Apply a good chunk of linting

packages/pipeline/src/pyearthtools/pipeline/branching/unify.py

@@ -59,7 +59,7 @@ def check_validity(self, sample: tuple) -> Union[None, int]:  # pragma: no cover
                 Which sub_sample to be returned.
                 Return `None` if invalid.
         """
-        raise NotImplementedError(f"Child class must supply `check_validity` function.")
+        raise NotImplementedError("Child class must supply `check_validity` function.")
 
     def unify(self, sample: tuple) -> Any:
         index = self.check_validity(sample)

packages/pipeline/src/pyearthtools/pipeline/controller.py

@@ -99,13 +99,13 @@ def set_parent_record(
     def parent_pipeline(self) -> Pipeline:
         """Get parent pipeline of this `PipelineIndex`, will not include self"""
         if self._partial_parent is None:
-            raise ValueError(f"Parent record has not been set with `set_parent_record`, cannot get parent pipeline")
+            raise ValueError("Parent record has not been set with `set_parent_record`, cannot get parent pipeline")
         return self._partial_parent(*self._steps)
 
     def as_pipeline(self) -> Pipeline:
         """Get `PipelineIndex` as full pipeline, will include self"""
         if self._partial_parent is None:
-            raise ValueError(f"Parent record has not been set with `set_parent_record`, cannot get step as pipeline")
+            raise ValueError("Parent record has not been set with `set_parent_record`, cannot get step as pipeline")
         return self._partial_parent(*self._steps, self)
 
     @abstractmethod

packages/pipeline/src/pyearthtools/pipeline/iterators.py

@@ -23,7 +23,7 @@
 from functools import cached_property
 from abc import ABCMeta, abstractmethod
 
-from typing import Any, Callable, Generator, Hashable, Iterable, Optional, Union, Set
+from typing import Any, Callable, Generator, Hashable, Iterable, Optional, Union
 from pathlib import Path
 
 import numpy as np

packages/pipeline/src/pyearthtools/pipeline/operations/dask/filters.py

@@ -60,7 +60,7 @@ def filter(self, sample: da.Array):
                 If sample contains nan's
         """
         if not bool(da.array(list(da.isnan(sample))).any()):
-            raise PipelineFilterException(sample, f"Data contained nan's.")
+            raise PipelineFilterException(sample, "Data contained nan's.")
 
 
 class DropAllNan(daskFilter):
@@ -86,7 +86,7 @@ def filter(self, sample: da.Array):
                 If sample contains nan's
         """
         if not bool(da.array(list(da.isnan(sample))).all()):
-            raise PipelineFilterException(sample, f"Data contained all nan's.")
+            raise PipelineFilterException(sample, "Data contained all nan's.")
 
 
 class DropValue(daskFilter):

packages/pipeline/src/pyearthtools/pipeline/operations/dask/reshape.py

@@ -195,7 +195,7 @@ def __init__(
         self.shape_attempt = shape_attempt
 
         if isinstance(flatten_dims, int) and flatten_dims < 1:
-            raise ValueError(f"'flatten_dims' cannot be smaller than 1.")
+            raise ValueError("'flatten_dims' cannot be smaller than 1.")
         self.flatten_dims = flatten_dims
 
     def _prod_shape(self, shape):
@@ -205,8 +205,8 @@ def _prod_shape(self, shape):
 
     def _configure_shape_attempt(self) -> tuple[Union[str, int], ...]:
         if not self._fillshape or not self.shape_attempt:
-            raise RuntimeError(f"Cannot find shape to unflatten with, try flattening first.")
-        if not "..." in self.shape_attempt:
+            raise RuntimeError("Cannot find shape to unflatten with, try flattening first.")
+        if "..." not in self.shape_attempt:
             return self.shape_attempt
 
         shape_attempt = list(self.shape_attempt)
@@ -235,15 +235,15 @@ def apply(self, data: da.Array) -> da.Array:
 
     def undo(self, data: da.Array) -> da.Array:
         if self._unflattenshape is None:
-            raise RuntimeError(f"Shape not set, therefore cannot undo")
+            raise RuntimeError("Shape not set, therefore cannot undo")
 
         def _unflatten(data, shape):
             while len(data.shape) > len(shape):
                 shape = (data[-len(shape)], *shape)
             return data.reshape(shape)
 
         if self.flatten_dims is None:
-            raise RuntimeError(f"`flatten_dims` was not set, and this set hasn't been used. Cannot Unflatten.")
+            raise RuntimeError("`flatten_dims` was not set, and this set hasn't been used. Cannot Unflatten.")
 
         data_shape = data.shape
         parsed_shape = data_shape[: -1 * min(1, (self.flatten_dims - 1))] if len(data_shape) > 1 else data_shape

packages/pipeline/src/pyearthtools/pipeline/operations/numpy/filters.py

@@ -58,7 +58,7 @@ def filter(self, sample: np.ndarray):
                 If sample contains nan's
         """
         if not bool(np.array(list(np.isnan(sample))).any()):
-            raise PipelineFilterException(sample, f"Data contained nan's.")
+            raise PipelineFilterException(sample, "Data contained nan's.")
 
 
 class DropAllNan(NumpyFilter):
@@ -86,7 +86,7 @@ def filter(self, sample: np.ndarray):
                 If sample contains nan's
         """
         if not bool(np.array(list(np.isnan(sample))).all()):
-            raise PipelineFilterException(sample, f"Data contained all nan's.")
+            raise PipelineFilterException(sample, "Data contained all nan's.")
 
 
 class DropValue(NumpyFilter):

packages/pipeline/src/pyearthtools/pipeline/operations/numpy/reshape.py

@@ -190,7 +190,7 @@ def _prod_shape(self, shape):
     def _configure_shape_attempt(self) -> tuple[Union[str, int], ...]:
         if not self._fillshape or not self.shape_attempt:
             raise RuntimeError("Cannot find shape to unflatten with, try flattening first.")
-        if not "..." in self.shape_attempt:
+        if "..." not in self.shape_attempt:
             return self.shape_attempt
 
         shape_attempt = list(self.shape_attempt)
@@ -219,15 +219,15 @@ def apply(self, data: np.ndarray) -> np.ndarray:
 
     def undo(self, data: np.ndarray) -> np.ndarray:
         if self._unflattenshape is None:
-            raise RuntimeError(f"Shape not set, therefore cannot undo")
+            raise RuntimeError("Shape not set, therefore cannot undo")
 
         def _unflatten(data, shape):
             # while len(data.shape) > len(shape):
             #     shape = (data[-len(shape)], *shape)
             return data.reshape(shape)
 
         if self.flatten_dims is None:
-            raise RuntimeError(f"`flatten_dims` was not set, and this set hasn't been used. Cannot Unflatten.")
+            raise RuntimeError("`flatten_dims` was not set, and this set hasn't been used. Cannot Unflatten.")
 
         data_shape = data.shape
         # parsed_shape = data_shape[: -1 * min(1, (self.flatten_dims - 1))] if len(data_shape) > 1 else []

packages/pipeline/src/pyearthtools/pipeline/operations/numpy/select.py

@@ -13,7 +13,7 @@
 # limitations under the License.
 
 
-from typing import Any, Optional
+from typing import Optional
 
 import numpy as np
 

packages/pipeline/src/pyearthtools/pipeline/operations/numpy/split.py

@@ -56,7 +56,7 @@ def split(self, sample: np.ndarray) -> tuple[np.ndarray]:
     def join(self, sample: tuple[np.ndarray]) -> np.ndarray:
         """Join `sample` together, recovering initial shape"""
         if self.axis_size is None:
-            raise RuntimeError(f"`axis_size` not set.")
+            raise RuntimeError("`axis_size` not set.")
 
         data = np.concatenate(sample, axis=0)
         shape = data.shape

packages/pipeline/src/pyearthtools/pipeline/operations/transforms.py

@@ -13,7 +13,7 @@
 # limitations under the License.
 
 
-from typing import Any, TypeVar, Union, Optional
+from typing import TypeVar, Union, Optional
 
 import xarray as xr
 

packages/pipeline/src/pyearthtools/pipeline/operations/xarray/_align_dates.py

@@ -13,7 +13,7 @@
 # limitations under the License.
 
 
-from typing import TypeVar, Optional
+from typing import TypeVar
 
 import pandas as pd
 import xarray as xr

packages/pipeline/src/pyearthtools/pipeline/operations/xarray/_recode_calendar.py

@@ -13,7 +13,7 @@
 # limitations under the License.
 
 
-from typing import TypeVar, Optional
+from typing import TypeVar
 
 import xarray as xr
 

packages/pipeline/src/pyearthtools/pipeline/operations/xarray/filters.py

@@ -72,7 +72,7 @@ def _check(self, sample: xr.Dataset):
             sample = sample[self.variables]
 
         if not bool(np.array(list(np.isnan(sample).values())).any()):
-            raise PipelineFilterException(sample, f"Data contained nan's.")
+            raise PipelineFilterException(sample, "Data contained nan's.")
 
 
 class DropAllNan(XarrayFilter):
@@ -109,7 +109,7 @@ def _check(self, sample: xr.Dataset):
             sample = sample[self.variables]
 
         if not bool(np.array(list(np.isnan(sample).values())).all()):
-            raise PipelineFilterException(sample, f"Data contained all nan's.")
+            raise PipelineFilterException(sample, "Data contained all nan's.")
 
 
 class DropValue(XarrayFilter):

packages/pipeline/tests/operations/xarray/test_xarray_conversion.py

@@ -16,7 +16,6 @@
 
 import numpy as np
 import xarray as xr
-import dask
 import pytest
 
 

packages/pipeline/tests/pipeline/operations/dask/test_dask_compute.py

@@ -16,7 +16,6 @@
 from pyearthtools.pipeline.operations.dask.compute import Compute
 
 import xarray as xr
-import dask
 import numpy as np
 
 

packages/pipeline/tests/pipeline/test_sequence.py

@@ -14,7 +14,6 @@
 
 
 from __future__ import annotations
-from typing import Any
 
 import pytest
 
@@ -24,10 +23,9 @@
 
 import pyearthtools.data
 
-from pyearthtools.pipeline import Pipeline, exceptions, modifications
+from pyearthtools.pipeline import Pipeline
 from pyearthtools.pipeline.modifications.idx_modification import SequenceRetrieval
 
-from pyearthtools.pipeline import Operation
 from pyearthtools.data import Index
 
 

packages/pipeline/tests/pipeline/test_temporal_idx_mod.py

@@ -14,7 +14,6 @@
 
 
 from __future__ import annotations
-from typing import Any
 
 import pytest
 
@@ -24,10 +23,9 @@
 
 import pyearthtools.data
 
-from pyearthtools.pipeline import Pipeline, exceptions
+from pyearthtools.pipeline import Pipeline
 from pyearthtools.pipeline.modifications.idx_modification import TemporalRetrieval
 
-from pyearthtools.pipeline import Operation
 from pyearthtools.data import Index
 
 

packages/utils/src/pyearthtools/utils/config.py

@@ -24,9 +24,7 @@
 from __future__ import annotations
 
 import ast
-import base64
 import builtins  # Explicitly use builtins.set as 'set' will be shadowed by a function
-import json
 import os
 import site
 import sys

packages/utils/src/pyearthtools/utils/data/__init__.py

@@ -19,3 +19,5 @@
 
 from pyearthtools.utils.data import converter
 from pyearthtools.utils.data.tesselator import Tesselator
+
+__all__ = ["converter", "Tesselator"]

packages/utils/src/pyearthtools/utils/data/converter.py

@@ -18,6 +18,8 @@
 
 from __future__ import annotations
 
+import dask
+import dask.array as da
 import importlib
 import importlib.util
 import json
@@ -326,10 +328,6 @@ def _rebuild_arrays(self, numpy_array: np.ndarray, xarray_distill: dict) -> xr.D
         full_coords.pop("Variables", None)
 
         ar = np
-        try:
-            import dask.array as da
-        except (ImportError, ModuleNotFoundError):
-            ar = da
 
         for i in range(numpy_array.shape[xarray_distill["dims"].index("Variables")]):
             data = ar.take(numpy_array, i, axis=xarray_distill["dims"].index("Variables"))
@@ -436,7 +434,6 @@ def convert_from_xarray(
             (dask.array.Array | tuple[dask.array.Array, ...]):
                 Generated array/s from Dataset/s
         """
-        import dask.array as da
 
         self._set_records(data, replace=replace)
 
@@ -456,7 +453,6 @@ def convert(dataset: xr.DataArray | xr.Dataset) -> da.Array:
         raise TypeError(f"Unable to convert data of {type(data)} to `da.array`")
 
     def convert_to_xarray(self, data, pop: bool = True):
-        import dask.array as da
 
         # if isinstance(data, da.Array):
         #     data = data.compute()

packages/utils/src/pyearthtools/utils/data/tesselator/__init__.py

@@ -245,12 +245,12 @@ def stitch(
         if (np.array(self.stride) > np.array(self.kernel_size)).any():
             raise TesselatorException(
                 "Stride is larger than kernel size, incoming data cannot be complete.\n"
-                f"Set stride smaller, or use another tesselator "
+                "Set stride smaller, or use another tesselator "
             )
 
         if self._layout is None:
             raise TesselatorException(
-                f"This tesselator has not be used to patch, therefore it has not recorded the layout, and cannot be used to stitch."
+                "This tesselator has not be used to patch, therefore it has not recorded the layout, and cannot be used to stitch."
             )
 
         if not input_data.shape == self._post_shape and not self.ignore_difference:
@@ -261,7 +261,7 @@ def stitch(
 
         all_patches = []
         for input_patch in input_data:
-            all_patches.append(_patching.reorder.reorder(input_patch, data_format, "TCHW"))
+            all_patches.append(_patching.reorder(input_patch, data_format, "TCHW"))
 
         all_patches = np.array(all_patches)
 
@@ -274,7 +274,7 @@ def stitch(
             full_prediction = _patching.subset.center(full_prediction, self._initial_shape[-2:])
         except TesselatorException:
             warnings.warn(
-                f"Could not trim to initial_shape, if 'padding' is None, an incomplete patch set is made. Padding with nans",
+                "Could not trim to initial_shape, if 'padding' is None, an incomplete patch set is made. Padding with nans",
                 TesselatorWarning,
             )
             pad_width = [

packages/utils/src/pyearthtools/utils/data/tesselator/_patching/__init__.py

@@ -15,11 +15,16 @@
 
 """
 Data processing tools for use by the [Tesselator][pyearthtools.utils.data.Tesselator]
+
 """
+from ._reorder import reorder
+
 DEFAULT_FORMAT_SUBSET: str = "...HW"
 
 DEFAULT_FORMAT_PATCH_ORGANISE: str = "P...HW"
 DEFAULT_FORMAT_PATCH: str = "RP...HW"
 DEFAULT_FORMAT_PATCH_AFTER: str = "...HW"
 
-from . import patches, reorder, subset
+from . import patches, subset  # noqa
+
+__all__ = ["patches", "reorder", "subset"]

packages/utils/src/pyearthtools/utils/data/tesselator/_patching/patches.py

@@ -29,8 +29,8 @@
     DEFAULT_FORMAT_PATCH_AFTER,
     DEFAULT_FORMAT_PATCH_ORGANISE,
 )
-from pyearthtools.utils.data.tesselator._patching.reorder import reorder
-from pyearthtools.utils.data.tesselator._patching.subset import center, cut_center
+from pyearthtools.utils.data.tesselator._patching._reorder import reorder
+from pyearthtools.utils.data.tesselator._patching.subset import cut_center
 
 
 def factors(value: int) -> list[list[int, int]]:
@@ -273,7 +273,7 @@ def find_dim_expand(length, kernel, stride, rounding_flip: bool = False):
         )
         # padd_width.append(((kernel_size[0] - stride[0])//2,(kernel_size[1] - stride[1])//2))
         if (np.array(padd_width) < 0).any():
-            raise ValueError(f"Padding width cannot be negative, try setting `padding` to None")
+            raise ValueError("Padding width cannot be negative, try setting `padding` to None")
 
         if padding == "constant":
             kwargs["constant_values"] = kwargs.get("constant_values", np.nan)

packages/utils/src/pyearthtools/utils/data/tesselator/_patching/subset.py

@@ -25,7 +25,7 @@
 import numpy as np
 
 from pyearthtools.utils.data.tesselator._patching import DEFAULT_FORMAT_SUBSET
-from pyearthtools.utils.data.tesselator._patching.reorder import move_to_end, reorder
+from pyearthtools.utils.data.tesselator._patching._reorder import move_to_end, reorder
 from pyearthtools.utils.exceptions import TesselatorException
 
 

packages/utils/src/pyearthtools/utils/initialisation/imports.py

@@ -45,11 +45,11 @@ def dynamic_import(object_path: str) -> Callable | ModuleType:
         pass
 
     if not object_path:
-        raise ImportError(f"object_path cannot be empty")
+        raise ImportError("object_path cannot be empty")
     try:
         return importlib.import_module(object_path)
     except ModuleNotFoundError:
         object_path_list = object_path.split(".")
         return getattr(dynamic_import(".".join(object_path_list[:-1])), object_path_list[-1])
-    except ValueError as e:
+    except ValueError:
         raise ModuleNotFoundError("End of module definition reached")