Merge pull request #39 from scverse/kevinyamauchi-patch-1

update readme and docs

Author: LucaMarconato

README.md

@@ -1,13 +1,21 @@
-# spatialdata-io
+![SpatialData banner](https://github.com/scverse/spatialdata/blob/main/docs/_static/img/spatialdata_horizontal.png?raw=true)
+
+# spatialdata-io: convenient readers for loading common formats into SpatialData
 
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
 
-[badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml/badge.svg
-[link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml
+[badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test_and_deploy.yaml/badge.svg
+[link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test_and_deploy.yaml
 [badge-docs]: https://img.shields.io/readthedocs/spatialdata-io
 
-SpatialData IO for common technologies.
+This package contains reader functions to load common spatial omics formats into SpatialData. Currently, we provide support for:
+
+-   NanoString CosMx
+-   MCMICRO
+-   Steinbock
+-   10x Genomics Visium
+-   10x Genomics Xenium
 
 ## Getting started
 
@@ -22,32 +30,26 @@ Python installed, we recommend installing [Miniconda](https://docs.conda.io/en/l
 
 There are several alternative options to install spatialdata-io:
 
-<!--
-1) Install the latest release of `spatialdata-io` from `PyPI <https://pypi.org/project/spatialdata-io/>`_:
+1. Install the latest release of `spatialdata-io` from [PyPI](https://pypi.org/project/spatialdata-io/):
 
 ```bash
 pip install spatialdata-io
 ```
--->
 
-1. Install the latest development version:
+2. Install the latest development version:
 
 ```bash
 pip install git+https://github.com/scverse/spatialdata-io.git@main
 ```
 
-## Release notes
-
-See the [changelog][changelog].
-
 ## Contact
 
 For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
 If you found a bug, please use the [issue tracker][issue-tracker].
 
 ## Citation
 
-> t.b.a
+[L Marconato*, G Palla*, KA Yamauchi*, I Virshup*, E Heidari, T Treis, M Toth, R Shrestha, H Vöhringer, W Huber, M Gerstung, J Moore, FJ Theis, O Stegle, bioRxiv, 2023](https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1). \* = equal contribution
 
 [scverse-discourse]: https://discourse.scverse.org/
 [issue-tracker]: https://github.com/scverse/spatialdata-io/issues

docs/template_usage.md

@@ -1,4 +1,4 @@
-# Using this template
+# Developer guide
 
 Welcome to the developer guidelines! This document is split into two parts: