[FIX] Write .h5ad files #347
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- convert any "object" dtype values in obs or uns to "category" or "str" for writing to .h5ad files
- current issues: 1.) Categories True/False cannot be written
2.) Non-numerical values in X have to be encoded before writing
- fixed an error that caused numerical detection to produce false positives while reading
- column with boolean values (as well as binary columns) are now casted to bool columns in obs - columns with 0 and 1 will be casted as well
Imipenem
commented
Mar 11, 2022
- fixed an error that caused dtype of X to be object despite all columns being numeric and the inital AnnData object had numerical X dtype
- writing unencoded AnnData objects to .h5ad files no longer raises an error and can be performed normally
- added tests + new test files - updated docs - pinned flake8-bandit to >=3.0.0 since this fixes the previous CI error
|
Please merge development into this and fix the dependencies, please. |
Imipenem
commented
Mar 11, 2022
| adata_cp = adata.copy() | ||
| adata_cp.uns["ehrapy_dummy_encoding"] = True | ||
| adata_cp.uns["columns_obs_only"] = list(adata_cp.obs.columns) | ||
| # TODO: THIS SHOULD BE FIXED WITH PR #348, SO NO COPY SHOULD BE NEEDED THEN SINCE THE ORIGINAL WILL NOT BE MUTATED |
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PR Checklist
docsis updatedDescription of changes
Fix #337 and #333
Issue: Cannot write
dtype objectto .h5adfiles.Fix:
category.booleanthough (see Unable to write categorical booleans in .obs to .h5ad scverse/anndata#724)objectdtype while reading from cacheNew feature:
.h5adfiles. (relates to Writing unencoded dataset results in error #333)Current Issues:
--> but this got added in 0.8.0 which should be released in the next few days