2025 update (#108)

Author: quantumjot

.github/workflows/linting.yml

@@ -11,18 +11,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Cache pre-commit
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pre-commit
           key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
 
       - name: Set up python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           cache: "pip"
           cache-dependency-path: "pyproject.toml"
 

.github/workflows/plugin_preview.yml

@@ -18,48 +18,66 @@ jobs:
     strategy:
       matrix:
         # Run all supported Python versions on linux
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         platform: [ubuntu-latest]
-        # Include one windows and macos run
+        # Include one macos run (Windows skipped due to OpenGL context issues)
         include:
           - platform: macos-latest
-            python-version: "3.9"
-          - platform: windows-latest
-            python-version: "3.9"
+            python-version: "3.11"
 
     steps:
+      # Checkout repository
+      - uses: actions/checkout@v4
       # Setup pyqt libraries
       - uses: tlambert03/setup-qt-libs@v1
-      # Run tests
-      - uses: UCL/composite-actions/python/tox@v1
+      # Setup Python
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .
+          python -m pip install pytest pytest-cov pytest-qt PySide6
+      - name: Install xvfb (Linux only)
+        if: runner.os == 'Linux'
+        run: python -m pip install pytest-xvfb
+      # Run tests
+      - name: Run tests
+        env:
+          DISPLAY: ":99.0"
+          # Disable napari GUI in headless environment
+          NAPARI_APPLICATION_IPY_INTERACTIVE: false
+          # Force matplotlib to use non-interactive backend
+          MPLBACKEND: Agg
+        run: pytest --cov --cov-report=xml
       # Upload code coverage
       - name: Coverage
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
 
   deploy:
     # this will run when you have tagged a commit, starting with "v*"
-    # and requires that you have put your twine API key in your
-    # github secrets (see readme for details)
+    # uses PyPI's trusted publishing via OIDC (no API key required)
     needs: [test]
     runs-on: ubuntu-latest
     if: contains(github.ref, 'tags')
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
-      - name: Install dependencies
+      - name: Install build dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install build twine
-      - name: Build and publish
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+          python -m pip install build
+      - name: Build package
         run: |
           git tag
           python -m build
-          twine upload dist/*
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test_and_deploy.yml

@@ -1,37 +1,18 @@
 repos:
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.246
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.4
     hooks:
       - id: ruff
-  - repo: https://github.com/Lucas-C/pre-commit-hooks
-    rev: v1.4.2
-    hooks:
-      - id: forbid-tabs
-  - repo: https://github.com/pappasam/toml-sort
-    rev: v0.22.3
-    hooks:
-      - id: toml-sort-fix
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.0.0
-    hooks:
-      - id: mypy
-        additional_dependencies: [numpy]
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.4
-    hooks:
-      - id: prettier
+        args: [--fix]
+      - id: ruff-format
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: check-case-conflict
-      - id: check-docstring-first
       - id: check-merge-conflict
       - id: check-toml
+      - id: check-yaml
       - id: end-of-file-fixer
       - id: mixed-line-ending
         args: [--fix=lf]
       - id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
-    hooks:
-      - id: black

.pre-commit-config.yaml

@@ -2,6 +2,7 @@
 Show a large tree in arboretum
 ==============================
 """
+
 import logging
 from copy import copy
 

examples/show_large_tree.py

@@ -7,6 +7,7 @@
 - loads the arboretum plugin
 - opens the napari viewer
 """
+
 import napari
 
 from napari_arboretum.sample.sample_data import load_sample_data

examples/show_sample_data.py

@@ -17,16 +17,17 @@ classifiers = [
     "License :: OSI Approved :: BSD License",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Programming Language :: Python",
     "Topic :: Scientific/Engineering :: Visualization",
 ]
 dependencies = [
     "matplotlib",
     "napari-matplotlib>=0.2.1",
-    "napari>=0.4.0",
+    "napari>=0.6.0",
     "numpy>=1.17.3",
     "pandas",
     "pooch>=1",
@@ -40,7 +41,7 @@ dynamic = [
 ]
 name = "napari-arboretum"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 entry-points."napari.manifest".napari-arboretum = "napari_arboretum:napari.yaml"
 license.file = "LICENCE.md"
 urls.homepage = "https://github.com/lowe-lab-ucl/arboretum"
@@ -68,9 +69,12 @@ testpaths = [
 [tool.ruff]
 fix = true
 force-exclude = true
+
+[tool.ruff.lint]
 ignore = [
     "B905", # python>=3.10
     "EM101",
+    "ISC001", # conflicts with ruff formatter
 ]
 per-file-ignores = {"test_*" = [
     "S101",
@@ -102,8 +106,12 @@ select = [
     "W",
     "YTT",
 ]
-isort.known-first-party = ["napari_arboretum"]
-mccabe.max-complexity = 18
+
+[tool.ruff.lint.isort]
+known-first-party = ["napari_arboretum"]
+
+[tool.ruff.lint.mccabe]
+max-complexity = 18
 
 [tool.setuptools_scm]
 write_to = "src/napari_arboretum/_version.py"
@@ -114,34 +122,3 @@ sort_inline_tables = true
 sort_table_keys = true
 spaces_indent_inline_array = 4
 trailing_comma_inline_array = true
-
-[tool.tox]
-legacy_tox_ini = """
-    [gh-actions]
-    python =
-        3.8: py38
-        3.9: py39
-        3.10: py310
-
-    [testenv]
-    passenv =
-        CI
-        DISPLAY
-        GITHUB_ACTIONS
-        NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
-        PYVISTA_OFF_SCREEN
-        XAUTHORITY
-    deps =
-        magicgui
-        napari
-        PySide2
-        pytest
-        pytest-cov
-        pytest-qt
-        pytest-xvfb ; sys_platform == 'linux'
-    commands = pytest --cov --cov-report=xml
-
-    [tox]
-    envlist = py{38,39,310}
-    isolated_build = True
-"""

pyproject.toml

@@ -4,6 +4,7 @@
 Note that this file should *not* contain code for laying out the graphs for
 visualisation. Code for this is kept in `tree.py`.
 """
+
 from __future__ import annotations
 
 from dataclasses import dataclass, field
@@ -66,7 +67,7 @@ def build_reverse_graph(graph: dict) -> tuple[list | set, dict[int, list[int]]]:
             else:
                 reverse_graph[parent].append(node)
 
-            if parent not in graph.keys():
+            if parent not in graph:
                 roots.add(parent)
 
     # sort the roots

src/napari_arboretum/graph.py

@@ -1,6 +1,7 @@
 """
 Classes and functions for laying out graphs for visualisation.
 """
+
 from __future__ import annotations
 
 import itertools
@@ -29,14 +30,14 @@ class Annotation:
     x: float
     y: float
     label: str
-    color: ColorType = field(default_factory=lambda: WHITE)
+    color: ColorType = field(default_factory=lambda: np.array([1.0, 1.0, 1.0, 1.0]))
 
 
 @dataclass
 class Edge:
     x: tuple[float, float]
     y: tuple[float, float]
-    color: ColorType = field(default_factory=lambda: WHITE)
+    color: ColorType = field(default_factory=lambda: np.array([1.0, 1.0, 1.0, 1.0]))
     track_id: int | None = None
     node: TreeNode | None = None
 

src/napari_arboretum/tree.py

@@ -28,7 +28,11 @@ class Bounds:
 @dataclass
 class TrackSubvisualProxy:
     pos: np.ndarray
-    color: np.ndarray = np.array([1.0, 1.0, 1.0, 1.0])
+    color: np.ndarray = None
+
+    def __post_init__(self):
+        if self.color is None:
+            self.color = np.array([1.0, 1.0, 1.0, 1.0])
 
     @property
     def connex(self):