Parse entire macsima metadata from OME metadata

[MSHelm]

Fixes #348

The parser now tries to use the filename stored in the tiff metadata, if it exists. This is more robust, as users typically do not modify these entries.
If this metadata doesnt exist (which is the case for older data), it falls back to the actual filename.

Since the lung dataset used for testing is using an old format, I added a newer data set that is publicy available (https://zenodo.org/records/14008816). I documented this in the tests as well.

Full disclosure: I am working for Miltenyi, but I love your work ;)

[codecov-commenter]

Codecov Report

❌ Patch coverage is 12.29050% with 157 lines in your changes missing coverage. Please review.
✅ Project coverage is 52.81%. Comparing base (23bcb72) to head (0aae9ce).

Files with missing lines	Patch %	Lines
src/spatialdata_io/readers/macsima.py	12.29%	157 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #349      +/-   ##
==========================================
- Coverage   55.07%   52.81%   -2.27%     
==========================================
  Files          26       26              
  Lines        2809     2969     +160     
==========================================
+ Hits         1547     1568      +21     
- Misses       1262     1401     +139     

Files with missing lines	Coverage Δ
src/spatialdata_io/readers/macsima.py	21.19% <12.29%> (-7.38%)	⬇️

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[MSHelm]

I checked the tests and the failing ones are all due to some Xenium and Visium HD readers, which I didnt touch XD Did they exist before this PR already?

[MSHelm]

Hey everyone,
with the last commits this turned into a bit of a bigger contribution. With this PR, we now solely rely on the metadata stored in the OME object. This should be significantly more robust than parsing file names, and enables us to add more metadata. In principle there would be even more information available than I currently implemented, but I think the most interesting bits are covered here.

I implemented 2 versions of the parser, as there are 2 different formats of the metadata. I removed the previously used data sets, as they are not part of the CI. Instead, I added 2 publicly available data sets, one for each version.

I tried modifying the github action to download them, but it seems that this was not really successful. If someone can give me some pointers that would be wonderful.

Cheers!

[LucaMarconato]

Hi @MSHelm, thanks for the contribution! I’ve fixed the unrelated failing tests on main, and your PR is now green.

I had a quick look but before full review I kindly ask you to verify and confirm which items from the contribution guide checklist apply to this PR. Ensuring the contributions guidelines are followed help streamline our review process and improve long-term code maintainability. Much appreciated!