Update dependencies

Author: VesnaT

.github/workflows/test.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install dependencies
         run: |

orangecontrib/explain/explainer.py

@@ -60,12 +60,17 @@ def _join_shap_values(
     of lists with the np.ndarray for each class, when explaining regression,
     the result is the list of one np.ndarrays.
     """
-    if isinstance(shap_values[0], np.ndarray):
-        # regression
+    shape = shap_values[0].shape
+    if len(shape) == 1 or (len(shape) == 2 and shape[0] == 1):
+        # regression and xgb with two classes
         return [np.vstack(shap_values)]
     else:
         # classification
-        return [np.vstack(s) for s in zip(*shap_values)]
+        if len(shape) == 3:
+            transformed = [(np.squeeze(v, axis=0)).T for v in shap_values]
+        else:
+            transformed = [v.T for v in shap_values]
+        return [np.vstack(s) for s in zip(*transformed)]
 
 
 def _explain_trees(

orangecontrib/explain/inspection.py

@@ -4,6 +4,7 @@
 import numpy as np
 import scipy.sparse as sp
 from sklearn.inspection import partial_dependence
+from sklearn.utils import Tags, TargetTags
 
 from Orange.base import Model
 from Orange.classification import Model as ClsModel
@@ -202,11 +203,13 @@ def dummy_fit(*_, **__):
     model.fit = dummy_fit
     model.fit_ = dummy_fit
     if model.domain.class_var.is_discrete:
-        model._estimator_type = "classifier"
         model.classes_ = np.array(model.domain.class_var.values)
+        estimator_type = "classifier"
     else:
-        model._estimator_type = "regressor"
+        estimator_type = "regressor"
 
+    model.__sklearn_tags__ = lambda: Tags(estimator_type=estimator_type,
+                                          target_tags=TargetTags(required=True))
     progress_callback(0.1)
 
     dep = partial_dependence(model,

orangecontrib/explain/widgets/owice.py

@@ -26,6 +26,7 @@
     create_annotated_table
 from Orange.widgets.utils.concurrent import TaskState, ConcurrentWidgetMixin
 from Orange.widgets.utils.itemmodels import VariableListModel, DomainModel
+from Orange.widgets.utils.multi_target import check_multiple_targets_input
 from Orange.widgets.utils.sql import check_sql_input
 from Orange.widgets.utils.widgetpreview import WidgetPreview
 from Orange.widgets.visualize.owdistributions import LegendItem
@@ -37,10 +38,6 @@
 
 from orangecontrib.explain.inspection import individual_condition_expectation
 from orangewidget.utils.visual_settings_dlg import VisualSettingsDialog
-try:
-    from Orange.widgets.utils.multi_target import check_multiple_targets_input
-except ImportError:
-    check_multiple_targets_input = lambda f: f
 
 
 class RunnerResults(SimpleNamespace):
@@ -734,7 +731,7 @@ def _apply_feature_sorting(self):
         if self.order_by_importance:
             def compute_score(feature):
                 values = self.__results_avgs[feature][self.target_index]
-                return -np.sum(np.abs(values - np.mean(values)))
+                return float(-np.sum(np.abs(values - np.mean(values))))
 
             try:
                 if self.__results_avgs is None:

orangecontrib/explain/widgets/tests/test_owpermutationimportance.py

@@ -281,19 +281,19 @@ def test_x_label(self):
         self.send_signal(self.widget.Inputs.model, self.rf_cls)
         self.wait_until_finished()
         label: QGraphicsTextItem = self.widget.plot.bottom_axis.label
-        self.assertEqual(label.toPlainText(), "Decrease in AUC ")
+        self.assertIn("Decrease in AUC", label.toPlainText())
 
         self.send_signal(self.widget.Inputs.data, self.housing)
         self.send_signal(self.widget.Inputs.model, self.rf_reg)
         self.wait_until_finished()
         label: QGraphicsTextItem = self.widget.plot.bottom_axis.label
-        self.assertEqual(label.toPlainText(), "Decrease in R2 ")
+        self.assertIn("Decrease in R2", label.toPlainText())
 
         score_cb: QComboBox = self.widget._score_combo
         simulate.combobox_activate_item(score_cb, "MSE")
         self.wait_until_finished()
         label: QGraphicsTextItem = self.widget.plot.bottom_axis.label
-        self.assertEqual(label.toPlainText(), "Increase in MSE ")
+        self.assertIn("Increase in MSE", label.toPlainText())
 
     @unittest.mock.patch("orangecontrib.explain.widgets."
                          "owpermutationimportance.OWPermutationImportance.run")

setup.py

@@ -38,18 +38,16 @@
 ]
 
 INSTALL_REQUIRES = [
-    "AnyQt",
-    # shap's requirement, force users for numba to get updated because compatibility
-    # issues with numpy - completely remove this pin after october 2024
-    "numba >=0.58",
-    "numpy",
-    "Orange3 >=3.36.2",
-    "orange-canvas-core >=0.1.30",
-    "orange-widget-base >=4.22.0",
-    "pyqtgraph",
-    "scipy",
-    "shap==0.42.1",
-    "scikit-learn>=1.3.0",
+    "AnyQt>=0.2.0",
+    "Orange3>=3.39.0",
+    "orange-canvas-core>=0.2.5",
+    "orange-widget-base>=4.26.0",
+    "pandas>=2.2.3",
+    "scikit-learn>=1.7.0",
+    "scipy>=1.13.0",
+    "pyqtgraph>=0.13.1",
+    "numpy>=2.0.0",
+    "shap>=0.50.0",
 ]
 
 EXTRAS_REQUIRE = {

tox.ini

@@ -22,13 +22,16 @@ deps =
     {env:PYQT_PYPI_NAME:PyQt5}=={env:PYQT_PYPI_VERSION:5.15.*}
     {env:WEBENGINE_PYPI_NAME:PyQtWebEngine}=={env:WEBENGINE_PYPI_VERSION:5.15.*}
     xgboost
-    oldest: orange3==3.36.2
-    oldest: orange-canvas-core==0.1.30
-    oldest: orange-widget-base==4.22.0
-    oldest: pandas==1.4.0
-    oldest: scikit-learn==1.3.0
-    oldest: scipy==1.9.0
+    oldest: orange3==3.39.0
+    oldest: orange-canvas-core==0.2.5
+    oldest: orange-widget-base==4.26.0
+    oldest: pandas~=2.2.3
+    oldest: scikit-learn~=1.7.0
+    oldest: scipy~=1.13.0
     oldest: xgboost==2.0.0
+    oldest: pyqtgraph==0.13.1
+    oldest: numpy~=2.0.0
+    oldest: shap==0.50.0
     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