Merge pull request #284 from comic/fix_flake8

Add flake8 checks

.pre-commit-config.yaml

@@ -12,6 +12,18 @@ repos:
     hooks:
       - id: black
         language: python
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.9
+    hooks:
+      - id: flake8
+        language: python
+        additional_dependencies:
+          - flake8-bugbear
+          - flake8-import-order
+          - pep8-naming
+          # The following is disabled due to a runtime error
+          # - flake8-docstrings
+          - mccabe
   - repo: https://github.com/mgedmin/check-manifest
     rev: "0.40"
     hooks:

docs/conf.py

@@ -22,7 +22,7 @@
 
 sys.path.insert(0, os.path.abspath(".."))
 
-import evalutils
+import evalutils  # noqa: E402
 
 # -- General configuration ---------------------------------------------
 
@@ -83,6 +83,7 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
+
 # Always document the __init__ method
 def skip(app, what, name, obj, skip, options):
     if name == "__init__":

evalutils/__init__.py

@@ -1,9 +1,9 @@
 from .__version__ import __version__ as _version
 from .evalutils import (
+    BaseAlgorithm,
     ClassificationEvaluation,
     DetectionEvaluation,
     Evaluation,
-    BaseAlgorithm,
 )
 
 __author__ = """James Meakin"""

evalutils/cli.py

@@ -1,5 +1,4 @@
 import re
-
 from pathlib import Path
 
 import click

evalutils/evalutils.py

@@ -3,31 +3,38 @@
 from abc import ABC, abstractmethod
 from os import PathLike
 from pathlib import Path
-from typing import Tuple, Dict, Set, Callable, List, Union, Pattern
+from typing import Callable, Dict, List, Pattern, Set, Tuple, Union
 from warnings import warn
 
-from pandas import DataFrame, merge, Series, concat
+from pandas import DataFrame, Series, concat, merge
 
-from .exceptions import FileLoaderError, ValidationError, ConfigurationError
-from .io import first_int_in_filename_key, FileLoader, CSVLoader
+from .exceptions import ConfigurationError, FileLoaderError, ValidationError
+from .io import CSVLoader, FileLoader, first_int_in_filename_key
 from .scorers import score_detection
 from .validators import DataFrameValidator
 
 logger = logging.getLogger(__name__)
 
 
+DEFAULT_INPUT_PATH = Path("/input/")
+DEFAULT_ALGORITHM_OUTPUT_IMAGES_PATH = Path("/output/images/")
+DEFAULT_ALGORITHM_OUTPUT_FILE_PATH = Path("/output/results.json")
+DEFAULT_GROUND_TRUTH_PATH = Path("/opt/evaluation/ground-truth/")
+DEFAULT_EVALUATION_OUTPUT_FILE_PATH = Path("/output/metrics.json")
+
+
 class BaseAlgorithm(ABC):
     def __init__(
         self,
         *,
         index_key: str,
         file_loaders: Dict[str, FileLoader],
         file_filters: Dict[str, Pattern[str]] = None,
-        input_path: Path = Path("/input/"),
-        output_path: Path = Path("/output/images/"),
+        input_path: Path = DEFAULT_INPUT_PATH,
+        output_path: Path = DEFAULT_ALGORITHM_OUTPUT_IMAGES_PATH,
         file_sorter_key: Callable = None,
         validators: Dict[str, Tuple[DataFrameValidator, ...]],
-        output_file: PathLike = Path("/output/results.json"),
+        output_file: PathLike = DEFAULT_ALGORITHM_OUTPUT_FILE_PATH,
     ):
         """
         The base class for all algorithms. Sets the environment and controls
@@ -159,14 +166,14 @@ class BaseEvaluation(ABC):
     def __init__(
         self,
         *,
-        ground_truth_path: Path = Path("/opt/evaluation/ground-truth/"),
-        predictions_path: Path = Path("/input/"),
+        ground_truth_path: Path = DEFAULT_GROUND_TRUTH_PATH,
+        predictions_path: Path = DEFAULT_INPUT_PATH,
         file_sorter_key: Callable = first_int_in_filename_key,
         file_loader: FileLoader,
         validators: Tuple[DataFrameValidator, ...],
         join_key: str = None,
         aggregates: Set[str] = None,
-        output_file: PathLike = Path("/output/metrics.json"),
+        output_file: PathLike = DEFAULT_EVALUATION_OUTPUT_FILE_PATH,
     ):
         """
         The base class for all evaluations. Sets the environment and controls

evalutils/io.py

@@ -2,12 +2,12 @@
 import re
 from abc import ABC, abstractmethod
 from pathlib import Path
-from typing import Union, Dict, List
+from typing import Dict, List, Union
 
-from SimpleITK import ReadImage, GetArrayFromImage
+from SimpleITK import GetArrayFromImage, ReadImage
 from imageio import imread
 from pandas import read_csv
-from pandas.errors import ParserError, EmptyDataError
+from pandas.errors import EmptyDataError, ParserError
 
 from .exceptions import FileLoaderError
 

evalutils/stats.py

@@ -8,7 +8,7 @@
 from scipy.ndimage.morphology import binary_erosion, generate_binary_structure
 
 
-def distance_transform_edt_float32(
+def distance_transform_edt_float32(  # noqa: C901
     input,
     sampling=None,
     return_distances=True,

evalutils/templates/algorithm/hooks/post_gen_project.py

@@ -1,12 +1,12 @@
 import os
 import shutil
 from pathlib import Path
+
 from evalutils.utils import (
     bootstrap_development_distribution,
     convert_line_endings,
 )
 
-
 ALGORITHM_NAME = "{{ cookiecutter.algorithm_name }}"
 IS_DEV_BUILD = int("{{ cookiecutter.dev_build }}") == 1
 
@@ -16,7 +16,6 @@
 for f in templated_files:
     shutil.move(f.name, f.stem)
 
-
 convert_line_endings()
 
 if IS_DEV_BUILD:

evalutils/templates/evaluation/hooks/post_gen_project.py

@@ -1,6 +1,7 @@
 import os
 import shutil
 from pathlib import Path
+
 from evalutils.utils import (
     bootstrap_development_distribution,
     convert_line_endings,
@@ -45,7 +46,6 @@ def remove_detection_files():
 if CHALLENGE_KIND.lower() != "classification":
     remove_classification_files()
 
-
 convert_line_endings()
 
 if IS_DEV_BUILD:

evalutils/utils.py

@@ -1,5 +1,5 @@
-from pathlib import Path
 import shutil
+from pathlib import Path
 
 EOL_UNIX = b"\n"
 EOL_WIN = b"\r\n"

setup.cfg

@@ -3,7 +3,7 @@ collect_ignore = ['setup.py']
 
 [flake8]
 application-import-names =
-    gcapi
+    evalutils
     tests
 import-order-style = pycharm
 docstring-convention = numpy

setup.py

@@ -2,7 +2,7 @@
 
 import os
 
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 NAME = "evalutils"
 REQUIRES_PYTHON = ">=3.6.0"
@@ -46,7 +46,10 @@
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
     ],
-    description="evalutils helps challenge administrators easily create evaluation containers for grand-challenge.org.",
+    description=(
+        "evalutils helps challenge administrators easily create evaluation "
+        "containers for grand-challenge.org."
+    ),
     extras_require={"test": test_requirements},
     install_requires=requirements,
     license="MIT license",

tests/test_algorithm.py

@@ -1,16 +1,18 @@
+import json
+import os
+import re
+import shutil
 from pathlib import Path
+
 import SimpleITK
-import shutil
 import numpy as np
 from pandas import DataFrame
-import re
-import os
-import json
+
 from evalutils import BaseAlgorithm
 from evalutils.io import SimpleITKLoader
 from evalutils.validators import (
-    UniquePathIndicesValidator,
     UniqueImagesValidator,
+    UniquePathIndicesValidator,
 )
 
 

tests/test_io.py

@@ -7,11 +7,11 @@
 
 from evalutils.exceptions import FileLoaderError
 from evalutils.io import (
-    get_first_int_in,
-    ImageIOLoader,
     CSVLoader,
+    ImageIOLoader,
     SimpleITKLoader,
     first_int_in_filename_key,
+    get_first_int_in,
 )