Merge pull request #63 from PrimozGodec/fix-deprecations

[FIX] Resolve deprecations

orangecontrib/explain/explainer.py

@@ -596,7 +596,7 @@ def get_instance_ordering(
     NotImplementedError if unknown order_by.
     """
     if isinstance(order_by, Variable):
-        x_data = data.get_column_view(order_by)[0]
+        x_data = data.get_column(order_by)
         clust_ord = np.argsort(hclust_ordering(shap_values))
         return np.lexsort([clust_ord, x_data])
     elif order_by == ORIGINAL_ORDER:

orangecontrib/explain/tests/test_explainer.py

@@ -276,7 +276,7 @@ def test_all_regressors(self):
                 if learner == CurveFitLearner:
                     attr = self.housing.domain.attributes
                     learner = CurveFitLearner(
-                        lambda x, a: np.sum(x[:, i] for i in range(len(attr))),
+                        lambda x, a: sum(x[:, i] for i in range(len(attr))),
                         [], [a.name for a in self.housing.domain.attributes]
                     )
                 else:

orangecontrib/explain/widgets/owexplainfeaturebase.py

@@ -549,16 +549,17 @@ def _update_plot(self):
     def _clear_selection(self):
         if self.selection:
             self.selection = ()
-            self.commit()
+            self.commit.deferred()
 
     def update_selection(self, *_):
         raise NotImplementedError
 
     def select_pending(self, pending_selection: Tuple):
         self.__pending_selection = pending_selection
-        self.unconditional_commit()
+        self.commit.now()
 
     # Outputs
+    @gui.deferred
     def commit(self):
         selected_data = self.get_selected_data()
         if not selected_data:

orangecontrib/explain/widgets/owexplainmodel.py

@@ -421,7 +421,7 @@ def update_selection(self, min_val: float, max_val: float, attr_name: str):
         if not self.selection and not any(mask):
             return
         self.selection = (attr_name, list(np.flatnonzero(mask)))
-        self.commit()
+        self.commit.deferred()
 
     def select_pending(self, pending_selection: Tuple):
         if not pending_selection or not pending_selection[1] \

orangecontrib/explain/widgets/owexplainpredictions.py

@@ -587,7 +587,7 @@ def _add_plot(self):
 
     def __on_selection_changed(self, selection: List[Tuple[float, float]]):
         self.selection_ranges = selection
-        self.commit()
+        self.commit.deferred()
 
     def _add_controls(self):
         box = gui.vBox(self.controlArea, "Target class")
@@ -624,12 +624,12 @@ def _add_controls(self):
     def __on_target_changed(self):
         self.selection_ranges = []
         self.setup_plot()
-        self.commit()
+        self.commit.deferred()
 
     def __on_order_changed(self):
         self.selection_ranges = []
         self.setup_plot()
-        self.commit()
+        self.commit.deferred()
 
     def __on_annot_changed(self):
         if not self.__results or not self.data:
@@ -717,7 +717,7 @@ def _setup_controls(self):
     def handleNewSignals(self):
         self.clear()
         self.start(run, self.data, self.background_data, self.model)
-        self.commit()
+        self.commit.deferred()
 
     def clear(self):
         self.__results = None
@@ -815,6 +815,7 @@ def apply_selection(self):
             self.__on_selection_changed(selection_ranges)
             self.__pending_selection = []
 
+    @gui.deferred
     def commit(self):
         selected = None
         selected_indices = []

orangecontrib/explain/widgets/owice.py

@@ -5,15 +5,15 @@
 
 import numpy as np
 from AnyQt.QtCore import Qt, QSortFilterProxyModel, QSize, QModelIndex, \
-    QItemSelection, QPointF, Signal, QLineF
+    QPointF, Signal, QLineF
 from AnyQt.QtGui import QColor
 from AnyQt.QtWidgets import QComboBox, QSizePolicy, QGraphicsSceneHelpEvent, \
     QToolTip, QGraphicsLineItem, QApplication
 
 import pyqtgraph as pg
 
 from orangecanvas.gui.utils import disconnected
-from orangewidget.utils.listview import ListViewSearch
+from orangewidget.utils.listview import ListViewFilter
 
 from Orange.base import Model
 from Orange.data import Table, ContinuousVariable, Variable, \
@@ -261,7 +261,7 @@ def __on_mouse_moved(self, point: QPointF):
         )
 
         # points
-        x_data = self.__data.get_column_view(self.__feature)[0][indices]
+        x_data = self.__data.get_column(self.__feature)[indices]
         n_dec = self.__feature.number_of_decimals
         y_data = []
         for i, x in zip(indices, x_data):
@@ -537,7 +537,7 @@ def __init__(self):
         self.domain: Optional[Domain] = None
         self.graph: ICEPlot = None
         self._target_combo: QComboBox = None
-        self._features_view: ListViewSearch = None
+        self._features_view: ListViewFilter = None
         self._features_model: VariableListModel = None
         self._color_model: DomainModel = None
 
@@ -571,10 +571,10 @@ def _add_controls(self):
         box = gui.vBox(self.controlArea, "Feature")
         self._features_model = VariableListModel()
         sorted_model = SortProxyModel(sortRole=Qt.UserRole)
-        sorted_model.setSourceModel(self._features_model)
         sorted_model.sort(0)
-        self._features_view = ListViewSearch()
-        self._features_view.setModel(sorted_model)
+        self._features_view = ListViewFilter(
+            model=self._features_model, proxy=sorted_model
+        )
         self._features_view.setMinimumSize(QSize(30, 100))
         self._features_view.setSizePolicy(QSizePolicy.Expanding,
                                           QSizePolicy.Expanding)
@@ -600,12 +600,9 @@ def __on_target_changed(self):
         self._apply_feature_sorting()
         self.__on_parameter_changed()
 
-    def __on_feature_changed(self, selection: QItemSelection):
-        if not selection:
-            return
-
-        self.feature = selection.indexes()[0].data(gui.TableVariable)
-        self._apply_feature_sorting()
+    def __on_feature_changed(self):
+        selection = self._features_view.selectionModel().selectedIndexes()
+        self.feature = selection[0].data(gui.TableVariable) if selection else None
         self._run()
 
     def __on_order_changed(self):
@@ -788,7 +785,7 @@ def setup_plot(self):
         color_labels = None
         if self.color_var and self.color_var.is_discrete:
             colors = self.color_var.colors
-            color_col = self.data[mask].get_column_view(self.color_var)[0]
+            color_col = self.data[mask].get_column(self.color_var)
             color_labels = self.color_var.values
 
         self.graph.set_data(self.data[mask], self.feature,

orangecontrib/explain/widgets/owpermutationimportance.py

@@ -315,7 +315,7 @@ def update_selection(self, attr_names: Set[str]):
             return
         assert self.results is not None
         self.selection = tuple(attr_names)
-        self.commit()
+        self.commit.deferred()
 
     def select_pending(self, pending_selection: Tuple):
         if not pending_selection or self.results is None:

orangecontrib/explain/widgets/tests/test_owice.py

@@ -1,12 +1,13 @@
 # pylint: disable=missing-docstring
 import unittest
-from unittest.mock import Mock
+from unittest.mock import Mock, patch
 
 from AnyQt.QtCore import Qt, QPointF
 
 from Orange.classification import RandomForestLearner, CalibratedLearner, \
     ThresholdLearner, SimpleRandomForestLearner as SimpleRandomForestClassifier
 from Orange.data import Table
+from Orange.data.table import DomainTransformationError
 from Orange.regression import RandomForestRegressionLearner, \
     SimpleRandomForestLearner
 from Orange.tests.test_classification import all_learners as all_cls_learners
@@ -39,15 +40,19 @@ def test_input_cls(self):
 
         self.send_signal(self.widget.Inputs.model, self.rf_reg)
         self.wait_until_finished()
-        self.assertTrue(self.widget.Error.unknown_err.is_shown())
+        # no error since no attributes in view and those no future is selected
+        self.assertFalse(self.widget.Error.unknown_err.is_shown())
 
         self.send_signal(self.widget.Inputs.model, None)
         self.assertFalse(self.widget.Error.unknown_err.is_shown())
 
-        self.send_signal(self.widget.Inputs.data, self.iris)
-        self.send_signal(self.widget.Inputs.model, self.rf_cls)
-        self.wait_until_finished()
-        self.assertTrue(self.widget.Error.domain_transform_err.is_shown())
+        with patch(
+            "orangecontrib.explain.widgets.owice.individual_condition_expectation",
+            side_effect=DomainTransformationError
+        ):
+            self.send_signal(self.widget.Inputs.model, self.rf_cls)
+            self.wait_until_finished()
+            self.assertTrue(self.widget.Error.domain_transform_err.is_shown())
 
     def test_output(self):
         self.send_signal(self.widget.Inputs.data, self.heart)

setup.py

@@ -40,9 +40,9 @@
 INSTALL_REQUIRES = [
     "AnyQt",
     "numpy",
-    "Orange3 >= 3.33.0",
-    "orange-widget-base",
-    "orange-canvas-core",
+    "Orange3 >=3.34.0",
+    "orange-canvas-core >=0.1.28",
+    "orange-widget-base >=4.19.0",
     "pyqtgraph",
     "scipy",
     "shap >=0.42.1",

tox.ini

@@ -23,9 +23,9 @@ deps =
     {env:WEBENGINE_PYPI_NAME:PyQtWebEngine}=={env:WEBENGINE_PYPI_VERSION:5.15.*}
     xgboost
     oldest: scikit-learn==1.0.1
-    oldest: orange3==3.33.0
-    oldest: orange-canvas-core==0.1.27
-    oldest: orange-widget-base==4.18.0
+    oldest: orange3==3.34.0
+    oldest: orange-canvas-core==0.1.28
+    oldest: orange-widget-base==4.19.0
     latest: https://github.com/biolab/orange3/archive/refs/heads/master.zip#egg=orange3
     latest: https://github.com/biolab/orange-canvas-core/archive/refs/heads/master.zip#egg=orange-canvas-core
     latest: https://github.com/biolab/orange-widget-base/archive/refs/heads/master.zip#egg=orange-widget-base