[python] Ingestion performance #2434
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Additional details and impacted files@@ Coverage Diff @@
## main #2434 +/- ##
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- Coverage 90.61% 79.93% -10.69%
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Files 37 92 +55
Lines 3900 8626 +4726
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+ Hits 3534 6895 +3361
- Misses 366 1731 +1365
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johnkerl
changed the title
nguyenv
reviewed
Apr 11, 2024
| soma_arr = DenseNDArray.create( | ||
| arr_uri, | ||
| type=pa_dtype, | ||
| shape=value.shape, | ||
| platform_config=platform_config, | ||
| context=context, | ||
| ) | ||
| except AlreadyExistsError: | ||
| soma_arr = _factory.open(arr_uri, "w", soma_type=DenseNDArray, context=context) |
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We can actually just directly call DenseNDArray.open here (and same with DataFrame.open above).
nguyenv
reviewed
Apr 11, 2024
|
@nguyenv @ryan-williams ready for re-review! :) |
nguyenv
approved these changes
Apr 12, 2024
Co-authored-by: nguyenv <[email protected]>
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* AlreadyExistsError; use for DataFrame in tiledbsoma.io * apply in `_create_or_open_collection` * apply in _create_from_matrix * apply in _ingest_uns_ndarray * lint * Run SO copying workflow on macos-13 to avoid SIP (#2435) * AlreadyExistsError; use for DataFrame in tiledbsoma.io * apply in `_create_or_open_collection` * apply in _create_from_matrix * apply in _ingest_uns_ndarray * lint * neaten * neaten * Update raises-notes * code-review feedback Co-authored-by: nguyenv <[email protected]> --------- Co-authored-by: John Blischak <[email protected]> Co-authored-by: nguyenv <[email protected]>
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* AlreadyExistsError; use for DataFrame in tiledbsoma.io * apply in `_create_or_open_collection` * apply in _create_from_matrix * apply in _ingest_uns_ndarray * lint * Run SO copying workflow on macos-13 to avoid SIP (#2435) * AlreadyExistsError; use for DataFrame in tiledbsoma.io * apply in `_create_or_open_collection` * apply in _create_from_matrix * apply in _ingest_uns_ndarray * lint * neaten * neaten * Update raises-notes * code-review feedback --------- Co-authored-by: John Kerl <[email protected]> Co-authored-by: John Blischak <[email protected]> Co-authored-by: nguyenv <[email protected]>
This was referenced Apr 12, 2024
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Issue and/or context: #2433
Changes: As narrated on #2433. The only additional details is that to balance the
DoesNotExistErrorforopen, we need a completely analogousAlreadyExistsErrorforcreate.Notes for Reviewer: There is a bit more performance improvement to be made, but it needs to be done in core; I will track that work separately. Also, as this is for Python; I'll track the R work -- both a needs-analysis, and any possible (maybe no) dev work -- separately.