Using autosummary to generate full API docs #51

C-Achard · 2023-09-28T13:23:25Z

Ideally, we would like to generate full API docs using autosummary in #50.

However, if one wants to include all members, attributes, etc, custom templates are needed, as per jupyter book documentation.

See example of custom template here.

A bug with sphinx-book-theme > 1.0.0 prevents one to use custom templates, however, as mentioned here :
executablebooks/sphinx-book-theme#729

Downgrading to sphinx-book-theme > 0.3.3 prevents this problem, but breaks other jupyter-book features.

Currently waiting for a fix from sphinx-book-theme, or another workaround.

The text was updated successfully, but these errors were encountered:

* Moved docs to source folder * Updated to jupyter-books * Update GH Action to jupyter-book * Updated guides * Update reqs for jupyter-books - Fixed typo * Fix typo and file duplicate * Added auto API docs * Update welcome.rst * Update interface docstrings * Update ruff to enforce docstring style * Updated docstrings in interface/config * Add additional docstring rule exceptions * Update utils docstring * Update plugins.py * Update dev_scripts * Updated code_plugin folder docstrings * Update code_models docstrings * Update tests docstrings * Update docstring rules to enforce docs * Fix warnings when building docs * Restore docs images * Remove old API docs * Added module docstring for all public modules * Update pyproject.toml * Update folder desc * Update inference and training guides * Update inference_module_guide.rst * Guides updates * Change indexing, guides updates * Fix unindent warning * Update _toc.yml * Fixed model list inconsistencies * Update model list * Trying to fully use autosummary (see #51) * Docs update * Fix missing refactor in CRF * Update cropping_module_guide.rst * Updated docs ref for code * Figs, refs, utils guide update * Update images to figures where relevant * Updated refs to source code * Improved utils guide layout and contents * Review update + crop/utils * Review update * Small inference tweaks for pipeline * Config changes * Update worker_inference.py * Small instance seg refactor * Added properties for instance seg params * Utils cleanup * Small refactor of unclear train/val split terminology * Fix log parameters incorrectly printing def dir * Enable sliding window for all instance seg methods * Update instance_segmentation.py Refactor sliding window to not shadow builtin "function" * Fixed mistake in auto-check for WNet results * Fix for restarting train worker after force stop * Docs & images update * mv welcome image * Improved inference docs * Update inference_module_guide.rst * Attempt to fix M1 yaml * Config docstring update * Welcome page update * Docs update * Add WandB for supervised models * Added auto contrast reset in cropping * Added checks for instance labels in training * Check for custom weights before locking window inference * Improve review plots makers * Documentation update (Timokleia) (#53) * Update cropping_module_guide.rst changes in the cropping module guide * Update cropping_module_guide.rst add `` * Update inference_module_guide.rst additions to inference module * Update metrics_module_guide.rst adjusting the metrics module * Update review_module_guide.rst review module updates * Update training_module_guide.rst changes in the training module * Update training_wnet.rst additions in the wnet module * Update utils_module_guide.rst utilities updates * review parameters image * Update cropping_module_guide.rst emoji * Update metrics_module_guide.rst emoji * Update training_module_guide.rst emoji * Update utils_module_guide.rst emoji * Update cropping_module_guide.rst mild style changes * Update review_module_guide.rst adjusting image code * Update welcome.rst changes to welcome * Add files via upload * Review and training tweaks - Fixed a few links, indents, typos - Replaced some emojis and added new ones for other pages * Welcome and inference tweaks - Fixed minor formatting, tables, broken links issues, etc * RM unused model wrappers attributes * Inference edits * Update WNet and inference * Images update * Update plots_train.png * Restore walkthrough * Update detailed_walkthrough.rst * Update detailed_walkthrough.rst editions * Minor edits --------- Co-authored-by: C-Achard <[email protected]> * Added floats in small remove * Try to fix issue with float/long * Add except handling for layer removal in train * Add first version of dedicated install page - Add install page - Refacto/clean up welcome page - Add more useful plugins - Update TODO * Improve training guide * Move M1 install * Added label stats utils * Added label stats doc * Added check for dtype in stats labels * Update utils_module_guide.rst * Experimental classifier to reject bad preds on empty * Experimental classifier to reject bad preds on empty * Update classifier_test.ipynb * WIP Trying to fix some QoL issues - Better exception handling in inference - Swapaxes at mode output - Remove small in Voronoi-Otsu * Fix exception handling * Locating csv issue * Enable ruff again * Handle empty labels in csv stats * Fix call to get_dict when stats is None * Ensure consistent rotation * Fix rotation checks + auto-channel select * Fix test for review * Update installation_guide.rst (#54) refining * Minor edits to install guide * [WIP] GUI-less training example script (#52) * Add remote train scripts * mv dockerfile * Paths for remote train * Change device * Update remote_training.py * Change results path to include more info * Update colab_training.py * Delete Dockerfile.cellseg3d * Make all wandb inits point to same project * Remove deprecated call to AddChannel * Fix tests issue with MONAI 1.3.0 * Create whole_brain_utils.py Add segmentation correction scripts * Update whole_brain_utils.py * Update whole_brain_utils.py * Update whole_brain_utils.py * Update whole_brain_utils.py * Update _config.yml --------- Co-authored-by: Timokleia <[email protected]> Co-authored-by: Mackenzie Mathis <[email protected]>

* WANDB integration for WNet * Colab training script * Update colab_training.py * Update colab_training.py * Update colab_training.py * Update colab_training.py * Update colab_training.py * Added minimal Colab notebook * ZeroCostDL4Mic-style notebook * Added WANDB to Colab notebook * Added softmax param * Fix reset of paths in training UI * WNet visualization * Disable intensity transforms in WNet * Fixed supervised loss saving * Update view_wnet.ipynb * Update view_wnet.ipynb * Fixed filepaths * Added more checks for csv + fix eval batch size * Utils+training fixes * Colab training improvements (#49) * Update colab_wnet_training.ipynb * Update colab_wnet_training.ipynb --------- Co-authored-by: Cyril Achard <[email protected]> * Reverted include_background=True in Dice * Reintroduced best Dice channel seeking + refacto * Improve filepath messages * Fix unsup image loading when not validating * Fixed deletion of Qt imports in interface * Added auto-check for which channel has foreground Preventing background to be shown first when using WNet inference, for better UX * Fixed eval_batch_size assignment * Fix training tests * Experimental auto-discard * Improved auto-discard utility * Create experimental sliding window Voronoi-Otsu for large volumes * Disable resize error handler * Docs update & jupyter-books port (#50) * Moved docs to source folder * Updated to jupyter-books * Update GH Action to jupyter-book * Updated guides * Update reqs for jupyter-books - Fixed typo * Fix typo and file duplicate * Added auto API docs * Update welcome.rst * Update interface docstrings * Update ruff to enforce docstring style * Updated docstrings in interface/config * Add additional docstring rule exceptions * Update utils docstring * Update plugins.py * Update dev_scripts * Updated code_plugin folder docstrings * Update code_models docstrings * Update tests docstrings * Update docstring rules to enforce docs * Fix warnings when building docs * Restore docs images * Remove old API docs * Added module docstring for all public modules * Update pyproject.toml * Update folder desc * Update inference and training guides * Update inference_module_guide.rst * Guides updates * Change indexing, guides updates * Fix unindent warning * Update _toc.yml * Fixed model list inconsistencies * Update model list * Trying to fully use autosummary (see #51) * Docs update * Fix missing refactor in CRF * Update cropping_module_guide.rst * Updated docs ref for code * Figs, refs, utils guide update * Update images to figures where relevant * Updated refs to source code * Improved utils guide layout and contents * Review update + crop/utils * Review update * Small inference tweaks for pipeline * Config changes * Update worker_inference.py * Small instance seg refactor * Added properties for instance seg params * Utils cleanup * Small refactor of unclear train/val split terminology * Fix log parameters incorrectly printing def dir * Enable sliding window for all instance seg methods * Update instance_segmentation.py Refactor sliding window to not shadow builtin "function" * Fixed mistake in auto-check for WNet results * Fix for restarting train worker after force stop * Docs & images update * mv welcome image * Improved inference docs * Update inference_module_guide.rst * Attempt to fix M1 yaml * Config docstring update * Welcome page update * Docs update * Add WandB for supervised models * Added auto contrast reset in cropping * Added checks for instance labels in training * Check for custom weights before locking window inference * Improve review plots makers * Documentation update (Timokleia) (#53) * Update cropping_module_guide.rst changes in the cropping module guide * Update cropping_module_guide.rst add `` * Update inference_module_guide.rst additions to inference module * Update metrics_module_guide.rst adjusting the metrics module * Update review_module_guide.rst review module updates * Update training_module_guide.rst changes in the training module * Update training_wnet.rst additions in the wnet module * Update utils_module_guide.rst utilities updates * review parameters image * Update cropping_module_guide.rst emoji * Update metrics_module_guide.rst emoji * Update training_module_guide.rst emoji * Update utils_module_guide.rst emoji * Update cropping_module_guide.rst mild style changes * Update review_module_guide.rst adjusting image code * Update welcome.rst changes to welcome * Add files via upload * Review and training tweaks - Fixed a few links, indents, typos - Replaced some emojis and added new ones for other pages * Welcome and inference tweaks - Fixed minor formatting, tables, broken links issues, etc * RM unused model wrappers attributes * Inference edits * Update WNet and inference * Images update * Update plots_train.png * Restore walkthrough * Update detailed_walkthrough.rst * Update detailed_walkthrough.rst editions * Minor edits --------- Co-authored-by: C-Achard <[email protected]> * Added floats in small remove * Try to fix issue with float/long * Add except handling for layer removal in train * Add first version of dedicated install page - Add install page - Refacto/clean up welcome page - Add more useful plugins - Update TODO * Improve training guide * Move M1 install * Added label stats utils * Added label stats doc * Added check for dtype in stats labels * Update utils_module_guide.rst * Experimental classifier to reject bad preds on empty * Experimental classifier to reject bad preds on empty * Update classifier_test.ipynb * WIP Trying to fix some QoL issues - Better exception handling in inference - Swapaxes at mode output - Remove small in Voronoi-Otsu * Fix exception handling * Locating csv issue * Enable ruff again * Handle empty labels in csv stats * Fix call to get_dict when stats is None * Ensure consistent rotation * Fix rotation checks + auto-channel select * Fix test for review * Update installation_guide.rst (#54) refining * Minor edits to install guide * [WIP] GUI-less training example script (#52) * Add remote train scripts * mv dockerfile * Paths for remote train * Change device * Update remote_training.py * Change results path to include more info * Update colab_training.py * Delete Dockerfile.cellseg3d * Make all wandb inits point to same project * Remove deprecated call to AddChannel * Fix tests issue with MONAI 1.3.0 * Create whole_brain_utils.py Add segmentation correction scripts * Update whole_brain_utils.py * Update whole_brain_utils.py * Update whole_brain_utils.py * Update whole_brain_utils.py * Update _config.yml --------- Co-authored-by: Timokleia <[email protected]> Co-authored-by: Mackenzie Mathis <[email protected]> --------- Co-authored-by: Timokleia <[email protected]> Co-authored-by: Mackenzie Mathis <[email protected]>

C-Achard added documentation Improvements or additions to documentation help wanted Extra attention is needed labels Sep 28, 2023

C-Achard self-assigned this Sep 28, 2023

C-Achard added a commit that referenced this issue Sep 28, 2023

Trying to fully use autosummary (see #51)

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Using autosummary to generate full API docs #51

Using autosummary to generate full API docs #51

C-Achard commented Sep 28, 2023

Using autosummary to generate full API docs #51

Using autosummary to generate full API docs #51

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C-Achard commented Sep 28, 2023