galaxy/packages

Package-centric Galaxy

You clone Galaxy as a Monorepo for its Python backend. This packages directory allows us to distribute smaller connected repositories out of individual Galaxy components. CI ensures these repositories have valid dependencies and such defined by running each components tests in isolation (see packages/test.sh, run from the repository root as bash packages/test.sh).

Development

Typically Galaxy developers develop against the monorepo but there are times when developing against a small unit of Galaxy might make sense - such as to keep an AI (or human cognitive) context as small as possible.

Development uses a single uv workspace rooted at the repository root. The root pyproject.toml (name = "galaxy-workspace", [tool.uv.workspace] members packages/*) is the only workspace: the former nested packages/pyproject.toml workspace has been removed, so every uv command run from a package directory resolves to the root workspace and its environment.

The exact uv version to use is pinned in .tool-versions at the repository root (uv 0.12.23). Both mise and asdf can read this file. Use the pinned version when syncing or regenerating the lock.

The root uv.lock is tracked and is the only workspace lockfile. The .gitignore exception for it keeps Galaxy runtime lock files ignored. Resolve manifest conflicts first, then regenerate the lock with the pinned uv version and review the dependency diff. Do not hand-edit the lock or run an unrelated broad upgrade in a source-move change.

Python sources live under lib/; package source directories link to their owned modules there. A root dev sync installs development tools and third-party dependencies; use a package-scoped command to install the relevant workspace members. Start Galaxy with ./run.sh.

Here is an example workflow that syncs the shared development environment once from the repository root and then runs tests for a specific package:

$ git clone https://github.com/galaxyproject/galaxy.git
$ cd galaxy
$ uv sync --locked --group dev
$ uv run --locked --package galaxy-util --group dev pytest packages/util/tests

uv lock --check verifies the lock is up to date without modifying it. The requirements exports used by startup and tooling live under lib/galaxy/dependencies/. Regenerate them from the existing lock without upgrading dependencies with sh lib/galaxy/dependencies/update.sh --export-only. Run the same script with --check to verify the lock and exports without changing them. CI runs this check on dependency changes. make update-dependencies deliberately upgrades dependencies and regenerates the exports; lint and conditional requirements retain their separate inputs.

The per-package Makefile (symlinked as e.g. packages/auth/Makefile) targets the same root workspace, so package commands can also be run from the package directory:

$ git clone https://github.com/galaxyproject/galaxy.git
$ cd galaxy/packages/auth
$ make test

This syncs the workspace environment scoped to that package (uv sync --locked --package ...) and runs its tests with uv run --locked --package ....

If the environment has already been setup and you wish to just re-run the tests. The make _test command be used to just do the testing in the existing environment without messing with sync and adjusting dependencies.

The Makefile can also be used for typechecking.

$ cd galaxy/packages/auth
$ make mypy
$ make _mypy  # a shortcut to just run mypy on an existing updated environment

This is equivalent to syncing the package environment and then adding Galaxy's type checking dependencies from lib/galaxy/dependencies/:

$ uv sync --locked --package galaxy-auth --all-extras
$ uv pip install -r ../../lib/galaxy/dependencies/pinned-typecheck-requirements.txt
$ uv run --locked --package galaxy-auth mypy .

The Makefile can also be used for linting.

$ cd galaxy/packages/auth
$ make lint
$ make _lint  # a shortcut to just run ruff on an existing updated environment

This is equivalent to syncing the package environment and then adding Galaxy's linting dependencies to it.

$ uv sync --locked --package galaxy-auth --all-extras
$ uv pip install -r ../../lib/galaxy/dependencies/pinned-lint-requirements.txt
$ uv run --locked --package galaxy-auth ruff check .

Isolated package checks

The shared-workspace commands above are convenient for development but prove nothing about package dependency isolation. The authoritative isolation check remains packages/test.sh (used by the test_galaxy_packages tox environments): it builds a throw-away virtualenv per package in dependency order, installs that package's own dependencies, and runs its tests, mypy, wheel build, and twine check there.