Reorganize README content (#1314)

* Readd newline required for rendering of code block

* Remove DOI badge

* Moving existing README to docs

* Add new README

* Add align=center attribute to README header

Author: matt-graham

README.md

@@ -0,0 +1,60 @@
+<div style="text-align: center" align="center">
+<img src="docs/thanzi-la-onse.png" alt="Thanzi La Onze" />
+<br />
+<h1>Thanzi la Onse model</h1>
+</div>
+
+[![License][license-badge]](./LICENSE.txt)
+[![DOI][doi-badge]][doi-link]
+[![Tests status][tests-badge]][tests-link]
+[![Checks status][checks-badge]][checks-link]
+[![Documentation status][documentation-badge]][documentation-link]
+
+The __Thanzi la Onse model (TLOmodel)__ is a part of the [Thanzi la Onse][thanzi-link]
+(Health for All) Collaboration. Our fundamental aim is to develop the use of epidemiological and economic science to effect a step-change in the way that health priorities are addressed through policy interventions in low-income countries. We are doing this by developing a model that represents explicitly the generation of health gains in a population, which can be used to examine the effect of resource allocation, management and clinical practice, in order to contribute to informing decision-making.
+
+- __Documentation__: <https://www.tlomodel.org>
+- __Getting started__: <https://www.tlomodel.org/getting_started.html>
+- __Contributing__: <https://www.tlomodel.org/contributing.html>
+- __Bug reports__: <https://github.com/UCL/TLOmodel/issues>
+- __Wiki__: <https://github.com/UCL/TLOmodel/wiki>
+
+## Project team
+
+TLOmodel is developed in a collaboration between:
+
+- [Kamuzu University of Health Sciences][kuhes-link]
+- [MRC Centre for Global Infectioous Disease Analysis][mrc-gida-link], [Imperial College London][imperial-link]
+- [Institute for Global Health][igh-link], [University College London][ucl-link]
+- [Centre for Advanced Research Computing][arc-link], [University College London][ucl-link]
+- [Centre for Health Economics][che-link], [University of York][york-link]
+
+It benefits from a close partnership between this team and the Ministry of Health, Malawi.
+
+A [full list of contributors][contributors-link] is available 
+in the documentation.
+
+## Acknowledgements
+
+This work has been funded by grants from [Wellcome](https://wellcome.org/),
+[GCRF](https://www.newton-gcrf.org/) and [UKRI](https://www.ukri.org/).
+ 
+[tests-badge]: https://github.com/UCL/TLOmodel/actions/workflows/tests.yml/badge.svg
+[tests-link]: https://github.com/UCL/TLOmodel/actions/workflows/tests.yml
+[checks-badge]: https://github.com/UCL/TLOmodel/actions/workflows/checks.yml/badge.svg
+[checks-link]: https://github.com/UCL/TLOmodel/actions/workflows/checks.yml
+[documentation-badge]: https://github.com/UCL/TLOmodel/actions/workflows/docs.yml/badge.svg
+[documentation-link]: https://github.com/UCL/TLOmodel/actions/workflows/docs.yml
+[license-badge]: https://img.shields.io/badge/License-MIT-blue.svg
+[doi-badge]: https://zenodo.org/badge/DOI/10.5281/zenodo.10144015.svg
+[doi-link]: https://doi.org/10.5281/zenodo.10144015
+[thanzi-link]: https://thanzi.org
+[kuhes-link]: https://www.kuhes.ac.mw/
+[imperial-link]: https://www.imperial.ac.uk
+[mrc-gida-link]: https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis
+[ucl-link]: https://www.ucl.ac.uk
+[igh-link]: https://www.ucl.ac.uk/global-health/
+[arc-link]: https://www.ucl.ac.uk/arc
+[york-link]: https://www.york.ac.uk/
+[che-link]: https://www.york.ac.uk/che/
+[contributors-link]: https://www.tlomodel.org/contributors.html

README.rst docs/getting_started.rst

@@ -1,6 +1,3 @@
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.10144015.svg
-  :target: https://zenodo.org/doi/10.5281/zenodo.10144015
-
 =====================
 Getting Started
 =====================
@@ -21,6 +18,7 @@ Please use the `Installation Guide <https://github.com/UCL/TLOmodel/wiki/Install
 you prefer, you can carry out the setup using the command line:
 
 ::
+
     cd TLOmodel
     conda create -n tlo python=3.11
     conda activate tlo

docs/index.rst

@@ -48,7 +48,7 @@ Contents
    aims
    writeups
    data_sources
-   readme
+   getting_started
    azure_batch
    reference/index
    resources/index

docs/readme.rst

@@ -40,7 +40,7 @@ dependencies = [
 description = "Thanzi la Onse Epidemiology Model"
 dynamic = ["version"]
 license = {file = "LICENSE.txt"}
-readme = "README.rst"
+readme = "README.md"
 requires-python = ">=3.8"
 
 [project.optional-dependencies]