MACSIMA parse subfolders only when explicitly requested#379
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Remove auto parsing style option entirely. By default, all tif files inside a folder and all its subdirectories are parsed into a single Image element inside a SpatialData object. Only if the user specifically requests parsing subfolders, then the first level underneath the specified directory defines the image elements. All tifs in these directories, and subdirectores, will be parsed into separate image elements, with corresponding tables and coordinate systems.
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #379 +/- ##
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+ Coverage 62.77% 62.92% +0.15%
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Files 26 26
Lines 3175 3172 -3
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+ Hits 1993 1996 +3
+ Misses 1182 1176 -6
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@LucaMarconato Great, thanks a lot. So far I haven't added tests for this PoC implementation, I will do this tomorrow. |
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Thanks for adding tests! I'll review. |
…xplicitly_requested
| _parse_v1_ome_metadata, | ||
| macsima, | ||
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| from tests._utils import skip_if_below_python_version |
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Good point! No need for the skip_if_below_python_version machinery, since you have
if not (Path("./data/OMAP10_small").exists() or Path("./data/OMAP23_small").exists()):
pytest.skip()And in the test.yaml workflow we already skip downloading the artifacts for python < 3.13
LucaMarconato
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LucaMarconato
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Looks great to me! I have just made some minor modifications, which make the pytest checks more explicits.
We can actually merge already! |
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Tests fail due to this line, which comes from spatialdata-io/src/spatialdata_io/__main__.py Line 873 in c8f6191 |
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This implements the proposed change of macsima parsing style options, described in #378