Merge branch 'main' into content/lock_dims_rolling

.circleci/config.yml

@@ -1,74 +1,55 @@
+# As much as possible, this file should be kept in sync with:
+# https://github.com/napari/napari/blob/main/.circleci/config.yaml
 # Use the latest 2.1 version of CircleCI pipeline process engine.
-# See: https://circleci.com/docs/2.0/configuration-reference
+# See: https://circleci.com/docs/2.1/configuration-reference
 version: 2.1
-
-# Orbs are reusable packages of CircleCI configuration that you may share across projects, enabling you to create encapsulated, parameterized commands, jobs, and executors that can be used across multiple projects.
-# See: https://circleci.com/docs/2.0/orb-intro/
+# Orbs are reusable packages of CircleCI configuration that you may share across projects.
+# See: https://circleci.com/docs/2.1/orb-intro/
 orbs:
-  # The python orb contains a set of prepackaged CircleCI configuration you can use repeatedly in your configuration files
-  # Orb commands and jobs help you with common scripting around a language/tool
-  # so you dont have to copy and paste it everywhere.
-  # See the orb documentation here: https://circleci.com/developer/orbs/orb/circleci/python
   python: circleci/[email protected]
-
-# Define a job to be invoked later in a workflow.
-# See: https://circleci.com/docs/2.0/configuration-reference/#jobs
 jobs:
-  build-docs: # This is the name of the job, feel free to change it to better match what you're trying to do!
-    # These next lines defines a Docker executors: https://circleci.com/docs/2.0/executor-types/
-    # You can specify an image from Dockerhub or use one of the convenience images from CircleCI's Developer Hub
-    # A list of available CircleCI Docker convenience images are available here: https://circleci.com/developer/images/image/cimg/python
-    # The executor is the environment in which the steps below will be executed - below will use a python 3.10.2 container
-    # Change the version below to your required version of python
+  build-docs:
     docker:
-      - image: cimg/python:3.10.2
-    # Checkout the code as the first step. This is a dedicated CircleCI step.
-    # The python orb's install-packages step will install the dependencies from a Pipfile via Pipenv by default.
-    # Here we're making sure we use just use the system-wide pip. By default it uses the project root's requirements.txt.
-    # Then run your tests!
-    # CircleCI will report the results back to your VCS provider.
+      # A list of available CircleCI Docker convenience images are available here: https://circleci.com/developer/images/image/cimg/python
+      - image: cimg/python:3.10.13
     steps:
-      - checkout
+      - checkout:
+          path: docs
+      - run:
+          name: Clone main repo into a subdirectory
+          command: git clone [email protected]:napari/napari.git napari
       - run:
           name: Install qt libs + xvfb
           command: sudo apt-get update && sudo apt-get install -y xvfb libegl1 libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 x11-utils
-
       - run:
           name: Setup virtual environment
-          # app-dir: ~/project/package-directory/  # If you're requirements.txt isn't in the root directory.
           command: |
             python -m venv venv
             . venv/bin/activate
             python -m pip install --upgrade pip
-      - run:
-          name: Clone main repo
-          command: git clone [email protected]:napari/napari.git napari
+
       - run:
           name: Install napari-dev
           command: |
             . venv/bin/activate
-            python -m pip install -e napari/".[pyside,dev]" -c "napari/resources/constraints/constraints_py3.10.txt"
-      - run:
-          name: Install python dependencies
-          command: |
-            . venv/bin/activate
-            python -m pip install -r requirements.txt
+            python -m pip install -e "napari/[pyside,dev]"
+          environment:
+            PIP_CONSTRAINT: napari/resources/constraints/constraints_py3.10_docs.txt
       - run:
           name: Build docs
           command: |
             . venv/bin/activate
-            xvfb-run --auto-servernum make docs GALLERY_PATH=../napari/examples/
+            cd docs
+            xvfb-run --auto-servernum make docs
+          environment:
+            PIP_CONSTRAINT: ../napari/resources/constraints/constraints_py3.10_docs.txt
       - store_artifacts:
-          path: docs/_build/
+          path: docs/docs/_build/
       - persist_to_workspace:
           root: .
           paths:
-            - docs/_build/
-
-# Invoke jobs via workflows
-# See: https://circleci.com/docs/2.0/configuration-reference/#workflows
+            - docs/docs/_build/
 workflows:
-  build-docs: # This is the name of the workflow, feel free to change it to better match your workflow.
-    # Inside the workflow, you define the jobs you want to run.
+  build-docs:
     jobs:
       - build-docs

.github/workflows/build_docs.yml

@@ -8,36 +8,44 @@ on:
       - main
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build-and-upload:
     name: Build & Upload Artifact
     runs-on: ubuntu-latest
     steps:
       - name: Clone docs repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+        with:
+          path: docs  # place in a named directory
 
       - name: Clone main repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: napari  # place in a named directory
           repository: napari/napari
           # ensure version metadata is proper
           fetch-depth: 0
 
-      - name: Copy examples to docs folder
-        run: |
-          cp -R napari/examples .
-
       - uses: actions/setup-python@v4
         with:
           python-version: "3.10"
+          cache-dependency-path: |
+            napari/setup.cfg
+            docs/requirements.txt
 
       - uses: tlambert03/setup-qt-libs@v1
 
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install "napari/[all]" -c "napari/resources/constraints/constraints_py3.10_docs.txt"
+          python -m pip install "napari/[all]"
+          python -m pip install -r docs/requirements.txt
+        env:
+          PIP_CONSTRAINT: ${{ github.workspace }}/napari/resources/constraints/constraints_py3.10_docs.txt
 
       - name: Testing
         run: |
@@ -49,11 +57,13 @@ jobs:
         env:
           GOOGLE_CALENDAR_ID: ${{ secrets.GOOGLE_CALENDAR_ID }}
           GOOGLE_CALENDAR_API_KEY: ${{ secrets.GOOGLE_CALENDAR_API_KEY }}
+          PIP_CONSTRAINT: ${{ github.workspace }}/napari/resources/constraints/constraints_py3.10_docs.txt
         with:
-          run: make docs GALLERY_PATH=../examples/
+          run:  make -C docs docs
+
 
       - name: Upload artifact
         uses: actions/upload-artifact@v3
         with:
           name: docs
-          path: docs/_build
+          path: docs/docs/_build

.github/workflows/circleci.yml

@@ -19,6 +19,6 @@ jobs:
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           api-token: ${{ secrets.CIRCLECI_TOKEN }}
-          artifact-path: 0/docs/_build/index.html
+          artifact-path: 0/docs/docs/_build/index.html
           circleci-jobs: build-docs
           job-title: Check the rendered docs here!

.github/workflows/deploy_docs.yml

@@ -47,7 +47,8 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install "napari-repo/[all]"  -c "napari-repo/resources/constraints/constraints_py3.10_docs.txt"
-
+          python -m pip install -r docs/requirements.txt -c "napari-repo/resources/constraints/constraints_py3.10_docs.txt"
+          
       - name: Testing
         run: |
           python -c 'import napari; print(napari.__version__)'

.github/workflows/labeler.yml

@@ -5,8 +5,11 @@ on:
 
 jobs:
   triage:
+    permissions:
+      contents: read
+      pull-requests: write
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/labeler@main
+    - uses: actions/labeler@v4
       with:
         repo-token: "${{ secrets.GITHUB_TOKEN }}"

docs/_scripts/update_preference_docs.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 from jinja2 import Template
-from pydantic.main import ModelMetaclass
+from napari._pydantic_compat import ModelMetaclass
 from qtpy.QtCore import QTimer
 from qtpy.QtWidgets import QMessageBox
 

docs/_toc.yml

@@ -145,6 +145,7 @@ subtrees:
           - file: naps/5-new-logo
           - file: naps/6-contributable-menus
           - file: naps/7-key-binding-dispatch
+          - file: naps/8-telemetry
       - file: developers/documentation/index
         subtrees:
         - entries:

docs/conf.py

@@ -163,7 +163,7 @@
 myst_heading_anchors = 4
 
 version_string = '.'.join(str(x) for x in __version_tuple__[:3])
-python_version = '3.9'
+python_version = '3.10'
 python_version_range = '3.8–3.10'
 
 myst_substitutions = {

docs/further-resources/napari-workshops.md

@@ -21,6 +21,10 @@ or contact the core developers on [zulip chat](https://napari.zulipchat.com/logi
 ## Workshops
 
 *Workshops are listed from newest to oldest.*
+* September 2023
+  * [Plugin design](https://chanzuckerberg.github.io/napari-plugin-accel-workshops/workshops/design23.html) and [software development workshop](https://chanzuckerberg.github.io/napari-plugin-accel-workshops/workshops/softwaredev.html) for [napari plugin grantees](https://chanzuckerberg.com/rfa/napari-plugin-grants/).
+  * [Bioimage Analysis with Python and Napari (video lecture)](https://www.youtube.com/watch?v=QDS5t7oZH-c) at the [EMBO Practical Course for Advanced Methods in Bioimage Analysis](https://www.embl.org/about/info/course-and-conference-office/events/bia23-01/)  
+
 * November 2022, napari foundation grant onboarding
   * [Getting started with napari plugin development slide deck](https://docs.google.com/presentation/d/15lrFRLPm9bfmU4hgcVwoduIJr5bqhoHo7ZeWLO6H_Us/edit?usp=sharing)
   * [Watch it here](https://drive.google.com/file/d/1IYDV-GTGEYh5j_tvBaWYEZ_tQXTqmJkr/view?usp=share_link)

docs/howtos/layers/points.md

@@ -153,8 +153,10 @@ additional points, or by dragging a bounding box around the points you want to
 select. You can quickly select the select points tool by pressing the `S` key
 when the points layer is selected.
 
-You can select all the points in the currently viewed slice by clicking the `A`
-key if you are in select mode.
+Additionally, you can select all the points in the currently viewed slice by pressing 
+the `A` key and all the points in the layer (across all slices) using `Shift-A`. 
+Note: Pressing either keybinding again will toggle the selection, so you can select 
+all points in a layer and the *deselect* points from a slice. 
 
 Once selected you can delete the selected points by clicking on the delete
 button in the layer controls panel or pressing the delete key.