John Chilton
605c4aec2a
Conflict: packages/tool_util/setup.cfg was deleted on dev by the
pyproject.toml migration (c329529e51) and modified on release_26.1 by
#23256, which moved jsonschema from install_requires to the test extra.
Kept the deletion and ported that move into packages/tool_util/pyproject.toml
so the dependency change isn't lost in the merge forward.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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.
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.
This can be done by treating Galaxy as a uv workspace. The pyproject.toml file in this directory defines a workspace for Galaxy and allows development and testing of individual packages with uv.
Here is an example workflow that will run tests for a specific package after setting up a virtual environment for that package.
$ git clone https://github.com/galaxyproject/galaxy.git
$ cd galaxy/packages
$ cd auth
$ uv sync --all-extras
$ uv run pytest tests
When switching between projects it is just important to remember to rerun the sync command for that project.
The package Makefile has been updated to use ux also, so the above can
be simplified to just:
$ git clone https://github.com/galaxyproject/galaxy.git
$ cd galaxy/packages
$ cd auth
$ make test
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.
$ git clone https://github.com/galaxyproject/galaxy.git
$ cd galaxy/packages
$ cd auth
$ make mypy
$ make _mypy # a shortcut to just run mypy on an existing updated environment
This is equivalent to syncing the uv environment and then adding Galaxy's type checking dependencies to it.
$ uv sync --all-extras
$ uv pip install -r ../../lib/galaxy/dependencies/pinned-typecheck-requirements.txt
$ uv run mypy .
The Makefile can also be used for linting.
$ git clone https://github.com/galaxyproject/galaxy.git
$ cd galaxy/packages
$ cd auth
$ make lint
$ make _lint # a shortcut to just run ruff on an existing updated environment
This is equivalent to syncing the uv environment and then adding Galaxy's linting dependencies to it.
$ uv sync --all-extras
$ uv pip install -r ../../lib/galaxy/dependencies/pinned-lint-requirements.txt
$ uv run ruff check .