contributing.rst

Contributing

Preparing environment

If you don't have Git installed on your system, follow these instructions.

Fork the main repository. Clone your fork (replace <username> with your GitHub account name) and change directory:

git clone git@github.com:<username>/RNAnorm.git
cd RNAnorm

Install the project for development:

pip install -e '.[docs,package,test]'

Note

We recommend using venv to create an isolated Python environment.

Ensuring reproducibility

Project package dependencies should be defined in pyproject.toml. Recommended is specifying a minimal version with some ability to update, i.e. using a tilde requirement (e.g., pandas~=1.4.2).

Running tests

Run unit tests and linters:

pytest --verbose --cov=rnanorm
black --check src tests
flake8 src tests
pydocstyle src
isort --check-only --diff src tests

To run the tests with Tox, use:

tox -r

Building documentation

sphinx-build docs build/sphinx

Preparing release

Describe the new features in changelog.rst. Replace the Unreleased heading with the new version, followed by the release date (e.g., 13.2.0 - 2018-10-23).

Add the new dependencies to pyproject.toml and update the package version. Use semantic versioning.

Commit changes to Git:

git commit -a -m "Prepare release <new-version>"

Push changes to your fork and open a pull request:

git push --set-upstream <RNAnorm-fork-name> release-<new-version>

Wait for tests to pass and pull request to be approved. Merge code to main:

git checkout main
git merge --ff-only release-<new-version>
git push <RNAnorm-upstream-name> main <new-version>

Tag the new release from the latest commit:

git checkout main
git tag -sm "Version <new-version>" <new-version>

Push the tag to the upstream repository:

git push <RNAnorm-upstream-name> main <new-version>