Merge remote-tracking branch 'upstream/main' into enable-gallery-melissa

Author: melissawm

.github/workflows/test_and_deploy.yml

@@ -48,6 +48,14 @@ jobs:
       - name: Test with tox
         run: python -m tox
 
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@v3
+        with:
+          name: pytest-results-${{ matrix.platform }} py${{ matrix.python-version }}
+          path: reports/
+        # Use always() to always run this step to publish test results when there are test failures
+        if: ${{ always() }}
+
       - name: Coverage
         uses: codecov/codecov-action@v2
 

docs/changelog.rst

@@ -4,6 +4,11 @@ Changelog
 0.3.0
 -----
 
+New features
+~~~~~~~~~~~~
+- Added `MPLWidget` as a widget containing just a Matplotlib canvas
+  without any association with a napari viewer.
+
 Visual improvements
 ~~~~~~~~~~~~~~~~~~~
 - The background of ``napari-matplotlib`` figures and axes is now transparent.
@@ -18,6 +23,9 @@ Changes
   you would be interested in please open an issue at https://github.com/matplotlib/napari-matplotlib.
 - Labels plotting with the features scatter widget no longer have underscores
   replaced with spaces.
+- ``NapariMPLWidget.update_layers()`` has been removed as it is intended to be
+  private API. Use `NapariMPLWidget.on_update_layers` instead to implement
+  funcitonality when layer selection is changed.
 
 Bug fixes
 ~~~~~~~~~

src/napari_matplotlib/base.py

@@ -17,40 +17,25 @@
 # Icons modified from
 # https://github.com/matplotlib/matplotlib/tree/main/lib/matplotlib/mpl-data/images
 ICON_ROOT = Path(__file__).parent / "icons"
-__all__ = ["NapariMPLWidget"]
+__all__ = ["MPLWidget", "NapariMPLWidget"]
 
 
-class NapariMPLWidget(QWidget):
-    """Widget containing a Matplotlib canvas and toolbar.
+class MPLWidget(QWidget):
+    """
+    Widget containing a Matplotlib canvas and toolbar.
 
     This creates a single FigureCanvas, which contains a single
     `~matplotlib.figure.Figure`, and an associated toolbar.
     It is not responsible for creating any Axes, because different
     widgets may want to implement different subplot layouts.
-
-    This class also handles callbacks to automatically update figures when
-    the layer selection or z-step is changed in the napari viewer. To take
-    advantage of this sub-classes should implement the ``clear()`` and
-    ``draw()`` methods.
-
-    Attributes
-    ----------
-    viewer : `napari.Viewer`
-        Main napari viewer.
-    canvas : matplotlib.backends.backend_qt5agg.FigureCanvas
-        Matplotlib canvas.
-    layers : `list`
-        List of currently selected napari layers.
     """
 
     def __init__(
         self,
-        napari_viewer: napari.viewer.Viewer,
         parent: Optional[QWidget] = None,
     ):
         super().__init__(parent=parent)
 
-        self.viewer = napari_viewer
         self.canvas = FigureCanvas()
 
         self.canvas.figure.patch.set_facecolor("none")
@@ -64,6 +49,87 @@ def __init__(
         self.layout().addWidget(self.toolbar)
         self.layout().addWidget(self.canvas)
 
+    @property
+    def figure(self) -> Figure:
+        """Matplotlib figure."""
+        return self.canvas.figure
+
+    def add_single_axes(self) -> None:
+        """
+        Add a single Axes to the figure.
+
+        The Axes is saved on the ``.axes`` attribute for later access.
+        """
+        self.axes = self.figure.subplots()
+        self.apply_napari_colorscheme(self.axes)
+
+    @staticmethod
+    def apply_napari_colorscheme(ax: Axes) -> None:
+        """Apply napari-compatible colorscheme to an Axes."""
+        # changing color of axes background to transparent
+        ax.set_facecolor("none")
+
+        # changing colors of all axes
+        for spine in ax.spines:
+            ax.spines[spine].set_color("white")
+
+        ax.xaxis.label.set_color("white")
+        ax.yaxis.label.set_color("white")
+
+        # changing colors of axes labels
+        ax.tick_params(axis="x", colors="white")
+        ax.tick_params(axis="y", colors="white")
+
+    def _replace_toolbar_icons(self) -> None:
+        # Modify toolbar icons and some tooltips
+        for action in self.toolbar.actions():
+            text = action.text()
+            if text == "Pan":
+                action.setToolTip(
+                    "Pan/Zoom: Left button pans; Right button zooms; "
+                    "Click once to activate; Click again to deactivate"
+                )
+            if text == "Zoom":
+                action.setToolTip(
+                    "Zoom to rectangle; Click once to activate; "
+                    "Click again to deactivate"
+                )
+            if len(text) > 0:  # i.e. not a separator item
+                icon_path = os.path.join(ICON_ROOT, text + ".png")
+                action.setIcon(QIcon(icon_path))
+
+
+class NapariMPLWidget(MPLWidget):
+    """
+    Widget containing a Matplotlib canvas and toolbar.
+
+    In addition to `BaseNapariMPLWidget`, this class handles callbacks
+    to automatically update figures when the layer selection or z-step
+    is changed in the napari viewer. To take advantage of this sub-classes
+    should implement the ``clear()`` and ``draw()`` methods.
+
+    When both the z-step and layer selection is changed, ``clear()`` is called
+    and if the number a type of selected layers are valid for the widget
+    ``draw()`` is then called. When layer selection is changed ``on_update_layers()``
+    is also called, which can be useful e.g. for updating a layer list in a
+    selection widget.
+
+    Attributes
+    ----------
+    viewer : `napari.Viewer`
+        Main napari viewer.
+    layers : `list`
+        List of currently selected napari layers.
+    """
+
+    def __init__(
+        self,
+        napari_viewer: napari.viewer.Viewer,
+        parent: Optional[QWidget] = None,
+    ):
+        super().__init__(parent=parent)
+
+        self.viewer = napari_viewer
         self._setup_callbacks()
         self.layers: List[napari.layers.Layer] = []
 
@@ -72,11 +138,6 @@ def __init__(
     #: Type of layer taken as input
     input_layer_types: Tuple[napari.layers.Layer, ...] = (napari.layers.Layer,)
 
-    @property
-    def figure(self) -> Figure:
-        """Matplotlib figure."""
-        return self.canvas.figure
-
     @property
     def n_selected_layers(self) -> int:
         """
@@ -102,14 +163,16 @@ def _setup_callbacks(self) -> None:
         # z-step changed in viewer
         self.viewer.dims.events.current_step.connect(self._draw)
         # Layer selection changed in viewer
-        self.viewer.layers.selection.events.changed.connect(self.update_layers)
+        self.viewer.layers.selection.events.changed.connect(
+            self._update_layers
+        )
 
-    def update_layers(self, event: napari.utils.events.Event) -> None:
+    def _update_layers(self, event: napari.utils.events.Event) -> None:
         """
         Update the ``layers`` attribute with currently selected layers and re-draw.
         """
         self.layers = list(self.viewer.layers.selection)
-        self._on_update_layers()
+        self.on_update_layers()
         self._draw()
 
     def _draw(self) -> None:
@@ -138,58 +201,13 @@ def draw(self) -> None:
         This is a no-op, and is intended for derived classes to override.
         """
 
-    def add_single_axes(self) -> None:
-        """
-        Add a single Axes to the figure.
-
-        The Axes is saved on the ``.axes`` attribute for later access.
+    def on_update_layers(self) -> None:
         """
-        self.axes = self.figure.subplots()
-        self.apply_napari_colorscheme(self.axes)
-
-    @staticmethod
-    def apply_napari_colorscheme(ax: Axes) -> None:
-        """Apply napari-compatible colorscheme to an Axes."""
-        # changing color of axes background to transparent
-        ax.set_facecolor("none")
-
-        # changing colors of all axes
-        for spine in ax.spines:
-            ax.spines[spine].set_color("white")
-
-        ax.xaxis.label.set_color("white")
-        ax.yaxis.label.set_color("white")
-
-        # changing colors of axes labels
-        ax.tick_params(axis="x", colors="white")
-        ax.tick_params(axis="y", colors="white")
-
-    def _on_update_layers(self) -> None:
-        """
-        Function is called when self.layers is updated via
-        ``self.update_layers()``.
+        Called when the selected layers are updated.
 
         This is a no-op, and is intended for derived classes to override.
         """
 
-    def _replace_toolbar_icons(self) -> None:
-        # Modify toolbar icons and some tooltips
-        for action in self.toolbar.actions():
-            text = action.text()
-            if text == "Pan":
-                action.setToolTip(
-                    "Pan/Zoom: Left button pans; Right button zooms; "
-                    "Click once to activate; Click again to deactivate"
-                )
-            if text == "Zoom":
-                action.setToolTip(
-                    "Zoom to rectangle; Click once to activate; "
-                    "Click again to deactivate"
-                )
-            if len(text) > 0:  # i.e. not a separator item
-                icon_path = os.path.join(ICON_ROOT, text + ".png")
-                action.setIcon(QIcon(icon_path))
-
 
 class NapariNavigationToolbar(NavigationToolbar2QT):
     """Custom Toolbar style for Napari."""

src/napari_matplotlib/histogram.py

@@ -27,7 +27,7 @@ def __init__(
     ):
         super().__init__(napari_viewer, parent=parent)
         self.add_single_axes()
-        self.update_layers(None)
+        self._update_layers(None)
 
     def clear(self) -> None:
         """

src/napari_matplotlib/scatter.py

@@ -132,7 +132,7 @@ def __init__(
             self.layout().addWidget(QLabel(f"{dim}-axis:"))
             self.layout().addWidget(self._selectors[dim])
 
-        self.update_layers(None)
+        self._update_layers(None)
 
     @property
     def x_axis_key(self) -> Union[str, None]:
@@ -230,7 +230,7 @@ def _get_data(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
 
         return x, y, x_axis_name, y_axis_name
 
-    def _on_update_layers(self) -> None:
+    def on_update_layers(self) -> None:
         """
         Called when the layer selection changes by ``self.update_layers()``.
         """

src/napari_matplotlib/slice.py

@@ -51,7 +51,7 @@ def __init__(
         for d in _dims_sel:
             self.slice_selectors[d].textChanged.connect(self._draw)
 
-        self.update_layers(None)
+        self._update_layers(None)
 
     @property
     def _layer(self) -> napari.layers.Layer:

tox.ini

@@ -11,6 +11,12 @@ python =
 
 [testenv]
 extras = testing
+allowlist_externals =
+    cp
+    ls
+    tree
 commands =
+    cp -R {toxinidir}/src/napari_matplotlib/tests/baseline {envdir}/baseline
+    ls {toxinidir}/src/napari_matplotlib/tests/baseline
     python -c 'from skimage import data; data.brain()'
-    python -m pytest --mpl -v --color=yes --cov=napari_matplotlib --cov-report=xml
+    python -m pytest --mpl --mpl-generate-summary=html --mpl-results-path={toxinidir}/reports -v --color=yes --cov=napari_matplotlib --cov-report=xml