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:

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 - 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):

Database	Environment variable	Default connection URI
AnyVLM DB (for `PostgresObjectStore`)	`ANYVLM_TEST_STORAGE_URI`	`"postgresql://postgres:postgres@localhost:5432/anyvlm_test"`
AnyVar DB (for testing `PythonAnyVarClient`)	`ANYVLM_ANYVAR_TEST_STORAGE_URI`	`"postgresql://postgres:postgres@localhost:5432/anyvlm_anyvar_test"`

Note

Ensure that the databases and roles are available in the PostgreSQL instance.

For example, to support the connection string "postgresql://anyvlm_test_user:anyvlm_test_pw@localhost:5432/anyvlm_test_db", run:

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:

make test

Documentation

To build documentation, use the docs Makefile target from the project root directory:

make docs

HTML output is built in the subdirectory docs/build/html/.

The docs use Sphinx GitHub Changelog to automatically generate the 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.