Backport PR #4100 on branch 1.12.x (docs: Highlight RSC & cleanup documentation) (#4104)

Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>

Author: meeseeksmachine

docs/api/index.md

@@ -7,7 +7,7 @@ import scanpy as sc
 ```
 
 ```{note}
-Additional functionality is available in the broader {doc}`ecosystem <../ecosystem>`, with some tools being wrapped in the {mod}`scanpy.external` module.
+Additional functionality is available across the broader [scverse ecosystem](https://scverse.org/packages/#ecosystem), with some tools wrapped in the {mod}`scanpy.external` module.
 ```
 
 (array-support)=

docs/community.md

@@ -1,10 +1,11 @@
 # Community
 
-Scanpy is a community driven project. There are multiple channels for users and developers to communicate and connect.
+Scanpy is a community driven project embedded in the [scverse consortium](https://scverse.org).
+There are multiple channels for users and developers to communicate and connect.
 
 ## [Discourse](https://discourse.scverse.org)
 
-The scverse Discourse forum is place to go to ask usage questions and for longer form discussions around the project.
+The scverse Discourse forum is the place to ask usage questions and for longer form discussions around the project.
 
 ## [Github Issue Tracker](https://github.com/scverse/scanpy/issues)
 

docs/ecosystem.md

@@ -7,13 +7,7 @@
 
 ```{warning}
 We are no longer accepting new tools into `scanpy.external`.
-Instead, please submit your tool to the [scverse ecosystem package listing](https://scverse.org/packages/#ecosystem).
-```
-
-```{note}
-For tools that integrate well with scanpy and anndata, see:
-* The [scverse ecosystem](https://scverse.org/packages/#ecosystem)
-* Scanpy's ecosystem {doc}`ecosystem page <../ecosystem>`
+For tools that integrate well with scanpy and anndata, or to submit your own, see the [scverse ecosystem](https://scverse.org/packages/#ecosystem).
 ```
 
 Import Scanpy's wrappers to external tools as:

docs/external/index.md

@@ -38,24 +38,24 @@ Need help? Reach out on our forum to get your questions answered!
 
 Find a bug? Interested in improving scanpy? Checkout our GitHub for the latest developments.
 :::
+
+:::{grid-item-card} GPU acceleration {octicon}`rocket;1em;`
+:link: https://rapids-singlecell.readthedocs.io
+
+Working with millions of cells and have a GPU available?
+[rapids-singlecell][rsc] mirrors the scanpy API with order-of-magnitude speedups on core preprocessing, neighbors, embedding, and clustering steps.
+:::
 ::::
 
+[rsc]: https://rapids-singlecell.readthedocs.io
+
 **Other resources**
 
 * Follow changes in the {ref}`release notes <release-notes>`.
-* Find tools that harmonize well with anndata & Scanpy at [scverse.org/packages/](https://scverse.org/packages/)
+* Discover tools that build on or complement scanpy in the [scverse ecosystem](https://scverse.org/packages/#ecosystem), and follow scverse-wide news at [scverse.org/blog](https://scverse.org/blog/).
 * Check out our {ref}`contribution guide <contribution-guide>` for development practices.
 * Consider citing [Genome Biology (2018)] along with original {doc}`references <references>`.
 
-## News
-
-```{include} news.md
-:start-after: '<!-- marker: after prelude -->'
-:end-before: '<!-- marker: before old news -->'
-```
-
-{ref}`(past news) <News>`
-
 % put references first so all references are resolved
 
 % NO! there is a particular meaning to this sequence
@@ -70,10 +70,8 @@ usage-principles
 how-to/index
 api/index
 external/index
-ecosystem
 release-notes/index
 community
-news
 dev/index
 contributors
 references

docs/index.md

@@ -109,6 +109,13 @@ For instructions on how to work with the code, see the {ref}`contribution guide
 
 [on github]: https://github.com/scverse/scanpy
 
+## GPU acceleration
+
+If you have a GPU, consider [rapids-singlecell][], which mirrors the scanpy API with order-of-magnitude speedups.
+See its [documentation][rapids-singlecell] for installation and usage instructions.
+
+[rapids-singlecell]: https://rapids-singlecell.readthedocs.io
+
 ## Docker
 
 If you're using [Docker][], you can use e.g. the image [gcfntnu/scanpy][] from Docker Hub.

docs/installation.md

@@ -0,0 +1 @@
+Highlighting rapids-singlecell for GPU users & cleanup documentation.

docs/news.md

@@ -23,7 +23,7 @@ plotting/index
 ## Trajectory inference
 
 ```{seealso}
-For more powerful tools for analysing single cell dynamics, check out the Scverse ecosystem packages:
+For more powerful tools for analysing single cell dynamics, check out the scverse ecosystem packages:
 
 * [CellRank](https://cellrank.readthedocs.io)
 * [Dynamo](https://dynamo-release.readthedocs.io/en/latest/)
@@ -35,9 +35,6 @@ For more powerful tools for analysing single cell dynamics, check out the Scvers
 trajectories/index
 ```
 
-## Spatial data
-
-
 ## Experimental
 
 ```{toctree}
@@ -53,7 +50,7 @@ A number of older tutorials can be found at:
 * The [`scanpy_usage`](https://github.com/scverse/scanpy_usage) repository
 
 ```{seealso}
-Scanpy used to have tutorials for its (now deprecated) spatial data functionality.x
+Scanpy used to have tutorials for its (now deprecated) spatial data functionality.
 For up-to-date tutorials on working with spatial data, see:
 
 * SquidPy {doc}`squidpy:notebooks/tutorials/index`

docs/release-notes/4100.docs.md

@@ -2,16 +2,15 @@
 
 Import Scanpy as:
 
-```
+```python
 import scanpy as sc
 ```
 
 ## Workflow
 
-The typical workflow consists of subsequent calls of data analysis tools
-in `sc.tl`, e.g.:
+The typical workflow consists of subsequent calls of data analysis tools in `sc.tl`, e.g.:
 
-```
+```python
 sc.tl.umap(adata, **tool_params)  # embed a neighborhood graph of the data using UMAP
 ```
 
@@ -20,7 +19,7 @@ Each of these calls adds annotation to an expression matrix *X*,
 which stores *n_obs* observations (cells) of *n_vars* variables (genes).
 For each tool, there typically is an associated plotting function in `sc.pl`:
 
-```
+```python
 sc.pl.umap(adata, **plotting_params)
 ```
 
@@ -41,24 +40,21 @@ Scanpy is based on {mod}`anndata`, which provides the {class}`~anndata.AnnData`
 :width: 300px
 ```
 
-At the most basic level, an {class}`~anndata.AnnData` object `adata` stores
-a data matrix `adata.X`, annotation of observations
-`adata.obs` and variables `adata.var` as `pd.DataFrame` and unstructured
-annotation `adata.uns` as `dict`. Names of observations and
-variables can be accessed via `adata.obs_names` and `adata.var_names`,
-respectively. {class}`~anndata.AnnData` objects can be sliced like
-dataframes, for example, `adata_subset = adata[:, list_of_gene_names]`.
+At the most basic level, an {class}`~anndata.AnnData` object `adata` stores a data matrix `adata.X`, annotation of observations
+`adata.obs` and variables `adata.var` as `pd.DataFrame` and unstructured annotation `adata.uns` as `dict`.
+Names of observations and variables can be accessed via `adata.obs_names` and `adata.var_names`, respectively.
+{class}`~anndata.AnnData` objects can be sliced like dataframes, for example, `adata_subset = adata[:, list_of_gene_names]`.
 For more, see this [blog post].
 
 To read a data file to an {class}`~anndata.AnnData` object, call:
 
-```
-adata = sc.read(filename)
+```python
+adata = sc.read_h5ad(filename).  # or sc.read_zarr(filename)
 ```
 
 to initialize an {class}`~anndata.AnnData` object. Possibly add further annotation using, e.g., `pd.read_csv`:
 
-```
+```python
 import pandas as pd
 anno = pd.read_csv(filename_sample_annotation)
 adata.obs['cell_groups'] = anno['cell_groups']  # categorical annotation of type pandas.Categorical
@@ -69,7 +65,7 @@ adata.obs['time'] = anno['time']                # numerical annotation of type f
 
 To write, use:
 
-```
+```python
 adata.write_h5ad(filename)
 adata.write_zarr(filename)
 adata.write_csvs(filename)