Use standard pre-commit config (#69)

* Add standard pre-commit config * Automated pre-commit fixes * Make ruff happy * Make mypy happy * Fix setup.py line length
brainglobe · Feb 21, 2023 · 3e5043c · 3e5043c
1 parent 7bc8263
commit 3e5043c
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Showing 12 changed files with 98 additions and 77 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,8 +1,4 @@
 repos:
-    - repo: https://github.com/pycqa/isort
-      rev: 5.12.0
-      hooks:
-          - id: isort
     - repo: https://github.com/pre-commit/pre-commit-hooks
       rev: v4.4.0
       hooks:
@@ -15,14 +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: 6.0.0
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.240
       hooks:
-          - id: flake8
+        - id: ruff
     - repo: https://github.com/psf/black
       rev: 23.1.0
       hooks:
           - id: black
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v0.991
+      hooks:
+          - id: mypy
+            additional_dependencies:
+                - types-setuptools
+                - types-requests
diff --git a/brainreg_segment/atlas/utils.py b/brainreg_segment/atlas/utils.py
@@ -75,9 +75,10 @@ def structure_from_viewer(status, atlas_layer, atlas):
 
     # Using a regex, extract list of coordinates from status string
     assert hasattr(atlas_layer, "data"), "Atlas layer appears to be empty"
-    assert (
-        atlas_layer.data.ndim == 3
-    ), f'Atlas layer data does not have the right dim ("{atlas_layer.data.ndim}")'
+    assert atlas_layer.data.ndim == 3, (
+        "Atlas layer data does not have the right dim "
+        f'("{atlas_layer.data.ndim}")'
+    )
 
     try:
         coords = re.findall(r"\[\d{1,5}\s+\d{1,5}\s+\d{1,5}\]", status)[0][

diff --git a/brainreg_segment/layout/gui_elements.py b/brainreg_segment/layout/gui_elements.py
@@ -1,5 +1,6 @@
 # GUI ELEMENTS
-# from napari.resources import build_icons # Contains .SVGPATH to all icons for napari
+# from napari.resources import build_icons # Contains .SVGPATH to all icons
+# for napari
 
 from qtpy.QtWidgets import (
     QCheckBox,
@@ -91,7 +92,8 @@ def add_button(
 #             "QRadioButton { text-align: right; padding: 0; spacing: 30px;}"
 #         )
 
-#     # Too change indicator button ... needs to dynamically retrieve icon from Napari.
+#     # Too change indicator button ... needs to dynamically retrieve icon
+#     # from Napari.
 #     # Icons are saved as .svg files under napari.resources SVGPATH
 #     # "QRadioButton::indicator"
 #     # "{"
@@ -104,7 +106,8 @@ def add_button(
 #     # "}"
 #     # "QRadioButton::indicator::checked"
 #     # "{"
-#     # "image: url(/opt/miniconda3/envs/analysis/lib/python3.6/site-packages/napari/resources/icons/visibility.svg);"
+#     # "image: url(/opt/miniconda3/envs/analysis/lib/python3.6/site-packages/
+#                   napari/resources/icons/visibility.svg);"
 #     # "}"
 #     # )
 

diff --git a/brainreg_segment/measurement/measurement.py b/brainreg_segment/measurement/measurement.py
@@ -13,7 +13,7 @@
 #  (anteroposterior, mediolateral, vectical)
 def get_angles_and_distances_between_consecutive_points(
     point_layer: "napari.layers.Points",
-) -> Tuple[List[float]]:
+) -> Tuple[List[float], List[float], List[float]]:
     """Returns the distance and angles  for each pair of consecutive points.
 
     Receives a points layer and for each pair of consecutive points it
@@ -45,13 +45,15 @@ def get_angles_and_distances_between_consecutive_points(
         # projecting the vector in the sagital plane is just removing
         #  the "y/mediolateral" coordinate
         segment_vector_zx = segment_vector[[2, 0]]
-        # for the angle, z is used as the first direction/axis and x as the other
+        # for the angle, z is used as the first direction/axis and x as the
+        # other
         ap_angle = math.atan2(segment_vector_zx[1], segment_vector_zx[0])
         ap_angles.append(ap_angle)
         # projecting the vector in the frontal plane is just removing
         #  the anterioposterior coordinate.
         segment_vector_zy = segment_vector[[2, 1]]
-        # for the angle, z is used as the first direction/axis and y as the other
+        # for the angle, z is used as the first direction/axis and y as the
+        # other
         mp_angle = math.atan2(segment_vector_zy[1], segment_vector_zy[0])
         mp_angles.append(mp_angle)
         distances.append(np.linalg.norm(segment_vector))
@@ -100,9 +102,12 @@ def get_vectors_joining_points(
 def analyze_points_layer(
     point_layer: "napari.layers.Points",
     save_resuts_to_output_folder: bool = False,
-    output_folder: pathlib.Path = "results_folder",
+    output_folder: pathlib.Path = pathlib.Path("results_folder"),
 ) -> List[napari.types.LayerDataTuple]:
-    """Analyzes a point layer and saves distances and angles for consecutive points
+    """
+    Analyzes a point layer and saves distances and angles for consecutive
+    points
+
     points.csv
     id, coordx,  coordy,  coordz
     0,   ..
@@ -119,7 +124,8 @@ def analyze_points_layer(
         point_layer: A points layer to analyze.
         save_resuts_to_output_folder: A boolean, whether to save the results
             to the output folder below. If False, output_folder is ignored.
-        output_folder: Name of the folder where the output is going to be saved.
+        output_folder: Name of the folder where the output is going to be
+            saved.
     """
     if save_resuts_to_output_folder and not os.path.exists(output_folder):
         os.mkdir(output_folder)
@@ -171,7 +177,10 @@ def analyze_points_layer(
 
     # Adding vectors as a shapes layer.
     vectors_text = {
-        "text": "distance: {distance:.4f}\nap_angle: {ap_angle:.4f}\n mp_angle: {mp_angle:.4f}",
+        "text": (
+            "distance: {distance:.4f}\nap_angle: {ap_angle:.4f}\n"
+            "mp_angle: {mp_angle:.4f}"
+        ),
         "size": 8,
         "color": "green",
         "anchor": "upper_left",

diff --git a/brainreg_segment/segment.py b/brainreg_segment/segment.py
@@ -1,12 +1,13 @@
 from pathlib import Path
+from typing import List, Optional
 
 import napari
 import numpy as np
+from bg_atlasapi import BrainGlobeAtlas
 from napari.qt.threading import thread_worker
 from qtpy import QtCore
 from qtpy.QtWidgets import QFileDialog, QGridLayout, QGroupBox, QLabel, QWidget
 
-from bg_atlasapi import BrainGlobeAtlas
 from brainreg_segment.atlas.utils import (
     get_available_atlases,
     structure_from_viewer,
@@ -26,12 +27,12 @@
 from brainreg_segment.paths import Paths
 from brainreg_segment.regions.IO import export_label_layers, save_label_layers
 
-# SEGMENTATION  ################################################################################
+### SEGMENTATION
 from brainreg_segment.segmentation_panels.regions import RegionSeg
 from brainreg_segment.segmentation_panels.tracks import TrackSeg
 from brainreg_segment.tracks.IO import export_splines, save_track_layers
 
-# LAYOUT HELPERS ################################################################################
+### LAYOUT HELPERS
 
 
 class SegmentationWidget(QWidget):
@@ -46,17 +47,20 @@ def __init__(
         self.viewer = viewer
 
         # Main layers
-        self.base_layer = []  # Contains registered brain / reference brain
-        self.atlas_layer = []  # Contains annotations / region information
+
+        # Contains registered brain / reference brain
+        self.base_layer: Optional[napari.layers.Image] = None
+        # Contains annotations / region information
+        self.atlas_layer: Optional[napari.layers.Labels] = None
 
         # Other data
-        self.hemispheres_data = []
+        self.hemispheres_data: Optional[np.ndarray] = None
 
         # Track variables
-        self.track_layers = []
+        self.track_layers: List[napari.layers.Tracks] = []
 
         # Region variables
-        self.label_layers = []
+        self.label_layers: List[napari.layers.Labels] = []
 
         # Atlas variables
         self.current_atlas_name = ""

diff --git a/brainreg_segment/segmentation_panels/regions.py b/brainreg_segment/segmentation_panels/regions.py
@@ -89,31 +89,40 @@ def add_region_panel(self, row):
 
     def toggle_region_panel(self):
         # TODO: Change color scheme directly when theme is switched
-        # TODO: "text-align" property should follow constant SEGM_METHODS_PANEL_ALIGN
+        # TODO: "text-align" property should follow constant
+        # SEGM_METHODS_PANEL_ALIGN
         if self.region_panel.isVisible():
             self.region_panel.setVisible(False)
             if self.parent.viewer.theme == "dark":
                 self.parent.show_regionseg_button.setStyleSheet(
-                    f"QPushButton {{ background-color: #414851; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
-                    f"QPushButton:pressed {{ background-color: #414851; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton {{ background-color: #414851; text-align:"
+                    f"{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton:pressed {{ background-color: #414851; "
+                    f"text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
                 )
             else:
                 self.parent.show_regionseg_button.setStyleSheet(
-                    f"QPushButton {{ background-color: #d6d0ce; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
-                    f"QPushButton:pressed {{ background-color: #d6d0ce; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton {{ background-color: #d6d0ce; text-align:"
+                    f"{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton:pressed {{ background-color: #d6d0ce; "
+                    f"text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
                 )
 
         else:
             self.region_panel.setVisible(True)
             if self.parent.viewer.theme == "dark":
                 self.parent.show_regionseg_button.setStyleSheet(
-                    f"QPushButton {{ background-color: #7e868f; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
-                    f"QPushButton:pressed {{ background-color: #7e868f; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton {{ background-color: #7e868f; text-align:"
+                    f"{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton:pressed {{ background-color: #7e868f; "
+                    f"text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
                 )
             else:
                 self.parent.show_regionseg_button.setStyleSheet(
-                    f"QPushButton {{ background-color: #fdf194; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
-                    f"QPushButton:pressed {{ background-color: #fdf194; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton {{ background-color: #fdf194; text-align:"
+                    f"{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton:pressed {{ background-color: #fdf194; "
+                    f"text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
                 )
 
     def check_saved_region(self):

diff --git a/brainreg_segment/segmentation_panels/tracks.py b/brainreg_segment/segmentation_panels/tracks.py
@@ -139,31 +139,40 @@ def add_track_panel(self, row):
 
     def toggle_track_panel(self):
         # TODO: Change color scheme directly when theme is switched
-        # TODO: "text-align" property should follow constant SEGM_METHODS_PANEL_ALIGN
+        # TODO: "text-align" property should follow constant
+        # SEGM_METHODS_PANEL_ALIGN
         if self.track_panel.isVisible():
             self.track_panel.setVisible(False)
             if self.parent.viewer.theme == "dark":
                 self.parent.show_trackseg_button.setStyleSheet(
-                    f"QPushButton {{ background-color: #414851; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
-                    f"QPushButton:pressed {{ background-color: #414851; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton {{ background-color: #414851; text-align:"
+                    f"{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton:pressed {{ background-color: #414851; "
+                    f"text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
                 )
             else:
                 self.parent.show_trackseg_button.setStyleSheet(
-                    f"QPushButton {{ background-color: #d6d0ce; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
-                    f"QPushButton:pressed {{ background-color: #d6d0ce; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton {{ background-color: #d6d0ce; text-align:"
+                    f"{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton:pressed {{ background-color: #d6d0ce; "
+                    f"text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
                 )
 
         else:
             self.track_panel.setVisible(True)
             if self.parent.viewer.theme == "dark":
                 self.parent.show_trackseg_button.setStyleSheet(
-                    f"QPushButton {{ background-color: #7e868f; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
-                    f"QPushButton:pressed {{ background-color: #7e868f; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton {{ background-color: #7e868f; text-align:"
+                    f"{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton:pressed {{ background-color: #7e868f; "
+                    f"text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
                 )
             else:
                 self.parent.show_trackseg_button.setStyleSheet(
-                    f"QPushButton {{ background-color: #fdf194; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
-                    f"QPushButton:pressed {{ background-color: #fdf194; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton {{ background-color: #fdf194; text-align:"
+                    f"{SEGM_METHODS_PANEL_ALIGN};}}"
+                    f"QPushButton:pressed {{ background-color: #fdf194; "
+                    f"text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
                 )
 
     def check_saved_track(self):

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,27 +1,10 @@
 [tool.black]
-target-version = ['py36', 'py37', 'py38']
+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
-sections=["FUTURE","STDLIB","THIRDPARTY","BRAINGLOBE","FIRSTPARTY","LOCALFOLDER"]
-known_brainglobe=["brainreg", "brainreg_segment", "brainglobe_napari_io", "bg_space", "bg_atlasapi"]
+[tool.ruff]
+line-length = 79
+exclude = ["__init__.py","build",".eggs"]
+select = ["I", "E", "F"]
+fix = true
diff --git a/setup.cfg b/setup.cfg
@@ -4,14 +4,14 @@ 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}
 
 [bumpversion:part:release]
 optional_value = prod
 first_value = rc
-values = 
+values =
 	rc
 	prod
 

diff --git a/setup.py b/setup.py
@@ -26,7 +26,10 @@
     author="Adam Tyson, Horst Obenhaus",
     author_email="code@adamltyson.com",
     license="BSD-3-Clause",
-    description="Manual segmentation of 3D brain structures in a common anatomical space",
+    description=(
+        "Manual segmentation of 3D brain structures "
+        "in a common anatomical space"
+    ),
     long_description=long_description,
     long_description_content_type="text/markdown",
     install_requires=requirements,

diff --git a/tests/tests/test_integration/test_tracks/test_track_analysis.py b/tests/tests/test_integration/test_tracks/test_track_analysis.py
@@ -2,8 +2,8 @@
 
 import numpy as np
 import pandas as pd
-
 from bg_atlasapi import BrainGlobeAtlas
+
 from brainreg_segment.tracks.analysis import run_track_analysis
 
 atlas_name = "allen_mouse_50um"

diff --git a/tests/tests/test_unit/test_atlas/test_atlas_utils.py b/tests/tests/test_unit/test_atlas/test_atlas_utils.py
@@ -1,6 +1,6 @@
 import numpy as np
-
 from bg_atlasapi import BrainGlobeAtlas
+
 from brainreg_segment.atlas import utils as atlas_utils
 
 atlas_name = "allen_mouse_50um"