broadinstitute/gnomad-project-template

Cookiecutter template for gnomAD projects using Python and Hail

gnomAD project template

Cookiecutter template for gnomAD projects.

This template sets up a Python project with:

• Nox for managing Python environments.
• Black for code formatting.
• isort for sorting imports.
• pydocstyle for docstring conventions.
• Pre-commit hooks to run Black and pydocstyle.
• Pylint for static analysis.
• pytest for tests.
• Sphinx for generating documentation.
• GitHub Actions workflows for...
  • Running checks on PRs
  • Publishing documentation to GitHub Pages.

Getting started

• Install cookiecutter.

• Generate the project directory. Enter a project name when prompted.

  cookiecutter gh:broadinstitute/gnomad-project-template
  

GitHub repository settings

To make full use of the GitHub Actions workflows defined in the template, configure these settings in the project's GitHub repository.

• Create a branch protection rule for the main branch.

  • Require pull requests.
  • Enable required status checks. Require the Checks and Build documentation status checks.

• On each commit to the main branch, documentation is automatically built and pushed to the gh-pages branch. To make the documentation available through GitHub Pages, configure GitHub Pages to publish from the root of the gh-pages branch. Note that GitHub Pages websites are always public, even if the repository is private.

gnomad-project-template's Issues

Add mypy?

Consider adding mypy for static type checking.

Not sure how useful this will be for Hail types. Some discussion about that going on in Slack.

Fails when attempting to clone https://github.com/broadinstitute/gnomad-project-template.git

It's trying to use password-based auth with github and failing due to "Support for password authentication was removed on August 13, 2021. Please use a personal access token instead."

wm103-772:~/code $ cookiecutter gh:broadinstitute/gnomad-project-template
Username for 'https://github.com': bw2
Password for 'https://[email protected]':
Traceback (most recent call last):
  File "/usr/local/Cellar/[email protected]/3.7.10_3/Frameworks/Python.framework/Versions/3.7/bin/cookiecutter", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/usr/local/lib/python3.7/site-packages/cookiecutter/cli.py", line 152, in main
    skip_if_file_exists=skip_if_file_exists,
  File "/usr/local/lib/python3.7/site-packages/cookiecutter/main.py", line 74, in cookiecutter
    directory=directory,
  File "/usr/local/lib/python3.7/site-packages/cookiecutter/repository.py", line 114, in determine_repo_dir
    no_input=no_input,
  File "/usr/local/lib/python3.7/site-packages/cookiecutter/vcs.py", line 104, in clone
    stderr=subprocess.STDOUT,
  File "/usr/local/Cellar/[email protected]/3.7.10_3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 411, in check_output
    **kwargs).stdout
  File "/usr/local/Cellar/[email protected]/3.7.10_3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 512, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['git', 'clone', 'https://github.com/broadinstitute/gnomad-project-template.git']' returned non-zero exit status 128.

wm103-772:~/code $ git clone https://github.com/broadinstitute/gnomad-project-template.git
Cloning into 'gnomad-project-template'...
Username for 'https://github.com': bw2
Password for 'https://[email protected]':
remote: Support for password authentication was removed on August 13, 2021. Please use a personal access token instead.
remote: Please see https://github.blog/2020-12-15-token-authentication-requirements-for-git-operations/ for more information.
fatal: Authentication failed for 'https://github.com/broadinstitute/gnomad-project-template.git/'