add flake pre-commit

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+repos:
+-   repo: https://github.com/python/black
+    rev: 19.10b0
+    hooks:
+    - id: black
+      pass_filenames: true
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.9
+    hooks:
+    - id: flake8
+      pass_filenames: true
+#      exclude: __init__.py

brainreg/backend/niftyreg/run.py

@@ -132,7 +132,7 @@ def run_niftyreg(
                 registration_output_folder, f"downsampled_standard_{name}.tiff"
             )
 
-            ## do the tiff part at the beginning
+            # do the tiff part at the beginning
             downsampled_brain = imio.load_any(
                 target_brain_path,
                 x_scaling,

brainreg/main.py

@@ -1,8 +1,6 @@
 import logging
 import numpy as np
 
-from pathlib import Path
-
 import bg_space as bg
 import imio
 

brainreg/utils/misc.py

@@ -1,9 +1,4 @@
-from argparse import (
-    ArgumentParser,
-    ArgumentDefaultsHelpFormatter,
-    ArgumentTypeError,
-    Namespace,
-)
+from argparse import Namespace
 
 
 def get_arg_groups(args, parser):

brainreg/utils/volume.py

@@ -132,7 +132,7 @@ def calculate_volumes(
         "total_volume_mm3",
     )
     for atlas_value in unique_vals_left:
-        if atlas_value is not 0:  # outside brain
+        if atlas_value != 0:  # outside brain
             try:
                 df = add_structure_volume_to_df(
                     df,

pyproject.toml

@@ -0,0 +1,16 @@
+[tool.black]
+line-length = 79
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | _build
+  | buck-out
+  | build
+  | dist
+)/
+'''

setup.cfg

@@ -10,3 +10,9 @@ replace = version="{new_version}"
 [bumpversion:file:brainreg/__init__.py]
 search = __version__ = "{current_version}"
 replace = __version__ = "{new_version}"
+
+[flake8]
+ignore = E203, E231, W503
+max-line-length = 79
+;max-complexity = 5
+exclude = __init__.py

setup.py

@@ -31,7 +31,14 @@
     long_description_content_type="text/markdown",
     install_requires=requirements,
     extras_require={
-        "dev": ["black", "pytest-cov", "pytest", "coverage", "bump2version"]
+        "dev": [
+            "black",
+            "pytest-cov",
+            "pytest",
+            "coverage",
+            "bump2version",
+            "pre-commit",
+        ]
     },
     python_requires=">=3.6, <3.8",
     packages=find_namespace_packages(exclude=("docs", "tests*")),