use pytest to manage docker container startup for tests

[d-v-b]

This change declares the minio and mysql docker services as pytest fixtures, which allows running the test suite without invoking docker-compose.

It also declares a test dependency group in pyproject.toml, so that tests can be run with uv sync --group test && pytest tests

[d-v-b]

@dimitri-yatsenko have a look. some tests are failing, which means the services are not exactly configured correctly, but I think this is a promising workflow

[Copilot]

Pull Request Overview

This PR refactors the test infrastructure to use pytest fixtures for managing Docker containers (MySQL and MinIO) instead of relying on docker-compose. This enables running tests with a simpler uv sync --group test && pytest tests command and provides better container lifecycle management within the pytest framework.

Key changes:

• Replace docker-compose based test execution with pytest-managed Docker containers
• Add comprehensive Docker container management with proper cleanup mechanisms
• Update test dependencies to use new dependency groups format

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
tests/conftest.py	Adds Docker container fixtures for MySQL and MinIO with lifecycle management
tests/test_json.py	Converts module-level MySQL version check to pytest fixture
src/datajoint/settings.py	Adds support for DJ_PORT environment variable configuration
pyproject.toml	Updates dependency structure and adds test dependencies
docker-compose.yaml	Updates comments to reflect new pytest-based testing approach
.github/workflows/test.yaml	Simplifies CI workflow to use pytest instead of docker-compose

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[d-v-b]

The graphviz dependency is outside of what pypi can provide, so I brought in pixi to declare that dependency from conda-forge. All tests are passing for me locally now.

You can try this with

pixi run -e test pytest tests

To see the logs related to the standup / shutdown of the docker container images, run

pixi run -e test pytest tests/ --log-cli-level INFO

[d-v-b]

@dimitri-yatsenko it would be great to get tests running as part of CI. Should I open a new ticket for this?