Correct dysfunctional test cases

[rmassei]

This PR contains:

• a new test-case for the benchmark
  • I hereby confirm that NO LLM-based technology (such as github copilot) was used while writing this benchmark
• new dependencies in requirements.txt
  • The environment.yml file was updated using the command conda env export > environment.yml
• new generator-functions allowing to sample from other LLMs
• new samples (sample_....jsonl files)
• new benchmarking results (..._results.jsonl files)
• documentation update
• bug fixes

Related github issue (if relevant):
closes #144
closes #145
closes #146

Short description:

• Bug fixes of the case-studies:
  • image_metadata_reading.ipynb
    Action take: I rephrase the docstring and the assert-statement in a more clear way
  • read_ome_xml_from_ome_tiff.ipynb
    Action take: Problem solved by including the xml encoding
  • tiff_metadata_reading.ipynb
    Action take: Working for me on Windows with bioio 1.1.0 and bioiotifffile 1.0.0

How do you think will this influence the benchmark results?

• Same reasons of the PR New Test-Case - Metadata Reading plus some basics image processing #142

Why do you think it makes sense to merge this PR?

• It is nice to have some bug-fixes case-studies

[haesleinhuepf]

Hi @rmassei ,

thanks for sending this PR so timely! Just a quick question: There is a "oryx-build-commands.txt" in the submission. What is it necessary for?

Thanks again!

Best,
Robert

[rmassei]

Ah, I did not noticed, probably a mistake.