Merge pull request #22 from biolab/dev

[FIX] Output selected data in the correct order

.pre-commit-config.yaml

@@ -1,21 +1,21 @@
 repos:
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.7.4
+    rev: v2.29.0
     hooks:
       - id: pyupgrade
         args: ["--py36-plus"]
   - repo: https://github.com/psf/black
-    rev: stable
+    rev: 21.9b0
     hooks:
       - id: black
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.3.0
+    rev: v4.0.1
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: mixed-line-ending
   - repo: https://gitlab.com/pycqa/flake8
-    rev: '3.8.4'
+    rev: '3.9.2'
     hooks:
       - id: flake8
         additional_dependencies:

orangecontrib/survival_analysis/widgets/owranksurvivalfeatures.py

@@ -71,7 +71,6 @@ def worker(table: Table, covariates: List, time_var: str, event_var: str, state:
             results = stacked_result[:, 1:].astype(float)
             _, pvals_corrected = fdrcorrection(results[:, -1], is_sorted=False)
             results = np.hstack((results, pvals_corrected.reshape(pvals_corrected.shape[0], -1)))
-
             return covariate_names, results
 
 
@@ -105,6 +104,7 @@ def __init__(self):
 
         self.data: Optional[Table] = None
         self.attr_name_to_variable: Optional[Table] = None
+        self.covariates_from_worker_result = None
 
         time_var_model = DomainModel(valid_types=(ContinuousVariable,), order=(4,))
         box = gui.vBox(self.controlArea, 'Time', margin=0)
@@ -150,7 +150,7 @@ def button(text, buttonid, toolTip=None):
         self.commit_button = gui.auto_commit(self.buttonsArea, self, 'auto_commit', '&Commit', box=False)
 
         # Main area
-        self.model = PyTableModel()
+        self.model = PyTableModel(parent=self)
         self.table_view = TableView(parent=self)
         self.table_view.setModel(self.model)
         self.model.setHorizontalHeaderLabels(['Log-Likelihood', 'Log-Likelihood Ratio', f'{"p".center(13)}', 'FDR'])
@@ -175,6 +175,7 @@ def covariates(self) -> Optional[List[str]]:
     def set_data(self, data: Table):
         self.closeContext()
         self.selected_attrs = []
+        self.covariates_from_worker_result = []
         self.model.clear()
         self.model.resetSorting()
 
@@ -229,6 +230,9 @@ def on_done(self, worker_result):
         # wrap everything except covariate names
         self.model.wrap(results.tolist())
 
+        # this is temp solution because covariate orders gets mixed when using multiprocessing
+        self.covariates_from_worker_result = covariate_names.tolist()
+
         # match covariate names to domain variables and set vertical header
         self.model.setVerticalHeaderLabels([self.attr_name_to_variable[name] for name in covariate_names])
         self.table_view.setVHeaderFixedWidthFromLabel(max((a.name for a in self.data.domain.attributes), key=len))
@@ -260,7 +264,7 @@ def auto_select(self):
         else:
             selection = QItemSelection()
             if self.selected_attrs is not None:
-                attr_indices = [self.data.domain.attributes.index(var) for var in self.selected_attrs]
+                attr_indices = [self.covariates_from_worker_result.index(var.name) for var in self.selected_attrs]
                 for row in self.model.mapFromSourceRows(attr_indices):
                     selection.append(
                         QItemSelectionRange(self.model.index(row, 0), self.model.index(row, column_count - 1))
@@ -272,7 +276,7 @@ def on_select(self):
         selected_rows = self.table_view.selectionModel().selectedRows(0)
         row_indices = [i.row() for i in selected_rows]
         attr_indices = self.model.mapToSourceRows(row_indices)
-        self.selected_attrs = [self.data.domain[idx] for idx in attr_indices]
+        self.selected_attrs = [self.model._headers[Qt.Vertical][row] for row in attr_indices]
         self.commit()
 
 

orangecontrib/survival_analysis/widgets/tests/test_owkaplanmeier.py

@@ -1,14 +1,39 @@
 import pyqtgraph as pg
-from pyqtgraph.tests import mouseMove, mousePress, mouseRelease, mouseClick
 from pyqtgraph.graphicsItems.LegendItem import LabelItem
-from pyqtgraph.Qt import QtTest
 
 from Orange.data.table import Table, Domain, StringVariable, ContinuousVariable, DiscreteVariable
-from orangewidget.tests.base import WidgetTest
+from Orange.widgets.tests.base import WidgetTest
 from orangecontrib.survival_analysis.widgets.owkaplanmeier import OWKaplanMeier
 
 
-from AnyQt.QtCore import Qt
+from AnyQt.QtCore import Qt, QEvent
+from AnyQt.QtGui import QMouseEvent
+from AnyQt.QtWidgets import QApplication, QGraphicsView
+from AnyQt.QtTest import QTest
+
+
+def mouse_press_and_hold(widget, pos, mouse_button=Qt.LeftButton):
+    if isinstance(widget, QGraphicsView):
+        widget = widget.viewport()
+
+    event = QMouseEvent(QEvent.MouseButtonPress, pos, mouse_button, Qt.NoButton, Qt.NoModifier)
+    QApplication.sendEvent(widget, event)
+
+
+def mouse_release(widget, pos, mouse_button=Qt.LeftButton):
+    if isinstance(widget, QGraphicsView):
+        widget = widget.viewport()
+
+    event = QMouseEvent(QEvent.MouseButtonRelease, pos, mouse_button, Qt.NoButton, Qt.NoModifier)
+    QApplication.sendEvent(widget, event)
+
+
+def mouse_move(widget, pos, buttons=Qt.NoButton):
+    if isinstance(widget, QGraphicsView):
+        widget = widget.viewport()
+
+    event = QMouseEvent(QEvent.MouseMove, pos, Qt.NoButton, buttons, Qt.NoModifier)
+    QApplication.sendEvent(widget, event)
 
 
 class TestOWKaplanMeier(WidgetTest):
@@ -54,12 +79,17 @@ def simulate_mouse_drag(self, start: tuple, end: tuple):
         start = self.widget.graph.view_box.mapViewToScene(pg.Point(start[0], start[1])).toPoint()
         end = self.widget.graph.view_box.mapViewToScene(pg.Point(end[0], end[1])).toPoint()
 
-        mouseMove(self.widget.graph, start)
-        QtTest.QTest.qWait(100)
-        mousePress(self.widget.graph, start, Qt.LeftButton)
-        mouseMove(self.widget.graph, end, Qt.LeftButton)
-        mouseRelease(self.widget.graph, end, Qt.LeftButton)
-        QtTest.QTest.qWait(100)
+        mouse_move(self.widget.graph, start)
+        # this is somehow not respected in KaplanMeierViewBox.mouseDragEvent so we do it here manualy
+        self.widget.graph.plotItem.scene().blockSignals(True)
+
+        QTest.qWait(100)
+        mouse_press_and_hold(self.widget.graph, start)
+        mouse_move(self.widget.graph, end, Qt.LeftButton)
+        QTest.qWait(100)
+        mouse_release(self.widget.graph, end)
+
+        self.widget.graph.plotItem.scene().blockSignals(False)
 
     def test_group_variable(self):
         # we expect only one curve
@@ -98,14 +128,14 @@ def test_curve_highlight(self):
         self.widget.on_controls_changed()
 
         pos = self.widget.graph.view_box.mapViewToScene(pg.Point(1.5, 0.5)).toPoint()
-        mouseMove(self.widget.graph, pos)
+        mouse_move(self.widget.graph, pos)
         # We need to wait for events to process
-        QtTest.QTest.qWait(100)
+        QTest.qWait(100)
         self.assertTrue(self.widget.graph.highlighted_curve == 1)
 
         pos = self.widget.graph.view_box.mapViewToScene(pg.Point(1.5, 0.85)).toPoint()
-        mouseMove(self.widget.graph, pos)
-        QtTest.QTest.qWait(100)
+        mouse_move(self.widget.graph, pos)
+        QTest.qWait(100)
         self.assertTrue(self.widget.graph.highlighted_curve == 0)
 
     def test_selection(self):
@@ -163,8 +193,8 @@ def test_selection(self):
 
         # reset selection
         pos = self.widget.graph.view_box.mapViewToScene(pg.Point(0, 0)).toPoint()
-        mouseClick(self.widget.graph, pos, Qt.LeftButton)
-        QtTest.QTest.qWait(100)
+        QTest.mouseClick(self.widget.graph.viewport(), Qt.LeftButton, pos=pos)
+        QTest.qWait(100)
 
         selected_data = self.get_output(self.widget.Outputs.selected_data)
         self.assertIsNone(selected_data)

setup.cfg

@@ -27,6 +27,7 @@ setup_requires =
 install_requires =
 	Orange3
 	lifelines
+	statsmodels
 
 [options.extras_require]
 doc =