Development

Set up a development environment, run the tests against a local OMERO server, and preview the documentation.

Setup

uv sync --dev
uv run pre-commit install

The pre-commit hooks run ruff (lint and format) and the ty type checker. Fix what they report rather than bypassing them with --no-verify. CI type-checks the whole workspace:

uv run ty check

ty is pinned to an exact version in the dev group, because it is still beta and its diagnostics change between releases; bump it deliberately. It reads # ty: ignore[<rule>] comments, not mypy’s # type: ignore[<code>]. Configuration is in [tool.ty] in the root pyproject.toml.

Tests

Unit tests live in tests/unit_tests, one directory per package:

uv run pytest                                      # everything
uv run pytest tests/unit_tests/omero_screen_tests  # one package

End-to-end tests in tests/e2e_tests run against an OMERO server under production-like conditions. Run one by name:

uv run omero-integration-test e2e_connection
uv run omero-integration-test e2e_excel

Local OMERO test server

A separate OMERO server for development runs in Docker on 127.0.0.2:4064 (user root, password omero):

./scripts/manage_test_server.sh start
./scripts/manage_test_server.sh status
./scripts/manage_test_server.sh stop

Import Operetta screens into it with load_plates.sh. Nothing is imported without -x:

./scripts/load_plates.sh -d /path/to/plates -x

Try it on sample data walks through a full run on this server.

Documentation

The docs are built with Great Docs: six sites, one per package, assembled into one tree.

./scripts/build_docs.sh            # build everything into ./_site
./scripts/build_docs.sh --serve    # build, then serve on localhost:8000
./scripts/dev_docs.py              # root site, rebuilt and reloaded on save
./scripts/dev_docs.py --package packages/cellview

Use dev_docs.py rather than great-docs build --watch, which watches copies of the sources and never sees your edits. CLI references are generated from the Click commands, so change the command’s help text rather than writing option tables by hand.

Commits and releases

Work goes from an issue to a branch to a pull request (Closes #N), and is squash-merged once CI is green. Use conventional commits (uv run cz commit). After the merge, the release workflow bumps the version, tags it and updates the changelog. With squash merges, the PR title decides the release:

PR title type	Release
fix(<scope>): …	patch
feat(<scope>): …	minor
docs, ci, chore, dev	none

Don’t run cz bump or create version tags by hand.