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.

🐳 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.

Please see the CONTRIBUTING.md in this repository!