Merge remote-tracking branch 'upstream/RELEASE_next_patch' into RELEA…

…SE_next_minor

# Conflicts:
#	.github/workflows/tests.yml

.github/workflows/tests.yml

@@ -11,44 +11,35 @@ jobs:
       MPLBACKEND: agg
       PIP_ARGS: --upgrade -e
       PYTEST_ARGS: --pyargs hyperspy --reruns 3 -n 2 --instafail
-      PYTEST_ARGS_COVERAGE:
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu, windows, macos]
         PYTHON_VERSION: ['3.8', '3.9']
-        PIP_SELECTOR: ['[all, tests]']
+        PIP_SELECTOR: ['[all, tests, coverage]']
         include:
-          # test oldest supported version of main dependencies on python 3.6
+          # test oldest supported version of main dependencies on python 3.7
           - os: ubuntu
             PYTHON_VERSION: '3.7'
-            OLDEST_SUPPORTED_VERSION: true
-            DEPENDENCIES: matplotlib==3.1.3 numpy==1.17.1 scipy==1.1 imagecodecs==2020.1.31 tifffile==2020.2.16 dask==2.11.0 distributed==2.11.0 scikit-image==0.15 numba==0.52
             PIP_SELECTOR: '[all, tests, coverage]'
-            # Hang at the end of the test suite run...
-            #PYTEST_ARGS_COVERAGE: --cov=. --cov-report=xml
+            OLDEST_SUPPORTED_VERSION: true
+            DEPENDENCIES: matplotlib==3.1.3 numpy==1.17.1 scipy==1.1 imagecodecs==2020.1.31 tifffile==2020.2.16 dask==2.11.0 distributed==2.11.0 scikit-image==0.15 numba==0.52 scikit-learn==1.0.1
             LABEL: -oldest
           # test minimum requirement
           - os: ubuntu
             PYTHON_VERSION: '3.8'
-            PIP_SELECTOR: '[tests]'
+            PIP_SELECTOR: '[tests, coverage]'
             LABEL: -minimum
           # Run coverage
           - os: ubuntu
-            PYTHON_VERSION: '3.8'
+            PYTHON_VERSION: '3.7'
             PIP_SELECTOR: '[all, tests, coverage]'
-            PYTEST_ARGS_COVERAGE: --cov=. --cov-report=xml
-            LABEL: -coverage
           - os: ubuntu
-            PYTHON_VERSION: '3.7'
-            PIP_SELECTOR: '[all, tests]'
+            PYTHON_VERSION: '3.8'
+            PIP_SELECTOR: '[all, tests, coverage]'
           - os: ubuntu
             PYTHON_VERSION: '3.10'
-            PIP_SELECTOR: '[all, tests]'
-        exclude:
-          # redundant build (same as coverage)
-          - os: ubuntu
-            PYTHON_VERSION: '3.8'
+            PIP_SELECTOR: '[all, tests, coverage]'
 
     steps:
       - uses: actions/checkout@v3.3.0
@@ -79,8 +70,8 @@ jobs:
 
       - name: Run test suite
         run: |
-          pytest ${{ env.PYTEST_ARGS }} ${{ matrix.PYTEST_ARGS_COVERAGE }}
+          pytest ${{ env.PYTEST_ARGS }} --cov=. --cov-report=xml
 
       - name: Upload coverage to Codecov
-        if: ${{ always() }} && ${{ matrix.PYTEST_ARGS_COVERAGE }}
+        if: ${{ always() }}
         uses: codecov/codecov-action@v3

hyperspy/drawing/_markers/horizontal_line.py

@@ -67,7 +67,7 @@ def __repr__(self):
     def update(self):
         if self.auto_update is False:
             return
-        self.marker.set_ydata(self.get_data_position('y1'))
+        self.marker.set_ydata([self.get_data_position('y1')])
 
     def _plot_marker(self):
         self.marker = self.ax.axhline(self.get_data_position('y1'),

hyperspy/drawing/_markers/vertical_line.py

@@ -66,7 +66,7 @@ def __repr__(self):
     def update(self):
         if self.auto_update is False:
             return
-        self.marker.set_xdata(self.get_data_position('x1'))
+        self.marker.set_xdata([self.get_data_position('x1')])
 
     def _plot_marker(self):
         self.marker = self.ax.axvline(self.get_data_position('x1'),

hyperspy/drawing/_widgets/horizontal_line.py

@@ -28,7 +28,7 @@ class HorizontalLineWidget(Widget1DBase):
 
     def _update_patch_position(self):
         if self.is_on and self.patch:
-            self.patch[0].set_ydata(self._pos[0])
+            self.patch[0].set_ydata([self._pos[0]])
             self.draw_patch()
 
     def _add_patch_to(self, ax):

hyperspy/drawing/_widgets/scalebar.py

@@ -18,7 +18,7 @@
 
 
 from hyperspy.misc.math_tools import closest_nice_number
-
+import numpy as np
 
 class ScaleBar(object):
 
@@ -95,8 +95,8 @@ def calculate_text_position(self, pad=1 / 100.):
 
     def calculate_size(self, max_size_ratio=0.25):
         ps = self.pixel_size if self.pixel_size is not None else 1
-        size = closest_nice_number(ps * (self.xmax - self.xmin) *
-                                   max_size_ratio)
+        size = closest_nice_number(np.abs(ps * (self.xmax - self.xmin) *
+                                   max_size_ratio))
         self.length = size
 
     def remove(self):

hyperspy/drawing/_widgets/vertical_line.py

@@ -28,7 +28,7 @@ class VerticalLineWidget(Widget1DBase):
 
     def _update_patch_position(self):
         if self.is_on and self.patch:
-            self.patch[0].set_xdata(self._pos[0])
+            self.patch[0].set_xdata([self._pos[0]])
             self.draw_patch()
 
     def _add_patch_to(self, ax):

hyperspy/drawing/image.py

@@ -563,7 +563,11 @@ def format_coord(x, y):
                 ims[0].set_norm(norm)
                 ims[0].norm.vmax, ims[0].norm.vmin = vmax, vmin
             if redraw_colorbar:
-                self._colorbar.draw_all()
+                # `draw_all` is deprecated in matplotlib 3.6.0
+                if Version(matplotlib.__version__) <= Version("3.6.0"):
+                    self._colorbar.draw_all()
+                else:
+                    self.figure.draw_without_rendering()
                 self._colorbar.solids.set_animated(
                     self.figure.canvas.supports_blit
                 )

hyperspy/drawing/utils.py

@@ -876,7 +876,7 @@ def __check_single_colorbar(cbar):
     # Set overall figure size and define figure (if not pre-existing)
     if fig is None:
         w, h = plt.rcParams['figure.figsize']
-        dpi = plt.rcParams['figure.dpi']  
+        dpi = plt.rcParams['figure.dpi']
         if overlay and axes_decor == 'off':
             shape = images[0].axes_manager.signal_shape
             if pixel_size_factor is None:
@@ -971,7 +971,7 @@ def transparent_single_color_cmap(color):
                 images[0].axes_manager[0].scale):
                 raise ValueError("Images are not the same scale and so should"
                                  "not be overlayed.")
-        
+
         if vmin is not None:
             _logger.warning('`vmin` is ignored when overlaying images.')
 
@@ -1003,7 +1003,7 @@ def transparent_single_color_cmap(color):
             #Set vmin and vmax
             centre = next(centre_colormaps)   # get next value for centreing
             data = _parse_array(im)
-            
+
             _vmin = data.min()
             _vmax = vmax[idx] if isinstance(vmax, (tuple, list)) else vmax
             _vmin, _vmax = contrast_stretching(data, _vmin, _vmax)
@@ -1203,30 +1203,31 @@ def transparent_single_color_cmap(color):
     # Replot: connect function
     def on_dblclick(event):
         # On the event of a double click, replot the selected subplot
-        if not event.inaxes:
+        if not event.inaxes or not event.dblclick:
             return
-        if not event.dblclick:
-            return
-        subplots = [axi for axi in f.axes if isinstance(axi, mpl.axes.Subplot)]
-        inx = list(subplots).index(event.inaxes)
-        im = replot_ims[inx]
+
+        idx_ = axes_list.index(event.inaxes)
+        ax_ = axes_list[idx_]
+        im_ = replot_ims[idx_]
 
         # Use some of the info in the subplot
-        cm = subplots[inx].images[0].get_cmap()
-        clim = subplots[inx].images[0].get_clim()
+        cm = ax_.images[0].get_cmap()
+        clim = ax_.images[0].get_clim()
 
         sbar = False
-        if (scalelist and inx in scalebar) or scalebar == 'all':
+        if (scalelist and idx_ in scalebar) or scalebar == 'all':
             sbar = True
 
-        im.plot(colorbar=bool(colorbar),
-                vmin=clim[0],
-                vmax=clim[1],
-                no_nans=no_nans,
-                aspect=asp,
-                scalebar=sbar,
-                scalebar_color=scalebar_color,
-                cmap=cm)
+        im_.plot(
+            colorbar=bool(colorbar),
+            vmin=clim[0],
+            vmax=clim[1],
+            no_nans=no_nans,
+            aspect=asp,
+            scalebar=sbar,
+            scalebar_color=scalebar_color,
+            cmap=cm,
+            )
 
     f.canvas.mpl_connect('button_press_event', on_dblclick)
 
@@ -1306,7 +1307,12 @@ def make_cmap(colors, name='my_colormap', position=None,
     cmap = mpl.colors.LinearSegmentedColormap(name, cdict, 256)
 
     if register:
-        mpl.cm.register_cmap(name, cmap)
+        try:
+            # Introduced in matplotlib 3.5
+            mpl.colormaps.register(cmap, name=name)
+        except AttributeError:
+            # Deprecated in matplotlib 3.5
+            mpl.cm.register_cmap(name, cmap)
     return cmap
 
 
@@ -1427,8 +1433,13 @@ def _reverse_legend(ax_, legend_loc_):
         """
         l = ax_.get_legend()
         labels = [lb.get_text() for lb in list(l.get_texts())]
-        handles = l.legendHandles
-        ax_.legend(handles[::-1], labels[::-1], loc=legend_loc_)
+        # "legendHandles" is deprecated in matplotlib 3.7.0 in favour of
+        # "legend_handles".
+        if Version(mpl.__version__) >= Version("3.7"):
+            handles = l.legend_handles
+        else:
+            handles = l.legendHandles
+        ax_.legend(reversed(handles), reversed(labels), loc=legend_loc_)
 
     # Before v1.3 default would read the value from prefereces.
     if style == "default":
@@ -1481,7 +1492,7 @@ def _reverse_legend(ax_, legend_loc_):
         _make_cascade_subplot(spectra, ax, color, linestyle, padding=padding,
                               drawstyle=drawstyle)
         if legend is not None:
-            plt.legend(legend, loc=legend_loc)
+            ax.legend(legend, loc=legend_loc)
             _reverse_legend(ax, legend_loc)
             if legend_picking is True:
                 animate_legend(fig=fig, ax=ax)

hyperspy/drawing/widget.py

@@ -19,7 +19,7 @@
 from __future__ import division
 
 import matplotlib.pyplot as plt
-from matplotlib.backend_bases import MouseEvent
+from matplotlib.backend_bases import MouseEvent, PickEvent
 import numpy as np
 
 from hyperspy.drawing.utils import on_figure_window_close
@@ -198,13 +198,17 @@ def select(self):
         if not self.patch or not self.is_on or not self.ax:
             return
 
-        canvas = self.ax.figure.canvas
+        figure = self.ax.figure
         # Simulate a pick event
         x, y = self.patch[0].get_transform().transform_point((0, 0))
-        mouseevent = MouseEvent('pick_event', canvas, x, y)
-        # when the widget is added programatically, mouseevent can be "empty"
+        mouseevent = MouseEvent('pick_event', figure.canvas, x, y)
         if mouseevent.button:
-            canvas.pick_event(mouseevent, self.patch[0])
+            try:
+                # Introduced in matplotlib 3.6 and `pick_event` deprecated
+                event = PickEvent('pick_event', figure, mouseevent, self.patch[0])
+                figure.canvas.callbacks.process('pick_event', event)
+            except: # Deprecated in matplotlib 3.6
+                figure.canvas.pick_event(mouseevent, self.patch[0])
         self.picked = False
 
     def connect(self, ax):