Client side tests for analysis-runner

[Alexander-Stuckey]

Adding some client side tests for analysis-runner, before I make any changes to include Nextflow tower as a supported dispatch mode.

ALSO centralise dependency management into pyproject.toml

• Add tests for both cli.py and cli_analysisrunner.py.
• Minimal tests to ensure that jobs route correctly to cromwell.
• Bump version of mypy and ruff, as they were quite outdated.
• Centralise dependencies into pyproject.toml, delete setup.py etc, update build references.

[MattWellie]

Good start. You can push the pre-commit versions even higher - pre-commit in general is at 6.0.0+, mypy has a version v2.1.0.

The get_repository_specific_information method is probably running as part of this call, and will pass if this testing branch is currently pushed to github which is a bit meta. Probably worth adding those checks in, as it's something we'll be re-using in TW... unless we exclusively stick with named workflows, I can't remember if we came to a decision on this.

[MattWellie]

Confirming a few things from playing locally -

1. the dev dependencies aren't present, ideally requirements-dev.in should have pytest and pytest-mock listed
2. the dev dependencies are kinda... distributed at the moment in a couple of requirements files. Might be a nice upgrade to roll these into a extras_require section in the setup.py. The more modern approach would be to roll all the requirements, setup.py, and pyproject.toml into just a pyproject.toml... easier to manage too

in the tests:

1. the git checks are present and un-mocked, this is doing a real check against the local and remote git history, and will fail if an un-pushed commit it added locally - failing stdout example

The commit "fe7d23eab841cf77619ec6c05270f2a82489d012" was not found on the remote (Github). 
Please confirm if you want to proceed anyway. (y/n): 

--

Feels bad raising these as issues and just... passing them over, lmk if you want to combine on this

[MattWellie]

LGTMatt - doesn't touch functional code, adds tests, updates/modernises requirements and packaging. What's not to love? Maybe a version bump and a second approval from software 👀

[violetbrina]

Thanks so much for your work adding tests to the analysis-runner, a much overdue addition for sure. I have some very minor comments, and I'm not sure if @dancoates or anyone else from @populationgenomics/software-team wants eyes on this as well.

But looking good.

[Alexander-Stuckey]

@violetbrina , I believe I've addressed everything, thanks for the feedback.

[MattWellie]

Suggested change

	analysis-runner[test] @ file:///opt/deps
	analysis-runner[test]

This is breaking CI

[MattWellie]

I've made a side PR stacked on this branch - it un-nests the analysis-runner [dev] and [test] optional dependencies, and changes how the package is installed in CI.

It also rebuilds the requirements-dev file with uv instead of pip - it should be equivalent, but the file header is explicit about being created with UV Which we may not want

#760

[Alexander-Stuckey]

@nevoodoo This is a package of tests that I wrote for the client side of analysis-runner. I had some packaging changes here as well, but in light of the work you are doing, have taken them out.