add more docs stuff

Author: jsstevenson

README.md

@@ -1 +1,30 @@
-# AnyVLM
+# *AnyVLM* - Lightweight, Portable Variant-Level Matching
+
+AnyVLM is a Python-based web service that supports the [GA4GH Variant-Level Matching (VLM) Protocol](https://www.ga4gh.org/what-we-do/ga4gh-implementation-forum/federated-variant-level-matching-vlm-project/). It is designed to be dependency-light and trivial to stand up in environments ranging from local development to modern cloud platforms. AnyVLM provides a minimal VLM implementation suitable for institutions interested in adding their data to a federated knowledge network.
+
+## Information
+
+[![rtd](https://img.shields.io/badge/docs-readthedocs-green.svg)](http://anyvlm.readthedocs.io/) [![changelog](https://img.shields.io/badge/docs-changelog-green.svg)](https://anyvlm.readthedocs.io/en/latest/changelog.html) [![GitHub license](https://img.shields.io/github/license/genomicmedlab/anyvlm.svg)](https://github.com/genomicmedlab/anyvlm/blob/main/LICENSE) [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.18249699-blue)](https://doi.org/10.5281/zenodo.18249699)
+
+## Latest Release
+
+[![GitHub tag](https://img.shields.io/github/tag/genomicmedlab/anyvlm.svg)](https://github.com/genomicmedlab/anyvlm) [![pypi_rel](https://img.shields.io/pypi/v/genomicmedlab.anyvlm.svg)](https://pypi.org/project/genomicmedlab.anyvlm/)
+
+## Development
+
+[![action status](https://github.com/genomicmedlab/anyvlm/actions/workflows/python-package.yml/badge.svg)](https://github.com/genomicmedlab/anyvlm/actions/workflows/python-cqa.yml) [![issues](https://img.shields.io/github/issues-raw/genomicmedlab/anyvlm.svg)](https://github.com/genomicmedlab/anyvlm/issues) [![GitHub Open Pull Requests](https://img.shields.io/github/issues-pr/genomicmedlab/anyvlm.svg)](https://github.com/genomicmedlab/anyvlm/pull/) [![GitHub Contributors](https://img.shields.io/github/contributors/genomicmedlab/anyvlm.svg)](https://github.com/genomicmedlab/anyvlm/graphs/contributors/) [![GitHub stars](https://img.shields.io/github/stars/genomicmedlab/anyvlm.svg?style=social&label=Stars)](https://github.com/genomicmedlab/anyvlm/stargazers) [![GitHub forks](https://img.shields.io/github/forks/genomicmedlab/anyvlm.svg?style=social&label=Forks)](https://github.com/genomicmedlab/anyvlm/forks)
+
+## Installation
+
+A set of Docker Compose resources are provided as part of the AnyVLM project. See the [Docker-based installation instructions](https://anyvlm.readthedocs.org/en/stable/getting_started/docker_compose.html).
+
+## Examples
+
+Populate the DB TODO
+
+Make a request TODO
+
+
+## Feedback and contributing
+
+We welcome [bug reports](https://github.com/genomicmedlab/anyvlm/issues/new?template=bug-report.md), [feature requests](https://github.com/genomicmedlab/anyvlm/issues/new?template=feature-request.md), and code contributions from users and interested collaborators. The [documentation](https://anyvlm.readthedocs.io/en/latest/contributing.html) contains guidance for submitting feedback and contributing new code.

docs/source/contributing.rst

@@ -0,0 +1,52 @@
+Contributing to AnyVLM
+!!!!!!!!!!!!!!!!!!!!!!
+
+Installing For Development
+==========================
+
+Clone and enter the repo, use the ``devready`` Makefile target to set up a virtual environment, then activate it and install pre-commit hooks:
+
+.. code-block:: shell
+
+    git clone https://github.com/genomicmedlab/anyvlm.git
+    cd anyvlm
+    make devready
+    source venv/3.11/bin/activate
+    pre-commit install
+
+Testing
+=======
+
+Some configuration is required to run tests:
+
+* **Install test dependencies** - in your AnyVLM environment, ensure that the ``test`` dependency group is available by running ``make testready`` in the root directory.
+* **Configure test database** - unit and integration tests will set up a storage instance using the connection string defined by the environment variable ``ANYVLM_TEST_STORAGE_URI`` (not ``ANYVLM_STORAGE_URI``!), which defaults to ``"postgresql://postgres:postgres@localhost:5432/anyvlm_test"``.
+
+.. note::
+
+    Ensure that the database and role are available in the PostgreSQL instance.
+
+    For example, to support the connection string ``"postgresql://anyvar_test_user:anyvar_test_pw@localhost:5432/anyvar_test_db"``, run ``psql -U postgres -C "CREATE USER anyvar_test_user WITH PASSWORD anyvar_test_pw; CREATE DATABASE anyvar_test_db WITH OWNER anyvar_test_user;"``
+
+* **Ensure Celery backend and broker are available, and that Celery workers are NOT running** - the task queueing tests create and manage their own Celery workers, but they do require access to a broker/backend for message transport and result storage. See `async task queuing setup instructions <todo>`_ for more. If an existing AnyVar Celery worker is running, they may not function properly.
+
+.. TODO fix celery reference above
+
+Tests are invoked with the ``pytest`` command. The project Makefile includes an easy shortcut:
+
+.. code-block:: shell
+
+   make test
+
+Documentation
+=============
+
+To build documentation, use the ``docs`` Makefile target from the project root directory:
+
+.. code-block::
+
+   make docs
+
+HTML output is built in the subdirectory ``docs/build/html/``.
+
+The docs use `Sphinx GitHub Changelog <https://github.com/ewjoachim/sphinx-github-changelog>`_ to automatically generate the :doc:`changelog <changelog>` page. A GitHub API token must be provided for the Sphinx build process to fetch GitHub release history and generate this page. If not provided, an error will be logged during the build and the page will be blank.

docs/source/index.rst

@@ -6,4 +6,12 @@ AnyVLM
    :caption: Contents
    :hidden:
 
+   Getting Started<getting_started/index>
+   Features<features>
+   Usage<usage>
    Configuration<configuration/index>
+   API Reference<api_reference/index>
+   Getting Help<getting_help>
+   Changelog<changelog>
+   Contributing<contributing>
+   License<license>