On this branch, I made changes related to Docker, environment variables, and testing. ### Main changes - **Environment variable-based configuration**: I updated the server to use Pydantic's `pydantic-settings` package (documented [here](https://docs.pydantic.dev/latest/concepts/pydantic_settings/#the-basics), and also used by `microbiomedata/nmdc-server`) to get the MongoDB connection parameters from environment variables. The precedence order (from highest to lowest) is: OS, `.env` file, class attribute defaults. Fixes #53. - **Example `.env` file**: I included an example `.env` file named `.env.example` and instructions on creating one's own `.env` file. Here's an example `.env` file: ```ini MONGO_HOST=mongo MONGO_PORT=27017 MONGO_DATABASE=bertron MONGO_USERNAME=admin MONGO_PASSWORD=root ``` - **Name of test database**: I added a pytest fixture that automatically sets the test database name in the context of all tests, overriding whatever the user might have in their `.env` file. The test database is always named `bertron_test` (we can make this, too, be read from an environment variable in a future PR). As a protective measure, tests will not run if the non-test database is also named `bertron_test`. - **New test**: I added a test that involves accessing the MongoDB database. Previously, no tests did this. Fixes #75. ### Tangential changes - **Fix bug involving silent failures**: I fixed a bug in the GitHub Actions workflow, where the status code returned by the `test` container was not being propagated to the `docker compose` command, itself. With that bug in place, even if a test had failed, the GHA step would have succeeded. Now, GHA "sees" that status code, so the step fails when a test fails. - **Speed up container image builds**: I created a `.dockerignore` file so Docker omits some unnecessary directories from the container image it builds. I did this while working on the GHA workflow (see next bullet point). - **Avoiding `.venv/` collisions between host and container**: I updated the GHA workflow to run the tests in the `test` container only, instead of also running them locally. That eliminated the need to handle collisions between the `.venv/` directory created by the containers and the one the local `uv` program tries to create. This can be un-done, in case team members want the GHA workflow to also run the tests locally. Note: Previously, the "run tests locally" step was only running tests defined in the top-level `tests/` directory, which was only the "hello world" test. - **Preventing redundant GHA workflow runs**: Previously, whenever someone would add a commit to a PR, the CI GHA workflow would run twice—once, because a PR was being updated, and again, because a commit was being pushed to any branch. Now, whenever someone adds a commit to a PR, the CI GHA workflow will only run once. --------- Co-authored-by: eecavanna <eecavanna@users.noreply.github.com>

Update FastAPI application obtain MongoDB credentials from environment (not hard-coded) #53

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