docs: Sphinx + ReadTheDocs site and reorganized documentation#13
Merged
Conversation
Reorganize docs/ into a Diátaxis-style tree (guide / reference / studies /
maintenance / archive) and add a Sphinx + MyST documentation site wired for
ReadTheDocs.
Site / toolchain:
* .readthedocs.yaml + docs/conf.py (furo, MyST-Parser, autodoc + napoleon for
the NumPy-style docstrings, intersphinx to cobra/numpy/pandas/scipy).
* docs/requirements.txt; docs/index.md landing page + master toctree.
* Full API reference auto-generated from docstrings — one automodule page per
subpackage, honoring each __all__.
* 7 task-oriented user-guide pages + quickstart; section index pages.
* CHANGELOG.md / IMPROVEMENTS.md are {include}-d into the site.
Link hygiene (the move + include changed relative depth):
* All intra-docs cross-links updated to the new section paths.
* Repo-file links (src/scripts/tests) and the included root files use absolute
GitHub URLs so they resolve on both GitHub and the RTD site.
* README/CHANGELOG/IMPROVEMENTS doc links remapped to the new paths.
Quality / CI:
* Tiny docstring formatting fixes (blank line before Parameters / bullet lists,
literal block in binaries.py) so autodoc renders cleanly. Build is
warning-clean under `sphinx-build -W`.
* New `docs` CI job builds the site with `-W --keep-going`.
edkerk
force-pushed
the
feature/readthedocs-docs
branch
from
bb269d6 to
d1be3ca
Compare
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Sets up a Sphinx + MyST documentation site wired for ReadTheDocs, and reorganizes
docs/into a navigable, sectioned tree.Organization (Diátaxis-style)
All existing docs were preserved (via
git mv) and grouped:guide/reference/reference/api/automodulepage per subpackage (honors each__all__)studies/maintenance/archive/Toolchain
.readthedocs.yaml+docs/conf.py: furo theme, MyST-Parser, autodoc + napoleon (NumPy docstrings), intersphinx (cobra/numpy/pandas/scipy), viewcode, copybutton.docs/requirements.txt; landing page + master toctree indocs/index.md.CHANGELOG.md/IMPROVEMENTS.mdare{include}-d into the site.Link hygiene
The move + includes changed relative depth, so: intra-docs links were repointed to the new section paths; repo-file links (
src/scripts/tests) and the included root files now use absolute GitHub URLs so they resolve on both GitHub and the RTD site; README/CHANGELOG/IMPROVEMENTS doc links were remapped.Quality / CI
Parameters/ bullet lists; literal block inbinaries.py) so autodoc renders cleanly.ruff+ imports still pass.docsCI job builds the site with-W --keep-going.sphinx-build -W.