Forbid implicit optional in typing (#449)

fm3 · web-flow · commit 29376eb7f5e3 · 2021-10-13T12:36:43.000Z
diff --git a/webknossos/typecheck.sh b/webknossos/typecheck.sh
@@ -1,11 +1,11 @@
 #!/usr/bin/env bash
 set -eEuo pipefail
 
-echo -n "Typecheck webknossos: "
-python -m mypy -p webknossos --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages
+echo "Typecheck webknossos..."
+python -m mypy -p webknossos --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages --no-implicit-optional
 
-echo -n "Typecheck tests:      "
-python -m mypy -p tests --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages
+echo "Typecheck tests..."
+python -m mypy -p tests --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages --no-implicit-optional
 
-echo -n "Typecheck examples:   "
-python -m mypy -p examples --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages
+echo "Typecheck examples..."
+python -m mypy -p examples --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages --no-implicit-optional
diff --git a/webknossos/webknossos/dataset/dataset.py b/webknossos/webknossos/dataset/dataset.py
@@ -163,9 +163,9 @@ def add_layer(
         self,
         layer_name: str,
         category: str,
-        dtype_per_layer: Union[str, np.dtype, type] = None,
-        dtype_per_channel: Union[str, np.dtype, type] = None,
-        num_channels: int = None,
+        dtype_per_layer: Optional[Union[str, np.dtype, type]] = None,
+        dtype_per_channel: Optional[Union[str, np.dtype, type]] = None,
+        num_channels: Optional[int] = None,
         **kwargs: Any,
     ) -> Layer:
         """
@@ -262,9 +262,9 @@ def get_or_add_layer(
         self,
         layer_name: str,
         category: str,
-        dtype_per_layer: Union[str, np.dtype, type] = None,
-        dtype_per_channel: Union[str, np.dtype, type] = None,
-        num_channels: int = None,
+        dtype_per_layer: Optional[Union[str, np.dtype, type]] = None,
+        dtype_per_channel: Optional[Union[str, np.dtype, type]] = None,
+        num_channels: Optional[int] = None,
         **kwargs: Any,
     ) -> Layer:
         """
@@ -409,7 +409,7 @@ def add_symlink_layer(
         self,
         foreign_layer: Union[str, Path, Layer],
         make_relative: bool = False,
-        new_layer_name: str = None,
+        new_layer_name: Optional[str] = None,
     ) -> Layer:
         """
         Creates a symlink to the data at `foreign_layer` which belongs to another dataset.
@@ -454,7 +454,9 @@ def add_symlink_layer(
         return self.layers[layer_name]
 
     def add_copy_layer(
-        self, foreign_layer: Union[str, Path, Layer], new_layer_name: str = None
+        self,
+        foreign_layer: Union[str, Path, Layer],
+        new_layer_name: Optional[str] = None,
     ) -> Layer:
         """
         Copies the data at `foreign_layer` which belongs to another dataset to the current dataset.
@@ -495,8 +497,8 @@ def copy_dataset(
         self,
         new_dataset_path: Union[str, Path],
         scale: Optional[Tuple[float, float, float]] = None,
-        block_len: int = None,
-        file_len: int = None,
+        block_len: Optional[int] = None,
+        file_len: Optional[int] = None,
         compress: Optional[bool] = None,
         args: Optional[Namespace] = None,
     ) -> "Dataset":
diff --git a/webknossos/webknossos/dataset/mag_view.py b/webknossos/webknossos/dataset/mag_view.py
@@ -167,7 +167,7 @@ def get_view(
         self,
         offset: Optional[Vec3IntLike] = None,
         size: Optional[Vec3IntLike] = None,
-        read_only: bool = None,
+        read_only: Optional[bool] = None,
     ) -> View:
         """
         Returns a view that is limited to the specified bounding box.
@@ -261,7 +261,9 @@ def get_bounding_boxes_on_disk(
             self.close()
 
     def compress(
-        self, target_path: Union[str, Path] = None, args: Namespace = None
+        self,
+        target_path: Optional[Union[str, Path]] = None,
+        args: Optional[Namespace] = None,
     ) -> None:
         """
         Compresses the files on disk. This has consequences for writing data (see `write`).
diff --git a/webknossos/webknossos/dataset/view.py b/webknossos/webknossos/dataset/view.py
@@ -222,7 +222,7 @@ def get_view(
         self,
         offset: Vec3IntLike = Vec3Int(0, 0, 0),
         size: Optional[Vec3IntLike] = None,
-        read_only: bool = None,
+        read_only: Optional[bool] = None,
     ) -> "View":
         """
         Returns a view that is limited to the specified bounding box.
@@ -346,7 +346,7 @@ def _assert_bounds(
         self,
         offset: Vec3Int,
         size: Vec3Int,
-        strict: bool = None,
+        strict: Optional[bool] = None,
     ) -> None:
         if strict is None:
             strict = self._is_bounded
diff --git a/webknossos/webknossos/skeleton/group.py b/webknossos/webknossos/skeleton/group.py
@@ -65,7 +65,7 @@ def children(self) -> Iterator[GroupOrGraph]:
     def add_group(
         self,
         name: str,
-        _enforced_id: int = None,
+        _enforced_id: Optional[int] = None,
     ) -> "Group":
         new_group = Group(name, nml=self._nml, enforced_id=_enforced_id)
         self._children.add(new_group)
diff --git a/webknossos/webknossos/skeleton/nml/from_skeleton.py b/webknossos/webknossos/skeleton/nml/from_skeleton.py
@@ -35,7 +35,7 @@ def _random_color_rgba() -> Tuple[float, float, float, float]:
 
 def from_skeleton(
     group: "Group",
-    parameters: Dict[str, Any] = None,
+    parameters: Optional[Dict[str, Any]] = None,
     volume_dict: Optional[Dict[str, Any]] = None,
 ) -> NML:
     """
diff --git a/wkcuber/typecheck.sh b/wkcuber/typecheck.sh
@@ -1,7 +1,8 @@
 #!/bin/bash
 set -eEuo pipefail
-echo "Typecheck wkcuber module:"
-python -m mypy -p wkcuber --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages
 
-echo "Typecheck tests:"
-python -m mypy -p tests --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages
+echo "Typecheck wkcuber module..."
+python -m mypy -p wkcuber --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages --no-implicit-optional
+
+echo "Typecheck tests..."
+python -m mypy -p tests --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages --no-implicit-optional
diff --git a/wkcuber/wkcuber/check_equality.py b/wkcuber/wkcuber/check_equality.py
@@ -1,7 +1,7 @@
 import logging
 from argparse import ArgumentParser, Namespace
 from pathlib import Path
-from typing import Any, Callable
+from typing import Any, Callable, Optional
 
 from wkcuber.api.dataset import Dataset
 from wkcuber.api.bounding_box import BoundingBox, BoundingBoxNamedTuple
@@ -80,7 +80,7 @@ def assert_equality_for_chunk(
 
 
 def check_equality(
-    source_path: Path, target_path: Path, args: Namespace = None
+    source_path: Path, target_path: Path, args: Optional[Namespace] = None
 ) -> None:
 
     logging.info(f"Comparing {source_path} with {target_path}")
diff --git a/wkcuber/wkcuber/compress.py b/wkcuber/wkcuber/compress.py
@@ -3,6 +3,7 @@
 import shutil
 import logging
 from argparse import ArgumentParser, Namespace
+from typing import Optional
 from os import makedirs
 
 from wkcuber.api.dataset import Dataset
@@ -51,25 +52,25 @@ def compress_mag(
     layer_name: str,
     target_path: Path,
     mag: Mag,
-    args: Namespace = None,
+    args: Optional[Namespace] = None,
 ) -> None:
     Dataset(source_path).get_layer(layer_name).get_mag(mag).compress(
         target_path=Path(target_path), args=args
     )
 
 
 def compress_mag_inplace(
-    target_path: Path, layer_name: str, mag: Mag, args: Namespace = None
+    target_path: Path, layer_name: str, mag: Mag, args: Optional[Namespace] = None
 ) -> None:
     Dataset(target_path).get_layer(layer_name).get_mag(mag).compress(args=args)
 
 
 def compress_mags(
     source_path: Path,
     layer_name: str,
-    target_path: Path = None,
-    mags: List[Mag] = None,
-    args: Namespace = None,
+    target_path: Optional[Path] = None,
+    mags: Optional[List[Mag]] = None,
+    args: Optional[Namespace] = None,
 ) -> None:
     if target_path is None:
         target = source_path.with_suffix(".tmp")
diff --git a/wkcuber/wkcuber/convert_knossos.py b/wkcuber/wkcuber/convert_knossos.py
@@ -1,7 +1,7 @@
 import time
 import logging
 from pathlib import Path
-from typing import Tuple, cast
+from typing import Tuple, cast, Optional
 
 import wkw
 from argparse import ArgumentParser, Namespace
@@ -84,7 +84,7 @@ def convert_knossos(
     layer_name: str,
     dtype: str,
     mag: int = 1,
-    args: Namespace = None,
+    args: Optional[Namespace] = None,
 ) -> None:
     source_knossos_info = KnossosDatasetInfo(source_path, dtype)
     target_wkw_info = WkwDatasetInfo(
diff --git a/wkcuber/wkcuber/convert_nifti.py b/wkcuber/wkcuber/convert_nifti.py
@@ -127,7 +127,7 @@ def convert_nifti(
     scale: Tuple[float, ...],
     is_segmentation_layer: bool = False,
     file_len: int = DEFAULT_WKW_FILE_LEN,
-    bbox_to_enforce: BoundingBox = None,
+    bbox_to_enforce: Optional[BoundingBox] = None,
     use_orientation_header: bool = False,
     flip_axes: Optional[Union[int, Tuple[int, ...]]] = None,
 ) -> None:
@@ -229,7 +229,7 @@ def convert_folder_nifti(
     segmentation_subpath: str,
     scale: Tuple[float, ...],
     use_orientation_header: bool = False,
-    bbox_to_enforce: BoundingBox = None,
+    bbox_to_enforce: Optional[BoundingBox] = None,
     flip_axes: Optional[Union[int, Tuple[int, ...]]] = None,
 ) -> None:
     paths = list(source_folder_path.rglob("**/*.nii"))
diff --git a/wkcuber/wkcuber/cubing.py b/wkcuber/wkcuber/cubing.py
@@ -150,7 +150,7 @@ def read_image_file(
 
 
 def prepare_slices_for_wkw(
-    slices: List[np.ndarray], num_channels: int = None
+    slices: List[np.ndarray], num_channels: Optional[int] = None
 ) -> np.ndarray:
     # Write batch buffer which will have shape (x, y, channel_count, z)
     # since we concat along the last axis (z)
diff --git a/wkcuber/wkcuber/downsampling.py b/wkcuber/wkcuber/downsampling.py
@@ -1,5 +1,7 @@
 from pathlib import Path
 
+from typing import Optional
+
 from argparse import ArgumentParser, Namespace
 import os
 
@@ -97,13 +99,13 @@ def create_parser() -> ArgumentParser:
 
 def downsample_mags(
     path: Path,
-    layer_name: str = None,
-    from_mag: Mag = None,
-    max_mag: Mag = None,
+    layer_name: Optional[str] = None,
+    from_mag: Optional[Mag] = None,
+    max_mag: Optional[Mag] = None,
     interpolation_mode: str = "default",
-    buffer_edge_len: int = None,
+    buffer_edge_len: Optional[int] = None,
     compress: bool = True,
-    args: Namespace = None,
+    args: Optional[Namespace] = None,
     sampling_mode: str = SamplingModes.ANISOTROPIC,
     force_sampling_scheme: bool = False,
 ) -> None:
diff --git a/wkcuber/wkcuber/export_wkw_as_nifti.py b/wkcuber/wkcuber/export_wkw_as_nifti.py
@@ -146,7 +146,7 @@ def export_wkw_as_nifti(args: Namespace) -> None:
     )
 
 
-def export_wkw_as_nifti_from_arg_list(arg_list: List = None) -> None:
+def export_wkw_as_nifti_from_arg_list(arg_list: Optional[List] = None) -> None:
     parsed_args = create_parser().parse_args(arg_list)
     setup_logging(parsed_args)
     export_wkw_as_nifti(parsed_args)
diff --git a/wkcuber/wkcuber/metadata.py b/wkcuber/wkcuber/metadata.py
@@ -340,7 +340,7 @@ def detect_segmentation_layer(
     layer_name: str,
     max_id: int,
     compute_max_id: bool = False,
-    exact_bounding_box: dict = None,
+    exact_bounding_box: Optional[dict] = None,
 ) -> dict:
     layer_info = detect_standard_layer(
         dataset_path, layer_name, exact_bounding_box, category="segmentation"
diff --git a/wkcuber/wkcuber/tile_cubing.py b/wkcuber/wkcuber/tile_cubing.py
@@ -85,7 +85,7 @@ def replace_coordinates_with_glob_regex(pattern: str, coord_ids: Dict[str, int])
 
 
 def get_digit_counts_for_dimensions(pattern: str) -> Dict[str, int]:
-    """ Counts how many digits the dimensions x, y and z occupy in the given pattern. """
+    """Counts how many digits the dimensions x, y and z occupy in the given pattern."""
     occurrences = re.findall("({x+}|{y+}|{z+})", pattern)
     decimal_lengths = {"x": 0, "y": 0, "z": 0}
 
@@ -275,7 +275,7 @@ def tile_cubing(
     layer_name: str,
     batch_size: int,
     input_path_pattern: str,
-    args: Namespace = None,
+    args: Optional[Namespace] = None,
 ) -> None:
     decimal_lengths = get_digit_counts_for_dimensions(input_path_pattern)
     (
diff --git a/wkcuber/wkcuber/upsampling.py b/wkcuber/wkcuber/upsampling.py
@@ -2,6 +2,8 @@
 import os
 from pathlib import Path
 
+from typing import Optional
+
 from wkcuber.api.dataset import Dataset
 from wkcuber.downsampling_utils import SamplingModes
 from .mag import Mag
@@ -85,12 +87,12 @@ def create_parser() -> ArgumentParser:
 
 def upsample_mags(
     path: Path,
-    layer_name: str = None,
-    from_mag: Mag = None,
+    layer_name: Optional[str] = None,
+    from_mag: Optional[Mag] = None,
     target_mag: Mag = Mag(1),
-    buffer_edge_len: int = None,
+    buffer_edge_len: Optional[int] = None,
     compress: bool = True,
-    args: Namespace = None,
+    args: Optional[Namespace] = None,
     sampling_mode: str = SamplingModes.ANISOTROPIC,
 ) -> None:
     assert layer_name and from_mag or not layer_name and not from_mag, (
diff --git a/wkcuber/wkcuber/vendor/dm3.py b/wkcuber/wkcuber/vendor/dm3.py
@@ -220,7 +220,7 @@ def readLEDouble(f):
 
 
 class DM3(object):
-    """DM3 object. """
+    """DM3 object."""
 
     ## utility functions
     def _makeGroupString(self):
