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Fix IO error reporting #1273

Merged
merged 13 commits into from Jan 4, 2024
Merged

Fix IO error reporting #1273

merged 13 commits into from Jan 4, 2024

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flying-sheep
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@flying-sheep flying-sheep commented Dec 20, 2023

This PR makes it so group path reporting in IO errors actually works.

It also fixes test_only_child_key_reported_on_failure, which did nothing before:
re.search searches anywhere in the string, so every string can be successfully searched for (?s)((?!Error raised while writing key '/?a').)*$. Only with the ^ at the start will that regex successfully fail when the substring is contained.

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codecov bot commented Dec 20, 2023

Codecov Report

Attention: 24 lines in your changes are missing coverage. Please review.

Comparison is base (63e6b29) 85.26% compared to head (0a51b54) 52.00%.

Additional details and impacted files
@@             Coverage Diff             @@
##             main    #1273       +/-   ##
===========================================
- Coverage   85.26%   52.00%   -33.26%     
===========================================
  Files          34       34               
  Lines        5421     5432       +11     
===========================================
- Hits         4622     2825     -1797     
- Misses        799     2607     +1808     
Flag Coverage Δ
gpu-tests 52.00% <58.62%> (-0.07%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Coverage Δ
anndata/_core/anndata.py 57.40% <100.00%> (-27.67%) ⬇️
anndata/_io/h5ad.py 18.90% <100.00%> (-74.13%) ⬇️
anndata/_io/zarr.py 29.26% <100.00%> (-53.66%) ⬇️
anndata/experimental/_dispatch_io.py 40.00% <0.00%> (-45.72%) ⬇️
anndata/_io/specs/registry.py 81.59% <80.00%> (-14.09%) ⬇️
anndata/compat/__init__.py 42.34% <44.44%> (-36.73%) ⬇️
anndata/_io/utils.py 36.88% <42.30%> (-39.79%) ⬇️

... and 17 files with indirect coverage changes

@flying-sheep flying-sheep added this to the 0.10.4 milestone Dec 20, 2023
@flying-sheep flying-sheep changed the title Fix error reporting Fix IO error reporting Dec 20, 2023
@flying-sheep flying-sheep marked this pull request as ready for review January 2, 2024 14:08
anndata/_io/utils.py Outdated Show resolved Hide resolved
@flying-sheep flying-sheep enabled auto-merge (squash) January 4, 2024 12:58
@flying-sheep flying-sheep merged commit 45a65f0 into main Jan 4, 2024
14 checks passed
@flying-sheep flying-sheep deleted the fix-io-error-notes branch January 4, 2024 13:04
meeseeksmachine pushed a commit to meeseeksmachine/anndata that referenced this pull request Jan 4, 2024
flying-sheep added a commit that referenced this pull request Jan 4, 2024
Co-authored-by: Philipp A <flying-sheep@web.de>
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Write error reporting got worse
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