Doc overhaul (scverse#2220)

* Update conf.py * add req * add override path * Create override.css * add pygments, remove scvi-tools colors * add myst extensions * remove github edit links * move css * add sphinx design, opengraph * move contributors out of index * show source * add submodule * add submodule * temp old tutorials rename * remove github links * remove github url from template * disable warning fail * disable warning fail * nbsphinx * fix headings * rtd use submodule * add viewcode * more headings fixes * tutorials index * add nbsphinx ext * remove sphinx pygments * fix colab link * add ipython as docs req * no signatures in tables * make ci happy * add sphinx design cards * break up api * fix icons * link to new api index in card * update colors * no latest release in index * release notes * colors * color typo * back to default colors * Update override.css * add module * move external * Make border color override work * grid * hoverxref and linkcode * fix grid * comment * grid spacing * intersphinx hoverxref * extlinks * extlinks * fix contributors * fix tutorials to use old page * hidden toc tree * toctree for tutorials hidden * clean up conf * fix extlinks * tutorial extlink * add leiden to docs build * buttons * small role * try rst badge * extlinks * fix image link * Update docs/conf.py * update submodule * remove hoverxref * warning code * add how to update submodule * remove unnecessary css * remove more scanpydoc * tutorials link * switch to sphinx book * pre commit' * update reqs * logo only * deps * linkcode * linkcode * exclude patterns * sidebar levels * remove external tools * fix external --------- Co-authored-by: Philipp A <[email protected]>
ducminhnguyenle · Feb 15, 2023 · 2b28b57 · 2b28b57
1 parent 619bd77
commit 2b28b57
Show file tree

Hide file tree

Showing 39 changed files with 1,036 additions and 882 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "docs/tutorials"]
+	path = docs/tutorials
+	url = https://github.com/scverse/scanpy-tutorials.git
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -11,3 +11,7 @@ python:
     path: .
     extra_requirements:
     - doc
+    - leiden
+submodules:
+  include:
+     - "docs/tutorials"
diff --git a/docs/_key_contributors.rst b/docs/_key_contributors.rst
diff --git a/docs/_static/css/override.css b/docs/_static/css/override.css
@@ -0,0 +1,20 @@
+/* for the sphinx design cards */
+body {
+    --sd-color-shadow: dimgrey;
+}
+
+dl.citation>dt {
+    float: left;
+    margin-right: 15px;
+    font-weight: bold;
+}
+
+/* for custom small role */
+.small {
+    font-size: 40% !important
+}
+
+.smaller,
+.pr {
+    font-size: 70% !important
+}
diff --git a/docs/_templates/autosummary/base.rst b/docs/_templates/autosummary/base.rst
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
@@ -1,5 +1,3 @@
-:github_url: {{ fullname | github_url }}
-
 {{ fullname | escape | underline}}
 
 .. currentmodule:: {{ module }}

diff --git a/docs/tutorials.md → docs/_tutorials.md b/docs/tutorials.md → docs/_tutorials.md
@@ -2,7 +2,7 @@
 
 ## Clustering
 
-For getting started, we recommend Scanpy’s reimplementation {tutorial}`pbmc3k`
+For getting started, we recommend Scanpy’s reimplementation {doc}`/tutorials/pbmc3k`
 of Seurat’s [^cite_satija15] clustering tutorial for 3k PBMCs from 10x Genomics,
 containing preprocessing, clustering and the identification of cell types via
 known marker genes.
@@ -29,15 +29,15 @@ known marker genes.
 
 ## Visualization
 
-This tutorial shows how to visually explore genes using scanpy. {tutorial}`plotting/core`
+This tutorial shows how to visually explore genes using scanpy. {doc}`/tutorials/plotting/core`
 
 ```{image} _static/img/stacked_violin_dotplot_matrixplot.png
 :width: 550px
 ```
 
 ## Trajectory inference
 
-Get started with the following example for hematopoiesis for data of [^cite_paul15]: {tutorial}`paga-paul15`
+Get started with the following example for hematopoiesis for data of [^cite_paul15]: {doc}`/tutorials/paga-paul15`
 
 ```{image} _static/img/tutorials/paga_paul15.png
 :width: 450px
@@ -56,16 +56,16 @@ for two hematopoiesis datasets: [DPT example 1] [^cite_paul15] and [DPT example
 
 ## Integrating datasets
 
-Map labels and embeddings of reference data to new data: {tutorial}`integrating-data-using-ingest`
+Map labels and embeddings of reference data to new data: {doc}`/tutorials/integrating-data-using-ingest`
 
 ```{image} https://scanpy-tutorials.readthedocs.io/en/latest/_images/integrating-data-using-ingest_21_0.png
 :width: 350px
 ```
 
 ## Spatial data
 
-- Basic analysis of spatial data: {tutorial}`spatial/basic-analysis`
-- Integrating spatial data with scRNA-seq using scanorama: {tutorial}`spatial/integration-scanorama`
+- Basic analysis of spatial data: {doc}`/tutorials/spatial/basic-analysis`
+- Integrating spatial data with scRNA-seq using scanorama: {doc}`/tutorials/spatial/integration-scanorama`
 
 ```{image} _static/img/spatial-basic-analysis.png
 :width: 250px
@@ -77,7 +77,7 @@ Map labels and embeddings of reference data to new data: {tutorial}`integrating-
 
 ### Conversion: AnnData, SingleCellExperiment, and Seurat objects
 
-```{image} https://github.com/scverse/scanpy-in-R/raw/master/logo.png
+```{image} https://github.com/theislab/scanpy-in-R/raw/master/logo.png
 :align: right
 :width: 200px
 ```
@@ -96,7 +96,7 @@ See the [cell cycle] notebook.
 
 ### Normalization with Pearson Residuals
 
-Normalization of scRNA-seq data with Pearson Residuals, from [^cite_lause21]: {tutorial}`tutorial_pearson_residuals`
+Normalization of scRNA-seq data with Pearson Residuals, from [^cite_lause21]: {doc}`/tutorials/tutorial_pearson_residuals`
 
 ### Scaling Computations
 
@@ -138,3 +138,17 @@ See pseudotime-time inference on deep-learning based features for [cell cycle re
 [scanpy in r]: https://theislab.github.io/scanpy-in-R/
 [seurat to anndata]: https://github.com/LuckyMD/Code_snippets/blob/master/Seurat_to_anndata.ipynb
 [toggleswitch]: https://nbviewer.jupyter.org/github/scverse/scanpy_usage/blob/master/170430_krumsiek11/toggleswitch.ipynb
+
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+
+tutorials/pbmc3k
+tutorials/paga-paul15
+tutorials/plotting/core
+tutorials/integrating-data-using-ingest
+tutorials/spatial/basic-analysis
+tutorials/spatial/integration-scanorama
+tutorials/tutorial_pearson_residuals
+```