Merge branch 'main' into feat/hist-bin-params

Author: p-j-smith

.github/workflows/docs.yml

@@ -32,7 +32,7 @@ jobs:
           sudo apt install graphviz --yes
 
       - name: Build Docs
-        uses: aganders3/headless-gui@v1
+        uses: aganders3/headless-gui@v2
         with:
           run: make html
           working-directory: ./docs

.github/workflows/napari_hub_preview.yml

@@ -12,6 +12,10 @@ on:
   workflow_dispatch:
   merge_group:
 
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
 jobs:
   test:
     name: ${{ matrix.platform }} py${{ matrix.python-version }}
@@ -20,7 +24,7 @@ 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
@@ -58,13 +62,15 @@ jobs:
         if: ${{ always() }}
 
       - name: Coverage
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         # 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*"

.github/workflows/test_and_deploy.yml

@@ -1,13 +1,13 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/psf/black
-    rev: 24.1.1
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.4.2
     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: v1.10.0
     hooks:
      - id: mypy
        additional_dependencies: [numpy, matplotlib]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.2.1'
+    rev: 'v0.4.2'
     hooks:
       - id: ruff
 

.pre-commit-config.yaml

@@ -1,5 +1,14 @@
 Changelog
 =========
+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
+
 2.0.1
 -----
 Bug fixes

docs/changelog.rst

@@ -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

docs/conf.py

@@ -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 +12,15 @@ 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"
 ]
 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 +30,11 @@ 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
@@ -35,24 +44,25 @@ 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 = "3.10"
 # 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
 ignore_missing_imports = true
 
+enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
+
 [[tool.mypy.overrides]]
 module = [
     "napari_matplotlib/tests/*",

pyproject.toml

@@ -29,9 +29,9 @@ packages = find:
 install_requires =
     matplotlib
     napari
-    numpy
+    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

setup.cfg

@@ -1,6 +1,5 @@
 import os
 from pathlib import Path
-from typing import Optional
 
 import matplotlib.style as mplstyle
 import napari
@@ -38,7 +37,7 @@ 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
@@ -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()
@@ -282,7 +281,7 @@ 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()

src/napari_matplotlib/base.py

@@ -78,7 +78,7 @@ 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)
 
@@ -168,7 +168,7 @@ def on_update_layers(self) -> None:
 
     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)
 
@@ -285,7 +285,7 @@ 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)
 
@@ -301,12 +301,12 @@ 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()
 
@@ -330,7 +330,7 @@ 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