Setup instructions in CONTRIBUTING.md fail with ModuleNotFoundError: pytest_cases on fresh clone

[Stu-ops]

Description:

When following the setup instructions in CONTRIBUTING.md for a fresh clone of the repository, running poetry install --extras dev results in a failure due to a missing pytest_cases module. This prevents contributors from setting up their development environment correctly.

Steps to Reproduce:

1. Clone the repository: git clone https://github.com/malariagen/malariagen-data-python.git
2. Navigate to the directory: cd malariagen-data-python
3. Run poetry install --extras dev as per CONTRIBUTING.md instructions.
4. Observe the error: ModuleNotFoundError: No module named 'pytest_cases'

Expected Behavior:

• poetry install --extras dev should complete successfully, installing all required dependencies including dev tools like pytest-cases.

Actual Behavior:

• Installation fails with the above error, halting the setup process.

Root Cause:

• Although pytest-cases is declared in [tool.poetry.extras] dev, Poetry's extras mechanism may not be resolving or locking the dependency correctly in all cases. Additionally, Poetry has deprecated extras in favor of dependency-groups for better dependency management. The project should migrate to dependency-groups to ensure reliable installation of dev dependencies.

Environment:

• Python version: 3.10+ (as per pyproject.toml)
• Poetry version: Latest (dependency-groups require Poetry 1.2+)
• OS: Any (reproducible on Windows, likely others)

Additional Context:

• This issue blocks new contributors from contributing, as they cannot run tests or set up the dev environment.
• The package pytest-cases is used for separating test code from test cases in pytest, and is essential for running the test suite.
• CONTRIBUTING.md currently uses --extras dev, but modern Poetry recommends --with dev for dependency-groups.

[NayerBasim]

Hi, I’d like to work on this issue if that’s okay.

I can open a PR to:
migrate dev tooling from tool.poetry.extras to tool.poetry.group.dev.dependencies,
update setup docs from poetry install --extras dev to poetry install --with dev,
and update CI setup to use --with dev as well.
Please let me know if this approach is acceptable, otherwise I’m happy to adjust.

[khushthecoder]

Hi @jonbrenas

Why this issue matters:

Currently,

CONTRIBUTING.md
instructs new contributors to run poetry install --extras dev, but the dev dependencies in
pyproject.toml
are not properly modeled as optional extras — they're listed as regular dependencies under [tool.poetry.dependencies] without optional = true. This means --extras dev doesn't reliably install packages like pytest-cases, leading to ModuleNotFoundError: pytest_cases on fresh clones. This is a barrier for anyone trying to contribute for the first time.

Impact on the project:

New contributors following the setup guide hit an immediate ModuleNotFoundError and may assume the project is broken or abandon their contribution attempt.
CI reliability is at risk since the same --extras dev command is used in
.github/actions/setup-python/action.yaml
, making all workflows (tests, linting, coverage, docs, notebooks) potentially fragile across Poetry version updates.
Dev tools are incorrectly modeled as runtime dependencies, which means pip install malariagen_data pulls in pytest, sphinx, ruff, etc. — packages that end users should never need.

Myapproach:

We migrated the dev/test/docs tooling from [tool.poetry.extras] to proper Poetry dependency groups (the recommended pattern since Poetry 1.2):

[tool.poetry.group.test.dependencies] — pytest, pytest-cases, pytest-mock, pytest-xdist, pytest-cov
[tool.poetry.group.dev.dependencies] — pre-commit, ruff, mypy, memory-profiler, snakeviz, notebook, jupyterlab
[tool.poetry.group.docs.dependencies] — sphinx, pydata-sphinx-theme, sphinx_design, pandas-stubs
Updated the CI action and

CONTRIBUTING.md
to use poetry install --with dev,test,docs. Verified locally that all imports (pytest_cases, pytest, sphinx, ruff) work correctly after a clean install.

I've opened PR #1136 with these changes — would appreciate your review when you get a chance!