Contribution guide
Maintaining a repository is a lot of work and it is only possible with the input for its users. That's why we love to get your feedback and continuously improve! We want to contibuting to this project as easy and transparent as possible. That's why we ask all contributions to go through a GitHub workflow.
Ask a question, report a bug, or suggest new features
Wether you wish to report a bug, discuss the current state of the code, how to use it, or propose new features, the GitHub repository is the place to start.
Go to 'Issues' in the repository's menu and use the search bar to look for your issue/question, maybe the discussion already exists! if you don't find what you are looking for, use the green button 'New Issue' and select the correct template (Question, Bug report or New feature).
Bug reports
Solving Bugs is not always easy and usually requires to be able to precisely understand what happened. Try to include the following in your report, so we can solve the problems quickly:
- A quick summary and/or background
- The software versions
- A precise description of the problem
- Join input data that reproduce the problem if possible
- Attach relevant log files to the issue
Improving the documentation
Writting a documentation is a big task and we are gratefull for any help to expand and improve it.
If you find a specific section of the documentaiton unclear, or would like to see it in other languages, we would love to hear about it, or if you feel like it, try suggesting modifications.
Writting tests
The critical parts of the workflow are currently verified by unit tests.
These could always be improved and/or expanded. If you like to write tests,
check the .tests/unit folder and suggest changes.
Submitting changes
All changes in the repository are made through pull requests.
Github worflow
To submitt a pull request:
- Fork the repository and create your branch from
main - Make your changes to the code base/documentation/tests
- If you have added code that shoul dbe testes, add tests
- If you have changed the parameters or formating of the inputs, update the documentation
- Ensure that your code passes the tests and lints, this will be automatically tested when you submit your pull request
- Issue your pull request and wait for a maintainer to review the changes
Please provide precise and sufficient information on the changes you performed when you submit your pull request.
Tests
It is a good idea to locally run tests before submitting your pull request.
Unit tests
We use pytest for running unit tests. Make sure your current environment supports a recent version of python (3.9 or 3.10).
python -m pip install --upgrade pip
pip install pytest
pip install -r .tests/unit/requirements.txt # Install tests dependencies
pytest .tests/unit
Integration test
It is always a good idea to verify that the workflow runs properly as a whole. For this activate a conda enviroment with a recent version of snakemake (see the documentation) and run the following test:
License
By submitting changes to this repository, you agree that your contributions will be licensed under its BSD-3 Clauses License.