Bump tiledbsoma version, address deprecations (#1235)

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~=1.11.4",
+    "tiledbsoma~=1.12.3",
     "anndata",
     "numpy>=1.21,<2.0",
     "requests",

api/python/cellxgene_census/src/cellxgene_census/experimental/ml/pytorch.py

@@ -541,7 +541,7 @@ def __init__(
             experimental
         """
         self.exp_uri = experiment.uri
-        self.aws_region = experiment.context.tiledb_ctx.config().get("vfs.s3.region")
+        self.aws_region = experiment.context.tiledb_config.get("vfs.s3.region")
         self.measurement_name = measurement_name
         self.layer_name = X_name
         self.obs_query = obs_query

api/python/cellxgene_census/tests/test_open.py

@@ -37,7 +37,7 @@ def test_open_soma_stable() -> None:
     with cellxgene_census.open_soma() as default_census:
         assert default_census.uri == census.uri
         for k, v in DEFAULT_TILEDB_CONFIGURATION.items():
-            assert census.context.tiledb_ctx.config()[k] == str(v)
+            assert census.context.tiledb_config[k] == str(v)
 
 
 @pytest.fixture(scope="module")
@@ -68,7 +68,7 @@ def test_open_soma_with_customized_tiledb_config(latest_locator: CensusLocator)
     with cellxgene_census.open_soma(uri=latest_locator["uri"], tiledb_config=tiledb_config) as census:
         assert census.uri == latest_locator["uri"]
         # Verify that user-provided custom config is passed through correctly
-        assert census.context.tiledb_ctx.config()["soma.init_buffer_bytes"] == soma_init_buffer_bytes
+        assert census.context.tiledb_config["soma.init_buffer_bytes"] == soma_init_buffer_bytes
 
 
 @pytest.mark.live_corpus
@@ -90,7 +90,7 @@ def test_open_soma_with_customized_plain_soma_context(
     context = soma.SOMATileDBContext().replace(**cfg)
     with cellxgene_census.open_soma(uri=latest_locator["uri"], context=context) as census:
         # Verify that the user-provided config settings are set correctly in the TileDB context object.
-        assert census.context.tiledb_ctx.config()["soma.init_buffer_bytes"] == soma_init_buffer_bytes
+        assert census.context.tiledb_config["soma.init_buffer_bytes"] == soma_init_buffer_bytes
         assert census.context.timestamp_ms == timestamp_ms
 
 
@@ -108,12 +108,12 @@ def test_open_soma_with_customized_default_soma_context(
 
     with cellxgene_census.open_soma(census_version="latest", context=custom_context) as census:
         # Verify the non-overriden soma context defaults are set correctly in the TileDB context object.
-        assert census.context.tiledb_ctx.config()["vfs.s3.no_sign_request"] == "true"
-        assert census.context.tiledb_ctx.config()["vfs.s3.region"] == latest_locator.get("s3_region")
-        assert census.context.tiledb_ctx.config()["py.init_buffer_bytes"] == f"{1 * 1024 ** 3}"
+        assert census.context.tiledb_config["vfs.s3.no_sign_request"] == "true"
+        assert census.context.tiledb_config["vfs.s3.region"] == latest_locator.get("s3_region")
+        assert census.context.tiledb_config["py.init_buffer_bytes"] == f"{1 * 1024 ** 3}"
 
         # Verify that the user-overridden config settings are set correctly in the TileDB context object.
-        assert census.context.tiledb_ctx.config()["soma.init_buffer_bytes"] == soma_init_buffer_bytes
+        assert census.context.tiledb_config["soma.init_buffer_bytes"] == soma_init_buffer_bytes
         assert census.context.timestamp_ms == timestamp_ms
 
 

tools/cellxgene_census_builder/tests/test_builder.py

@@ -10,7 +10,6 @@
 import psutil
 import pyarrow as pa
 import pytest
-import tiledb
 import tiledbsoma as soma
 
 from cellxgene_census_builder.build_soma import build
@@ -95,7 +94,7 @@ def proxy_psutil_virtual_memory() -> psutil._pslinux.svmem:
         # Query the census and do assertions
         with soma.Collection.open(
             uri=census_build_args.soma_path.as_posix(),
-            context=soma.options.SOMATileDBContext(tiledb_ctx=tiledb.Ctx({"vfs.s3.region": "us-west-2"})),
+            context=soma.options.SOMATileDBContext(tiledb_config={"vfs.s3.region": "us-west-2"}),
         ) as census:
             # There are 16 cells in total (4 in each dataset). They all belong to homo_sapiens
             human_obs = census[CENSUS_DATA_NAME]["homo_sapiens"]["obs"].read().concat().to_pandas()

tools/models/geneformer/generate-geneformer-embeddings.py

@@ -36,13 +36,11 @@ def main(argv):
         except Exception:  # noqa: BLE001
             pass
         tiledbsoma_context = tiledbsoma.options.SOMATileDBContext(
-            tiledb_ctx=tiledb.Ctx(
-                {
-                    "py.init_buffer_bytes": 4 * 1024**3,
-                    "soma.init_buffer_bytes": 4 * 1024**3,
-                    "vfs.s3.region": aws_region,
-                }
-            )
+            tiledb_config={
+                "py.init_buffer_bytes": 4 * 1024**3,
+                "soma.init_buffer_bytes": 4 * 1024**3,
+                "vfs.s3.region": aws_region,
+            }
         )
 
         with tiledbsoma.SparseNDArray.open(args.outfile, "r", context=tiledbsoma_context):

tools/models/geneformer/wdl/generate_embeddings.wdl

@@ -62,7 +62,7 @@ task init_embeddings_array {
             type=pa.float32(),
             shape=(2**31-2, ~{embedding_dim}),
             context = tiledbsoma.options.SOMATileDBContext(
-                tiledb_ctx=tiledb.Ctx({"vfs.s3.region": '~{s3_region}'})
+                tiledb_config={"vfs.s3.region": '~{s3_region}'}
             )
         ).close()
         EOF