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[python] Use new shape in one more spot #3321

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Nov 13, 2024
Merged

[python] Use new shape in one more spot #3321

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048f09b
[python] Use new shape in one more spot
johnkerl Nov 12, 2024
230bdd9
update a test case
johnkerl Nov 13, 2024
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13 changes: 8 additions & 5 deletions apis/python/src/tiledbsoma/io/outgest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -443,11 +443,14 @@
num_cols = width_configs.get(element_name, None)

if num_cols is None:
try:
used_shape = soma_nd_array.used_shape()
num_cols = used_shape[1][1] + 1
except SOMAError:
pass # We tried; moving on to next option
if soma_nd_array.tiledbsoma_has_upgraded_shape:
num_cols = soma_nd_array.shape[1]
else:
try:
used_shape = soma_nd_array.used_shape()
num_cols = used_shape[1][1] + 1
except SOMAError:
pass # We tried; moving on to next option

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apis/python/src/tiledbsoma/io/outgest.py#L449-L453 

Added lines #L449 - L453 were not covered by tests

if num_cols is None:
num_rows_times_width, coo_column_count = matrix_tbl.shape
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10 changes: 5 additions & 5 deletions apis/python/tests/test_basic_anndata_io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -822,14 +822,14 @@ def test_export_obsm_with_holes(h5ad_file_with_obsm_holes, tmp_path):
meta["soma_dim_1_domain_upper"]
assert meta["soma_object_type"] == "SOMASparseNDArray"

# Now try the remaining options for outgest.
with pytest.raises(tiledbsoma.SOMAError):
tiledbsoma.io.to_anndata(exp, "RNA")
# No longer throws as of new-shape feature in TileDB-SOMA 1.15.
try3 = tiledbsoma.io.to_anndata(exp, "RNA")
assert try3.obsm["X_pca"].shape == (2638, 50)

try3 = tiledbsoma.io.to_anndata(
try4 = tiledbsoma.io.to_anndata(
exp, "RNA", obsm_varm_width_hints={"obsm": {"X_pca": 50}}
)
assert try3.obsm["X_pca"].shape == (2638, 50)
assert try4.obsm["X_pca"].shape == (2638, 50)


def test_X_empty(h5ad_file_X_empty):
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