docs: consolidate tutorials and convert guides to notebooks#104
Merged
Conversation
…es to notebooks Merge the parallel docs/single_compartment and docs/multi_compartment trees into a single progressive docs/tutorials/ path, moving examples to docs/examples/. Merge and translate the channel/ion tutorials (previously duplicated, with the multi-compartment versions written in Chinese) into one English notebook each. Convert the 19 code-bearing Markdown guides (concepts, getting_started, file_formats, developer, troubleshooting) to executable notebooks; prose-only pages stay Markdown. Update toctrees and cross-references accordingly. Fix all Sphinx build warnings (clean build, 0 warnings): - conf.py: napoleon_use_ivar to stop Attributes duplicating autodoc members; autodoc-process-docstring hook restoring the blank line that sphinx_autodoc_typehints drops before a trailing section. - Move footnote citations out of one-line summaries (RK steps, HCN_HM1992) so autosummary no longer fails to resolve the footnote target. - Tidy Channel/Ion/IonInfo docstrings and a morphology forward reference.
![sourcery-ai[bot]](https://avatars.githubusercontent.com/in/48477?s=60&v=4){kind=small}
Contributor
There was a problem hiding this comment.
Sorry @chaoming0625, your pull request is larger than the review limit of 150000 diff characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
docs/single_compartment/anddocs/multi_compartment/trees into one progressivedocs/tutorials/path; move examples to top-leveldocs/examples/.channel/iontutorials (the multi-compartment versions were written in Chinese) into one English notebook each.napoleon_use_ivarso NumPy-doc Attributes no longer duplicate autodoc members.autodoc-process-docstringhook that restores the blank linesphinx_autodoc_typehintsdrops before a trailing section (Field list ends without a blank line).HCN_HM1992) soautosummaryresolves footnote targets.Channel/Ion/IonInfodocstrings and amorphologyforward reference.Test plan
sphinx-build -b html docs docs/_build/html— build succeeds with 0 warnings.nbformat.read(..., 4).docs/tutorials/*.ipynb.single_compartment/index/multi_compartment/indexreferences.