Handle corrupted HDF5 files gracefully in split_containers#114
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zcapjdb wants to merge 6 commits intoumami-hep:mainfrom
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Handle corrupted HDF5 files gracefully in split_containers#114zcapjdb wants to merge 6 commits intoumami-hep:mainfrom
zcapjdb wants to merge 6 commits intoumami-hep:mainfrom
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zcapjdb
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #114 +/- ##
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+ Coverage 94.91% 95.39% +0.48%
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Files 23 23
Lines 2044 2062 +18
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+ Hits 1940 1967 +27
+ Misses 104 95 -9 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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When creating a virtual dataset from multiple h5 files, validate each file before creating symlinks. Corrupted files are logged with a warning and skipped rather than crashing the entire process. Only raises an error if all files are corrupted. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Use 'import logging as log' to match codebase convention - Fix typo: "fiules" -> "files" Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Reorder imports to satisfy ruff linter - Add changelog entry for corrupted HDF5 file handling Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Tests cover: - Valid HDF5 files returning True - Corrupt files returning False - Non-existent files returning False - Empty files returning False - String path input Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
zcapjdb
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Tests cover: - Single file path/string handling (yields directly) - All corrupted files (raises RuntimeError) - Mixed files (filters corrupted with warnings) - All valid files (creates VDS without warnings) - Symlink creation (only valid files get symlinked) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Nice fix! I wonder if the better approach is to do this check at the prep stage so that we can have this for the resampling approach too. What do you think @afroch, @dkobylianskii? |
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Tbh. I think this might be a better addition for |
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When creating a virtual dataset from multiple h5 files, validate each file before creating symlinks. Corrupted files are logged with a warning and skipped rather than crashing the entire process. Only raises an error if all files are corrupted.
Conformity