Merge branch 'main' into add-feature-histogram

Author: jo-mueller

.github/workflows/docs.yml

@@ -0,0 +1,35 @@
+name: Build docs
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build-and-upload:
+    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]"
+      - 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

.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 +10,15 @@ on:
     branches:
       - main
   workflow_dispatch:
+  merge_group:
 
 jobs:
   test:
     name: ${{ matrix.platform }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
-        platform: [ubuntu-latest]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ['3.8', '3.9', '3.10']
 
     steps:
@@ -50,6 +48,14 @@ 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
 

.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

.pre-commit-config.yaml

@@ -1,43 +1,37 @@
 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
+    rev: v2.2.0
     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: 23.3.0
     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: v1.3.0
     hooks:
      - id: mypy
-       args: ["--disallow-incomplete-defs", "--ignore-missing-imports"]
+       additional_dependencies: [numpy, matplotlib]
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: 'v0.0.270'
+    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

CHANGELOG.rst

@@ -1,10 +1,11 @@
 # napari-matplotlib
 
-[![License](https://img.shields.io/pypi/l/napari-matplotlib.svg?color=green)](https://github.com/dstansby/napari-matplotlib/raw/main/LICENSE)
+[![License](https://img.shields.io/pypi/l/napari-matplotlib.svg?color=green)](https://github.com/matplotlib/napari-matplotlib/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/napari-matplotlib.svg?color=green)](https://pypi.org/project/napari-matplotlib)
 [![Python Version](https://img.shields.io/pypi/pyversions/napari-matplotlib.svg?color=green)](https://python.org)
-[![tests](https://github.com/dstansby/napari-matplotlib/workflows/tests/badge.svg)](https://github.com/dstansby/napari-matplotlib/actions)
-[![codecov](https://codecov.io/gh/dstansby/napari-matplotlib/branch/main/graph/badge.svg)](https://codecov.io/gh/dstansby/napari-matplotlib)
+[![tests](https://github.com/matplotlib/napari-matplotlib/workflows/tests/badge.svg)](https://github.com/matplotlib/napari-matplotlib/actions)
+[![codecov](https://codecov.io/gh/matplotlib/napari-matplotlib/branch/main/graph/badge.svg)](https://codecov.io/gh/matplotlib/napari-matplotlib)
+[![readthedocs](https://readthedocs.org/projects/napari-matplotlib/badge/?version=latest)](https://napari-matplotlib.readthedocs.io/en/latest/)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/matplotlib/pytest-mpl/master.svg)](https://results.pre-commit.ci/latest/github/matplotlib/pytest-mpl/master)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-matplotlib)](https://napari-hub.org/plugins/napari-matplotlib)
 
@@ -19,15 +20,15 @@ A plugin to create Matplotlib plots from napari layers
 
 ### `Slice`
 Plots 1D slices of data along a specified axis.
-![](https://raw.githubusercontent.com/dstansby/napari-matplotlib/main/examples/slice.png)
+![](https://raw.githubusercontent.com/matplotlib/napari-matplotlib/main/examples/slice.png)
 
 ### `Histogram`
 Plots histograms of individual image layers, or RGB histograms of an RGB image
-![](https://raw.githubusercontent.com/dstansby/napari-matplotlib/main/examples/hist.png)
+![](https://raw.githubusercontent.com/matplotlib/napari-matplotlib/main/examples/hist.png)
 
 ### `Scatter`
 Scatters the values of two similarly sized images layers against each other.
-![](https://raw.githubusercontent.com/dstansby/napari-matplotlib/main/examples/scatter.png)
+![](https://raw.githubusercontent.com/matplotlib/napari-matplotlib/main/examples/scatter.png)
 
 ## Installation
 
@@ -39,7 +40,7 @@ You can install `napari-matplotlib` via [pip]:
 
 To install latest development version :
 
-    pip install git+https://github.com/dstansby/napari-matplotlib.git
+    pip install git+https://github.com/matplotlib/napari-matplotlib.git
 
 
 ## Contributing

README.md

@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
-SPHINXOPTS    ?= -W
+SPHINXOPTS    ?= -W --keep-going
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build
@@ -12,6 +12,11 @@ BUILDDIR      = _build
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
+clean:
+	@echo Removing files created by sphinx-build
+	rm -rf $(BUILDDIR)
+	rm -rf $(SOURCEDIR)/api/
+
 .PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new

docs/Makefile

@@ -0,0 +1,40 @@
+Changelog
+=========
+
+0.3.0
+-----
+
+New features
+~~~~~~~~~~~~
+- Added ``MPLWidget`` as a widget containing just a Matplotlib canvas
+  without any association with a napari viewer.
+- Added text to each widget indicating how many layers need to be selected
+  for the widget to plot something.
+
+Visual improvements
+~~~~~~~~~~~~~~~~~~~
+- The background of ``napari-matplotlib`` figures and axes is now transparent, and the text and axis colour respects the ``napari`` theme.
+- The icons in the Matplotlib toolbar are now the same size as icons in the napari window.
+
+Changes
+~~~~~~~
+- The scatter widgets no longer use a LogNorm() for 2D histogram scaling.
+  This is to move the widget in line with the philosophy of using Matplotlib default
+  settings throughout ``napari-matplotlib``. This still leaves open the option of
+  adding the option to change the normalization in the future. If this is something
+  you would be interested in please open an issue at https://github.com/matplotlib/napari-matplotlib.
+- Labels plotting with the features scatter widget no longer have underscores
+  replaced with spaces.
+- ``NapariMPLWidget.update_layers()`` has been removed as it is intended to be
+  private API. Use ``NapariMPLWidget.on_update_layers`` instead to implement
+  funcitonality when layer selection is changed.
+
+Bug fixes
+~~~~~~~~~
+- Importing ``napari-matplotlib`` no longer affects how plots are rendered in
+  Jupyter notebooks.
+
+Other
+~~~~~
+- ``napari-matplotlib`` is now tested on macOS and Windows.
+- Type annotations have been completed throughout the code base.