Use standard pre-commit config (#77)

* Add standard pre-commit config

* Add known-first-party config

* Add automatic pre-commit fixes

* Fix deprecated bool alias

.pre-commit-config.yaml

@@ -1,12 +1,6 @@
 repos:
-    - repo: https://github.com/pycqa/isort
-      rev: 5.10.1
-      hooks:
-          - id: isort
-            types: [text]
-            types_or: [python, cython]
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.3.0
+      rev: v4.4.0
       hooks:
           - id: check-docstring-first
           - id: check-executables-have-shebangs
@@ -17,20 +11,18 @@ repos:
             args: [--fix=lf]
           - id: requirements-txt-fixer
           - id: trailing-whitespace
-            # bump2version produces whitespace in setup.cfg, so exclude to
-            # not inferfere with versioning
-            exclude: setup.cfg
-    - repo: https://github.com/pycqa/flake8
-      rev: 5.0.4
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.240
       hooks:
-          - id: flake8
+        - id: ruff
     - repo: https://github.com/psf/black
-      rev: 22.10.0
+      rev: 23.1.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.990
+      rev: v0.991
       hooks:
           - id: mypy
             additional_dependencies:
                 - types-setuptools
+                - types-requests

pyproject.toml

@@ -2,32 +2,19 @@
 requires = ['setuptools', 'wheel', 'cython']
 build-backend = 'setuptools.build_meta'
 
+[tool.cibuildwheel]
+build = "cp38-* cp39-* cp310-*"
+
 [tool.black]
 target-version = ['py38', 'py39', 'py310']
 skip-string-normalization = false
 line-length = 79
-exclude = '''
-(
-  /(
-      \.eggs
-    | \.git
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | buck-out
-    | build
-    | dist
-    | examples
-  )/
-)
-'''
-
-[tool.isort]
-profile = "black"
-line_length = 79
 
+[tool.ruff]
+line-length = 79
+exclude = ["__init__.py","build",".eggs"]
+select = ["I", "E", "F"]
+fix = true
 
-[tool.cibuildwheel]
-build = "cp38-* cp39-* cp310-*"
+[tool.ruff.isort]
+known-first-party = ["cellfinder_core"]

setup.cfg

@@ -4,12 +4,12 @@ commit = True
 tag = True
 tag_name = {new_version}
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<rc>\d+))?
-serialize = 
+serialize =
 	{major}.{minor}.{patch}-{release}{rc}
 	{major}.{minor}.{patch}
 
 [options]
-package_dir = 
+package_dir =
 	=src
 packages = find:
 
@@ -19,7 +19,7 @@ where = src
 [bumpversion:part:release]
 optional_value = prod
 first_value = rc
-values = 
+values =
 	rc
 	prod
 

src/cellfinder_core/classify/augment.py

@@ -51,7 +51,6 @@ def augment(augmentation_parameters, image, scale_back=True):
 
 
 def rescale_to_isotropic(image, relative_pixel_sizes, interpolation_order):
-
     if not all_elements_equal(relative_pixel_sizes):
         min_pixel_size = min(relative_pixel_sizes)
         normalised_pixel_sizes = []

src/cellfinder_core/classify/resnet.py

@@ -171,7 +171,6 @@ def residual_block(
     bn_epsilon=1e-5,
     axis=3,
 ):
-
     """
     Residual unit from He et al. (2015)
 
@@ -314,7 +313,6 @@ def get_shortcut(
     bn_epsilon=1e-5,
     axis=3,
 ):
-
     """
     Create shortcut. For none-bottleneck residual units, this is just the
     identity. Otherwise, the input is reshaped to match the output of the

src/cellfinder_core/classify/tools.py

@@ -48,7 +48,6 @@ def get_model(
 
 
 def make_lists(tiff_files, train=True):
-
     signal_list = []
     background_list = []
     if train:

src/cellfinder_core/detect/filters/setup_filters.py

@@ -42,7 +42,6 @@ def setup(
 
 
 def setup_tile_filtering(plane):
-
     max_value = get_max_value(plane)
     clipping_value = max_value - 2
     thrsh_val = max_value - 1

src/cellfinder_core/train/train_yml.py

@@ -313,7 +313,6 @@ def run(
     save_progress=False,
     epochs=100,
 ):
-
     from cellfinder_core.main import suppress_tf_logging
 
     suppress_tf_logging(tf_suppress_log_messages)

tests/tests/test_integration/test_detection.py

@@ -32,7 +32,6 @@ def background_array():
 # FIXME: This isn't a very good example
 @pytest.mark.slow
 def test_detection_full(signal_array, background_array):
-
     cells_test = main(
         signal_array,
         background_array,

tests/tests/test_unit/test_tools/test_geometry.py

@@ -8,7 +8,7 @@ def test_make_sphere():
 
 
 def test_four_connected_kernel():
-    assert (
-        (np.array([[0, 1, 0], [1, 1, 1], [0, 1, 0]], dtype=np.bool))
-        == geometry.four_connected_kernel()
-    ).all()
+    np.testing.assert_array_equal(
+        geometry.four_connected_kernel(),
+        np.array([[0, 1, 0], [1, 1, 1], [0, 1, 0]], dtype=bool),
+    )