20.22 Python

Use a current version of Python, but not a pre-release version. See status of Python versions.

Python packages

• Poetry is recommended for package management.
• pyOpenSci provides a useful guide.

Virtual environments

Virtual environments (venv) are required to run Python code.

sudo apt-get install python3-venv
python3 -m venv venv
source venv/bin/activate
python3 -m pip install --upgrade pip
python3 -m pip install -e .
deactivate

Dependencies

If the Python code is not managed as a package, a requirements.txt file should be created.

Linter

Black and pylint are recommended linters. They should be used part of the .pre-commit-config.yaml:

repos:
-   repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.6.0
    hooks:
    -   id: trailing-whitespace
        exclude: status.txt|readme.md
    -   id: end-of-file-fixer
        exclude: bib$|txt$
    -   id: check-docstring-first
    -   id: debug-statements
    -   id: name-tests-test
-   repo: https://github.com/psf/black-pre-commit-mirror
    rev: 24.4.2
    hooks:
      - id: black
        language_version: python3
-   repo: https://github.com/PyCQA/autoflake
    rev: v2.3.1
    hooks:
    -   id: autoflake
-   repo: https://github.com/PyCQA/flake8
    rev: 7.0.0
    hooks:
    -   id: flake8
        additional_dependencies: [flake8-typing-imports==1.12.0]
        args: ['--max-line-length=110', '--extend-ignore=E203,TYP006']
-   repo: https://github.com/asottile/reorder-python-imports
    rev: v3.13.0
    hooks:
    -   id: reorder-python-imports
        args: [--py3-plus]
-   repo: https://github.com/asottile/pyupgrade
    rev: v3.16.0
    hooks:
    -   id: pyupgrade
        args: [--py36-plus, --keep-runtime-typing]
-   repo: https://github.com/pre-commit/mirrors-mypy
    rev: 'v1.10.0'
    hooks:
    -   id: mypy
        args: [--disallow-untyped-defs, --disallow-incomplete-defs, --disallow-untyped-calls]
        additional_dependencies: [types-toml]
- repo: https://github.com/astral-sh/ruff-pre-commit
  rev: v0.4.8
  hooks:
    - id: ruff # runs faster than pylint
      args: [--fix, --exit-non-zero-on-fix]
- repo: local
  hooks:
    - id: pylint
      name: pylint
      entry: pylint
      language: system
      types: [python]
      files: colrev
      args:
        [
          "-rn", # Only display messages
          "-sn", # Don't display the score
        ]