round n+1 of code review

single-cell-data · Nov 21, 2023 · 080b5c2 · 080b5c2
1 parent 81e2c66
commit 080b5c2
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Showing 27 changed files with 5 additions and 78 deletions.
diff --git a/apis/python/src/tiledbsoma/__init__.py b/apis/python/src/tiledbsoma/__init__.py
@@ -96,6 +96,11 @@
 from somacore import AxisColumnNames, AxisQuery, ExperimentAxisQuery
 from somacore.options import ResultOrder
 
+# TODO: once we no longer support Python 3.7, remove this and pin to pyarrow >= 14.0.1
+# https://github.com/single-cell-data/TileDB-SOMA/issues/1926
+# ruff: noqa
+import pyarrow_hotfix
+
 from ._collection import Collection
 from ._constants import SOMA_JOINID
 from ._dataframe import DataFrame

diff --git a/apis/python/src/tiledbsoma/_arrow_types.py b/apis/python/src/tiledbsoma/_arrow_types.py
@@ -32,9 +32,6 @@
 import numpy.typing as npt
 import pandas as pd
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import tiledb
 
 _ARROW_TO_TDB_ATTR: Dict[Any, Union[str, TypeError]] = {

diff --git a/apis/python/src/tiledbsoma/_common_nd_array.py b/apis/python/src/tiledbsoma/_common_nd_array.py
@@ -9,9 +9,6 @@
 
 import numpy as np
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import somacore
 import tiledb
 from somacore import options

diff --git a/apis/python/src/tiledbsoma/_dataframe.py b/apis/python/src/tiledbsoma/_dataframe.py
@@ -11,9 +11,6 @@
 import numpy as np
 import pandas as pd
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import somacore
 import tiledb
 from somacore import options

diff --git a/apis/python/src/tiledbsoma/_dense_nd_array.py b/apis/python/src/tiledbsoma/_dense_nd_array.py
@@ -10,9 +10,6 @@
 from typing import Optional, Tuple
 
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import somacore
 from somacore import options
 from typing_extensions import Self

diff --git a/apis/python/src/tiledbsoma/_read_iters.py b/apis/python/src/tiledbsoma/_read_iters.py
@@ -26,9 +26,6 @@
 import numpy.typing as npt
 import pandas as pd
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import somacore
 from scipy import sparse
 from somacore import options

diff --git a/apis/python/src/tiledbsoma/_sparse_nd_array.py b/apis/python/src/tiledbsoma/_sparse_nd_array.py
@@ -19,9 +19,6 @@
 
 import numpy as np
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pyarrow.compute as pacomp
 import somacore
 import tiledb

diff --git a/apis/python/src/tiledbsoma/_tiledb_array.py b/apis/python/src/tiledbsoma/_tiledb_array.py
@@ -9,9 +9,6 @@
 from typing import Any, Dict, List, Optional, Sequence, Tuple
 
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import tiledb
 from somacore.options import ResultOrder, ResultOrderStr
 

diff --git a/apis/python/src/tiledbsoma/_types.py b/apis/python/src/tiledbsoma/_types.py
@@ -11,9 +11,6 @@
 import numpy.typing as npt
 import pandas as pd
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 from somacore import types
 from typing_extensions import Literal
 

diff --git a/apis/python/src/tiledbsoma/experiment_query.py b/apis/python/src/tiledbsoma/experiment_query.py
@@ -8,9 +8,6 @@
 import pandas as pd
 import pyarrow as pa
 
-# ruff: noqa
-import pyarrow_hotfix
-
 from ._types import NPNDArray, PDSeries
 
 

diff --git a/apis/python/src/tiledbsoma/io/_registration/signatures.py b/apis/python/src/tiledbsoma/io/_registration/signatures.py
@@ -5,9 +5,6 @@
 import attrs
 import pandas as pd
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 from typing_extensions import Self
 
 import tiledbsoma

diff --git a/apis/python/src/tiledbsoma/io/ingest.py b/apis/python/src/tiledbsoma/io/ingest.py
@@ -33,9 +33,6 @@
 import numpy as np
 import pandas as pd
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import scipy.sparse as sp
 import tiledb
 from anndata._core import file_backing

diff --git a/apis/python/tests/__init__.py b/apis/python/tests/__init__.py
@@ -1,7 +1,4 @@
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 from typeguard.importhook import install_import_hook
 
 # avoid typeguard by importing before calling install_import_hook

diff --git a/apis/python/tests/test_collection.py b/apis/python/tests/test_collection.py
@@ -6,9 +6,6 @@
 import numpy as np
 import pandas as pd
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 from typing_extensions import Literal
 

diff --git a/apis/python/tests/test_dataframe.py b/apis/python/tests/test_dataframe.py
@@ -4,9 +4,6 @@
 import numpy as np
 import pandas as pd
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 import somacore
 import tiledb

diff --git a/apis/python/tests/test_dataframe_index_columns.py b/apis/python/tests/test_dataframe_index_columns.py
@@ -1,8 +1,5 @@
 import numpy as np
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 import tiledb
 

diff --git a/apis/python/tests/test_dense_nd_array.py b/apis/python/tests/test_dense_nd_array.py
@@ -3,9 +3,6 @@
 
 import numpy as np
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 import tiledb
 

diff --git a/apis/python/tests/test_experiment_basic.py b/apis/python/tests/test_experiment_basic.py
@@ -2,9 +2,6 @@
 
 import numpy as np
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 
 import tiledbsoma as soma

diff --git a/apis/python/tests/test_experiment_query.py b/apis/python/tests/test_experiment_query.py
@@ -3,9 +3,6 @@
 import numpy as np
 import pandas as pd
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 from scipy import sparse
 from somacore import options

diff --git a/apis/python/tests/test_io.py b/apis/python/tests/test_io.py
@@ -1,8 +1,5 @@
 import numpy as np
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 from scipy import sparse as sp
 

diff --git a/apis/python/tests/test_metadata.py b/apis/python/tests/test_metadata.py
@@ -3,9 +3,6 @@
 
 import numpy as np
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 
 import tiledbsoma as soma

diff --git a/apis/python/tests/test_sparse_nd_array.py b/apis/python/tests/test_sparse_nd_array.py
@@ -8,9 +8,6 @@
 
 import numpy as np
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 import scipy.sparse as sparse
 import tiledb

diff --git a/apis/python/tests/test_tiledbobject.py b/apis/python/tests/test_tiledbobject.py
@@ -1,7 +1,4 @@
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 
 import tiledbsoma as soma

diff --git a/apis/python/tests/test_type_system.py b/apis/python/tests/test_type_system.py
@@ -1,9 +1,6 @@
 import pathlib
 
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 
 import tiledbsoma as soma

diff --git a/apis/python/tests/test_unicode.py b/apis/python/tests/test_unicode.py
@@ -1,9 +1,6 @@
 import numpy as np
 import pandas as pd
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 
 import tiledbsoma as soma

diff --git a/apis/python/tests/test_update_dataframes.py b/apis/python/tests/test_update_dataframes.py
@@ -5,9 +5,6 @@
 import numpy as np
 import pandas as pd
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 
 import tiledbsoma

diff --git a/apis/python/tests/test_util_tiledb.py b/apis/python/tests/test_util_tiledb.py
@@ -1,7 +1,4 @@
 import pyarrow as pa
-
-# ruff: noqa
-import pyarrow_hotfix
 import pytest
 import tiledb