DOCS: Update sphinx configuration, docs, citations #94
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* Adds `.readthedocs.yaml` * Converts citation to use `BibTex` via the `sphinxcontrib.bibtex` extension. References are now stored in `docs/references.bib` and can be cited using `:footcite:`. Citations for each page will show at the bottom by adding `.. footbibliography::`. * Adds brief description of `BibTex` citations to `docs/README.md` * Fixes issues with equation formatting in `calculations.py` and `diagrams.py` * Fixes issues with citations in `calculations.py` and `diagrams.py` * Removes "Kinetic Diagram Analysis" from titles of main modules (e.g. `calculations.py`) * Adds `usage.rst` which covers KDA installation and basic usage, including generating state probabilities and plotting diagrams * Updates `index.rst` such that some kinetic diagrams are rendered on the home page * Changes `version` and `release` in `conf.py` to automatically update based on imported `kda` version
* Add `docs/requirements.txt` with single package to install, `sphinxcontrib-bibtex` * Update `readthedocs.yaml` to install packages from `docs/requirements.txt`
* Updates `docs/requirements.txt` in accordance with the recommendations provided in the following link: https://docs.readthedocs.io/en/stable/guides/reproducible- builds.html#use-a-requirements-file-for-python-dependencies
* Update `docutils` version to `0.20.1` for compatibility between `sphinxcontrib-bibtex` and `sphinx-rtd-theme`
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Okay it looks like the docs are finally building. I'm gonna squash & merge this, any other changes to the docs can be handled in much smaller bite sizes. |
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Changes
Adds
.readthedocs.yamlConverts citation to use
BibTexvia thesphinxcontrib.bibtexextension. References are now stored indocs/references.biband can be cited using:footcite:. Citations for each page will show at the bottom by adding.. footbibliography::.Adds brief description of
BibTexcitations todocs/README.mdFixes issues with equation formatting in
calculations.pyanddiagrams.pyFixes issues with citations in
calculations.pyanddiagrams.pyRemoves "Kinetic Diagram Analysis" from titles of main modules (e.g.
calculations.py)Adds
usage.rstwhich covers KDA installation and basic usage, including generating state probabilities and plotting diagramsUpdates
index.rstsuch that some kinetic diagrams are rendered on the home pageChanges
versionandreleaseinconf.pyto automatically update based on importedkdaversionFixes Fix _combine() function showing up in kda.diagrams page of kda.readthedocs.io #23
Fixes DOC: Fix ReadtheDocs configuration #93