cookiecutter-toil

A cookiecutter for the creation of toil pipelines.

pip install cookiecutter
cookiecutter https://github.com/papaemmelab/cookiecutter-toil

Live Example

Check out toil_example, this project is updated automatically with every new commit on cookiecutter-toil.

Features

• 🐳   Containerized System Calls

  The commands.BaseJob inherits from ContainerJob, a Job Class used to run commands with either Docker, Singularity or Python's subprocess. See toil_container to learn more.

  A Dockerfile example is included. If you use singularity, the generated README will include information on how to generate a singularity image.

• 📦   Pip Installable Project

  Check the setup.py and setup.json for pip configurations. The only place where you have to define the version of your project is in the VERSION file. After generated, your project can be installed with:

    # local install
    pip install --editable <your_project_dir>
  
    # after deployment - check the continuous integration section
    pip install <your_project_name>
  

• 🍉   Python Modules

  Module	Description
  cli.py	Include the function that is mapped to the cli command, see setup.json:entry_points
  commands.py	Include a toil example pipeline
  exceptions.py	Include package specific exceptions
  utils.py	Multiple util functions are available
  validators.py	Defines common validators

• 🚧   Contributing Features

  File	Description
  README.md	with some example sections
  .gitignore	with well curated python ignore patterns
  .gitmessage	with issue types mapped to emojis! Like 🚀 for a new feature, or 🐛 for a fix
  .github	Contributing guidelines, code of conduct, issue and PR templates

• ✅   Testing Suite

  Pytest: python test examples are included, give them a try with:

    py.test tests
  

  Pylint: Google style linting configuration is included with the .pylintrc. Additionally, Docstrings conventions are tested with pydocstyle and are defined in .pydocstylerc.

    # check linting conventions
    pylint --rcfile={your_project_dir}/.pylintrc {your_project}
  
    # check docstrings
    pydocstyle --config={your_project_dir}/.pydocstylerc {your_project}
  

  Tox: Run pytest, pylint, pydocstyle with coverage on isolated python environments at the same time:

    tox
  

• 🌀   Continuous Integration

  Travis CI configuration with automatic deployment to PyPi with tags on master. To encrypt your PyPi password simply run:

    # you need travis (e.g. brew install travis)
    travis encrypt --add deploy.password
  

  Check out this tutorial if you want to learn more about deployment.

• 🐁   Click Mode

  Click is an great package to seamlessly build CLI packages. Use cli_type="click" if you want to use the goodies of this cookiecutter but don't need the toil rocketry. By using this mode, some of the toil specific modules and tests will be removed.

Contributing

Please see the CONTRIBUTING.md in this repository!