isort: tiledbsoma before tiledb (#2381)

(hopefully temporary) workaround for #2293

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ repos:
     hooks:
     - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.291
+    rev: v0.3.5
     hooks:
     - id: ruff
       args: ["--config=apis/python/pyproject.toml"]

apis/python/devtools/desc-array-fragments

@@ -7,6 +7,7 @@
 import argparse
 
 import pandas as pd
+
 import tiledb
 
 

apis/python/devtools/ingestor

@@ -16,7 +16,6 @@ import os
 import sys
 from typing import Optional
 
-import tiledb
 from somacore import options
 
 import tiledbsoma
@@ -26,6 +25,7 @@ import tiledbsoma._util
 import tiledbsoma.io
 import tiledbsoma.logging
 from tiledbsoma.options import SOMATileDBContext
+import tiledb
 
 
 # ================================================================

apis/python/devtools/outgestor

@@ -18,11 +18,10 @@ import logging
 import os
 import sys
 
-import tiledb
-
 import tiledbsoma
 import tiledbsoma._util
 import tiledbsoma.io
+import tiledb
 
 logger = logging.getLogger("tiledbsoma")
 

apis/python/devtools/peek-exp.py

@@ -8,10 +8,10 @@
 import numpy
 import pandas
 import scipy  # noqa: F401
-import tiledb  # noqa: F401
 
 import tiledbsoma
 import tiledbsoma.io
+import tiledb  # noqa: F401
 
 # module aliases
 ad = anndata

apis/python/pyproject.toml

@@ -23,5 +23,11 @@ extend-select = ["I001"]
 fix = true
 exclude = ["*.cc"]
 
-[tool.ruff.isort]
-known-first-party = ["tiledbsoma"]
+[tool.ruff.lint.isort]
+# HACK: tiledb needs to come after tiledbsoma: https://github.com/single-cell-data/TileDB-SOMA/issues/2293
+section-order = ["future", "standard-library", "third-party", "tiledbsoma", "tiledb", "first-party", "local-folder"]
+no-lines-before = ["tiledb"]
+
+[tool.ruff.lint.isort.sections]
+"tiledbsoma" = ["tiledbsoma"]
+"tiledb" = ["tiledb"]

apis/python/src/tiledbsoma/_arrow_types.py

@@ -32,6 +32,7 @@
 import numpy.typing as npt
 import pandas as pd
 import pyarrow as pa
+
 import tiledb
 
 _ARROW_TO_TDB_ATTR: Dict[Any, Union[str, TypeError]] = {

apis/python/src/tiledbsoma/_collection.py

@@ -28,10 +28,11 @@
 import attrs
 import somacore
 import somacore.collection
-import tiledb
 from somacore import options
 from typing_extensions import Self
 
+import tiledb
+
 from . import _funcs, _tdb_handles
 from ._common_nd_array import NDArray
 from ._dataframe import DataFrame

apis/python/src/tiledbsoma/_common_nd_array.py

@@ -10,10 +10,11 @@
 import numpy as np
 import pyarrow as pa
 import somacore
-import tiledb
 from somacore import options
 from typing_extensions import Self
 
+import tiledb
+
 from . import _arrow_types, _util
 from ._tiledb_array import TileDBArray
 from ._types import OpenTimestamp

apis/python/src/tiledbsoma/_dataframe.py

@@ -12,10 +12,11 @@
 import pandas as pd
 import pyarrow as pa
 import somacore
-import tiledb
 from somacore import options
 from typing_extensions import Self
 
+import tiledb
+
 from . import _arrow_types, _util
 from . import pytiledbsoma as clib
 from ._constants import SOMA_JOINID

apis/python/src/tiledbsoma/_sparse_nd_array.py

@@ -21,11 +21,12 @@
 import pyarrow as pa
 import pyarrow.compute as pacomp
 import somacore
-import tiledb
 from somacore import options
 from somacore.options import PlatformConfig
 from typing_extensions import Self
 
+import tiledb
+
 from . import _util
 
 # This package's pybind11 code

apis/python/src/tiledbsoma/_tdb_handles.py

@@ -28,11 +28,12 @@
 import attrs
 import numpy as np
 import pyarrow as pa
-import tiledb
 from numpy.typing import DTypeLike
 from somacore import options
 from typing_extensions import Literal, Self
 
+import tiledb
+
 from . import pytiledbsoma as clib
 from ._exception import DoesNotExistError, SOMAError, is_does_not_exist_error
 from ._types import METADATA_TYPES, Metadatum, OpenTimestamp

apis/python/src/tiledbsoma/_tiledb_array.py

@@ -6,10 +6,11 @@
 from typing import Any, Dict, List, Optional, Sequence, Tuple, Union
 
 import pyarrow as pa
-import tiledb
 from somacore import options
 from typing_extensions import Self
 
+import tiledb
+
 from . import _tdb_handles, _util
 
 # This package's pybind11 code

apis/python/src/tiledbsoma/_tiledb_object.py

@@ -8,10 +8,11 @@
 from typing import Any, Generic, MutableMapping, Optional, Type, TypeVar, Union
 
 import somacore
-import tiledb
 from somacore import options
 from typing_extensions import Self
 
+import tiledb
+
 from . import _constants, _tdb_handles
 from ._exception import SOMAError
 from ._types import OpenTimestamp

apis/python/src/tiledbsoma/io/_util.py

@@ -13,9 +13,10 @@
 from unittest import mock
 
 import anndata as ad
-import tiledb
 from anndata._core import file_backing
 
+import tiledb
+
 from .._types import Path
 
 

apis/python/src/tiledbsoma/io/ingest.py

@@ -36,11 +36,12 @@
 import pandas as pd
 import pyarrow as pa
 import scipy.sparse as sp
-import tiledb
 from anndata._core.sparse_dataset import SparseDataset
 from somacore.options import PlatformConfig
 from typing_extensions import get_args
 
+import tiledb
+
 from .. import (
     Collection,
     DataFrame,

apis/python/src/tiledbsoma/options/_soma_tiledb_context.py

@@ -10,10 +10,11 @@
 from concurrent.futures import ThreadPoolExecutor
 from typing import Any, Dict, Literal, Mapping, Optional, Union
 
-import tiledb
 from somacore import ContextBase
 from typing_extensions import Self
 
+import tiledb
+
 from .. import pytiledbsoma as clib
 from .._types import OpenTimestamp
 from .._util import ms_to_datetime, to_timestamp_ms

apis/python/src/tiledbsoma/options/_tiledb_create_options.py

@@ -15,10 +15,11 @@
 
 import attrs as attrs_  # We use the name `attrs` later.
 import attrs.validators as vld  # Short name because we use this a bunch.
-import tiledb
 from somacore import options
 from typing_extensions import Self
 
+import tiledb
+
 # Most defaults are configured directly as default attribute values
 # within TileDBCreateOptions.
 DEFAULT_TILE_EXTENT = 2048

apis/python/tests/test_basic_anndata_io.py

@@ -10,13 +10,13 @@
 import pytest
 import scipy
 import somacore
-import tiledb
 
 import tiledbsoma
 import tiledbsoma.io
 from tiledbsoma import Experiment, _constants, _factory
 from tiledbsoma._tiledb_object import TileDBObject
 from tiledbsoma._util import verify_obs_var
+import tiledb
 
 from ._util import TESTDATA
 

apis/python/tests/test_collection.py

@@ -11,11 +11,12 @@
 from typing_extensions import Literal
 
 import tiledbsoma as soma
-from tests._util import raises_no_typeguard
 from tiledbsoma import _collection, _factory, _tiledb_object
 from tiledbsoma._exception import DoesNotExistError
 from tiledbsoma.options import SOMATileDBContext
 
+from tests._util import raises_no_typeguard
+
 
 # ----------------------------------------------------------------
 def create_and_populate_dataframe(path: str) -> soma.DataFrame:

apis/python/tests/test_context.py

@@ -3,9 +3,9 @@
 from unittest import mock
 
 import pytest
-import tiledb
 
 import tiledbsoma.options._soma_tiledb_context as stc
+import tiledb
 
 
 @pytest.fixture(autouse=True)

apis/python/tests/test_dataframe.py

@@ -6,10 +6,11 @@
 import pyarrow as pa
 import pytest
 import somacore
-import tiledb
 from pandas.api.types import union_categoricals
 
 import tiledbsoma as soma
+import tiledb
+
 from tests._util import raises_no_typeguard
 
 

apis/python/tests/test_dataframe_index_columns.py

@@ -1,9 +1,9 @@
 import numpy as np
 import pyarrow as pa
 import pytest
-import tiledb
 
 import tiledbsoma as soma
+import tiledb
 
 
 @pytest.fixture

apis/python/tests/test_dense_nd_array.py

@@ -4,10 +4,10 @@
 import numpy as np
 import pyarrow as pa
 import pytest
-import tiledb
 
 import tiledbsoma as soma
 from tiledbsoma.options import SOMATileDBContext
+import tiledb
 
 from . import NDARRAY_ARROW_TYPES_NOT_SUPPORTED, NDARRAY_ARROW_TYPES_SUPPORTED
 from ._util import raises_no_typeguard

apis/python/tests/test_experiment_query.py

@@ -7,16 +7,17 @@
 import pandas as pd
 import pyarrow as pa
 import pytest
-import tiledb
 from pyarrow import ArrowInvalid
 from scipy import sparse
 from somacore import AxisQuery, options
 
 import tiledbsoma as soma
-from tests._util import raises_no_typeguard
 from tiledbsoma import SOMATileDBContext, _factory
 from tiledbsoma._collection import CollectionBase
 from tiledbsoma.experiment_query import X_as_series
+import tiledb
+
+from tests._util import raises_no_typeguard
 
 # Number of features for the embeddings layer
 N_FEATURES = 50

apis/python/tests/test_factory.py

@@ -3,10 +3,10 @@
 
 import numpy as np
 import pytest
-import tiledb
 
 import tiledbsoma as soma
 from tiledbsoma import _constants
+import tiledb
 
 UNKNOWN_ENCODING_VERSION = "3141596"
 

apis/python/tests/test_metadata.py

@@ -7,9 +7,10 @@
 from typeguard import suppress_type_checks
 
 import tiledbsoma as soma
-from tests._util import raises_no_typeguard
 from tiledbsoma import _factory
 
+from tests._util import raises_no_typeguard
+
 """"
 Metadata handling tests for all SOMA foundational datatypes.
 """

apis/python/tests/test_notebook_sparse_dense.py

@@ -2,6 +2,7 @@
 
 import tiledbsoma
 import tiledbsoma.io
+
 from tests._util import PY_ROOT
 
 

apis/python/tests/test_platform_config.py

@@ -1,12 +1,12 @@
 import tempfile
 
 import pytest
-import tiledb
 
 import tiledbsoma
 import tiledbsoma.io
 import tiledbsoma.options._tiledb_create_options as tco
 from tiledbsoma._util import verify_obs_var
+import tiledb
 
 
 @pytest.mark.skip(reason="No longer return ArraySchema - see note in test")

apis/python/tests/test_query_condition.py

@@ -3,12 +3,12 @@
 import os
 
 import pytest
-import tiledb
 
 import tiledbsoma.pytiledbsoma as clib
 from tiledbsoma._arrow_types import tiledb_schema_to_arrow
 from tiledbsoma._exception import SOMAError
 from tiledbsoma._query_condition import QueryCondition
+import tiledb
 
 VERBOSE = False
 

apis/python/tests/test_sparse_nd_array.py

@@ -12,11 +12,11 @@
 import pyarrow as pa
 import pytest
 import scipy.sparse as sparse
-import tiledb
 
 import tiledbsoma as soma
 from tiledbsoma import _factory
 from tiledbsoma.options import SOMATileDBContext
+import tiledb
 
 from . import NDARRAY_ARROW_TYPES_NOT_SUPPORTED, NDARRAY_ARROW_TYPES_SUPPORTED
 from ._util import raises_no_typeguard