Contributing

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

Developer Installation

If something goes wrong at any point during installing the library please see how our CI/CD on GitHub Actions installs and builds the project as it will always be the most up-to-date.

Test Resources and Git LFS

This project uses Git Large File Storage (LFS) to store large test resources under /tests/resources/. Before cloning, make sure you have Git LFS installed:

macOS

brew install git-lfs
git lfs install

Debian/Ubuntu

sudo apt-get install git-lfs
git lfs install

Or install manually: https://git-lfs.github.com/

⚠️ If you skip git lfs install, large files will appear as plain-text pointers and your tests may fail.

Get Started!

Ready to contribute? Here's how to set up bioio-dv for local development.

1. Fork the bioio-dv repo on GitHub.

2. Clone your fork locally:

   git clone git@github.com:{your_name_here}/bioio-dv.git
   

3. Install the project in editable mode. (It is also recommended to work in a virtualenv or anaconda environment):

   cd bioio-dv/
   just install
   

4. Create a branch for local development:

   git checkout -b {your_development_type}/short-description
   

   Ex: feature/read-tiff-files or bugfix/handle-file-not-found
   Now you can make your changes locally.

5. When you're done making changes, check that your changes pass linting and tests with just:

   just build
   

6. Commit your changes and push your branch to GitHub:

   git add .
   git commit -m "Your detailed description of your changes."
   git push origin {your_development_type}/short-description
   

7. Submit a pull request through the GitHub website.

Just Commands

For development commands we use just.

just

Available recipes:
    build                    # run lint and then run tests
    clean                    # clean all build, python, and lint files
    default                  # list all available commands
    install                  # install with all deps
    lint                     # lint, format, and check all files
    release                  # release a new version
    tag-for-release version  # tag a new version
    test                     # run tests
    update-from-cookiecutter # update this repo using latest cookiecutter-bioio-reader

Deploying

A reminder for the maintainers on how to deploy. Make sure the main branch is checked out and all desired changes are merged. Then run:

just tag-for-release "vX.Y.Z"
just release

The presence of a tag starting with "v" will trigger the publish step in the main github workflow, which will build the package and upload it to PyPI. The version will be injected into the package metadata by setuptools-scm