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CONTRIBUTING.md

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Contributing Code

The preferred workflow for contributing is to clone the main repository on GitHub and develop on a branch.

Steps:

  • Clone the repo from your GitHub account to your local disk: git clone https://github.com/neurodata/brainlit.git
  • Create a feature branch to hold your development changes: git checkout -b <my-feature>
  • Develop the feature on your feature branch. Add changed files using git add and then git commit files: git add <modified_files> git commit to record your changes in Git, push the changes to your branch with: git pull origin develop git push origin <my-feature>

The repository is structured according to this model (source)

Pull Request Checklist

We recommended that your contribution complies with the following rules before you submit a pull request:

  • Give your pull request a helpful title that summarises what your contribution does. In some cases Fix is enough. Fix # is not enough.
  • All public methods should have informative docstrings with sample usage presented as doctests when appropriate.
  • All major functions and classes should have at least one paragraph of narrative documentation with links to references in the literature (with PDF links when possible) and the example.
  • All functions and classes must have pytest unit tests. These should include, at the very least, type checking and ensuring correct computation/outputs. Test files should be located in a folder next to the files they are testing. Reminder that just because the code is covered does not mean it is tested. For example, code that is tested on a single type of s3 data may not work on other types of data.
  • Ensure all tests are passing locally using pytest. Install the necessary packages by: pip install pytest pytest-cov then run pytest or you can run pytest on a single test file by pytest path/to/test.py
  • Run an autoformatter. We use black and would like for you to format all files using black. You can run the following lines to format your files. pip install black black path/to/module.py
  • Ensure that your jupyter notebooks run successfully when you restart the kernel and run all cells. They should be located in docs/notebooks.
  • You are responsible for updating our documentation page according to your changes. This may involve updating .rst files for core code and notebooks:
    • For core code edit index.rst and your submodule's .rst file such as algs.rst.
    • For notebooks, edit tutorial.rst.
    • Run ./docs/build_docs.sh from brainlit's root directory. Output will be in docs/_build/. You should open docs/_build/html/index.html to preview the new documentation.
    • After your PR is merged, please (if appropriate) close any relevant issues and delete any relevant branches.