Update ASCII storage for dataframes

Author: johnkerl

apis/python/src/tiledbsoma/annotation_dataframe.py

@@ -1,7 +1,6 @@
 from concurrent.futures import ThreadPoolExecutor
 from typing import Optional, Sequence, Set, Tuple, Union
 
-import numpy as np
 import pandas as pd
 import pyarrow as pa
 import tiledb
@@ -86,9 +85,10 @@ def ids(self) -> Sequence[str]:
             self.timing_end(s1)
             self.dim_name = A.domain.dim(0).name
 
-            # TileDB string dims are ASCII not UTF-8. Decode them so they readback
-            # not like `b"AKR1C3"` but rather like `"AKR1C3"`.
             s2 = self.timing_start("ids", "tiledb_query")
+            # TileDB string dims are ASCII not UTF-8. Decode them so they readback not like
+            # `b"AKR1C3"` but rather like `"AKR1C3"`. Update as of
+            # https://github.com/TileDB-Inc/TileDB-Py/pull/1304 these dims will read back OK.
             retval = A.query(attrs=[], dims=[self.dim_name])[:][self.dim_name].tolist()
             self.timing_end(s2)
 
@@ -97,7 +97,12 @@ def ids(self) -> Sequence[str]:
             self.timing_end(s3)
 
             self.timing_end(s0)
-            return list(retval)  # coerce to list to appease the linter
+
+            if len(retval) > 0 and isinstance(retval[0], bytes):
+                return [e.decode() for e in retval]
+            else:
+                # list(...) is there to appease the linter which thinks we're returning `Any`
+                return list(retval)
 
     # ----------------------------------------------------------------
     def __repr__(self) -> str:
@@ -268,14 +273,8 @@ def _query_aux(
             #   (('__pandas_index_dims', '{"obs_id": "<U0"}'),)
             # so the set_index is already done for us.
             #
-<<<<<<< HEAD:apis/python/src/tiledbsoma/annotation_dataframe.py
             # However if the data was written somehow else (e.g. by tiledbsoma-r) then we do.
-||||||| parent of 19963aa (tiledbsc-py stats experiment):apis/python/src/tiledbsc/annotation_dataframe.py
-            # However if the data was written somehow else (e.g. by tiledbscr-r) then we do.
-=======
-            # However if the data was written somehow else (e.g. by tiledbscr-r) then we do.
             s3 = self.timing_start("query", "set_index")
->>>>>>> 19963aa (tiledbsc-py stats experiment):apis/python/src/tiledbsc/annotation_dataframe.py
             if not return_arrow:
                 if isinstance(df.index, pd.RangeIndex) and self.dim_name in df.columns:
                     df.set_index(self.dim_name, inplace=True)
@@ -451,7 +450,7 @@ def from_dataframe(self, dataframe: pd.DataFrame, extent: int = 2048) -> None:
             dfc = dataframe[column_name]
             if len(dfc) > 0 and type(dfc[0]) == str:
                 # Force ASCII storage if string, in order to make obs/var columns queryable.
-                column_types[column_name] = np.dtype("S")
+                column_types[column_name] = "ascii"
 
         tiledb.from_pandas(
             uri=self.uri,