Integrate body part regression

[surajpaib]

Switching base branch.

Original PR: #85

[LennyN95]

Please note, we updated our base image. All mhub dependencies are now installed in a virtual environment under /app/.venv running Python 3.11. Python, virtual environment and dependencies are now managed with uv. If required, you can create custom virtual environments, e.g., uv venv -p 3.8 .venv38 and use uv pip install -p .venv38 packge-name to install dependencies and uv run -p .venv3.8 python script.py to run a python script.

We also simplified our test routine. Sample and reference data now have to be uploaded to Zenodo and provided in a mhub.tom file at the project root. The process how to create and provide these sample data is explained in the updated testing phase article of our documentation. Under doi.org/10.5281/zenodo.13785615 we provide sample data as a reference.

[LennyN95]

If we parse the BPE results in MHub value outputs (using the dedicated IO decorators) the output format can be customized through a report exporter. What do you think?

[surajpaib]

@LennyN95 I'll take a look at this! I'm thinking Deepa might having something that we can use here as well as she did BPR -> Structured Report.

But maybe we get in the first json version of this integrated and then add a workflow. I'll add tests based on the update!

[surajpaib]

@LennyN95 I'm running into some challenges with the python environment for body part regression. I will debug this further and see. I think it might be better to use a custom fork with updated dependencies.

Is there an mhub policy on this?

[surajpaib]

I think this is from the new mhub container. Was there an OS upgrade as well?

I've tried to use Python3.8 - which it worked on earlier but breaks now

[LennyN95]

No so far I only updated Python. Have you tried installing bpr into a separate environment?

[surajpaib]

I have yes - on two separate machines but both of them have had OS upgrades in the past weeks so I was attributing it to that. But now I am not sure anymore.

[surajpaib]

@LennyN95 I've added a test for the default workflow but it seems like the compliance check fails because I haven't added tests for other workflows. Is this intended? Any way I can skip and only add tests for default as before?