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PhenoMePhenoMe

Testing and local quality checks

Commands used in CI and recommended before opening a PR.

Install dev tools

Section titled “Install dev tools”
Terminal window
pip install -e ".[dev]"

Lint and format

Section titled “Lint and format”
Terminal window
python -m ruff check phenome tests
python -m ruff format phenome tests --check

Auto-fix (local only):

Terminal window
python -m ruff check phenome tests --fix
python -m ruff format phenome tests

Type checking

Section titled “Type checking”
Terminal window
python -m mypy phenome

Docstring coverage

Section titled “Docstring coverage”
Terminal window
interrogate phenome

The project targets ≥95% coverage (pyproject.toml → [tool.interrogate]).

Spell check

Section titled “Spell check”
Terminal window
codespell

Documentation build

Section titled “Documentation build”
Terminal window
cd docs
npm install
npm run build

Dependency compatibility smoke

Section titled “Dependency compatibility smoke”
Terminal window
python -m pytest

This matches the main CI workflow. The suite:

  • Runs pip check so conflicting installed packages fail
  • Imports the public PhenoMe API and every phenome.* module
  • Constructs PhenoMe on CPU, reads PNG/NPY images, and runs a tiny find → embed → properties → clustering loop
  • Reloads embeddings from an HDF5 checkpoint and checks that advertised property presets resolve