Run package-installed Galaxy through Gravity

[jmchilton]

Run package-installed Galaxy through Gravity

This supersedes #1690 and #1691 with a narrower implementation of the package-installed Galaxy idea.

Motivation

#1690 explored running Galaxy directly inside Planemo's Python process. The discussion there, particularly this review comment, made a good case that Planemo should not own a second Galaxy process-management implementation.

#1691 moved the package-installed approach to Gravity, but retained history and interface surface from the broader experiment. This PR rebuilds that approach cleanly on current master.

What this PR does

• Adds one explicit installed_galaxy engine for planemo serve, run, and test.
• Runs the Galaxy packages installed alongside Planemo exclusively through Gravity.
• Adds an installed_galaxy package extra, currently bounded to Galaxy 26.1 and Gravity 1.2.
• Supports Galaxy XML tools, YAML GalaxyTool definitions, native Galaxy workflows, Tool Shed dependency installation, and the existing postgres_singularity database mode.
• Gives foreground and daemon executions explicit process-group cleanup so Galaxy, Gunicorn, and Celery do not leak across Planemo invocations.
• Exercises the released packages in a Python 3.13 CI job.

Install the optional runtime with:

pip install 'planemo[installed_galaxy]'

Then select it explicitly, for example:

planemo test --engine installed_galaxy path/to/tool.xml

Deliberate differences from #1690

This does not expose the embedded_galaxy engine, an in-process/non-Gravity entry point, or knobs for choosing between embedded and Gravity lifecycle implementations. installed_galaxy has one meaning: use the packaged Galaxy runtime and let Gravity manage its services. Existing Galaxy checkout and Docker engine defaults are unchanged.

The original embed_galaxy and gravity-installed branches remain available for comparison, while #1690 and #1691 are closed in favor of this consolidated implementation.

Validation

• Focused unit and lifecycle suite: 48 passed.
• Released-package integration suite with Galaxy 26.1.1 and Gravity 1.2.4: 3 passed, 1 external-service test deselected.
• Real Tool Shed workflow integration test: passed separately.
• tox -e lint: passed.
• tox -e mypy: passed.

The deterministic released-package tests run in CI. The real Tool Shed case remains an opt-in integration test so Tool Shed availability does not gate every pull request.

[jmchilton]

Correction: reopened. #1708 is intentionally stacked on this PR and adds the engine-level test --serve workflow for #1175 on top of this Gravity-backed installed_galaxy implementation. #1701 remains the prerequisite.