Doc overhaul

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "docs/tutorials"]
+	path = docs/tutorials
+	url = https://github.com/scverse/scanpy-tutorials.git

.readthedocs.yml

@@ -11,3 +11,7 @@ python:
     path: .
     extra_requirements:
     - doc
+    - leiden
+submodules:
+  include:
+     - "docs/tutorials"

docs/_static/css/override.css

@@ -0,0 +1,86 @@
+/* for the sphinx design cards */
+body {
+    --sd-color-shadow: dimgrey;
+}
+
+dt:target,
+span.highlighted {
+    background-color: #f0f0f0;
+}
+
+dl.citation>dt {
+    float: left;
+    margin-right: 15px;
+    font-weight: bold;
+}
+
+/* Parameters normalize size and captialized, */
+dl .field-list dt {
+    font-size: var(--font-size--normal) !important;
+    text-transform: none !important;
+}
+
+/* examples and headings in classes */
+p.rubric {
+    font-size: var(--font-size--normal);
+    text-transform: none;
+    font-weight: 500;
+}
+
+/* so that api methods are small in sidebar */
+li.toctree-l3 {
+    font-size: 81.25% !important;
+}
+
+li.toctree-l4 {
+    font-size: 75% !important;
+}
+
+/* for custom small role */
+.small {
+    font-size: 40% !important
+}
+
+.smaller,
+.pr {
+    font-size: 70% !important
+}
+
+
+/* nbsphinx specific */
+
+.nbinput .prompt,
+.nboutput .prompt {
+    display: none;
+}
+
+.nboutput .stderr {
+    display: none;
+}
+
+div.nblast.container {
+    padding-bottom: 10px !important;
+    padding-right: 0px;
+    padding-left: 0px;
+}
+
+div.nbinput.container {
+    padding-top: 10px !important;
+    padding-right: 0px;
+    padding-left: 0px;
+}
+
+div.nbinput.container div.input_area {
+    /* Code cell border that works in both dark and light mode */
+    border-color: rgba(127, 127, 127, .25) !important;
+}
+
+
+div.nbinput.container div.input_area div[class*="highlight"]>pre {
+    padding: 10px !important;
+    margin: 0;
+}
+
+p.topic-title {
+    margin-top: 0;
+}

docs/_templates/autosummary/class.rst

@@ -1,5 +1,3 @@
-:github_url: {{ fullname | github_url }}
-
 {{ fullname | escape | underline}}
 
 .. currentmodule:: {{ module }}

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 +138,16 @@ 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
+```