Rename tiledb.cc->tiledb.libtiledb (alias removed)

Author: jp-dark

apis/python/tests/test_tiledbvcf.py

@@ -1,10 +1,8 @@
-import math
 import numpy as np
 import subprocess
 import os
 import pandas as pd
 import pyarrow as pa
-import re
 import glob
 import shutil
 import platform
@@ -41,7 +39,7 @@ def check_if_compatible(uri):
     try:
         with tiledb.open(uri):
             return True
-    except tiledb.cc.TileDBError as e:
+    except tiledb.libtiledb.TileDBError as e:
         if "incompatible format version" in str(e).lower():
             raise pytest.skip.Exception(
                 "Test skipped due to incompatible format version"
@@ -127,7 +125,9 @@ def test_retrieve_samples(test_ds):
 
 def test_read_unsupported_regions_type(test_ds):
     unsupported_region = 3.14
-    unsupported_type_error = f'"regions" parameter cannot have type: {type(unsupported_region)}'
+    unsupported_type_error = (
+        f'"regions" parameter cannot have type: {type(unsupported_region)}'
+    )
     wrong_dimension_region = np.array([["1:12700-13400"], ["1:12700-13400"]])
     ndarray_wrong_dimension_error = f'"regions" parameter of type {type(wrong_dimension_region)} must be 1-dimensional'
     with pytest.raises(Exception, match=unsupported_type_error):
@@ -277,13 +277,15 @@ def test_basic_reads(test_ds):
 
     # Regions as numpy.ndarray
     df = test_ds.read(
-        attrs=["sample_name", "pos_start", "pos_end"], regions=np.array(["1:12700-13400"])
+        attrs=["sample_name", "pos_start", "pos_end"],
+        regions=np.array(["1:12700-13400"]),
     )
     _check_dfs(
         expected_df, df.sort_values(ignore_index=True, by=["sample_name", "pos_start"])
     )
     df = test_ds.read_arrow(
-        attrs=["sample_name", "pos_start", "pos_end"], regions=np.array(["1:12700-13400"])
+        attrs=["sample_name", "pos_start", "pos_end"],
+        regions=np.array(["1:12700-13400"]),
     ).to_pandas()
     _check_dfs(
         expected_df, df.sort_values(ignore_index=True, by=["sample_name", "pos_start"])
@@ -438,12 +440,12 @@ def test_incomplete_read_generator():
     cfg = tiledbvcf.ReadConfig(memory_budget_mb=0)
     test_ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
     expected_df = pd.DataFrame.from_dict(
-            {
-                "pos_end": np.array(
-                    [12771, 12771, 13374, 13389, 13395, 13413], dtype=np.int32
-                )
-            }
-        )
+        {
+            "pos_end": np.array(
+                [12771, 12771, 13374, 13389, 13395, 13413], dtype=np.int32
+            )
+        }
+    )
 
     # NOTE: Running multiple test shows that the iterator can be reused