Clean file when writing H5AD #156
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Error if file exists and overwrite = FALSE Fixes #121
* origin/main: (52 commits)
Use {cli} for alerts (#231)
Seurat metadata granularity (#224)
Tidy DESCRIPTION (#234)
Add more comprehensive to_Seurat tests (#225)
Add logo (#226)
Update README.md with trademark (#233)
Standardise styling (#230)
Make HDF5AnnData$finalize() private (#228)
Fix linting issues after breaking changes in lintr (#229)
Update URL in DESCRIPTION (#227)
Conversion from & to SingleCellExperiment (#212)
fix recursive default (#222)
dimension issue has been fixed (#221)
Support writing dgeMatrix (#219)
Support arrays with >2 dimensions (#218)
fix issue by explicitly adding dimensions to arrays and vectors (#216)
update list of vignettes in readme (#217)
remove known issue (#215)
Compare writing h5ad in Python & in R with h5diff (#207)
Rework documentation (#213)
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rcannood
reviewed
Mar 10, 2025
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I'm not sure whether it's currently possible to trigger this condition:
Line 283 in ee9ee49
Either the file doesn't exist yet, or the constructor will fail if you try to open an H5AD file and change stuff at the same time.
Could you take a look? 🙇
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Address #121 where old fields are not removed from files when writing to an existing H5AD file. This PR currently solves this by adding an
overwriteargument towrite_h5ad(). Possibly needs more work depending on what interfaces we want exposed to the user.