adds documentation setup and skeleton

README.md

@@ -31,6 +31,7 @@ Use [Black](https://black.readthedocs.io/en/stable/).
 
 ## Testing
 ```shell
+pip install -r requirements-dev.txt
 pytest
 ```
 
@@ -51,4 +52,18 @@ python manage.py runserver
 ```
 
 ## Deployment
-TODO
+TODO
+
+## Documentation
+There is an [mkdocs](https://www.mkdocs.org/) based documentation pack in the `docs/` folder
+configured by `mkdocs.yml`.
+This is suitable for serving on [ReadTheDocs](https://readthedocs.org/).
+
+To develop documentation:
+```shell
+pip install -r requirements-docs.txt
+mkdocs serve
+```
+and edit the Markdown files in `docs/*.md`.
+
+If you add a new file (page), add it to the navigation by editing the `nav` field of `mkdocs.yml`.

docs/api.md

@@ -0,0 +1 @@
+# API for programmatic access

docs/data.md

@@ -0,0 +1,15 @@
+# Datasets
+
+## ENA Projects
+
+## ENA Samples
+
+## ENA Checklist Metadata
+
+## Biosamples Metadata
+
+## MGnify: Metagenomics
+
+## MetaboLights: Metabolomics
+
+## Summary analyses

docs/index.md

@@ -0,0 +1,13 @@
+# HoloFood Data Portal - Documentation
+
+## Holofood Data Portal
+The database and website to present [Holofood](https://www.holofood.eu) samples,
+and unify the datasets stored in supporting services.
+
+## Background
+HoloFood is a consortium and project focussed on understanding the biomolecular 
+and physiological processes  triggered by incorporating feed additives and novel
+sustainable feeds in farmed animals.
+
+The data portal is a public website and API for browsing the Samples and datasets
+created by the project, which are stored in publicly-accessible data repositories. 

docs/partners.md

@@ -0,0 +1,7 @@
+# Admin access for HoloFood partners
+
+## Managing the database
+
+## Authoring new Summary Analysis documents
+
+## Editing and publishing Summary Analysis documents

docs/website.md

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+# Browsing the website
+
+## Finding Samples
+
+## Downloading sample lists and metadata
+
+## Finding analysis summaries

mkdocs.yml

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+site_name: HoloFood Data Portal Documentation
+repo_url: https://github.com/EBI-Metagenomics/holofood-database/
+site_description: Documentation for the HoloFood Data Portal – a hub for accessing datasets and samples creating by the HoloFood Project
+site_author: HoloFood Consortium
+
+theme:
+    name: readthedocs
+    highlightjs: true
+
+nav:
+    - 'index.md'
+    - 'data.md'
+    - 'website.md'
+    - 'api.md'
+    - 'partners.md'

requirements-docs.txt

@@ -0,0 +1 @@
+mkdocs==1.3.0