Merge branch 'main' into paul/fix-contrast-limits

Author: p-j-smith

.github/dependabot.yml

@@ -0,0 +1,11 @@
+---
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      github-actions:
+        patterns:
+          - "*"

.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@v2
+        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/[email protected]
       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 }}

.github/workflows/test_and_deploy.yml

@@ -1,4 +1,6 @@
 name: tests
+permissions:
+  contents: read
 
 on:
   push:
@@ -17,6 +19,19 @@ concurrency:
     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 }}
@@ -27,15 +42,17 @@ jobs:
         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
@@ -54,15 +71,15 @@ 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/
         # Use always() to always run this step to publish test results when there are test failures
         if: ${{ always() }}
 
       - name: Coverage
-        uses: codecov/codecov-action@v4
+        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'
@@ -83,9 +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
@@ -99,4 +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

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
+    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: v1.10.0
+    rev: v1.15.0
     hooks:
      - id: mypy
        additional_dependencies: [numpy, matplotlib]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.4.2'
+    rev: 'v0.11.9'
     hooks:
       - id: ruff
 

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
 

docs/changelog.rst

@@ -1,13 +1,30 @@
 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 <https://scientific-python.org/specs/spec-0000/>`_, 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
 -----

pyproject.toml

@@ -13,10 +13,18 @@ filterwarnings = [
     "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"
+    "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", "--strict-config", "--strict-markers", "-ra"]
+addopts = [
+    "--mpl",
+    "--mpl-baseline-relative",
+    "--strict-config",
+    "--strict-markers",
+    "-ra",
+]
 minversion = "7"
 testpaths = ["src/napari_matplotlib/tests"]
 log_cli_level = "INFO"
@@ -54,17 +62,15 @@ ignore = [
 convention = "numpy"
 
 [tool.mypy]
-python_version = "3.10"
+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

setup.cfg

@@ -28,7 +28,7 @@ project_urls =
 packages = find:
 install_requires =
     matplotlib
-    napari
+    napari>=0.5
     numpy>=1.23
     tinycss2
 python_requires = >=3.10

src/napari_matplotlib/base.py

@@ -42,7 +42,7 @@ def __init__(
         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
@@ -84,7 +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()
 
@@ -97,7 +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
 
@@ -224,14 +224,24 @@ 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.
         """
         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:
         """
@@ -243,10 +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]