Pre-commit autofixes

Author: BrianMichell

src/mdio/builder/dataset_builder.py

@@ -101,7 +101,9 @@ def add_dimension(self, name: str, size: int) -> "MDIODatasetBuilder":
         self._state = _BuilderState.HAS_DIMENSIONS
         return self
 
-    def push_dimension(self, dimension: NamedDimension, position: int, new_dim_chunk_size: int=1, new_dim_size: int=1) -> "MDIODatasetBuilder":
+    def push_dimension(
+        self, dimension: NamedDimension, position: int, new_dim_chunk_size: int = 1, new_dim_size: int = 1
+    ) -> "MDIODatasetBuilder":
         """Pushes a dimension to all Coordiantes and Variables.
         The position argument is the domain index of the dimension to push.
         If a Variable is within the position domain, it will be inserted at the position and all remaining dimensions will be shifted to the right.
@@ -130,23 +132,25 @@ def push_dimension(self, dimension: NamedDimension, position: int, new_dim_chunk
 
         def propogate_dimension(variable: Variable, position: int, new_dim_chunk_size: int) -> Variable:
             """Propogates the dimension to the variable or coordinate."""
-            from mdio.builder.schemas.chunk_grid import RegularChunkGrid, RegularChunkShape
+            from mdio.builder.schemas.chunk_grid import RegularChunkGrid
+            from mdio.builder.schemas.chunk_grid import RegularChunkShape
+
             if len(variable.dimensions) + 1 <= position:
                 # Don't do anything if the new dimension is not within the Variable's domain
                 return variable
             new_dimensions = variable.dimensions[:position] + [dimension] + variable.dimensions[position:]
-            
+
             # Get current chunk shape from metadata
             current_chunk_shape = (1,) * len(variable.dimensions)  # Default fallback
             if variable.metadata is not None and variable.metadata.chunk_grid is not None:
                 current_chunk_shape = variable.metadata.chunk_grid.configuration.chunk_shape
-            
+
             # Insert new chunk size at the correct position
             new_chunk_shape = current_chunk_shape[:position] + (new_dim_chunk_size,) + current_chunk_shape[position:]
-            
+
             # Create new chunk grid configuration
             new_chunk_grid = RegularChunkGrid(configuration=RegularChunkShape(chunk_shape=new_chunk_shape))
-            
+
             # Update metadata with new chunk grid
             new_metadata = variable.metadata.model_copy() if variable.metadata else VariableMetadata()
             new_metadata.chunk_grid = new_chunk_grid

src/mdio/builder/templates/abstract_dataset_template.py

@@ -1,11 +1,11 @@
 """Template method pattern implementation for MDIO v1 dataset template."""
 
 import copy
+import logging
 from abc import ABC
 from abc import abstractmethod
-import logging
+from collections.abc import Callable
 from typing import Any
-from typing import Callable
 
 from mdio.builder.dataset_builder import MDIODatasetBuilder
 from mdio.builder.schemas import compressors
@@ -21,6 +21,7 @@
 
 logger = logging.getLogger(__name__)
 
+
 class AbstractDatasetTemplate(ABC):
     """Abstract base class that defines the template method for Dataset building factory.
 
@@ -80,7 +81,6 @@ def build_dataset(
         if header_dtype:
             self._add_trace_headers(header_dtype)
 
-
         # This seems to be breaking the dataset, but adds the trace dimension.
         for transform in self._queued_transforms:
             logger.debug(f"Applying transform: {transform.__name__}")
@@ -163,7 +163,6 @@ def _add_dimensions(self) -> None:
         for i in range(len(self._dim_sizes) - len(self._dim_names)):
             self._builder.add_dimension(f"dim_{i}", self._dim_sizes[len(self._dim_names) + i])
 
-
     def _add_coordinates(self) -> None:
         """Add custom coordinates.
 

src/mdio/converters/segy.py

@@ -516,7 +516,7 @@ def segy_to_mdio(  # noqa PLR0913
     if "trace" in grid.dim_names:
         # Find the trace dimension index and remove it from sizes
         trace_idx = grid.dim_names.index("trace")
-        dataset_sizes = grid.shape[:trace_idx] + grid.shape[trace_idx + 1:]
+        dataset_sizes = grid.shape[:trace_idx] + grid.shape[trace_idx + 1 :]
 
     mdio_ds: Dataset = mdio_template.build_dataset(
         name=mdio_template.name,

src/mdio/segy/geometry.py

@@ -247,7 +247,9 @@ def create_trace_index(
     return index_headers
 
 
-def analyze_non_indexed_headers(index_headers: HeaderArray, dtype: DTypeLike = np.int16, index_names: Sequence[str] = None) -> NDArray:
+def analyze_non_indexed_headers(
+    index_headers: HeaderArray, dtype: DTypeLike = np.int16, index_names: Sequence[str] = None
+) -> NDArray:
     """Check input headers for SEG-Y input to help determine geometry.
 
     This function reads in trace_qc_count headers and finds the unique cable values. Then, it
@@ -436,7 +438,7 @@ def transform(
         self,
         index_headers: HeaderArray,
         grid_overrides: dict[str, bool | int],
-        index_names = None,
+        index_names=None,
     ) -> NDArray:
         """Perform the grid transform."""
         self.validate(index_headers, grid_overrides)
@@ -474,7 +476,7 @@ def transform(
         self,
         index_headers: HeaderArray,
         grid_overrides: dict[str, bool | int],
-        index_names = None,
+        index_names=None,
     ) -> NDArray:
         """Perform the grid transform."""
         self.validate(index_headers, grid_overrides)
@@ -538,7 +540,6 @@ def run(
         chunksize: Sequence[int] | None = None,
     ) -> tuple[HeaderArray, tuple[str], tuple[int]]:
         """Run grid overrides and return result."""
-
         for override in grid_overrides:
             if override in self.parameters:
                 continue

src/mdio/segy/parsers.py

@@ -11,11 +11,11 @@
 
 import numpy as np
 from psutil import cpu_count
+from segy.arrays import HeaderArray
 from tqdm.auto import tqdm
 
 from mdio.segy._workers import header_scan_worker
 
-from segy.arrays import HeaderArray
 if TYPE_CHECKING:
     from segy import SegyFile
 

src/mdio/segy/utilities.py

@@ -10,10 +10,10 @@
 import numpy as np
 from dask.array.core import normalize_chunks
 
+from mdio.builder.schemas.dimension import NamedDimension
 from mdio.core import Dimension
 from mdio.segy.geometry import GridOverrider
 from mdio.segy.parsers import parse_headers
-from mdio.builder.schemas.dimension import NamedDimension
 
 if TYPE_CHECKING:
     from numpy.typing import DTypeLike
@@ -28,41 +28,42 @@
 
 def _create_delayed_trace_dimension_transform(headers_subset: HeaderArray, position: int) -> callable:
     """Create a delayed transform function that adds a trace dimension and its coordinate.
-    
+
     This function creates a closure that captures the headers_subset and position,
     but defers the actual computation until the transform is executed by the dataset builder.
     The transform adds both the trace dimension and a corresponding coordinate.
-    
+
     Args:
         headers_subset: The header array containing trace information
         position: The position where the trace dimension should be inserted
-        
+
     Returns:
         A callable that can be used as a transform function
     """
+
     def delayed_transform(builder):
         from mdio.builder.schemas.dtype import ScalarType
-        
+
         # Calculate the trace dimension size at execution time
         if "trace" in headers_subset.dtype.names:
             trace_size = int(np.max(headers_subset["trace"]))
         else:
             # Fallback: if trace field doesn't exist, we need to determine size differently
             raise ValueError("Trace field not found in headers_subset when executing delayed transform")
-        
+
         # Add the trace dimension
         trace_dimension = NamedDimension(name="trace", size=trace_size)
         builder.push_dimension(trace_dimension, position=position, new_dim_chunk_size=1, new_dim_size=trace_size)
-        
+
         # Add the corresponding coordinate for the trace dimension
         builder.add_coordinate(
             "trace",
             dimensions=("trace",),
             data_type=ScalarType.INT32,
         )
-        
+
         return builder
-    
+
     return delayed_transform
 
 

tests/integration/test_import_streamer_grid_overrides.py

@@ -7,7 +7,6 @@
 
 import dask
 import numpy as np
-import numpy.testing as npt
 import pytest
 import xarray.testing as xrt
 from tests.integration.conftest import get_segy_mock_4d_spec