Change hypotheses boxes to QListWidget to reduce space

.pre-commit-config.yaml

@@ -1,10 +1,10 @@
 repos:
     - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.262
+      rev: v0.0.272
       hooks:
         - id: ruff
     - repo: https://github.com/Lucas-C/pre-commit-hooks
-      rev: v1.5.1
+      rev: v1.5.3
       hooks:
         - id: remove-tabs
           exclude: Makefile|docs/Makefile|\.bat$
@@ -22,15 +22,15 @@ repos:
           - id: trailing-whitespace
             args: [--markdown-linebreak-ext=md]
     - repo: https://github.com/psf/black
-      rev: 23.3.0
+      rev: 23.7.0
       hooks:
           - id: black
     - repo: https://github.com/pappasam/toml-sort
-      rev: v0.23.0
+      rev: v0.23.1
       hooks:
         - id: toml-sort-fix
     - repo: https://github.com/pre-commit/mirrors-clang-format
-      rev: v15.0.7
+      rev: v16.0.6
       hooks:
       - id: clang-format
         types_or: [c++, c, cuda]

btrack/btypes.py

@@ -175,7 +175,7 @@ def from_dict(properties: dict[str, Any]) -> PyTrackObject:
 
         # we can add any extra details to the properties dictionary
         obj.properties = {
-            k: v for k, v in properties.items() if k not in fields.keys()
+            k: v for k, v in properties.items() if k not in fields
         }
         return obj
 
@@ -353,7 +353,7 @@ class Tracklet:
     x values.
     """
 
-    def __init__(
+    def __init__(  # noqa: PLR0913
         self,
         ID: int,
         data: list[PyTrackObject],

btrack/io/_localization.py

@@ -178,7 +178,7 @@ def __call__(
         return nodes
 
 
-def segmentation_to_objects(
+def segmentation_to_objects(  # noqa: PLR0913
     segmentation: Union[np.ndarray, Generator],
     *,
     intensity_image: Optional[Union[np.ndarray, Generator]] = None,

btrack/io/exporters.py

@@ -112,7 +112,10 @@ def export_LBEP(filename: os.PathLike, tracks: list):
 
 
 def _export_HDF(
-    filename: os.PathLike, tracker, obj_type=None, filter_by: str = None
+    filename: os.PathLike,
+    tracker,
+    obj_type=None,
+    filter_by: Optional[str] = None,
 ):
     """Export to HDF."""
 

btrack/io/hdf.py

@@ -391,7 +391,7 @@ def write_properties(
 
         grp = self._hdf[f"objects/{self.object_type}"]
 
-        if "properties" not in grp.keys():
+        if "properties" not in grp:
             props_grp = grp.create_group("properties")
         else:
             props_grp = self._hdf[f"objects/{self.object_type}/properties"]

btrack/napari/config.py

@@ -38,7 +38,7 @@ def __getitem__(self, matrix_name):
         return self.__dict__[matrix_name]
 
     def __setitem__(self, matrix_name, sigma):
-        if matrix_name not in self.__dict__.keys():
+        if matrix_name not in self.__dict__:
             _msg = f"Unknown matrix name '{matrix_name}'"
             raise ValueError(_msg)
         self.__dict__[matrix_name] = sigma

btrack/napari/sync.py

@@ -10,6 +10,8 @@
     import btrack.napari.widgets
     from btrack.napari.config import Sigmas, UnscaledTrackerConfig
 
+from qtpy import QtCore
+
 import btrack.napari.constants
 
 
@@ -41,8 +43,9 @@ def update_config_from_widgets(
     hypothesis_model = config.hypothesis_model
     hypothesis_model.hypotheses = [
         hypothesis
-        for hypothesis in btrack.optimise.hypothesis.H_TYPES
-        if btrack_widget[hypothesis].isChecked()
+        for i, hypothesis in enumerate(btrack.optimise.hypothesis.H_TYPES)
+        if btrack_widget["hypotheses"].item(i).checkState()
+        == QtCore.Qt.CheckState.Checked
     ]
 
     # Update HypothesisModel scaling factors
@@ -91,9 +94,13 @@ def update_widgets_from_config(
 
     # Update widgets from HypothesisModel.hypotheses values
     hypothesis_model = config.hypothesis_model
-    for hypothesis in btrack.optimise.hypothesis.H_TYPES:
-        is_checked = hypothesis in hypothesis_model.hypotheses
-        btrack_widget[hypothesis].setChecked(is_checked)
+    for i, hypothesis in enumerate(btrack.optimise.hypothesis.H_TYPES):
+        is_checked = (
+            QtCore.Qt.CheckState.Checked
+            if hypothesis in hypothesis_model.hypotheses
+            else QtCore.Qt.CheckState.Unchecked
+        )
+        btrack_widget["hypotheses"].item(i).setCheckState(is_checked)
 
     # Update widgets from HypothesisModel scaling factors
     for scaling_factor in btrack.napari.constants.HYPOTHESIS_SCALING_FACTORS:

btrack/napari/widgets/_general.py

@@ -3,7 +3,7 @@
 from qtpy import QtWidgets
 
 
-def create_input_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
+def create_input_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
     """Create widgets for selecting labels layer and TrackerConfig"""
 
     # TODO: annotation=napari.layers.Labels,
@@ -26,7 +26,7 @@ def create_input_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
     return widgets
 
 
-def create_update_method_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
+def create_update_method_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
     """Create widgets for selecting the update method"""
 
     update_method = QtWidgets.QComboBox()

btrack/napari/widgets/_hypothesis.py

@@ -1,14 +1,16 @@
 from __future__ import annotations
 
-from qtpy import QtWidgets
+from qtpy import QtCore, QtWidgets
 
 import btrack.napari.constants
 
 
-def _create_hypotheses_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
+def _create_hypotheses_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
     """Create widgets for selecting which hypotheses to generate."""
 
-    hypotheses = btrack.optimise.hypothesis.H_TYPES
+    hypotheses = [
+        h.replace("_", " ") for h in btrack.optimise.hypothesis.H_TYPES
+    ]
     tooltips = [
         "Hypothesis that a tracklet is a false positive detection. Always required.",
         "Hypothesis that a tracklet starts at the beginning of the movie or edge of the field of view.",  # noqa: E501
@@ -19,25 +21,31 @@ def _create_hypotheses_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
         "Hypothesis that two tracklets merge into one tracklet.",
     ]
 
-    hypotheses_widgets = {}
-    for hypothesis, tooltip in zip(hypotheses, tooltips):
-        widget = QtWidgets.QCheckBox()
-        widget.setChecked(True)  # noqa: FBT003
-        widget.setToolTip(tooltip)
-        widget.setTristate(False)  # noqa: FBT003
-        hypotheses_widgets[hypothesis] = (hypothesis.replace("_", " "), widget)
+    widget = QtWidgets.QListWidget()
+    widget.addItems(hypotheses)
+    flags = QtCore.Qt.ItemFlags(
+        QtCore.Qt.ItemIsUserCheckable + QtCore.Qt.ItemIsEnabled
+    )
+    for i, tooltip in enumerate(tooltips):
+        widget.item(i).setCheckState(QtCore.Qt.CheckState.Checked)
+        widget.item(i).setFlags(flags)
+        widget.item(i).setToolTip(tooltip)
 
     # P_FP is always required
-    hypotheses_widgets["P_FP"][1].setEnabled(False)  # noqa: FBT003
+    widget.item(hypotheses.index("P FP")).setFlags(
+        QtCore.Qt.ItemIsUserCheckable,
+    )
 
-    # P_merge should be disabled by default
-    hypotheses_widgets["P_merge"][1].setChecked(False)  # noqa: FBT003
+    # # P_merge should be disabled by default
+    widget.item(hypotheses.index("P merge")).setCheckState(
+        QtCore.Qt.CheckState.Unchecked
+    )
 
-    return hypotheses_widgets
+    return {"hypotheses": ("hypotheses", widget)}
 
 
 def _create_scaling_factor_widgets() -> (
-    dict[str, tuple(str, QtWidgets.QWidget)]
+    dict[str, tuple[str, QtWidgets.QWidget]]
 ):
     """Create widgets for setting the scaling factors of the HypothesisModel"""
 
@@ -74,7 +82,7 @@ def _create_scaling_factor_widgets() -> (
     return scaling_factor_widgets
 
 
-def _create_threshold_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
+def _create_threshold_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
     """Create widgets for setting thresholds for the HypothesisModel"""
 
     distance_threshold = QtWidgets.QDoubleSpinBox()
@@ -113,7 +121,7 @@ def _create_threshold_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
     return widgets
 
 
-def _create_bin_size_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
+def _create_bin_size_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
     """Create widget for setting bin sizes for the HypothesisModel"""
 
     distance_bin_size = QtWidgets.QDoubleSpinBox()
@@ -142,9 +150,9 @@ def _create_bin_size_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
 
 
 def create_hypothesis_model_widgets() -> (
-    dict[str, tuple(str, QtWidgets.QWidget)]
+    dict[str, tuple[str, QtWidgets.QWidget]]
 ):
-    """Create widgets for setting parameters of the MotionModel"""
+    """Create widgets for setting parameters of the HypothesisModel"""
 
     widgets = {
         **_create_hypotheses_widgets(),

btrack/napari/widgets/_motion.py

@@ -9,7 +9,7 @@ def _make_label_bold(label: str) -> str:
     return f"<b>{label}</b>"
 
 
-def _create_sigma_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
+def _create_sigma_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
     """Create widgets for setting the magnitudes of the MotionModel matrices"""
 
     P_sigma = QtWidgets.QDoubleSpinBox()
@@ -43,7 +43,7 @@ def _create_sigma_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
     return widgets
 
 
-def create_motion_model_widgets() -> dict[str, tuple(str, QtWidgets.QWidget)]:
+def create_motion_model_widgets() -> dict[str, tuple[str, QtWidgets.QWidget]]:
     """Create widgets for setting parameters of the MotionModel"""
 
     widgets = _create_sigma_widgets()

btrack/napari/widgets/create_ui.py

@@ -14,20 +14,6 @@
 from btrack.napari.widgets._motion import create_motion_model_widgets
 
 
-def create_widgets() -> (
-    dict[str, QtWidgets.QWidget | tuple[str, QtWidgets.QWidget]]
-):
-    """Create all the widgets for the plugin"""
-
-    return (
-        create_input_widgets()
-        | create_update_method_widgets()
-        | create_motion_model_widgets()
-        | create_hypothesis_model_widgets()
-        | create_io_widgets()
-    )
-
-
 class BtrackWidget(QtWidgets.QScrollArea):
     """Main btrack widget"""
 

tests/test_shared_lib.py

@@ -16,7 +16,7 @@ def test_load_library():
 def test_fails_load_library_debug(tmp_path):
     """Test loading a fake shared library."""
     fake_lib_filename = Path(tmp_path) / "fakelib"
-    with pytest.raises(Exception):
+    with pytest.raises(Exception):  # noqa: B017
         load_library(fake_lib_filename)