Collection of EPPs for the Scilifelab Stockholm node.

Table of contents

• scilifelab_epps
  • Overview
  • Installation
  • Development
    • Automated linting
      • GitHub Actions
      • Pre-commit
      • VS Code automation
    • Git blame suppression

The repo is installed inside a designated conda environment on a server hosting Illumina Clarity LIMS.

After installation, the scripts in scripts/ are addded to the bin of the Conda environment, from which they can be called by LIMS.

Inside the repo, run pip install .

Run pip install requirements-dev.txt to install packages used for development and pip install -e . to make the installation editable.

This repo is configured for automated linting. Linter parameters are defined in pyproject.toml.

As of now, we use:

• ruff to perform automated formatting and a variety of lint checks.

  • Run with ruff check . and ruff format .

• mypy for static type checking and to prevent contradictory type annotation.

  • Run with mypy **/*.py

• pipreqs to check that the requirement files are up-to-date with the code.

  • This is run with a custom Bash script in GitHub Actions which will only compare the list of package names.

    # Extract and sort package names
    awk '{print $1}' $1 | sort -u > "$1".compare
    awk -F'==' '{print $1}' $2 | sort -u > "$2".compare
    
    # Compare package lists
    if cmp -s "$1".compare "$2".compare
    then
      echo "Requirements are the same"
      exit 0
    else
      echo "Requirements are different"
      exit 1
    fi
    

• prettier to format common languages.

  • Run with prettier .

• editorconfig-checker to enforce .editorconfig rules for all files not covered by the tools above.

  • Run with

    editorconfig-checker $(git ls-files | grep -v '.py\|.md\|.json\|.yml\|.yaml\|.html')
    

Configured in .github/workflows/lint-code.yml. Will test all commits in pushes or pull requests, but not change code or prevent merges.

Will prevent local commits that fail linting checks. Configured in .pre-commit-config.yml.

To set up pre-commit checking:

1. Run pip install pre-commit
2. Navigate to the repo root
3. Run pre-commit install

This can be disabled with pre-commit uninstall

To enable automated linting in VS Code, go the the user settings.json and include the following lines:

"[python]": {
    "editor.defaultFormatter": "charliermarsh.ruff",
}

This will run the ruff-mediated linting with the same parameters as the GitHub Actions and pre-commit every time VS Code is used to format the code in the repository.

To run formatting on save, include the lines:

"[python]": {
    "editor.formatOnSave": true,
}

When a non-invasive tool is used to tidy up a lot of code, it is useful to supress the Git blame for that particular commit, so the original author can still be traced.

To do this, add the hash of the commit containing the changes to .git-blame-ignore-revs, headed by an explanatory comment.