[misc] Prepare for 1.12.0 release (#1061)

* [misc] Prepare for 1.12.0 release

* Update tiledbsoma to 1.9.1

* Set tiledbsoma version to 1.9.0 to pass unit tests

* Use new re-indexer class in tiledbsoma 1.9.1

* Remove placeholder comment

Author: prathapsridharan

api/python/cellxgene_census/pyproject.toml

@@ -31,7 +31,7 @@ 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",
+    "tiledbsoma~=1.9.1",
     "anndata",
     "numpy>=1.21",
     "requests",

api/python/cellxgene_census/src/cellxgene_census/experimental/_embedding.py

@@ -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()

api/python/cellxgene_census/src/cellxgene_census/experimental/pp/_highly_variable_genes.py

@@ -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

api/r/cellxgene.census/DESCRIPTION

@@ -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"))