Fix links (#2953)

Co-authored-by: Philipp A <[email protected]>

Author: ivirshup

CONTRIBUTING.md

@@ -17,4 +17,4 @@ Contributing code
 -----------------
 
 We love code contributions!
-If you're interested in contributing code, please take a look over the [contributing guide](https://scanpy.readthedocs.io/en/latest/dev/index.html) in the main documentation.
+If you're interested in contributing code, please take a look over the [contribution guide](https://scanpy.readthedocs.io/en/latest/dev/index.html) in the main documentation.

README.md

@@ -11,13 +11,17 @@
 # Scanpy – Single-Cell Analysis in Python
 
 Scanpy is a scalable toolkit for analyzing single-cell gene expression data
-built jointly with [anndata](https://anndata.readthedocs.io).  It includes
+built jointly with [anndata][].  It includes
 preprocessing, visualization, clustering, trajectory inference and differential
 expression testing.  The Python-based implementation efficiently deals with
 datasets of more than one million cells.
 
-Discuss usage on the scverse [Discourse]. Read the [documentation].
-If you'd like to contribute by opening an issue or creating a pull request, please take a look at our [contributing guide].
+Discuss usage on the scverse [Discourse][]. Read the [documentation][].
+If you'd like to contribute by opening an issue or creating a pull request, please take a look at our [contribution guide][].
+
+[anndata]: https://anndata.readthedocs.io
+[discourse]: https://discourse.scverse.org/
+[documentation]: https://scanpy.readthedocs.io
 
 [//]: # (numfocus-fiscal-sponsor-attribution)
 
@@ -52,6 +56,5 @@ You can cite the scverse publication as follows:
 >
 > _Nat Biotechnol._ 2023 Apr 10. doi: [10.1038/s41587-023-01733-8](https://doi.org/10.1038/s41587-023-01733-8).
 
-[contributing guide]: CONTRIBUTING.md
-[discourse]: https://discourse.scverse.org/
-[documentation]: https://scanpy.readthedocs.io
+
+[contribution guide]: CONTRIBUTING.md

docs/index.md

@@ -1,5 +1,5 @@
 ```{include} ../README.md
-:end-line: 36
+:end-line: 40
 ```
 
 ```{eval-rst}
@@ -51,7 +51,7 @@ Find a bug? Interested in improving scanpy? Checkout our GitHub for the latest d
 **Other resources**
 * Follow changes in the {ref}`release notes <release-notes>`.
 * Find tools that harmonize well with anndata & Scanpy via the {doc}`external API <external/index>` and the {doc}`ecosystem page <ecosystem>`.
-* Check out our {ref}`contributing guide <contribution-guide>` for development practices.
+* Check out our {ref}`contribution guide <contribution-guide>` for development practices.
 * Consider citing [Genome Biology (2018)] along with original {doc}`references <references>`.
 
 ## News
@@ -85,6 +85,6 @@ contributors
 references
 ```
 
-[discourse]: https://discourse.scverse.org/
+[contribution guide]: dev/index.md
 [genome biology (2018)]: https://doi.org/10.1186/s13059-017-1382-0
 [github]: https://github.com/scverse/scanpy

docs/installation.md

@@ -65,7 +65,7 @@ flit install -s --deps=develop
 On Windows, you might have to use `flit install --pth-file`
 if you are not able to give yourself the [create symbolic links] privilege.
 
-For instructions on how to work with the code, see the {ref}`contributing guide <contribution-guide>`.
+For instructions on how to work with the code, see the {ref}`contribution guide <contribution-guide>`.
 
 ## Docker