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Contribute to This Plugin

Structure of this repository

The software is located inside src/nomad_eosc_galaxy_actions, with unit tests in tests, standalone scripts (not part of the installed package) in scripts, and the Galaxy-team-facing demo in examples/galaxy_demo.

Setup

Requires Python 3.10+. We recommend uv, an extremely fast Python package and project manager; a more classical venv/pip approach works too.

uv venv

python3 -m venv .venv
. .venv/bin/activate

Development installation

git clone https://github.com/FAIRmat-NFDI/nomad-eosc-galaxy-actions.git
cd nomad-eosc-galaxy-actions

Install the package in editable mode, together with its dev dependencies:

uv pip install -e ".[dev]"

pip install --upgrade pip
pip install -e ".[dev]"

Linting, formatting, and pre-commit hooks

We use Ruff for linting/formatting and mypy for type checking, run via pre-commit:

pre-commit install          # installs the git hook, once per clone
pre-commit run --all-files  # run all hooks against the whole repo once

You can also run Ruff directly:

ruff check .
ruff format . --check

In the pre-commit as well as in the GitHub CI, we use cspell for spellchecking. If cspell flags a real (correctly spelled) word, add it to .cspell/custom-dictionary.txt through this script:

scripts/generate_custom_dict.sh

Testing

Unit tests are written with pytest:

pytest -sv tests

The Galaxy round trip itself isn't exercised by the unit test suite — it needs a real Galaxy account. scripts/test_galaxy_roundtrip.py covers that separately; see the tutorial.

Contributing on GitHub

Commit your changes on a separate branch and open a pull request. CI checks linting, runs the tests, and builds the docs; once those pass and a review happens, the PR can be merged. Before releasing, keep the version in sync between pyproject.toml and CITATION.cff — publish.yml's cff-version-check job fails the release otherwise.

Changing something in docs/? See How-to guides > Contribute to the Documentation for the writing conventions, how to build the docs locally, and how to add a new page.

Developing this plugin as part of NOMAD

If you're working on this plugin's NOMAD integration (the Action, the trigger entry schema) rather than just galaxy_client.py in isolation, use nomad-distro-dev, FAIRmat's development environment for NOMAD and its plugins. See How-to guides > Install this Plugin for how this repo is wired into that workspace.

Troubleshooting

If you hit an issue with the plugin or with setting up the development environment, open a GitHub issue.