Update docs (#35)

* Add bug report template * Add more templates * Adding deploy to pypi * First stab at running CI tests * Unit tests only for Python 3.13 * Fix libgit * Whitespace * Should work now * Explain why we need this * Stick to python 3.12 for now * Add codecov, improve pyproject toml * Install test environment * Improve readme with autogenerated screenshots :) * Add more screenshots * Adding in quarto pip tests requirements * Quarto via pip * Add pandocfilters * Move towards trusted publishing * Autofixing * Panflutes * Typo * Flute, not flutes * Not necessary * Use quarto GH action to setup quarto * Don't enforce quarto version * Fix v8 options * update release workflow * Update pre-commit * autoformat * run rich codex automatically * disable codecov for now; can revisit later * attempt fix rich codex autocommits * Pre-commit * Bootstrap docs from template * Try fix rich * test pre-commit action * Try fix rich * test pre-commit action * Generate new screengrabs with rich-codex * Rich codex to separate PR * rich codex separate PR * Commit pre-commit changes even when pre-commit failed (intended for autofixing) * Apply automatic changes * trigger ci * Bootstrap docs from template * Try fix rich * Apply automatic changes * cleanup * Fix sphinx build * Add docs action * test * update workflows * update workflows * test * fix reference to changelog * fix contributing * use hatch envs * migrate pre-commit config * update contributing guide * pre-structure docs * fix sphinx build --------- Co-authored-by: Alexander Peltzer <[email protected]> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: grst <[email protected]>
Boehringer-Ingelheim · Oct 18, 2024 · cd7f4c1 · cd7f4c1
1 parent fa898a3
commit cd7f4c1
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Showing 9 changed files with 38 additions and 21 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -29,7 +29,7 @@
 # The full version, including alpha/beta/rc tags
 release = info["Version"]
 
-bibtex_bibfiles = ["references.bib"]
+# bibtex_bibfiles = ["references.bib"]
 templates_path = ["_templates"]
 nitpicky = True  # Warn about broken links
 needs_sphinx = "4.0"
@@ -53,7 +53,7 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
-    "sphinxcontrib.bibtex",
+    # "sphinxcontrib.bibtex",
     "sphinx_autodoc_typehints",
     "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",

diff --git a/docs/contributing.md b/docs/contributing.md
@@ -127,7 +127,7 @@ This project uses [sphinx][] with the following features:
 -   The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
 -   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
 -   [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
--   Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+-   Citations can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
 
 See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
 

diff --git a/docs/api.md → docs/dso_python.md b/docs/api.md → docs/dso_python.md
@@ -1,4 +1,6 @@
-# API
+# Python API
+
+TODO
 
 ```{eval-rst}
 .. module:: dso

diff --git a/docs/dso_r.md b/docs/dso_r.md
@@ -0,0 +1,3 @@
+# DSO R package
+
+TODO
diff --git a/docs/getting_started.md b/docs/getting_started.md
@@ -0,0 +1,3 @@
+# Getting started
+
+TODO
diff --git a/docs/index.md b/docs/index.md
@@ -5,9 +5,32 @@
 ```{toctree}
 :hidden: true
 :maxdepth: 1
+:caption: User Guide
+
+getting_started.md
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+:caption: DSO CLI
 
-api.md
 CHANGELOG.md
 contributing.md
-references.md
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+:caption: DSO Python API
+
+dso_python.md
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+:caption: DSO R API
+
+dso_r.md
 ```
diff --git a/docs/references.bib b/docs/references.bib
diff --git a/docs/references.md b/docs/references.md
diff --git a/pyproject.toml b/pyproject.toml
@@ -46,6 +46,7 @@ optional-dependencies.doc = [
   # For notebooks
   "ipykernel",
   "ipython",
+  "matplotlib",
   "myst-nb>=1.1",
   "sphinx>=4",
   "sphinx-autodoc-typehints",