Merge branch 'main' into add_feature_histograms

.github/workflows/docs.yml

@@ -0,0 +1,61 @@
+name: Build docs
+
+on:
+
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+
+jobs:
+  build-docs:
+    name: Build & Upload Artifact
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+
+      - uses: tlambert03/setup-qt-libs@v1
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[docs]"
+          sudo apt install graphviz --yes
+
+      - name: Build Docs
+        uses: aganders3/headless-gui@v1
+        with:
+          run: make html
+          working-directory: ./docs
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: docs
+          path: docs/_build
+
+  upload-docs:
+    name: Upload docs to GitHub pages
+    runs-on: ubuntu-latest
+    needs: build-docs
+    if: contains(github.ref, 'tags')
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/download-artifact@v3
+      with:
+        name: docs
+
+    - name: Push to GitHub pages
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        folder: html
+        ssh-key: ${{ secrets.DEPLOY_KEY }}
+        repository-name: napari-matplotlib/napari-matplotlib.github.io

.github/workflows/napari_hub_preview.yml

@@ -13,9 +13,9 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: napari hub Preview Page Builder
-        uses: chanzuckerberg/[email protected].5
+        uses: chanzuckerberg/[email protected]
         with:
           hub-ref: main

.github/workflows/test_and_deploy.yml

@@ -1,6 +1,3 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: tests
 
 on:
@@ -13,14 +10,16 @@ on:
     branches:
       - main
   workflow_dispatch:
+  merge_group:
 
 jobs:
   test:
     name: ${{ matrix.platform }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.platform }}
     strategy:
+      fail-fast: false
       matrix:
-        platform: [ubuntu-latest]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ['3.8', '3.9', '3.10']
 
     steps:
@@ -50,8 +49,22 @@ jobs:
       - name: Test with tox
         run: python -m tox
 
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@v3
+        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@v2
+        uses: codecov/codecov-action@v3
+        # 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
 
   deploy:
     # this will run when you have tagged a commit, starting with "v*"
@@ -60,21 +73,24 @@ jobs:
     needs: [test]
     runs-on: ubuntu-latest
     if: contains(github.ref, 'tags')
+    environment: pypi-deploy
+    permissions:
+      id-token: write
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
           python-version: "3.x"
-      - name: Install dependencies
+      - name: Install build
         run: |
           python -m pip install --upgrade pip
-          pip install -U setuptools setuptools_scm wheel twine build
-      - name: Build and publish
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+          python -m pip install --upgrade build
+
+      - name: Build package
         run: |
           git tag
           python -m build .
-          twine upload dist/*
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -37,6 +37,7 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+report/
 .coverage
 .coverage.*
 .cache
@@ -84,3 +85,6 @@ venv/
 
 # written by setuptools_scm
 **/_version.py
+
+# Generated by test runs
+reports

.napari/config.yml

@@ -0,0 +1,8 @@
+labels:
+  ontology: EDAM-BIOIMAGING:alpha06
+  terms:
+  - 2D Image
+  - 3D Image
+  - Plotting
+  - Slice rendering
+  - Scientific visualisation

.pre-commit-config.yaml

@@ -1,43 +1,32 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.4.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
-  - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v1.20.1
-    hooks:
-      - id: setup-cfg-fmt
-  - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
-    hooks:
-      - id: flake8
-        additional_dependencies: [flake8-typing-imports>=1.9.0]
-  - repo: https://github.com/myint/autoflake
-    rev: v1.4
-    hooks:
-      - id: autoflake
-        args: ["--in-place", "--remove-all-unused-imports"]
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
-    hooks:
-      - id: isort
+
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.7.0
     hooks:
       - id: black
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v2.32.0
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus, --keep-runtime-typing]
+
   - repo: https://github.com/tlambert03/napari-plugin-checks
-    rev: v0.2.0
+    rev: v0.3.0
     hooks:
       - id: napari-plugin-checks
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.910-1
+    rev: v1.5.1
     hooks:
      - id: mypy
-       args: ["--disallow-incomplete-defs", "--ignore-missing-imports"]
+       additional_dependencies: [numpy, matplotlib]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: 'v0.0.285'
+    hooks:
+      - id: ruff
+
+ci:
+  autofix_prs: false

.readthedocs.yaml

@@ -0,0 +1,15 @@
+version: 2
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+  apt_packages:
+    - xvfb

MANIFEST.in

@@ -1,5 +1,6 @@
 include LICENSE
 include README.md
+recursive-include * *.mplstyle
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]