Contributing guide

Contributing guide#

Do you want to add new metrics, models, or other features to seqme?

This document aims at summarizing the most important information for getting you started on contributing to this project. We assume that you are already familar with git and with making pull requests on GitHub.

Installing dev dependencies#

In addition to the required dependencies needed to use this package, you need additional python packages to run tests and build the documentation. It’s easy to set up the package for development using pip:

cd seqme
pip install -e ".[dev,doc]"

Code-style#

We use pre-commit to enforce consistent code-styles. On every commit, pre-commit checks will either automatically fix issues with the code, or raise an error message.

To enable pre-commit locally, simply run

pre-commit install

in the root of the repository. Pre-commit will automatically download all dependencies when it is run for the first time.

To run pre-commit without calling git commit, do

pre-commit

Writing tests#

This package uses pytest for automated testing. Please write tests in the tests directory for every function added to the package.

Most IDEs integrate with pytest and provide a GUI to run tests. Alternatively, you can run all tests from the command line by executing

pytest

in the root of the repository.

Each file in the test directory has to follow the naming convention: tests/test_foo.py

def helper(): # pytest does not check this function
    ...
def test_bar(): # pytest recognizes it as a test
    assert ...

Tests are run automatically with pre-commit.

Code checks#

Use ruff to check and format code:

ruff check
ruff check --fix
ruff format

Use mypy for typing errors:

mypy -p seqme

All checks are run automatically with pre-commit.

Notebook stripping#

Use nbstripout to strip notebook metadata before commiting to repository:

find . -name '*.ipynb' -exec nbstripout --drop-empty-cells --keep-output {} +

This command is run automatically with pre-commit.

Building sphinx docs#

To build the sphinx docs, do

cd docs
make clean & make html

which generates docs/_build directory with HTML files.

Note: Any changes to the sphinx docs, will automatically be built by readthedocs when merged into the main branch.

Tooling#

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