add more stuff

jsstevenson · jsstevenson · commit a84c90887e79 · 2026-01-20T08:56:11.000-05:00
diff --git a/docs/source/_templates/module_summary.rst b/docs/source/_templates/module_summary.rst
@@ -0,0 +1,8 @@
+{{ fullname | underline }}
+
+.. automodule:: {{ fullname }}
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
+
diff --git a/docs/source/_templates/module_summary_no_inherit.rst b/docs/source/_templates/module_summary_no_inherit.rst
@@ -0,0 +1,9 @@
+{{ fullname | underline }}
+
+.. automodule:: {{ fullname }}
+   :members:
+   :no-inherited-members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config, metadata
+
diff --git a/docs/source/api/api/anyvar/anyvlm.anyvar.http_client.rst b/docs/source/api/api/anyvar/anyvlm.anyvar.http_client.rst
@@ -0,0 +1,8 @@
+﻿anyvlm.anyvar.http_client
+=========================
+
+.. automodule:: anyvlm.anyvar.http_client
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/api/api/anyvar/anyvlm.anyvar.python_client.rst b/docs/source/api/api/anyvar/anyvlm.anyvar.python_client.rst
@@ -0,0 +1,8 @@
+﻿anyvlm.anyvar.python_client
+===========================
+
+.. automodule:: anyvlm.anyvar.python_client
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/api/api/storage/anyvlm.storage.base_storage.rst b/docs/source/api/api/storage/anyvlm.storage.base_storage.rst
@@ -0,0 +1,9 @@
+﻿anyvlm.storage.base_storage
+===========================
+
+.. automodule:: anyvlm.storage.base_storage
+   :members:
+   :no-inherited-members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config, metadata
diff --git a/docs/source/api/api/storage/anyvlm.storage.mapper_registry.rst b/docs/source/api/api/storage/anyvlm.storage.mapper_registry.rst
@@ -0,0 +1,9 @@
+﻿anyvlm.storage.mapper_registry
+==============================
+
+.. automodule:: anyvlm.storage.mapper_registry
+   :members:
+   :no-inherited-members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config, metadata
diff --git a/docs/source/api/api/storage/anyvlm.storage.mappers.rst b/docs/source/api/api/storage/anyvlm.storage.mappers.rst
@@ -0,0 +1,9 @@
+﻿anyvlm.storage.mappers
+======================
+
+.. automodule:: anyvlm.storage.mappers
+   :members:
+   :no-inherited-members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config, metadata
diff --git a/docs/source/api/api/storage/anyvlm.storage.orm.rst b/docs/source/api/api/storage/anyvlm.storage.orm.rst
@@ -0,0 +1,9 @@
+﻿anyvlm.storage.orm
+==================
+
+.. automodule:: anyvlm.storage.orm
+   :members:
+   :no-inherited-members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config, metadata
diff --git a/docs/source/api/api/storage/anyvlm.storage.postgres.rst b/docs/source/api/api/storage/anyvlm.storage.postgres.rst
@@ -0,0 +1,9 @@
+﻿anyvlm.storage.postgres
+=======================
+
+.. automodule:: anyvlm.storage.postgres
+   :members:
+   :no-inherited-members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config, metadata
diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst
@@ -0,0 +1,29 @@
+.. _api_reference:
+
+API Reference
+!!!!!!!!!!!!!
+
+Storage
+=======
+
+.. autosummary::
+   :nosignatures:
+   :toctree: api/storage/
+   :template: module_summary_no_inherit.rst
+
+   anyvlm.storage.base_storage
+   anyvlm.storage.mapper_registry
+   anyvlm.storage.mappers
+   anyvlm.storage.orm
+   anyvlm.storage.postgres
+
+AnyVar Clients
+==============
+
+.. autosummary::
+   :nosignatures:
+   :toctree: api/anyvar/
+   :template: module_summary.rst
+
+   anyvlm.anyvar.http_client
+   anyvlm.anyvar.python_client
diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -0,0 +1,6 @@
+Changelog
+!!!!!!!!!
+
+.. changelog::
+    :changelog-url: https://anylm.readthedocs.io/en/stable/#changelog
+    :github: https://github.com/genomicmedlab/anyvlm/releases/
diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
@@ -20,17 +20,30 @@ 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"``.
+* **Configure test database** - tests currently make use of two distinct database connection URIs (though they technically could both point to the same place without much issue at present):
+
+.. list-table::
+   :header-rows: 1
+
+   * - Database
+     - Environment variable
+     - Default connection URI
+   * - AnyVLM DB (for :py:class:`~anyvlm.storage.postgres.PostgresObjectStore`)
+     - ``ANYVLM_TEST_STORAGE_URI``
+     - ``"postgresql://postgres:postgres@localhost:5432/anyvlm_test"``
+   * - AnyVar DB (for testing :py:class:`~anyvlm.anyvar.python_client.PythonAnyVarClient`)
+     - ``ANYVLM_ANYVAR_TEST_STORAGE_URI``
+     - ``"postgresql://postgres:postgres@localhost:5432/anyvlm_anyvar_test"``
 
 .. note::
 
-    Ensure that the database and role are available in the PostgreSQL instance.
+    Ensure that the databases and roles 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;"``
+    For example, to support the connection string ``"postgresql://anyvlm_test_user:anyvlm_test_pw@localhost:5432/anyvlm_test_db"``, run:
 
-* **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.
+    .. code-block::
 
-.. TODO fix celery reference above
+       psql -U postgres -C "CREATE USER anyvlm_test_user WITH PASSWORD anyvlm_test_pw; CREATE DATABASE anyvlm_test_db WITH OWNER anyvlm_test_user;"``
 
 Tests are invoked with the ``pytest`` command. The project Makefile includes an easy shortcut:
 
diff --git a/docs/source/features.rst b/docs/source/features.rst
@@ -0,0 +1,12 @@
+AnyVLM Features
+!!!!!!!!!!!!!!!
+
+Variant-Level Matching (VLM) Protocol
+=====================================
+
+TODO
+
+Cohort Allele Frequency (CAF) Retrieval
+=======================================
+
+TODO
diff --git a/docs/source/getting_started/docker_compose.rst b/docs/source/getting_started/docker_compose.rst
@@ -0,0 +1,44 @@
+Quick Setup: Docker Compose
+!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+Prerequisites
+=============
+
+* `Docker Compose <https://docs.docker.com/compose/install/>`_
+
+Steps
+=====
+
+Clone the AnyVLM repository (optionally switching to a release tag), and enter the directory:
+
+.. code-block:: console
+
+   % git clone https://github.com/genomicmedlab/anyvlm
+   % cd anyvlm
+
+Create all required volumes:
+
+TODO fix this
+
+.. code-block:: bash
+
+   % docker volume create seqrepo_vol
+   % docker volume create uta_vol
+   % docker volume create anyvar_vol
+
+Then, launch the application:
+
+.. code-block:: console
+
+   % docker compose up
+
+This will:
+
+TODO clean this up
+
+* pull the necessary images,
+* start SeqRepo (or use your local SeqRepo if configured),
+* start UTA and AnyVar’s PostgreSQL database,
+* and launch AnyVar REST service.
+
+Once the containers are running, visit `http://127.0.0.1:8010/docs <http://127.0.0.1:8010/docs>`_ to view the interactive Swagger UI and confirm the service is responding.
diff --git a/docs/source/getting_started/index.rst b/docs/source/getting_started/index.rst
@@ -0,0 +1,10 @@
+Getting Started
+!!!!!!!!!!!!!!!
+
+TODO fill in description/links
+
+.. toctree::
+    :maxdepth: 2
+    :hidden:
+
+    Quick Start: Docker Compose <docker_compose>
diff --git a/docs/source/help.rst b/docs/source/help.rst
@@ -0,0 +1,10 @@
+Getting Help
+!!!!!!!!!!!!
+
+If you run into an issue, have an idea, or just need guidance using AnyVLM, we’re happy to help. Please choose the most appropriate channel so we can respond efficiently:
+
+* `Report a bug <https://github.com/genomicmedlab/anyvlm/issues/new?template=bug-report.yaml>`_
+* `Request a new feature <https://github.com/genomicmedlab/anyvlm/issues/new?template=feature-request.yaml>`_
+* `Ask a question (how-to, usage, clarifications) <https://github.com/genomicmedlab/anyvlm/discussions/new?category=q-a>`_
+
+Each link opens a pre-filled template to help you provide the details we need.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -10,8 +10,8 @@ AnyVLM
    Features<features>
    Usage<usage>
    Configuration<configuration/index>
-   API Reference<api_reference/index>
-   Getting Help<getting_help>
+   API Reference<api/index>
+   Getting Help<help>
    Changelog<changelog>
    Contributing<contributing>
    License<license>
diff --git a/docs/source/license.rst b/docs/source/license.rst
@@ -0,0 +1,4 @@
+License
+!!!!!!!
+
+.. literalinclude:: ../../LICENSE
diff --git a/docs/source/usage.rst b/docs/source/usage.rst
@@ -0,0 +1,14 @@
+Usage
+!!!!!
+
+Submitting VCFs
+===============
+
+
+TODO
+
+Retrieving CAFs
+===============
+
+
+TODO
