fix readme

Author: tristanpwdennis

README.md

@@ -1,15 +1,89 @@
-# Curation metadata
+# `malariagen_data` - analyse MalariaGEN data from Python
 
-Summary statistics used during our sequence QC process are available within each sample set subdirectory, in a file named "sequence_qc_stats.csv". Each file contains the following fields:
+This Python package provides methods for accessing and analysing data from MalariaGEN.
 
-- `sample_id` (string) - MalariaGEN sample identifier
-- `mean_cov` (float) - mean coverage
-- `median_cov` (int) - median coverage
-- `modal_cov` (int) - modal coverage
-- `mean_cov_{contig}` (float) - mean coverage for a particular contig
-- `median_cov_{contig}` (int) - median coverage for a particular contig
-- `mode_cov_{contig}` (int) - modal coverage for a particular contig
-- `frac_gen_cov` (float) - fraction of the genome covered
-- `divergence` (float) - divergence
+## Installation
 
-For further information or queries contact support@malariagen.net.
+The `malariagen_data` Python package is available from the Python
+package index (PyPI) and can be installed via `pip`, e.g.:
+
+```bash
+pip install malariagen-data
+```
+
+## Documentation
+
+Documentation of classes and methods in the public API are available
+from the following locations:
+
+-   [Ag3 API
+    docs](https://malariagen.github.io/malariagen-data-python/latest/Ag3.html)
+
+-   [Af1 API
+    docs](https://malariagen.github.io/malariagen-data-python/latest/Af1.html)
+
+-   [Amin1 API
+    docs](https://malariagen.github.io/malariagen-data-python/latest/Amin1.html)
+
+-  [Adir1 API
+    docs](https://malariagen.github.io/malariagen-data-python/latest/Adir1.html)
+
+-   [Pf8 API
+    docs](https://malariagen.github.io/parasite-data/pf8/api.html)
+
+-   [Pf7 API
+    docs](https://malariagen.github.io/parasite-data/pf7/api.html)
+
+-   [Pv4 API
+    docs](https://malariagen.github.io/parasite-data/pv4/api.html)
+
+## Release notes (change log)
+
+See [GitHub releases](https://github.com/malariagen/malariagen-data-python/releases)
+for release notes.
+
+## Developer setup
+
+To get setup for development, see [this video if you prefer VS Code](https://youtu.be/zddl3n1DCFM), or [this older video if you prefer PyCharm](https://youtu.be/QniQi-Hoo9A).
+
+For detailed setup instructions, see:
+- [Linux setup guide](LINUX_SETUP.md)
+- [macOS setup guide](MACOS_SETUP.md)
+- [Windows setup guide](WINDOWS_SETUP.md)
+- [Google Colab (TPU) setup guide](docs/source/colab_tpu_runtime.rst)
+Detailed instructions can be found in the [Contributors guide](https://github.com/malariagen/malariagen-data-python/blob/master/CONTRIBUTING.md).
+
+## AI use policy and guidelines
+
+See [AI use policy and guidelines](https://github.com/malariagen/malariagen-data-python/blob/master/AI-POLICY.md) for more details.
+
+## Release process
+
+Create a new GitHub release. That's it. This will automatically
+trigger publishing of a new release to PyPI and a new version of
+the documentation via GitHub Actions.
+
+The version switcher for the documentation can then be updated by
+modifying the `docs/source/_static/switcher.json` file accordingly.
+
+## Citation
+
+If you use the `malariagen_data` package in a publication
+or include any of its functions or code in other materials (_e.g._ training resources),
+please cite: [doi.org/10.5281/zenodo.11173411](https://doi.org/10.5281/zenodo.11173411)
+
+Some functions may require additional citations to acknowledge specific contributions. These are indicated in the description for each relevant function.
+
+For any questions, please feel free to contact us at: [support@malariagen.net](mailto:support@malariagen.net)
+
+
+## Sponsorship
+
+This project is currently supported by the following grants:
+
+* [BMGF INV-068808](https://www.gatesfoundation.org/about/committed-grants/2024/04/inv-068808)
+* [BMGF INV-062921](https://www.gatesfoundation.org/about/committed-grants/2024/07/inv-062921)
+
+This project was previously supported by the following grants:
+
+* [BMGF INV-001927](https://www.gatesfoundation.org/about/committed-grants/2019/11/inv001927)