Make ruff and black happy

funkelab · Apr 29, 2024 · d7c742d · d7c742d
1 parent f41e742
commit d7c742d
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Showing 10 changed files with 137 additions and 76 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -11,24 +11,6 @@ target-version = ['py38', 'py39', 'py310']
 
 [tool.ruff]
 line-length = 79
-select = [
-    "E", "F", "W", #flake8
-    "UP", # pyupgrade
-    "I", # isort
-    "BLE", # flake8-blind-exception
-    "B", # flake8-bugbear
-    "A", # flake8-builtins
-    "C4", # flake8-comprehensions
-    "ISC", # flake8-implicit-str-concat
-    "G", # flake8-logging-format
-    "PIE", # flake8-pie
-    "SIM", # flake8-simplify
-]
-ignore = [
-    "E501", # line too long. let black handle this
-    "UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
-    "SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9
-]
 
 exclude = [
     ".bzr",
@@ -54,3 +36,24 @@ exclude = [
 
 target-version = "py38"
 fix = true
+
+[tool.ruff.lint]
+select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "SIM", # flake8-simplify
+]
+
+ignore = [
+    "E501", # line too long. let black handle this
+    "UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
+    "SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9
+]
diff --git a/src/motile_plugin/__init__.py b/src/motile_plugin/__init__.py
@@ -1,6 +1,4 @@
 __version__ = "0.0.1"
 from .widgets.motile_widget import MotileWidget
 
-__all__ = (
-    "MotileWidget",
-)
+__all__ = ("MotileWidget",)
diff --git a/src/motile_plugin/_graph_layer_utils.py b/src/motile_plugin/_graph_layer_utils.py
@@ -17,7 +17,10 @@ def to_napari_graph_layer(graph, name, loc_keys=("t", "z", "y", "x")):
         napari_id += 1
     num_nodes = napari_id
 
-    edges = [[nx_id_to_napari_id[s], nx_id_to_napari_id[t]] for s, t in graph.edges()]
+    edges = [
+        [nx_id_to_napari_id[s], nx_id_to_napari_id[t]]
+        for s, t in graph.edges()
+    ]
     coords = [
         get_location(
             graph.nodes[napari_id_to_nx_id[nap_id]], loc_keys=loc_keys

diff --git a/src/motile_plugin/_tests/conftest.py b/src/motile_plugin/_tests/conftest.py
@@ -32,7 +32,11 @@ def multi_hypothesis_segmentation_2d():
 
     """
     frame_shape = (100, 100)
-    total_shape = (2, 2, *frame_shape)  # 2 time points, 2 hypotheses layers, H, W
+    total_shape = (
+        2,
+        2,
+        *frame_shape,
+    )  # 2 time points, 2 hypotheses layers, H, W
     segmentation = np.zeros(total_shape, dtype="int32")
     # make frame with one cell in center with label 1 (hypo 1)
     rr0, cc0 = disk(center=(50, 50), radius=20, shape=frame_shape)
@@ -90,8 +94,16 @@ def graph_2d():
         ),
     ]
     edges = [
-        ("0_1", "1_1", {EdgeAttr.DISTANCE.value: 42.43, EdgeAttr.IOU.value: 0.0}),
-        ("0_1", "1_2", {EdgeAttr.DISTANCE.value: 11.18, EdgeAttr.IOU.value: 0.395}),
+        (
+            "0_1",
+            "1_1",
+            {EdgeAttr.DISTANCE.value: 42.43, EdgeAttr.IOU.value: 0.0},
+        ),
+        (
+            "0_1",
+            "1_2",
+            {EdgeAttr.DISTANCE.value: 11.18, EdgeAttr.IOU.value: 0.395},
+        ),
     ]
     graph.add_nodes_from(nodes)
     graph.add_edges_from(edges)
@@ -159,8 +171,16 @@ def multi_hypothesis_graph_2d():
     ]
 
     edges = [
-        ("0_0_1", "1_0_1", {EdgeAttr.DISTANCE.value: 42.426, EdgeAttr.IOU.value: 0.0}),
-        ("0_0_1", "1_1_1", {EdgeAttr.DISTANCE.value: 43.011, EdgeAttr.IOU.value: 0.0}),
+        (
+            "0_0_1",
+            "1_0_1",
+            {EdgeAttr.DISTANCE.value: 42.426, EdgeAttr.IOU.value: 0.0},
+        ),
+        (
+            "0_0_1",
+            "1_1_1",
+            {EdgeAttr.DISTANCE.value: 43.011, EdgeAttr.IOU.value: 0.0},
+        ),
         (
             "0_0_1",
             "1_0_2",
@@ -171,9 +191,21 @@ def multi_hypothesis_graph_2d():
             "1_1_2",
             {EdgeAttr.DISTANCE.value: 11.180, EdgeAttr.IOU.value: 0.4768},
         ),
-        ("0_1_1", "1_0_1", {EdgeAttr.DISTANCE.value: 43.011, EdgeAttr.IOU.value: 0.0}),
-        ("0_1_1", "1_1_1", {EdgeAttr.DISTANCE.value: 42.426, EdgeAttr.IOU.value: 0.0}),
-        ("0_1_1", "1_0_2", {EdgeAttr.DISTANCE.value: 15.0, EdgeAttr.IOU.value: 0.2402}),
+        (
+            "0_1_1",
+            "1_0_1",
+            {EdgeAttr.DISTANCE.value: 43.011, EdgeAttr.IOU.value: 0.0},
+        ),
+        (
+            "0_1_1",
+            "1_1_1",
+            {EdgeAttr.DISTANCE.value: 42.426, EdgeAttr.IOU.value: 0.0},
+        ),
+        (
+            "0_1_1",
+            "1_0_2",
+            {EdgeAttr.DISTANCE.value: 15.0, EdgeAttr.IOU.value: 0.2402},
+        ),
         (
             "0_1_1",
             "1_1_2",
@@ -188,7 +220,9 @@ def multi_hypothesis_graph_2d():
 def sphere(center, radius, shape):
     assert len(center) == len(shape)
     indices = np.moveaxis(np.indices(shape), 0, -1)  # last dim is the index
-    distance = np.linalg.norm(np.subtract(indices, np.asarray(center)), axis=-1)
+    distance = np.linalg.norm(
+        np.subtract(indices, np.asarray(center)), axis=-1
+    )
     mask = distance <= radius
     return mask
 

diff --git a/src/motile_plugin/_tests/test_solver.py b/src/motile_plugin/_tests/test_solver.py
@@ -1,4 +1,3 @@
-
 from motile_plugin.backend.solve import solve
 from motile_plugin.backend.solver_params import SolverParamsWidget
 
@@ -12,11 +11,11 @@ def test_solve_2d(segmentation_2d, graph_2d):
     soln_graph = solve(params, segmentation_2d)
     assert set(soln_graph.nodes) == set(graph_2d.nodes)
 
+
 def test_solve_3d(segmentation_3d, graph_3d):
     params = SolverParamsWidget()
     params.merge_cost = None
     params.appear_cost = None
     params.disappear_cost = None
     soln_graph = solve(params, segmentation_3d)
     assert set(soln_graph.nodes) == set(graph_3d.nodes)
-
diff --git a/src/motile_plugin/backend/motile_run.py b/src/motile_plugin/backend/motile_run.py
@@ -17,8 +17,8 @@
 
 
 class MotileRun(BaseModel):
-    """An object representing a motile tracking run.
-    """
+    """An object representing a motile tracking run."""
+
     run_name: str
     solver_params: SolverParams
     input_segmentation: np.ndarray | None = None
@@ -40,20 +40,26 @@ def _make_directory(time, run_name):
     def _unpack_directory(directory):
         stamp_len = len(datetime.now().strftime(STAMP_FORMAT))
         stamp = directory[0:stamp_len]
-        run_name = directory[stamp_len+1:]
+        run_name = directory[stamp_len + 1 :]
         try:
             time = datetime.strptime(stamp, STAMP_FORMAT)
-        except:
-            raise ValueError(f"Cannot unpack directory {directory} into timestamp and run name.")
+        except ValueError as e:
+            raise ValueError(
+                f"Cannot unpack directory {directory} into timestamp and run name."
+            ) from e
         return time, run_name
 
     def save(self, base_path: str | Path):
         base_path = Path(base_path)
         run_dir = base_path / self._make_directory(self.time, self.run_name)
         Path.mkdir(run_dir)
         self._save_params(run_dir)
-        self._save_segmentation(run_dir, IN_SEG_FILEANME, self.input_segmentation)
-        self._save_segmentation(run_dir, OUT_SEG_FILEANME, self.output_segmentation)
+        self._save_segmentation(
+            run_dir, IN_SEG_FILEANME, self.input_segmentation
+        )
+        self._save_segmentation(
+            run_dir, OUT_SEG_FILEANME, self.output_segmentation
+        )
         self._save_tracks(run_dir)
         if self.gaps is not None:
             self._save_gaps(run_dir)
@@ -80,7 +86,7 @@ def load(cls, run_dir: Path | str):
 
     def _save_params(self, run_dir):
         params_file = run_dir / PARAMS_FILENAME
-        with open(params_file, 'w') as f:
+        with open(params_file, "w") as f:
             json.dump(self.solver_params.__dict__, f)
 
     @staticmethod
@@ -110,7 +116,7 @@ def _load_segmentation(
 
     def _save_tracks(self, run_dir: Path):
         tracks_file = run_dir / TRACKS_FILENAME
-        with open(tracks_file, 'w') as f:
+        with open(tracks_file, "w") as f:
             json.dump(nx.node_link_data(self.tracks), f)
 
     @staticmethod
@@ -127,8 +133,8 @@ def _load_tracks(run_dir: Path, required: bool = True) -> nx.DiGraph:
 
     def _save_gaps(self, run_dir: Path):
         gaps_file = run_dir / GAPS_FILENAME
-        with open(gaps_file, 'w') as f:
-            f.write(','.join(map(str, self.gaps)))
+        with open(gaps_file, "w") as f:
+            f.write(",".join(map(str, self.gaps)))
 
     @staticmethod
     def _load_gaps(run_dir, required: bool = True) -> list[float]:
@@ -142,8 +148,6 @@ def _load_gaps(run_dir, required: bool = True) -> list[float]:
         else:
             return None
 
-
-
     def delete(self, base_path: str | Path):
         base_path = Path(base_path)
         run_dir = base_path / self._make_directory(self.time, self.run_name)
@@ -155,4 +159,3 @@ def delete(self, base_path: str | Path):
         (run_dir / TRACKS_FILENAME).unlink()
         (run_dir / GAPS_FILENAME).unlink()
         run_dir.rmdir()
-
diff --git a/src/motile_plugin/widgets/motile_widget.py b/src/motile_plugin/widgets/motile_widget.py
@@ -85,7 +85,7 @@ def update_napari_layers(self, run: MotileRun) -> None:
             run.output_segmentation[:, 0], name=run.run_name + "_seg"
         )
         if run.tracks is None or run.tracks.number_of_nodes() == 0:
-            warn("No tracks found for run {run.run_name}")
+            warn(f"No tracks found for run {run.run_name}", stacklevel=2)
             self.tracks_layer = None
         else:
             track_data, track_props, track_edges = to_napari_tracks_layer(

diff --git a/src/motile_plugin/widgets/run_editor.py b/src/motile_plugin/widgets/run_editor.py
@@ -1,4 +1,3 @@
-
 from warnings import warn
 
 import numpy as np
@@ -23,15 +22,20 @@
 
 class RunEditor(QWidget):
     create_run = Signal(MotileRun)
+
     def __init__(self, run_name, solver_params, layers, multiseg=False):
         # TODO: Don't pass static layers
         super().__init__()
         self.run_name: QLineEdit
         self.layers: list
         self.layer_selection_box: QComboBox
-        self.solver_params_widget = SolverParamsWidget(solver_params, editable=True)
+        self.solver_params_widget = SolverParamsWidget(
+            solver_params, editable=True
+        )
         main_layout = QVBoxLayout()
-        main_layout.addWidget(self._ui_select_labels_layer(layers, multiseg=multiseg))
+        main_layout.addWidget(
+            self._ui_select_labels_layer(layers, multiseg=multiseg)
+        )
         main_layout.addWidget(self.solver_params_widget)
         main_layout.addWidget(self._ui_run_motile(run_name))
         self.setLayout(main_layout)
@@ -42,9 +46,13 @@ def _ui_select_labels_layer(self, layers, multiseg=False) -> QGroupBox:
         layer_layout = QHBoxLayout()
         self.layer_selection_box = QComboBox()
         if multiseg:
-            self.layer_selection_box.setSelectionMode(QAbstractItemView.SelectionMode.MultiSelection)
+            self.layer_selection_box.setSelectionMode(
+                QAbstractItemView.SelectionMode.MultiSelection
+            )
         self.update_labels_layers(layers)
-        self.layer_selection_box.setToolTip("Select the labels layer you want to use for tracking")
+        self.layer_selection_box.setToolTip(
+            "Select the labels layer you want to use for tracking"
+        )
         layer_layout.addWidget(self.layer_selection_box)
         layer_group.setLayout(layer_layout)
         return layer_group
@@ -76,7 +84,9 @@ def _ui_run_motile(self, run_name) -> QGroupBox:
         # Generate Tracks button
         generate_tracks_btn = QPushButton("Create Run")
         generate_tracks_btn.clicked.connect(self.emit_run)
-        generate_tracks_btn.setToolTip("Run tracking. Might take minutes or longer for larger samples.")
+        generate_tracks_btn.setToolTip(
+            "Run tracking. Might take minutes or longer for larger samples."
+        )
         run_layout.addWidget(generate_tracks_btn)
 
         # Add running widget
@@ -93,12 +103,16 @@ def get_run(self):
         run_name = self.get_run_name()
         input_layer = self.get_labels_layer()
         if input_layer is None:
-            warn("No input labels layer selected")
+            warn("No input labels layer selected", stacklevel=2)
             return None
         input_seg = np.expand_dims(input_layer.data, 1)
         print(f"{input_seg.shape=}")
         params = self.solver_params_widget.solver_params.copy()
-        return MotileRun(run_name=run_name, solver_params=params, input_segmentation=input_seg)
+        return MotileRun(
+            run_name=run_name,
+            solver_params=params,
+            input_segmentation=input_seg,
+        )
 
     def emit_run(self):
         run = self.get_run()