diff --git a/docs/Makefile b/docs/Makefile
index b50c24dc..5117fbf5 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -3,7 +3,7 @@
# You can set these variables from the command line, and also
# from the environment for the first two.
-SPHINXOPTS ?= -W
+SPHINXOPTS ?= -W --keep-going
SPHINXBUILD ?= sphinx-build
SOURCEDIR = .
BUILDDIR = _build
diff --git a/docs/conf.py b/docs/conf.py
index 2c04f853..efff247a 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -56,10 +56,18 @@
automodapi_inheritance_diagram = False
intersphinx_mapping = {
+ "python": ("https://docs.python.org/3/", None),
"napari": ("https://napari.org/", None),
+ "numpy": ("https://numpy.org/doc/stable/", None),
"matplotlib": ("https://matplotlib.org/", None),
+ "PyQT6": ("https://www.riverbankcomputing.com/static/Docs/PyQt6/", None),
}
+nitpicky = True
+# Can't work out how to link this properley using intersphinx and the PyQT6 docs.
+# TODO: fix at some point
+nitpick_ignore = [("py:class", "PyQt6.QtWidgets.QWidget")]
+
# Add any paths that contain templates here, relative to this directory.
templates_path = ["_templates"]
diff --git a/docs/make.bat b/docs/make.bat
index 32bb2452..4b78115a 100644
--- a/docs/make.bat
+++ b/docs/make.bat
@@ -7,6 +7,9 @@ REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
+if "%SPHINXOPTS%" == "" (
+ set SPHINXOPTS="--keep-going"
+)
set SOURCEDIR=.
set BUILDDIR=_build
diff --git a/src/napari_matplotlib/base.py b/src/napari_matplotlib/base.py
index b69d0310..fc8fa17f 100644
--- a/src/napari_matplotlib/base.py
+++ b/src/napari_matplotlib/base.py
@@ -22,11 +22,12 @@
class NapariMPLWidget(QWidget):
"""
- Base Matplotlib canvas. Widget that can be embedded as a napari widget.
+ Widget containing a Matplotlib canvas and toolbar.
- This creates a single FigureCanvas, which contains a single Figure.
- It is not responsible for creating any Axes, because different widgets
- may want to implement different subplot layouts.
+ 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
@@ -60,12 +61,12 @@ def __init__(self, napari_viewer: napari.viewer.Viewer):
self.layout().addWidget(self.toolbar)
self.layout().addWidget(self.canvas)
- self.setup_callbacks()
+ self._setup_callbacks()
self.layers: List[napari.layers.Layer] = []
- # Accept any number of input layers by default
+ #: Number of layers taken as input
n_layers_input = Interval(None, None)
- # Accept any type of input layer by default
+ #: Type of layer taken as input
input_layer_types: Tuple[napari.layers.Layer, ...] = (napari.layers.Layer,)
@property
@@ -83,17 +84,17 @@ def n_selected_layers(self) -> int:
@property
def current_z(self) -> int:
"""
- Current z-step of the viewer.
+ Current z-step of the napari viewer.
"""
return self.viewer.dims.current_step[0]
- def setup_callbacks(self) -> None:
+ def _setup_callbacks(self) -> None:
"""
Sets up callbacks.
- Sets up callbacks for:
- - Layer selection changing
- - z-step changing
+ Sets up callbacks for when:
+ - Layer selection is changed
+ - z-step is changed
"""
# z-step changed in viewer
self.viewer.dims.events.current_step.connect(self._draw)
@@ -102,7 +103,7 @@ def setup_callbacks(self) -> None:
def update_layers(self, event: napari.utils.events.Event) -> None:
"""
- Update the layers attribute with currently selected layers and re-draw.
+ Update the ``layers`` attribute with currently selected layers and re-draw.
"""
self.layers = list(self.viewer.layers.selection)
self._on_update_layers()
@@ -145,7 +146,7 @@ def add_single_axes(self) -> None:
@staticmethod
def apply_napari_colorscheme(ax: Axes) -> None:
- """Apply napari-compatible colorscheme to an axes object."""
+ """Apply napari-compatible colorscheme to an Axes."""
# changing color of axes background to transparent
ax.set_facecolor("none")
diff --git a/src/napari_matplotlib/scatter.py b/src/napari_matplotlib/scatter.py
index 405b7b09..858a42a8 100644
--- a/src/napari_matplotlib/scatter.py
+++ b/src/napari_matplotlib/scatter.py
@@ -8,7 +8,7 @@
from .base import NapariMPLWidget
from .util import Interval
-__all__ = ["ScatterWidget", "FeaturesScatterWidget"]
+__all__ = ["ScatterBaseWidget", "ScatterWidget", "FeaturesScatterWidget"]
class ScatterBaseWidget(NapariMPLWidget):
@@ -68,7 +68,7 @@ def _get_data(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
class ScatterWidget(ScatterBaseWidget):
"""
- Widget to display scatter plot of two similarly shaped image layers.
+ Scatter data in two similarly shaped layers.
If there are more than 500 data points, a 2D histogram is displayed instead
of a scatter plot, to avoid too many scatter points.
@@ -127,7 +127,7 @@ def __init__(self, napari_viewer: napari.viewer.Viewer):
@property
def x_axis_key(self) -> Optional[str]:
"""
- Key to access x axis data from the FeaturesTable.
+ Key for the x-axis data.
"""
return self._x_axis_key
@@ -139,7 +139,7 @@ def x_axis_key(self, key: Optional[str]) -> None:
@property
def y_axis_key(self) -> Optional[str]:
"""
- Key to access y axis data from the FeaturesTable.
+ Key for the y-axis data.
"""
return self._y_axis_key
diff --git a/src/napari_matplotlib/slice.py b/src/napari_matplotlib/slice.py
index 4e22bad8..c29fff5c 100644
--- a/src/napari_matplotlib/slice.py
+++ b/src/napari_matplotlib/slice.py
@@ -50,7 +50,7 @@ def __init__(self, napari_viewer: napari.viewer.Viewer):
self.update_layers(None)
@property
- def layer(self) -> napari.layers.Layer:
+ def _layer(self) -> napari.layers.Layer:
"""
Layer being plotted.
"""
@@ -73,28 +73,19 @@ def current_dim_index(self) -> int:
return _dims[::-1].index(self.current_dim)
@property
- def selector_values(self) -> Dict[str, int]:
+ def _selector_values(self) -> Dict[str, int]:
"""
Values of the slice selectors.
"""
return {d: self.slice_selectors[d].value() for d in _dims_sel}
- def update_slice_selectors(self) -> None:
- """
- Update range and enabled status of the slice selectors, and the value
- of the z slice selector.
- """
- # Update min/max
- for i, dim in enumerate(_dims_sel):
- self.slice_selectors[dim].setRange(0, self.layer.data.shape[i])
-
- def get_xy(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any]]:
+ def _get_xy(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any]]:
"""
Get data for plotting.
"""
- x = np.arange(self.layer.data.shape[self.current_dim_index])
+ x = np.arange(self._layer.data.shape[self.current_dim_index])
- vals = self.selector_values
+ vals = self._selector_values
vals.update({"z": self.current_z})
slices = []
@@ -109,7 +100,7 @@ def get_xy(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any]]:
# Reverse since z is the first axis in napari
slices = slices[::-1]
- y = self.layer.data[tuple(slices)].ravel()
+ y = self._layer.data[tuple(slices)].ravel()
return x, y
@@ -123,8 +114,8 @@ def draw(self) -> None:
"""
Clear axes and draw a 1D plot.
"""
- x, y = self.get_xy()
+ x, y = self._get_xy()
self.axes.plot(x, y)
self.axes.set_xlabel(self.current_dim)
- self.axes.set_title(self.layer.name)
+ self.axes.set_title(self._layer.name)
diff --git a/src/napari_matplotlib/util.py b/src/napari_matplotlib/util.py
index 4ae8ca19..17965caf 100644
--- a/src/napari_matplotlib/util.py
+++ b/src/napari_matplotlib/util.py
@@ -28,6 +28,12 @@ def __init__(self, lower_bound: Optional[int], upper_bound: Optional[int]):
self.lower = lower_bound
self.upper = upper_bound
+ def __repr__(self) -> str:
+ """
+ Get string representation.
+ """
+ return f"Interval({self.lower}, {self.upper})"
+
def __contains__(self, val: int) -> bool:
"""
Return True if val is in the current interval.