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Merged
merged 29 commits into from
Jun 13, 2025
Merged

Init sphinx docs #57

merged 29 commits into from
Jun 13, 2025

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@TimothyWillard
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@TimothyWillard TimothyWillard commented May 23, 2025 •
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  • Fix warnings like:
/Users/twillard/Desktop/GitHub/ACCIDDA/vaxflux/src/vaxflux/multilevel_model.py:docstring of vaxflux.multilevel_model.UptakeModelConfig.name:1: WARNING: duplicate object description of vaxflux.multilevel_model.UptakeModelConfig.name, other instance in api/vaxflux.multilevel_model, use :no-index: for one of them
  • Incorporate docs building/checking into GitHub actions CI pipeline.

@TimothyWillard TimothyWillard linked an issue May 23, 2025 that may be closed by this pull request
Sphinx Documentation Site #9
Closed
@TimothyWillard
Add sphinx to dev deps
ebba8f5
@TimothyWillard
Run sphinx-quickstart to create docs/ dir
8880203
@TimothyWillard
Switch sphinx to pydata theme
38d5766
@TimothyWillard
Add docs to make clean, format/lint docs
09988cf
@TimothyWillard
Add a make docs step to Makefile
82a9058
@TimothyWillard
Add light content to docs index page
dd9649c
@TimothyWillard
Add rstcheck for linting docs
e0e04f3
@TimothyWillard
Autogen API reference from source docstrings
fc33b83
@TimothyWillard
Autodoc order by entry in source
b390f06
@TimothyWillard
Remove 'Attributes:' section from classes
077c6ac 
Moved documentation to the attribute level itself with sphinx's native
'#:' comment. This is to avoid warnings about duplicate documentation
where sphinx was parsing the attribute itself as well as the
'Attributes:' section.
@TimothyWillard
Outline of documentation pages to write
b605a04
@TimothyWillard
Add mathjax to documentation
b5568f6
@TimothyWillard
Add docs target to all, ci in Makefile
3bdefdf
@TimothyWillard
Add docs/_static to fix html_static_path warn
88e794e
@TimothyWillard
Initial installation docs
c499cc8 
Will have to revisit these instructions once the repo becomes public.
@TimothyWillard
Hide section nav for individual pages
579ff99
@TimothyWillard
Helper script to modify generated API reference
684c87d
@TimothyWillard
Initial work on "Getting Started" documentation
1be4c7f
@TimothyWillard
Add 'Introduction' documentation page
26e46a4 
Added an 'Introduction' documentation page to give a high level summary
of the package and layout the problem statement this package is intended
to address.
@TimothyWillard
Fleshed out 'Getting Started' guide
8c58416 
Completed the 'Getting Started' guide in the documentation, covering a
start to finish tutorial.
@TimothyWillard
Adjust 'Getting Started' priors
7f7eff1
@TimothyWillard
Describe curves in 'Model Details' guide
bc3928b
@TimothyWillard
Outline for rest of 'Model Details'
f8cc157
@TimothyWillard
Link to NCIRD data set page directly
94fb244 
Swapped out a short url for the NCIRD weekly cumulative influenza
vaccinations data set with a proper link to the about page in the
docstring of
`vaxflux.data.get_ncird_weekly_cumulative_vaccination_coverage`. This
link now renders nicely in the documentation site. Also removed TODO
comment from that function since that has been extracted into #60.
@TimothyWillard
Correct curve equations
db7f298
@TimothyWillard
Change doc names to be more url friendly
7d1273b 
Changed getting started and model detail documentation pages from using
an underscore to using a dash.
@TimothyWillard TimothyWillard merged commit ba369cb into main Jun 13, 2025
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@TimothyWillard TimothyWillard deleted the init-sphinx-docs branch June 13, 2025 19:44
@TimothyWillard TimothyWillard mentioned this pull request Jun 13, 2025
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Sphinx Documentation Site

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@TimothyWillard