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[misc] Prepare for 1.12.0 release #1061

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merged 5 commits into from
Mar 28, 2024
Merged

[misc] Prepare for 1.12.0 release #1061

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237bf98
[misc] Prepare for 1.12.0 release
prathapsridharan Mar 21, 2024
3f734a4
Update tiledbsoma to 1.9.1
prathapsridharan Mar 27, 2024
f94c277
Set tiledbsoma version to 1.9.0 to pass unit tests
prathapsridharan Mar 28, 2024
644a7c7
Use new re-indexer class in tiledbsoma 1.9.1
prathapsridharan Mar 28, 2024
b1a300b
Remove placeholder comment
prathapsridharan Mar 28, 2024
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3 changes: 2 additions & 1 deletion api/python/cellxgene_census/pyproject.toml
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Expand Up @@ -31,7 +31,8 @@ dependencies= [
# NOTE: the tiledbsoma version must be >= to the version used in the Census builder, to
# ensure that the assets are readable (tiledbsoma supports backward compatible reading).
# Make sure this version does not fall behind the builder's tiledbsoma version.
"tiledbsoma~=1.8.0",
# TODO: When ready to release 1.12.0 update tiledbsoma version to 1.9.x and delete this temporary comment
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time to delete the comment?

BTW, I believe ~=1.9.1 means anything >1.9.1 and <1.10.0, so this pin should be fine (1.9.0 never existed in the wild)

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will remove comment.

I believe ~=1.9.1

Yea that is my understanding too

"tiledbsoma~=1.9.1",
"anndata",
"numpy>=1.21",
"requests",
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2 changes: 1 addition & 1 deletion api/python/cellxgene_census/src/cellxgene_census/experimental/_embedding.py
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Expand Up @@ -126,7 +126,7 @@ def get_embedding(
embedding_shape = (len(obs_soma_joinids), E.shape[1])
embedding = np.full(embedding_shape, np.NaN, dtype=np.float32, order="C")

obs_indexer = soma.tiledbsoma_build_index(obs_soma_joinids, context=E.context)
obs_indexer = soma.IntIndexer(obs_soma_joinids, context=E.context)
for tbl in E.read(coords=(obs_soma_joinids,)).tables():
obs_idx = obs_indexer.get_indexer(tbl.column("soma_dim_0").to_numpy())
feat_idx = tbl.column("soma_dim_1").to_numpy()
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4 changes: 1 addition & 3 deletions api/python/cellxgene_census/src/cellxgene_census/experimental/pp/_highly_variable_genes.py
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Expand Up @@ -89,9 +89,7 @@ def _highly_variable_genes_seurat_v3(
n_batches = len(batch_index.cat.categories)
n_samples = batch_index.value_counts().loc[batch_index.cat.categories.to_numpy()].to_numpy()
if n_batches > 1:
batch_indexer = soma.tiledbsoma_build_index(
batch_index.index.to_numpy(), context=query.experiment.context
).get_indexer
batch_indexer = soma.IntIndexer(batch_index.index.to_numpy(), context=query.experiment.context).get_indexer
batch_codes = batch_index.cat.codes.to_numpy().astype(np.int64)
else:
n_batches = 1
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2 changes: 1 addition & 1 deletion api/r/cellxgene.census/DESCRIPTION
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@@ -1,6 +1,6 @@
Package: cellxgene.census
Title: CZ CELLxGENE Discover Cell Census
Version: 1.11.1
Version: 1.12.0
Authors@R:
person("Chan Zuckerberg Initiative Foundation", email = "[email protected]",
role = c("aut", "cre", "cph", "fnd"))
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