v0.4.0

Added

• shelley clean removes built modules.
• Support build for tools with no shpc registry BioShell/#22
• Dependabot opens monthly, grouped PRs into dev for GitHub Actions and uv.lock
  updates; see docs/how-to/developer-setup.md.
• Release workflow: pushing a vX.Y.Z tag on main checks that the versions and
  CHANGELOG match, builds and smoke-tests the wheel, and creates the GitHub release
  with the wheel and sdist attached. See docs/how-to/developer-setup.md.
• Monthly data refresh workflow: regenerates rsec_meta.json.gz and
  galaxy_singularity_cache.json.gz, and opens a PR into
  dev when their content changes. See docs/how-to/maintain-corpus.md.
• Test coverage reporting with pytest-cov (in the dev extra). CI prints coverage
  for every test run and adds a summary table to the run's page. See
  docs/how-to/developer-setup.md.
• README badges for CI status, latest release, supported Python, licence, ruff and uv.
• Release docs cover Zenodo archiving and DOIs, and why shelley is not yet on PyPI.
  See docs/how-to/developer-setup.md.

Changed

• Local registries are now built in versioned subdirectories for shelley clean to
  correctly uninstall tool versions.
• Development tooling now uses ruff for linting and
  formatting, replacing the unused black and flake8 in the dev extra. CI enforces
  ruff check and ruff format --check on every pull request. The codebase was
  reformatted once to match; see docs/how-to/developer-setup.md.

Removed

• print_about() and ShelleyStyle.create_about_panel() from shelley.utils. They were
  unused and raised NameError if called.
• Support for Python 3.10. shelley now requires Python 3.11 or later.

Fixed

• docs/how-to/maintain-corpus.md pointed to a removed script for regenerating the
  Galaxy cache; it now uses shelley-build-galaxy.