NEW_REPO

This repository serves only as a Python template for new projects.

Create a new repository

• Create a new repo and select CellProfiling/cell-pro-template as template repository.
• Clone your new repo.
• Search and replace all occurences of NEW_REPO, AUTHOR_NAME and AUTHOR_EMAIL. Replace NEW_REPO with the name of the new repo.
• Add package requirements in install_requires in setup.py and in requirements.txt as needed.
• Update this README.md with a description of and instructions for your new repo.

Development

• Install and set up development environment.

  pip install -r requirements_dev.txt

  This will install all requirements. It will also install this package in development mode, so that code changes are applied immediately without reinstall necessary.

• Here's a list of development tools we use.

  • black
  • flake8
  • pydocstyle
  • pylint
  • pytest
  • tox

• It's recommended to use the corresponding code formatter and linters also in your code editor to get instant feedback. A popular editor that can do this is vscode.

• Run all tests, check formatting and linting.

  tox

• Run a single tox environment.

  tox -e lint

• Reinstall all tox environments.

  tox -r

• Run pytest and all tests.

  pytest

• Run pytest and calculate coverage for the package.

  pytest --cov-report term-missing --cov=NEW_REPO

• Continous integration is by default supported via GitHub actions. GitHub actions is free for public repos and comes with 2000 free Ubuntu build minutes per month for private repos.

• To activate continuous integration testing on Travis CI, add a .travis.yml file with this contents to the repo.

  dist: xenial
  language: python
  cache: pip
  python:
    - "3.6"
    - "3.7"
    - "3.8"
  install:
    - pip install -U tox-travis
  script: tox

  Note that Travis CI is free for public repos, but requires a subscription for private repos.