Reformat function help blocks to NumPy-style docstrings#616
Merged
Conversation
Rewrite the leading help comment block of every documented function (across the analysis, annotation, biomass, comparison, conditions, conversion, curation, gapfilling, io, localization, manipulation, omics, queries, reconstruction, solver, tasks, utils and visualization modules) to NumPy-style docstrings: a one-line summary, followed by Parameters, Returns, Examples and (where relevant) Notes / See also sections, with typed arguments. This renders as structured argument/return tables in the documentation site (via mkdocstrings-matlab) while remaining valid, readable MATLAB help text. Only comment lines are changed; function signatures and code are untouched.
edkerk
force-pushed
the
fix/numpy-style-help
branch
from
d915c40 to
5d959db
Compare
edkerk
added a commit
to edkerk/raven-docs
that referenced
this pull request
Jun 10, 2026
RAVEN's develop3 branch reorganises the toolbox into modular directories (reconstruction, manipulation, analysis, gapfilling, ...) that mirror raven-python's package layout, so the two line up by category. - .gitmodules: track the RAVEN submodule on develop3. - gen_api_pages.py: organise the API reference by develop3's modular categories. - mkdocs.yml: point the MATLAB mkdocstrings handler at the modular directories. The NumPy-style function help that renders these as argument/return tables lands in develop3 via SysBioChalmers/RAVEN#616; once merged, updating the submodule (it now tracks develop3) brings the reformatted docstrings in.
edkerk
added a commit
to edkerk/raven-docs
that referenced
this pull request
Jun 12, 2026
* Use numpy docstring style for the MATLAB API handler RAVEN's function help is being reformatted to NumPy-style docstrings, which mkdocstrings-matlab renders as structured argument/return tables. Set the matlab handler's docstring_style to numpy so the help is parsed accordingly. * Track RAVEN develop3 and document its modular structure RAVEN's develop3 branch reorganises the toolbox into modular directories (reconstruction, manipulation, analysis, gapfilling, ...) that mirror raven-python's package layout, so the two line up by category. - .gitmodules: track the RAVEN submodule on develop3. - gen_api_pages.py: organise the API reference by develop3's modular categories. - mkdocs.yml: point the MATLAB mkdocstrings handler at the modular directories. The NumPy-style function help that renders these as argument/return tables lands in develop3 via SysBioChalmers/RAVEN#616; once merged, updating the submodule (it now tracks develop3) brings the reformatted docstrings in. * Add daily submodule-update GitHub Action Track develop3 (RAVEN) and develop (raven-python) in .gitmodules and add a scheduled workflow that bumps the submodule pointers to the tip of their tracked branches once a day, with manual workflow_dispatch support.
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.
Main improvements in this PR:
analysis,annotation,biomass,comparison,conditions,conversion,curation,gapfilling,io,localization,manipulation,omics,queries,reconstruction,solver,tasks,utilsandvisualizationmodules) to NumPy-style docstrings: a one-line summary, followed byParameters,Returns,Examplesand (where relevant)Notes/See alsosections, with typed arguments (e.g.model : struct,verbose : logical, optional).mkdocstrings-matlab), while remaining valid, readable MATLABhelptext. A few inconsistent H1 lines (copy-paste leftovers) were corrected to match the file name.Instructions on merging this PR:
develop3branch, and will be resolved with a squash-merge.mainas target branch, and will be resolved as descriped here.