reduce number of deprecation warnings

.github/workflows/deploy.yml

@@ -9,7 +9,7 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v2

.github/workflows/etc/ilastik-env.yaml

@@ -3,11 +3,11 @@ channels:
   - conda-forge
   - ilastik-forge
 dependencies:
-  - python 3.7.*
+  - python 3.9.*
   - ilastik-core
   - qimage2ndarray
   - pyqtgraph
   - conda-build
-  - pytest >=3,<4
+  - pytest >4
   - pytest-qt
   - pytest-cov

.github/workflows/lint.yml

@@ -10,7 +10,7 @@ jobs:
   black:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true

.github/workflows/test.yml

@@ -13,7 +13,7 @@ jobs:
         os: [windows-latest, ubuntu-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           # for codecov
           fetch-depth: 5
@@ -43,7 +43,7 @@ jobs:
         # auto activation of env does not seem to work on win
         run: |
           pip install -e . & pytest
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v3
         if: matrix.os == 'ubuntu-latest'
         with:
           files: ./coverage.xml,
@@ -61,7 +61,7 @@ jobs:
 
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: ""

volumina/colortables.py

@@ -48,12 +48,12 @@ def matplotlib_to_qt4_colortable(cmap_name, N, asLong=True):
     cmap_name can be any matplotlib colortable
     """
     try:
-        import matplotlib.cm as cm
+        import matplotlib
     except:
         raise RuntimeError("this function requires matplotlib")
 
-    cmap = cm.get_cmap(cmap_name, N)
-    cmap = cmap(np.arange(N))[:, :-1]
+    cmap = matplotlib.colormaps.get_cmap(cmap_name).resampled(N)
+    cmap = cmap(np.arange(N))[:, :-1].astype(int)
     colortable = []
     for el in cmap:
         r, g, b = el * 255
@@ -400,7 +400,7 @@ def create_default_8bit():
     Repeatedly applies the default16 colortable to the whole 8bit range.
 
     """
-    return [color for color in itertools.islice(itertools.cycle(default16), 0, 2 ** 8)]
+    return [color for color in itertools.islice(itertools.cycle(default16), 0, 2**8)]
 
 
 def create_default_16bit():
@@ -409,7 +409,7 @@ def create_default_16bit():
     Repeatedly applies the default16 colortable to the whole 16bit range.
 
     """
-    return [color for color in itertools.islice(itertools.cycle(default16), 0, 2 ** 16)]
+    return [color for color in itertools.islice(itertools.cycle(default16), 0, 2**16)]
 
 
 def create_random_8bit():
@@ -423,7 +423,7 @@ def create_random_16bit():
     """Create a colortable suitable for 16bit data.
 
     Repeatedly applies a pseudo-random colortable to the whole 16bit range"""
-    return [color for color in itertools.islice(itertools.cycle(random256), 0, 2 ** 16)]
+    return [color for color in itertools.islice(itertools.cycle(random256), 0, 2**16)]
 
 
 if __name__ == "__main__":

volumina/layer.py

@@ -177,7 +177,7 @@ def isDifferentEnough(self, other_layer):
 
     def __init__(self, datasources, direct=False):
         super(Layer, self).__init__()
-        self._name = u"Unnamed Layer"
+        self._name = "Unnamed Layer"
         self._visible = True
         self._opacity = 1.0
         self._datasources = datasources
@@ -438,7 +438,7 @@ def generateRandomColors(M=256, colormodel="hsv", clamp=None, zeroIsTransparent=
                 colors.append(QColor(0, 0, 0, 0).rgba())
             else:
                 h, s, v = r[i, :]
-                color = numpy.asarray(colorsys.hsv_to_rgb(h, s, v)) * 255
+                color = (numpy.asarray(colorsys.hsv_to_rgb(h, s, v)) * 255).astype(int)
                 qColor = QColor(*color)
                 colors.append(qColor.rgba())
         return colors

volumina/sliceSelectorHud.py

@@ -195,7 +195,6 @@ def setNewValue(self, value):
         self.spinBox.setSuffix("/" + str(value))
 
     def on_upLabel(self):
-
         imgView = self.parent().parent().parent().parent()
         try:
             roi_3d = imgView._croppingMarkers.crop_extents_model.get_roi_3d()
@@ -207,7 +206,6 @@ def on_upLabel(self):
             self.spinBox.setValue(self.spinBox.value() + 1)
 
     def on_downLabel(self):
-
         imgView = self.parent().parent().parent().parent()
         try:
             roi_3d = imgView._croppingMarkers.crop_extents_model.get_roi_3d()
@@ -587,7 +585,7 @@ def createQuadViewStatusBar(
         self._registerTimeframeShortcuts()
 
     def _registerTimeframeShortcuts(self, enabled=True, remove=True):
-        """ Register or deregister "," and "." as keyboard shortcuts for scrolling in time """
+        """Register or deregister "," and "." as keyboard shortcuts for scrolling in time"""
         mgr = ShortcutManager()
         ActionInfo = ShortcutManager.ActionInfo
 
@@ -700,9 +698,9 @@ def updateShape5Dcropped(self, shape5DcropMin, shape5Dmax):
         self.timeSlider.setValue(shape5DcropMin[0])
 
     def setMouseCoords(self, x, y, z):
-        self.xSpinBox.setValueWithoutSignal(x)
-        self.ySpinBox.setValueWithoutSignal(y)
-        self.zSpinBox.setValueWithoutSignal(z)
+        self.xSpinBox.setValueWithoutSignal(int(x))
+        self.ySpinBox.setValueWithoutSignal(int(y))
+        self.zSpinBox.setValueWithoutSignal(int(z))
 
 
 if __name__ == "__main__":

volumina/widgets/layerwidget.py

@@ -103,7 +103,7 @@ def paintEvent(self, ev):
         painter.restore()
 
         # fraction indicator
-        painter.drawRect(QRect(QPoint(0, y_offset), QSize(self._barWidth() * self._fraction, self._barHeight())))
+        painter.drawRect(QRect(QPoint(0, y_offset), QSize(int(self._barWidth() * self._fraction), self._barHeight())))
 
     def sizeHint(self):
         return QSize(100, 10)
@@ -191,7 +191,7 @@ def __init__(self, parent=None):
         self.opacityLabel = QLabel(parent=self)
         self.opacityLabel.setAlignment(Qt.AlignRight)
         self.opacityLabel.setFont(self._font)
-        self.opacityLabel.setText(u"\u03B1=%0.1f%%" % (100.0 * (self.bar.fraction())))
+        self.opacityLabel.setText("\u03B1=%0.1f%%" % (100.0 * (self.bar.fraction())))
         self.toggleEye = ToggleEye(parent=self)
         self.toggleEye.setActive(False)
         self.toggleEye.setFixedWidth(35)
@@ -245,7 +245,6 @@ def _onFractionChanged(self, fraction):
 
     def _onEyeToggle(self, active):
         if self._layer and (active != self._layer.visible):
-
             if self._layer._allowToggleVisible:
                 self._layer.visible = active
             else:
@@ -259,7 +258,7 @@ def _updateState(self):
         if self._layer:
             self.toggleEye.setActive(self._layer.visible)
             self.bar.setFraction(self._layer.opacity)
-            self.opacityLabel.setText(u"\u03B1=%0.1f%%" % (100.0 * (self.bar.fraction())))
+            self.opacityLabel.setText(f"\u03B1={(100.0 * (self.bar.fraction())):0.1f}")
             self.nameLabel.setText(self._layer.name)
 
             if self._layer.numberOfChannels > 1: