diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..af3b9f02 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,11 @@ +--- +version: 2 +updates: + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "monthly" + groups: + github-actions: + patterns: + - "*" diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 5b721d92..6a5d182f 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -1,4 +1,6 @@ name: Build docs +permissions: + contents: read on: @@ -17,13 +19,15 @@ jobs: name: Build & Upload Artifact runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 + with: + persist-credentials: false - - uses: actions/setup-python@v3 + - uses: actions/setup-python@v5 with: python-version: "3.10" - - uses: tlambert03/setup-qt-libs@v1 + - uses: tlambert03/setup-qt-libs@19e4ef2d781d81f5f067182e228b54ec90d23b76 # v1 - name: Install Dependencies run: | @@ -32,13 +36,13 @@ jobs: sudo apt install graphviz --yes - name: Build Docs - uses: aganders3/headless-gui@v1 + uses: aganders3/headless-gui@f85dd6316993505dfc5f21839d520ae440c84816 # v2 with: run: make html working-directory: ./docs - name: Upload artifact - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: docs path: docs/_build @@ -49,13 +53,15 @@ jobs: needs: build-docs if: contains(github.ref, 'tags') steps: - - uses: actions/checkout@v3 - - uses: actions/download-artifact@v3 + - uses: actions/checkout@v4 + with: + persist-credentials: false + - uses: actions/download-artifact@v4.3.0 with: name: docs - name: Push to GitHub pages - uses: JamesIves/github-pages-deploy-action@v4 + uses: JamesIves/github-pages-deploy-action@6c2d9db40f9296374acc17b90404b6e8864128c8 # v4 with: folder: html ssh-key: ${{ secrets.DEPLOY_KEY }} diff --git a/.github/workflows/napari_hub_preview.yml b/.github/workflows/napari_hub_preview.yml deleted file mode 100644 index c204ac45..00000000 --- a/.github/workflows/napari_hub_preview.yml +++ /dev/null @@ -1,21 +0,0 @@ -name: napari hub Preview Page # we use this name to find your preview page artifact, so don't change it! -# For more info on this action, see https://github.com/chanzuckerberg/napari-hub-preview-action/blob/main/action.yml - -on: - pull_request: - types: [ labeled ] - -jobs: - preview-page: - if: ${{ github.event.label.name == 'napari hub preview' }} - name: Preview Page Deploy - runs-on: ubuntu-latest - - steps: - - name: Checkout repo - uses: actions/checkout@v3 - - - name: napari hub Preview Page Builder - uses: chanzuckerberg/napari-hub-preview-action@v0.1 - with: - hub-ref: main diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 8665e1d2..0521c9e6 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -1,4 +1,6 @@ name: tests +permissions: + contents: read on: push: @@ -12,7 +14,24 @@ on: workflow_dispatch: merge_group: +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: + pre-commit: + name: precommit + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + with: + fetch-depth: 0 + - uses: actions/setup-python@8d9ed9ac5c53483de85588cdf95a591a75ab9f55 # v5.5.0 + with: + python-version: "3.x" + - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 + with: + extra_args: --hook-stage manual --all-files test: name: ${{ matrix.platform }} py${{ matrix.python-version }} runs-on: ${{ matrix.platform }} @@ -20,18 +39,20 @@ jobs: fail-fast: false matrix: platform: [ubuntu-latest, macos-latest, windows-latest] - python-version: ['3.9', '3.10', '3.11'] + python-version: ['3.10', '3.11', '3.12'] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 + with: + persist-credentials: false - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} # these libraries enable testing on Qt on linux - - uses: tlambert03/setup-qt-libs@v1 + - uses: tlambert03/setup-qt-libs@19e4ef2d781d81f5f067182e228b54ec90d23b76 # v1 # strategy borrowed from vispy for installing opengl libs on windows - name: Install Windows OpenGL @@ -50,7 +71,7 @@ jobs: run: python -m tox - name: Upload pytest test results - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: pytest-results-${{ matrix.platform }} py${{ matrix.python-version }} path: reports/ @@ -58,13 +79,15 @@ jobs: if: ${{ always() }} - name: Coverage - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@18283e04ce6e62d37312384ff67231eb8fd56d24 # v5 # Don't run coverage on merge queue CI to avoid duplicating reports # to codecov. See https://github.com/matplotlib/napari-matplotlib/issues/155 if: github.event_name != 'merge_group' with: token: ${{ secrets.CODECOV_TOKEN }} - fail_ci_if_error: true + fail_ci_if_error: false + + deploy: # this will run when you have tagged a commit, starting with "v*" @@ -77,9 +100,11 @@ jobs: permissions: id-token: write steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 + with: + persist-credentials: false - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: "3.x" - name: Install build @@ -93,4 +118,4 @@ jobs: python -m build . - name: Publish package - uses: pypa/gh-action-pypi-publish@release/v1 + uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8df635ab..e592dea1 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,13 +1,13 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.5.0 + rev: v5.0.0 hooks: - id: check-docstring-first - id: end-of-file-fixer - id: trailing-whitespace - - repo: https://github.com/psf/black - rev: 23.12.1 + - repo: https://github.com/psf/black-pre-commit-mirror + rev: 25.1.0 hooks: - id: black @@ -17,14 +17,14 @@ repos: - id: napari-plugin-checks - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.8.0 + rev: v1.15.0 hooks: - id: mypy additional_dependencies: [numpy, matplotlib] - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.1.11' + rev: 'v0.11.9' hooks: - id: ruff diff --git a/README.md b/README.md index e4551d23..fb7aa635 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ A plugin to create Matplotlib plots from napari layers ## Introduction `napari-matplotlib` is a bridge between `napari` and `matplotlib`, making it easy to create publication quality `Matplotlib` plots based on the data loaded in `napari` layers. -Documentaiton can be found at https://napari-matplotlib.github.io/ +Documentation can be found at https://napari-matplotlib.github.io/ ## Contributing diff --git a/docs/changelog.rst b/docs/changelog.rst index 255982a3..60dd72ba 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -1,5 +1,31 @@ Changelog ========= + +2.1.0 +----- +New features +~~~~~~~~~~~~ +- Added a GUI element to manually set the number of bins in the histogram widgets. + +2.0.3 +----- +Bug fixes +~~~~~~~~~ +- Fix an error that happened when the histogram widget was open, but a layer that doesn't support + histogramming (e.g., a labels layer) was selected. + +2.0.2 +----- +Dependencies +~~~~~~~~~~~~ +napari-matplotlib now adheres to `SPEC 0 `_, and has: + +- Dropped support for Python 3.9 +- Added support for Python 3.12 +- Added a minimum required numpy verison of 1.23 +- Pinned the maximum napari version to ``< 0.5``. + Version 3.0 of ``napari-matplotlib`` will introduce support for ``napari`` version 0.5. + 2.0.1 ----- Bug fixes diff --git a/docs/conf.py b/docs/conf.py index 2517a59c..f1533830 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -13,7 +13,7 @@ # import os # import sys # sys.path.insert(0, os.path.abspath('.')) -import qtgallery +from sphinx_gallery import scrapers # -- Project information ----------------------------------------------------- @@ -35,18 +35,58 @@ "sphinx.ext.intersphinx", ] + +def reset_napari(gallery_conf, fname): # type: ignore[no-untyped-def] + from napari.settings import get_settings + from qtpy.QtWidgets import QApplication + + settings = get_settings() + settings.appearance.theme = "dark" + + # Disabling `QApplication.exec_` means example scripts can call `exec_` + # (scripts work when run normally) without blocking example execution by + # sphinx-gallery. (from qtgallery) + QApplication.exec_ = lambda _: None + + +def napari_scraper(block, block_vars, gallery_conf): # type: ignore[no-untyped-def] + """Basic napari window scraper. + + Looks for any QtMainWindow instances and takes a screenshot of them. + + `app.processEvents()` allows Qt events to propagateo and prevents hanging. + """ + import napari + + imgpath_iter = block_vars["image_path_iterator"] + + if app := napari.qt.get_app(): + app.processEvents() + else: + return "" + + img_paths = [] + for win, img_path in zip( + reversed(napari._qt.qt_main_window._QtMainWindow._instances), + imgpath_iter, + strict=False, + ): + img_paths.append(img_path) + win._window.screenshot(img_path, canvas_only=False) + + napari.Viewer.close_all() + app.processEvents() + + return scrapers.figure_rst(img_paths, gallery_conf["src_dir"]) + + sphinx_gallery_conf = { "filename_pattern": ".", - "image_scrapers": (qtgallery.qtscraper,), - "reset_modules": (qtgallery.reset_qapp,), + "image_scrapers": (napari_scraper,), + "reset_modules": (reset_napari,), } +suppress_warnings = ["config.cache"] -qtgallery_conf = { - "xvfb_size": (640, 480), - "xvfb_color_depth": 24, - "xfvb_use_xauth": False, - "xfvb_extra_args": [], -} numpydoc_show_class_members = False automodapi_inheritance_diagram = True diff --git a/examples/histogram.py b/examples/histogram.py index ccda491a..b9ceb377 100644 --- a/examples/histogram.py +++ b/examples/histogram.py @@ -2,6 +2,7 @@ Histograms ========== """ + import napari viewer = napari.Viewer() diff --git a/examples/scatter.py b/examples/scatter.py index cd812401..00e01ec9 100644 --- a/examples/scatter.py +++ b/examples/scatter.py @@ -2,6 +2,7 @@ Scatter plots ============= """ + import napari viewer = napari.Viewer() diff --git a/examples/slice.py b/examples/slice.py index 3e43443e..242a16cc 100644 --- a/examples/slice.py +++ b/examples/slice.py @@ -2,6 +2,7 @@ 1D slices ========= """ + import napari viewer = napari.Viewer() diff --git a/pyproject.toml b/pyproject.toml index ba9f9e66..f76831a3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["setuptools", "wheel", "setuptools_scm"] +requires = ["setuptools", "setuptools_scm"] build-backend = "setuptools.build_meta" [tool.setuptools_scm] @@ -12,9 +12,23 @@ filterwarnings = [ # Coming from vispy "ignore:distutils Version classes are deprecated:DeprecationWarning", "ignore:`np.bool8` is a deprecated alias for `np.bool_`:DeprecationWarning", + # Coming from pydantic via napari + "ignore:Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.:DeprecationWarning", + # Until we stop supporting older numpy versions (<2.1) + "ignore:(?s).*`newshape` keyword argument is deprecated.*$:DeprecationWarning", ] qt_api = "pyqt6" -addopts = "--mpl --mpl-baseline-relative" +addopts = [ + "--mpl", + "--mpl-baseline-relative", + "--strict-config", + "--strict-markers", + "-ra", +] +minversion = "7" +testpaths = ["src/napari_matplotlib/tests"] +log_cli_level = "INFO" +xfail_strict = true [tool.black] line-length = 79 @@ -24,8 +38,11 @@ profile = "black" line_length = 79 [tool.ruff] -target-version = "py39" -select = ["I", "UP", "F", "E", "W", "D"] +target-version = "py310" +fix = true + +[tool.ruff.lint] +select = ["B", "I", "UP", "F", "E", "W", "D"] ignore = [ "D100", # Missing docstring in public module "D104", # Missing docstring in public package @@ -35,26 +52,25 @@ ignore = [ "D401", # First line of docstring should be in imperative mood ] -fix = true -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "docs/*" = ["D"] "examples/*" = ["D"] "src/napari_matplotlib/tests/*" = ["D"] -[tool.ruff.pydocstyle] +[tool.ruff.lint.pydocstyle] convention = "numpy" [tool.mypy] -python_version = "3.9" +python_version = "3.12" # Block below are checks that form part of mypy 'strict' mode strict = true disallow_subclassing_any = false # TODO: fix -warn_return_any = false # TODO: fix +warn_return_any = false # TODO: fix ignore_missing_imports = true +enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"] + [[tool.mypy.overrides]] -module = [ - "napari_matplotlib/tests/*", -] +module = ["napari_matplotlib/tests/*"] disallow_untyped_defs = false diff --git a/setup.cfg b/setup.cfg index 41e4e34f..a3709e66 100644 --- a/setup.cfg +++ b/setup.cfg @@ -28,10 +28,10 @@ project_urls = packages = find: install_requires = matplotlib - napari - numpy + napari>=0.5 + numpy>=1.23 tinycss2 -python_requires = >=3.9 +python_requires = >=3.10 include_package_data = True package_dir = =src @@ -47,11 +47,10 @@ napari.manifest = [options.extras_require] docs = - napari[all]==0.4.19rc3 + napari[all] numpydoc pydantic<2 pydata-sphinx-theme - qtgallery sphinx sphinx-automodapi sphinx-gallery diff --git a/src/napari_matplotlib/base.py b/src/napari_matplotlib/base.py index fb9e485c..ca69a548 100644 --- a/src/napari_matplotlib/base.py +++ b/src/napari_matplotlib/base.py @@ -1,6 +1,5 @@ import os from pathlib import Path -from typing import Optional import matplotlib.style as mplstyle import napari @@ -38,12 +37,12 @@ class BaseNapariMPLWidget(QWidget): def __init__( self, napari_viewer: napari.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(parent=parent) self.viewer = napari_viewer self.napari_theme_style_sheet = style_sheet_from_theme( - get_theme(napari_viewer.theme, as_dict=False) + get_theme(napari_viewer.theme) ) # Sets figure.* style @@ -85,7 +84,7 @@ def _on_napari_theme_changed(self, event: Event) -> None: Event that triggered the callback. """ self.napari_theme_style_sheet = style_sheet_from_theme( - get_theme(event.value, as_dict=False) + get_theme(event.value) ) self._replace_toolbar_icons() @@ -98,7 +97,7 @@ def _napari_theme_has_light_bg(self) -> bool: bool True if theme's background colour has hsl lighter than 50%, False if darker. """ - theme = napari.utils.theme.get_theme(self.viewer.theme, as_dict=False) + theme = napari.utils.theme.get_theme(self.viewer.theme) _, _, bg_lightness = theme.background.as_hsl_tuple() return bg_lightness > 0.5 @@ -173,7 +172,7 @@ class NapariMPLWidget(BaseNapariMPLWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(napari_viewer=napari_viewer, parent=parent) self._setup_callbacks() @@ -225,6 +224,15 @@ def _setup_callbacks(self) -> None: self._update_layers ) + @property + def _valid_layer_selection(self) -> bool: + """ + Return `True` if layer selection is valid. + """ + return self.n_selected_layers in self.n_layers_input and all( + isinstance(layer, self.input_layer_types) for layer in self.layers + ) + def _update_layers(self, event: napari.utils.events.Event) -> None: """ Update the ``layers`` attribute with currently selected layers and re-draw. @@ -232,7 +240,8 @@ def _update_layers(self, event: napari.utils.events.Event) -> None: self.layers = list(self.viewer.layers.selection) self.layers = sorted(self.layers, key=lambda layer: layer.name) self.on_update_layers() - self._draw() + if self._valid_layer_selection: + self._draw() def _draw(self) -> None: """ @@ -244,10 +253,7 @@ def _draw(self) -> None: with mplstyle.context(self.napari_theme_style_sheet): # everything should be done in the style context self.clear() - if self.n_selected_layers in self.n_layers_input and all( - isinstance(layer, self.input_layer_types) - for layer in self.layers - ): + if self._valid_layer_selection: self.draw() self.canvas.draw() # type: ignore[no-untyped-call] @@ -282,7 +288,7 @@ class SingleAxesWidget(NapariMPLWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(napari_viewer=napari_viewer, parent=parent) self.add_single_axes() diff --git a/src/napari_matplotlib/histogram.py b/src/napari_matplotlib/histogram.py index 40765287..85bba9d2 100644 --- a/src/napari_matplotlib/histogram.py +++ b/src/napari_matplotlib/histogram.py @@ -1,4 +1,4 @@ -from typing import Any, Optional, cast +from typing import Any, cast import napari import numpy as np @@ -8,7 +8,10 @@ from napari.layers._multiscale_data import MultiScaleData from qtpy.QtWidgets import ( QComboBox, + QFormLayout, + QGroupBox, QLabel, + QSpinBox, QVBoxLayout, QWidget, ) @@ -22,15 +25,32 @@ _COLORS = {"r": "tab:red", "g": "tab:green", "b": "tab:blue"} -def _get_bins(data: npt.NDArray[Any]) -> npt.NDArray[Any]: +def _get_bins( + data: npt.NDArray[Any], + num_bins: int = 100, +) -> npt.NDArray[np.floating]: + """Create evenly spaced bins with a given interval. + + Parameters + ---------- + data : napari.layers.Layer.data + Napari layer data. + num_bins : integer, optional + Number of evenly-spaced bins to create. Defaults to 100. + + Returns + ------- + bin_edges : numpy.ndarray + Array of evenly spaced bin edges. + """ if data.dtype.kind in {"i", "u"}: # Make sure integer data types have integer sized bins - step = np.ceil(np.ptp(data) / 100) + step = np.ceil(np.ptp(data) / num_bins) return np.arange(np.min(data), np.max(data) + step, step) else: - # For other data types, just have 100 evenly spaced bins - # (and 101 bin edges) - return np.linspace(np.min(data), np.max(data), 101) + # For other data types we can use exactly `num_bins` bins + # (and `num_bins` + 1 bin edges) + return np.linspace(np.min(data), np.max(data), num_bins + 1) class HistogramWidget(SingleAxesWidget): @@ -44,9 +64,33 @@ class HistogramWidget(SingleAxesWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(napari_viewer, parent=parent) + + num_bins_widget = QSpinBox() + num_bins_widget.setRange(1, 100_000) + num_bins_widget.setValue(101) + num_bins_widget.setWrapping(False) + num_bins_widget.setKeyboardTracking(False) + + # Set bins widget layout + bins_selection_layout = QFormLayout() + bins_selection_layout.addRow("num bins", num_bins_widget) + + # Group the widgets and add to main layout + params_widget_group = QGroupBox("Params") + params_widget_group_layout = QVBoxLayout() + params_widget_group_layout.addLayout(bins_selection_layout) + params_widget_group.setLayout(params_widget_group_layout) + self.layout().addWidget(params_widget_group) + + # Add callbacks + num_bins_widget.valueChanged.connect(self._draw) + + # Store widgets for later usage + self.num_bins_widget = num_bins_widget + self._update_layers(None) self.viewer.events.theme.connect(self._on_napari_theme_changed) @@ -55,22 +99,33 @@ def on_update_layers(self) -> None: Called when the selected layers are updated. """ super().on_update_layers() - for layer in self.viewer.layers: - layer.events.contrast_limits.connect(self._update_contrast_lims) + if self._valid_layer_selection: + self.layers[0].events.contrast_limits.connect( + self._update_contrast_lims + ) + + if not self.layers: + return + + # Reset the num bins based on new layer data + layer_data = self._get_layer_data(self.layers[0]) + self._set_widget_nums_bins(data=layer_data) def _update_contrast_lims(self) -> None: for lim, line in zip( - self.layers[0].contrast_limits, self._contrast_lines + self.layers[0].contrast_limits, self._contrast_lines, strict=False ): line.set_xdata(lim) self.figure.canvas.draw() - def draw(self) -> None: - """ - Clear the axes and histogram the currently selected layer/slice. - """ - layer: Image = self.layers[0] + def _set_widget_nums_bins(self, data: npt.NDArray[Any]) -> None: + """Update num_bins widget with bins determined from the image data""" + bins = _get_bins(data) + self.num_bins_widget.setValue(bins.size - 1) + + def _get_layer_data(self, layer: napari.layers.Layer) -> npt.NDArray[Any]: + """Get the data associated with a given layer""" data = layer.data if isinstance(layer.data, MultiScaleData): @@ -85,9 +140,21 @@ def draw(self) -> None: # Read data into memory if it's a dask array data = np.asarray(data) + return data + + def draw(self) -> None: + """ + Clear the axes and histogram the currently selected layer/slice. + """ + layer: Image = self.layers[0] + data = self._get_layer_data(layer) + # Important to calculate bins after slicing 3D data, to avoid reading # whole cube into memory. - bins = _get_bins(data) + bins = _get_bins( + data, + num_bins=self.num_bins_widget.value(), + ) if layer.rgb: # Histogram RGB channels independently @@ -121,7 +188,7 @@ class FeaturesHistogramWidget(SingleAxesWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(napari_viewer, parent=parent) @@ -137,12 +204,12 @@ def __init__( self._update_layers(None) @property - def x_axis_key(self) -> Optional[str]: + def x_axis_key(self) -> str | None: """Key to access x axis data from the FeaturesTable""" return self._x_axis_key @x_axis_key.setter - def x_axis_key(self, key: Optional[str]) -> None: + def x_axis_key(self, key: str | None) -> None: self._x_axis_key = key self._draw() @@ -166,7 +233,7 @@ def _get_valid_axis_keys(self) -> list[str]: else: return self.layers[0].features.keys() - def _get_data(self) -> tuple[Optional[npt.NDArray[Any]], str]: + def _get_data(self) -> tuple[npt.NDArray[Any] | None, str]: """Get the plot data. Returns @@ -209,10 +276,12 @@ def draw(self) -> None: # get the colormap from the layer depending on its type if isinstance(self.layers[0], napari.layers.Points): colormap = self.layers[0].face_colormap - self.layers[0].face_color = self.x_axis_key + if self.x_axis_key: + self.layers[0].face_color = self.x_axis_key elif isinstance(self.layers[0], napari.layers.Vectors): colormap = self.layers[0].edge_colormap - self.layers[0].edge_color = self.x_axis_key + if self.x_axis_key: + self.layers[0].edge_color = self.x_axis_key else: colormap = None diff --git a/src/napari_matplotlib/scatter.py b/src/napari_matplotlib/scatter.py index 67d6896c..98ebe928 100644 --- a/src/napari_matplotlib/scatter.py +++ b/src/napari_matplotlib/scatter.py @@ -1,4 +1,4 @@ -from typing import Any, Optional, Union +from typing import Any import napari import numpy.typing as npt @@ -100,7 +100,7 @@ class FeaturesScatterWidget(ScatterBaseWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(napari_viewer, parent=parent) @@ -118,7 +118,7 @@ def __init__( self._update_layers(None) @property - def x_axis_key(self) -> Union[str, None]: + def x_axis_key(self) -> str | None: """ Key for the x-axis data. """ @@ -133,7 +133,7 @@ def x_axis_key(self, key: str) -> None: self._draw() @property - def y_axis_key(self) -> Union[str, None]: + def y_axis_key(self) -> str | None: """ Key for the y-axis data. """ diff --git a/src/napari_matplotlib/slice.py b/src/napari_matplotlib/slice.py index 9459fa97..1924bf2b 100644 --- a/src/napari_matplotlib/slice.py +++ b/src/napari_matplotlib/slice.py @@ -1,4 +1,4 @@ -from typing import Any, Optional +from typing import Any import matplotlib.ticker as mticker import napari @@ -30,7 +30,7 @@ class SliceWidget(SingleAxesWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): # Setup figure/axes super().__init__(napari_viewer, parent=parent) diff --git a/src/napari_matplotlib/tests/baseline/test_histogram_2D_bins.png b/src/napari_matplotlib/tests/baseline/test_histogram_2D_bins.png new file mode 100644 index 00000000..98e3cde1 Binary files /dev/null and b/src/napari_matplotlib/tests/baseline/test_histogram_2D_bins.png differ diff --git a/src/napari_matplotlib/tests/scatter/test_scatter.py b/src/napari_matplotlib/tests/scatter/test_scatter.py index a225863d..0c60660c 100644 --- a/src/napari_matplotlib/tests/scatter/test_scatter.py +++ b/src/napari_matplotlib/tests/scatter/test_scatter.py @@ -15,7 +15,9 @@ def test_scatter_2D(make_napari_viewer, astronaut_data): viewer.add_image(astronaut_data[0], **astronaut_data[1], name="astronaut") viewer.add_image( - astronaut_data[0] * -1, **astronaut_data[1], name="astronaut_reversed" + astronaut_data[0] * -1.0, + **astronaut_data[1], + name="astronaut_reversed", ) # De-select existing selection viewer.layers.selection.clear() @@ -36,7 +38,7 @@ def test_scatter_3D(make_napari_viewer, brain_data): viewer.add_image(brain_data[0], **brain_data[1], name="brain") viewer.add_image( - brain_data[0] * -1, **brain_data[1], name="brain_reversed" + brain_data[0] * -1.0, **brain_data[1], name="brain_reversed" ) # De-select existing selection viewer.layers.selection.clear() diff --git a/src/napari_matplotlib/tests/test_histogram.py b/src/napari_matplotlib/tests/test_histogram.py index 1ceca519..435973ba 100644 --- a/src/napari_matplotlib/tests/test_histogram.py +++ b/src/napari_matplotlib/tests/test_histogram.py @@ -10,6 +10,20 @@ ) +@pytest.mark.mpl_image_compare +def test_histogram_2D_bins(make_napari_viewer, astronaut_data): + viewer = make_napari_viewer() + viewer.theme = "light" + viewer.add_image(astronaut_data[0], **astronaut_data[1]) + widget = HistogramWidget(viewer) + viewer.window.add_dock_widget(widget) + widget.num_bins_widget.setValue(25) + fig = widget.figure + # Need to return a copy, as original figure is too eagerley garbage + # collected by the widget + return deepcopy(fig) + + @pytest.mark.mpl_image_compare def test_histogram_2D(make_napari_viewer, astronaut_data): viewer = make_napari_viewer() diff --git a/src/napari_matplotlib/tests/test_theme.py b/src/napari_matplotlib/tests/test_theme.py index 2310f32f..5fedc43d 100644 --- a/src/napari_matplotlib/tests/test_theme.py +++ b/src/napari_matplotlib/tests/test_theme.py @@ -29,7 +29,7 @@ def _mock_up_theme() -> None: Based on: https://napari.org/stable/gallery/new_theme.html """ - blue_theme = napari.utils.theme.get_theme("dark", False) + blue_theme = napari.utils.theme.get_theme("dark") blue_theme.label = "blue" blue_theme.background = "#4169e1" # my favourite shade of blue napari.utils.theme.register_theme( diff --git a/src/napari_matplotlib/tests/test_util.py b/src/napari_matplotlib/tests/test_util.py index a8792d41..e966cc26 100644 --- a/src/napari_matplotlib/tests/test_util.py +++ b/src/napari_matplotlib/tests/test_util.py @@ -26,7 +26,7 @@ def test_interval(): assert 10 not in interval with pytest.raises(ValueError, match="must be an integer"): - "string" in interval # type: ignore + assert "string" in interval # type: ignore[operator] with pytest.raises(ValueError, match="must be <= upper_bound"): Interval(5, 3) @@ -69,7 +69,10 @@ def test_fallback_if_missing_dimensions(mocker): test_css = " Flobble { background-color: rgb(0, 97, 163); } " mocker.patch("napari.qt.get_current_stylesheet").return_value = test_css with pytest.warns(RuntimeWarning, match="Unable to find DimensionToken"): - assert from_napari_css_get_size_of("Flobble", (1, 2)) == QSize(1, 2) + with pytest.warns(RuntimeWarning, match="Unable to find Flobble"): + assert from_napari_css_get_size_of("Flobble", (1, 2)) == QSize( + 1, 2 + ) def test_fallback_if_prelude_not_in_css(): diff --git a/src/napari_matplotlib/util.py b/src/napari_matplotlib/util.py index ed994256..8d4150c3 100644 --- a/src/napari_matplotlib/util.py +++ b/src/napari_matplotlib/util.py @@ -1,4 +1,3 @@ -from typing import Optional, Union from warnings import warn import napari.qt @@ -12,7 +11,7 @@ class Interval: An integer interval. """ - def __init__(self, lower_bound: Optional[int], upper_bound: Optional[int]): + def __init__(self, lower_bound: int | None, upper_bound: int | None): """ Parameters ---------- @@ -48,7 +47,7 @@ def __contains__(self, val: int) -> bool: return True @property - def _helper_text(self) -> Optional[str]: + def _helper_text(self) -> str | None: """ Helper text for widgets. """ @@ -86,9 +85,7 @@ def _has_id(nodes: list[tinycss2.ast.Node], id_name: str) -> bool: ) -def _get_dimension( - nodes: list[tinycss2.ast.Node], id_name: str -) -> Union[int, None]: +def _get_dimension(nodes: list[tinycss2.ast.Node], id_name: str) -> int | None: """ Get the value of the DimensionToken for the IdentToken `id_name`. @@ -97,14 +94,18 @@ def _get_dimension( None if no IdentToken is found. """ cleaned_nodes = [node for node in nodes if node.type != "whitespace"] - for name, _, value, _ in zip(*(iter(cleaned_nodes),) * 4): + for name, _, value, _ in zip(*(iter(cleaned_nodes),) * 4, strict=False): if ( name.type == "ident" and value.type == "dimension" and name.value == id_name ): return value.int_value - warn(f"Unable to find DimensionToken for {id_name}", RuntimeWarning) + warn( + f"Unable to find DimensionToken for {id_name}", + RuntimeWarning, + stacklevel=1, + ) return None @@ -137,6 +138,7 @@ def from_napari_css_get_size_of( f"Unable to find {qt_element_name} or unable to find its size in " f"the current Napari stylesheet, falling back to {fallback}", RuntimeWarning, + stacklevel=1, ) return QSize(*fallback) diff --git a/tox.ini b/tox.ini index 4ec0c702..f4aed6a8 100644 --- a/tox.ini +++ b/tox.ini @@ -1,12 +1,12 @@ [tox] -envlist = py{39,310,311} +envlist = py{310,311,312} isolated_build = true [gh-actions] python = - 3.9: py39 3.10: py310 3.11: py311 + 3.12: py312 [testenv] extras = testing pFad - Phonifier reborn

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