - caption: DeepLabCut-Live! - chapters: - - file: docs/deeplabcutlive - - - caption: "🦄 DeepLabCut Model Zoo" - chapters: - - file: docs/ModelZoo - - file: docs/recipes/UsingModelZooPupil - - - caption: DeepLabCut Benchmarking - chapters: - - file: docs/benchmark - - file: docs/pytorch/Benchmarking_shuffle_guide - - - caption: "Mission & Contribute" - chapters: - - file: docs/MISSION_AND_VALUES - - file: docs/roadmap - - file: docs/Governance - - file: CONTRIBUTING - - - caption: Citations for DeepLabCut - chapters: - - file: docs/citation +- caption: Getting Started + chapters: + - file: docs/UseOverviewGuide + - file: docs/course + +- caption: Installation + chapters: + - file: docs/installation + - file: docs/recipes/installTips + - file: docs/docker + +- caption: Main User Guides + chapters: + - file: docs/standardDeepLabCut_UserGuide + - file: docs/maDLC_UserGuide + - file: docs/Overviewof3D + - file: docs/HelperFunctions + +- caption: Graphical User Interfaces (GUIs) + chapters: + - file: docs/gui/PROJECT_GUI + - file: docs/gui/napari_GUI + +- caption: DLC3 PyTorch Specific Docs + chapters: + - file: docs/pytorch/user_guide.md + - file: docs/pytorch/pytorch_config.md + - file: docs/pytorch/architectures.md + +- caption: Quick Start Tutorials + chapters: + - file: docs/quick-start/single_animal_quick_guide + - file: docs/quick-start/tutorial_maDLC + +- caption: "🚀 Beginner's Guide to DeepLabCut" + chapters: + - file: docs/beginner-guides/beginners-guide + - file: docs/beginner-guides/manage-project + - file: docs/beginner-guides/labeling + - file: docs/beginner-guides/Training-Evaluation + - file: docs/beginner-guides/video-analysis + +- caption: "🚀 Main Demo Notebooks" + chapters: + - file: examples/COLAB/COLAB_DEMO_SuperAnimal + - file: examples/COLAB/COLAB_DEMO_mouse_openfield + - file: examples/COLAB/COLAB_3miceDemo + - file: examples/COLAB/COLAB_HumanPose_with_RTMPose + +- caption: "🚀 Notebooks For Your Data" + chapters: + - file: examples/COLAB/COLAB_YOURDATA_SuperAnimal + - file: examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis + - file: examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis + +- caption: "🚀 Special Feature Demos" + chapters: + - file: examples/COLAB/COLAB_transformer_reID + - file: examples/COLAB/COLAB_BUCTD_and_CTD_tracking + - file: examples/JUPYTER/Demo_3D_DeepLabCut + - file: examples/COLAB/COLAB_DLC_ModelZoo + +- caption: "🧑‍🍳 Cookbook (detailed helper guides)" + chapters: + - file: docs/convert_maDLC + - file: docs/recipes/OtherData + - file: docs/recipes/io + - file: docs/recipes/nn + - file: docs/recipes/post + - file: docs/recipes/BatchProcessing + - file: docs/recipes/DLCMethods + - file: docs/recipes/ClusteringNapari + - file: docs/recipes/OpenVINO + - file: docs/recipes/flip_and_rotate + - file: docs/recipes/pose_cfg_file_breakdown + - file: docs/recipes/publishing_notebooks_into_the_DLC_main_cookbook + +- caption: Hardware Tips + chapters: + - file: docs/recipes/TechHardware + +- caption: DeepLabCut-Live! + chapters: + - file: docs/deeplabcutlive + +- caption: "🦄 DeepLabCut Model Zoo" + chapters: + - file: docs/ModelZoo + - file: docs/recipes/UsingModelZooPupil + +- caption: DeepLabCut Benchmarking + chapters: + - file: docs/benchmark + - file: docs/pytorch/Benchmarking_shuffle_guide + +- caption: "Mission & Contribute" + chapters: + - file: docs/MISSION_AND_VALUES + - file: docs/roadmap + - file: docs/Governance + - file: CONTRIBUTING + +- caption: Citations for DeepLabCut + chapters: + - file: docs/citation From 612e5a3a4dc163981b491cf59b13480fa077d6d4 Mon Sep 17 00:00:00 2001 From: C-Achard Date: Fri, 6 Feb 2026 20:10:18 +0100 Subject: [PATCH 3/4] Update _toc.yml --- _toc.yml | 110 +++++++++++++++++++++++++++---------------------------- 1 file changed, 55 insertions(+), 55 deletions(-) diff --git a/_toc.yml b/_toc.yml index a0e45450e0..561574d5f5 100644 --- a/_toc.yml +++ b/_toc.yml @@ -4,106 +4,106 @@ root: README parts: - caption: Getting Started chapters: - - file: docs/UseOverviewGuide - - file: docs/course + - file: docs/UseOverviewGuide + - file: docs/course - caption: Installation chapters: - - file: docs/installation - - file: docs/recipes/installTips - - file: docs/docker + - file: docs/installation + - file: docs/recipes/installTips + - file: docs/docker - caption: Main User Guides chapters: - - file: docs/standardDeepLabCut_UserGuide - - file: docs/maDLC_UserGuide - - file: docs/Overviewof3D - - file: docs/HelperFunctions + - file: docs/standardDeepLabCut_UserGuide + - file: docs/maDLC_UserGuide + - file: docs/Overviewof3D + - file: docs/HelperFunctions - caption: Graphical User Interfaces (GUIs) chapters: - - file: docs/gui/PROJECT_GUI - - file: docs/gui/napari_GUI + - file: docs/gui/PROJECT_GUI + - file: docs/gui/napari_GUI - caption: DLC3 PyTorch Specific Docs chapters: - - file: docs/pytorch/user_guide.md - - file: docs/pytorch/pytorch_config.md - - file: docs/pytorch/architectures.md + - file: docs/pytorch/user_guide.md + - file: docs/pytorch/pytorch_config.md + - file: docs/pytorch/architectures.md - caption: Quick Start Tutorials chapters: - - file: docs/quick-start/single_animal_quick_guide - - file: docs/quick-start/tutorial_maDLC + - file: docs/quick-start/single_animal_quick_guide + - file: docs/quick-start/tutorial_maDLC - caption: "🚀 Beginner's Guide to DeepLabCut" chapters: - - file: docs/beginner-guides/beginners-guide - - file: docs/beginner-guides/manage-project - - file: docs/beginner-guides/labeling - - file: docs/beginner-guides/Training-Evaluation - - file: docs/beginner-guides/video-analysis + - file: docs/beginner-guides/beginners-guide + - file: docs/beginner-guides/manage-project + - file: docs/beginner-guides/labeling + - file: docs/beginner-guides/Training-Evaluation + - file: docs/beginner-guides/video-analysis - caption: "🚀 Main Demo Notebooks" chapters: - - file: examples/COLAB/COLAB_DEMO_SuperAnimal - - file: examples/COLAB/COLAB_DEMO_mouse_openfield - - file: examples/COLAB/COLAB_3miceDemo - - file: examples/COLAB/COLAB_HumanPose_with_RTMPose + - file: examples/COLAB/COLAB_DEMO_SuperAnimal + - file: examples/COLAB/COLAB_DEMO_mouse_openfield + - file: examples/COLAB/COLAB_3miceDemo + - file: examples/COLAB/COLAB_HumanPose_with_RTMPose - caption: "🚀 Notebooks For Your Data" chapters: - - file: examples/COLAB/COLAB_YOURDATA_SuperAnimal - - file: examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis - - file: examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis + - file: examples/COLAB/COLAB_YOURDATA_SuperAnimal + - file: examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis + - file: examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis - caption: "🚀 Special Feature Demos" chapters: - - file: examples/COLAB/COLAB_transformer_reID - - file: examples/COLAB/COLAB_BUCTD_and_CTD_tracking - - file: examples/JUPYTER/Demo_3D_DeepLabCut - - file: examples/COLAB/COLAB_DLC_ModelZoo + - file: examples/COLAB/COLAB_transformer_reID + - file: examples/COLAB/COLAB_BUCTD_and_CTD_tracking + - file: examples/JUPYTER/Demo_3D_DeepLabCut + - file: examples/COLAB/COLAB_DLC_ModelZoo - caption: "🧑‍🍳 Cookbook (detailed helper guides)" chapters: - - file: docs/convert_maDLC - - file: docs/recipes/OtherData - - file: docs/recipes/io - - file: docs/recipes/nn - - file: docs/recipes/post - - file: docs/recipes/BatchProcessing - - file: docs/recipes/DLCMethods - - file: docs/recipes/ClusteringNapari - - file: docs/recipes/OpenVINO - - file: docs/recipes/flip_and_rotate - - file: docs/recipes/pose_cfg_file_breakdown - - file: docs/recipes/publishing_notebooks_into_the_DLC_main_cookbook + - file: docs/convert_maDLC + - file: docs/recipes/OtherData + - file: docs/recipes/io + - file: docs/recipes/nn + - file: docs/recipes/post + - file: docs/recipes/BatchProcessing + - file: docs/recipes/DLCMethods + - file: docs/recipes/ClusteringNapari + - file: docs/recipes/OpenVINO + - file: docs/recipes/flip_and_rotate + - file: docs/recipes/pose_cfg_file_breakdown + - file: docs/recipes/publishing_notebooks_into_the_DLC_main_cookbook - caption: Hardware Tips chapters: - - file: docs/recipes/TechHardware + - file: docs/recipes/TechHardware - caption: DeepLabCut-Live! chapters: - - file: docs/deeplabcutlive + - file: docs/deeplabcutlive - caption: "🦄 DeepLabCut Model Zoo" chapters: - - file: docs/ModelZoo - - file: docs/recipes/UsingModelZooPupil + - file: docs/ModelZoo + - file: docs/recipes/UsingModelZooPupil - caption: DeepLabCut Benchmarking chapters: - - file: docs/benchmark - - file: docs/pytorch/Benchmarking_shuffle_guide + - file: docs/benchmark + - file: docs/pytorch/Benchmarking_shuffle_guide - caption: "Mission & Contribute" chapters: - - file: docs/MISSION_AND_VALUES - - file: docs/roadmap - - file: docs/Governance - - file: CONTRIBUTING + - file: docs/MISSION_AND_VALUES + - file: docs/roadmap + - file: docs/Governance + - file: CONTRIBUTING - caption: Citations for DeepLabCut chapters: - - file: docs/citation + - file: docs/citation From 0f943977b006c790a31aabdf56ff42022b04ebd0 Mon Sep 17 00:00:00 2001 From: Cyril Achard Date: Tue, 10 Feb 2026 17:24:29 +0100 Subject: [PATCH 4/4] Update _config.yml Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- _config.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/_config.yml b/_config.yml index c7582131f1..ca768b4469 100644 --- a/_config.yml +++ b/_config.yml @@ -11,9 +11,7 @@ sphinx: - ".venv/**" - "venv/**" - "**/site-packages/**" - - "_build/**" - "**/_build/**" - extra_extensions: - numpydoc - sphinxcontrib.mermaid