[STYLE] format with black (#215)

* format with black

* rm unused package data file

* flake8 ignore E701

pyproject.toml

@@ -92,15 +92,15 @@ Repository = "https://github.com/SBU-BMI/wsinfer"
 wsinfer = "wsinfer.cli.cli:cli"
 
 [tool.setuptools.package-data]
-wsinfer = ["py.typed", "patchlib/presets/*.csv", "schemas/*.json"]
+wsinfer = ["py.typed", "schemas/*.json"]
 
 [tool.setuptools.packages.find]
 include = ["wsinfer*"]
 
 # Flake8-pyproject (https://pypi.org/project/Flake8-pyproject/)
 [tool.flake8]
 max-line-length = 88
-extend-ignore = ['E203']
+extend-ignore = ['E203', 'E701']
 exclude = "wsinfer/_version.py"
 
 [tool.mypy]

wsinfer/errors.py

@@ -11,8 +11,7 @@ class UnknownArchitectureError(WsinferException):
     """Architecture is unknown and cannot be found."""
 
 
-class WholeSlideImageDirectoryNotFound(WsinferException, FileNotFoundError):
-    ...
+class WholeSlideImageDirectoryNotFound(WsinferException, FileNotFoundError): ...
 
 
 class DuplicateFilePrefixesFound(WsinferException):
@@ -23,24 +22,19 @@ class DuplicateFilePrefixesFound(WsinferException):
     """
 
 
-class WholeSlideImagesNotFound(WsinferException, FileNotFoundError):
-    ...
+class WholeSlideImagesNotFound(WsinferException, FileNotFoundError): ...
 
 
-class ResultsDirectoryNotFound(WsinferException, FileNotFoundError):
-    ...
+class ResultsDirectoryNotFound(WsinferException, FileNotFoundError): ...
 
 
-class PatchDirectoryNotFound(WsinferException, FileNotFoundError):
-    ...
+class PatchDirectoryNotFound(WsinferException, FileNotFoundError): ...
 
 
-class CannotReadSpacing(WsinferException):
-    ...
+class CannotReadSpacing(WsinferException): ...
 
 
-class NoBackendException(WsinferException):
-    ...
+class NoBackendException(WsinferException): ...
 
 
 class BackendNotAvailable(WsinferException):

wsinfer/modellib/models.py

@@ -11,8 +11,7 @@
 
 
 @dataclasses.dataclass
-class LocalModelTorchScript(Model):
-    ...
+class LocalModelTorchScript(Model): ...
 
 
 def get_registered_model(name: str) -> HFModelTorchScript:

wsinfer/modellib/run_inference.py

@@ -4,6 +4,7 @@
 > In the prediction (test) phase, no data augmentation was applied except for the
 > normalization of the color channels.
 """
+
 from __future__ import annotations
 
 import os

wsinfer/write_geojson.py

@@ -45,7 +45,7 @@ def _row_to_geojson(row: pd.Series, prob_cols: list[str]) -> dict:
             # measurements is a list of {"name": str, "value": float} dicts.
             # https://qupath.github.io/javadoc/docs/qupath/lib/measurements/MeasurementList.html
             "measurements": measurements,
-            "objectType": "tile"
+            "objectType": "tile",
             # classification is a dict of "name": str and optionally "color": int.
             # https://qupath.github.io/javadoc/docs/qupath/lib/objects/classes/PathClass.html
             # We do not include classification because we do not enforce a single class

wsinfer/wsi.py

@@ -47,13 +47,11 @@
 
 
 @overload
-def set_backend(name: Literal["openslide"]) -> type[openslide.OpenSlide]:
-    ...
+def set_backend(name: Literal["openslide"]) -> type[openslide.OpenSlide]: ...
 
 
 @overload
-def set_backend(name: Literal["tiffslide"]) -> type[tiffslide.TiffSlide]:
-    ...
+def set_backend(name: Literal["tiffslide"]) -> type[tiffslide.TiffSlide]: ...
 
 
 def set_backend(