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CONTRIBUTING.md

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Contributing

So you want to contribute to BioProv? That's great! Contributions are welcome, and every little bit helps.

There are many ways to contribute:

Types of Contributions

Report Bugs

Report bugs at https://github.com/vinisalazar/BioProv/issues.

If you are reporting a bug, please include:

  • Your operating system name and version.
  • Any details about your local setup that might be helpful in troubleshooting.
  • Detailed steps to reproduce the bug.
  • The full error log! Please format it by wrapping it around "```" as it makes it more readable.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it. Post a response to the issue so we can assign it to you!

Implement Features

Look through the GitHub issues for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it. Post a response to the issue so we can assign it to you!

Write Documentation

We could always use more documentation, whether as part of the official docs, in docstrings, or even as articles and use cases.

Saw a function or class in the source code without a docstring? Write it! Take other functions as examples of how to write docstrings.

Want to write a new tutorial for a functionality of BioProv you frequently use? Do it! We'd prefer if you wrote the tutorial as a Jupyter Notebook (.ipynb) and added it to the docs/tutorials directory.

Request a new feature

The best way to do so is to file an issue at https://github.com/vinisalazar/BioProv/issues.

If you are proposing a feature:

  • Explain in detail how it would work.
  • Keep the scope as narrow as possible, to make it easier to implement.
  • Remember that this is a volunteer-driven project, so don't take it the wrong way if we take a while to respond :)
  • Feeling like you could tackle writing it yourself? Go ahead!

Get Started!

Ready to contribute? Here's how to set up BioProv for local development.

  • Fork the BioProv repo on GitHub. (Top right)

  • Clone your fork locally:

git clone [email protected]:your_name_here/BioProv.git
  • Create a development environment. If you aren't yet familiar, get to know conda, the software used to manage our environment.
conda env create --file environment.yml

In case you've already created the environment and changes have been made to it, run:

conda activate bioprov
conda env update --file environment.yml
  • Assuming you've created the environment, install the package locally:
pip install -e .

This will make an "editable" version of the local installation.

  • Update the repository to its latest version:
git pull origin master
  • Create a branch for local development:
git checkout -b name-of-your-bugfix-or-feature

Now you can make your changes locally.

  • When you're done making changes, check that your changes are black-formatted and pass the tests:
black bioprov/
pytest

Some tests will require external tools, such as Prodigal, and if you haven't yet, you can either download them or run only a subset of tests, such as:

pytest bioprov/tests/test_bioprov_imports.py
  • Commit your changes and push your branch to GitHub:
git add .
git commit -m "Your detailed description of your changes."
git push origin name-of-your-bugfix-or-feature
  • Submit a pull request through the GitHub website.

Pull Request Guidelines

Before you submit a pull request, if your pull request includes code changes check that it meets these guidelines:

  • If the pull request adds functionality:
    • Put your new functionality into a function or class with a docstring;
    • Make a new test for said functionality.
  • Add a one-line description of the contribution to the CHANGELOG.md file under the current development version.
  • Make sure your code changes were formatted with the Black styling tool.