Merge branch 'main' into psobolewskiPhD-patch-8

napari · May 31, 2024 · 21582ca · 21582ca
2 parents 2076e50 + 21b8aa6
commit 21582ca
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -44,11 +44,11 @@ jobs:
           environment:
             PIP_CONSTRAINT: ../napari/resources/constraints/constraints_py3.10_docs.txt
       - store_artifacts:
-          path: docs/docs/_build/
+          path: docs/docs/_build/html/
       - persist_to_workspace:
           root: .
           paths:
-            - docs/docs/_build/
+            - docs/docs/_build/html/
 workflows:
   build-docs:
     jobs:

diff --git a/.github/workflows/build_docs.yml → .github/workflows/build_and_deploy.yml b/.github/workflows/build_docs.yml → .github/workflows/build_and_deploy.yml
@@ -1,8 +1,18 @@
 # As much as possible, this file should be kept in sync with
 # https://github.com/napari/napari/blob/main/.github/workflows/build_docs.yml
-name: Build PR Docs
+#
+# Note this workflow is also triggered by
+# https://github.com/napari/napari/blob/main/.github/workflows/deploy_docs.yml when a
+# commit to `main` occurs in `napari/napari`
+
+name: Build & Deploy PR Docs
 
 on:
+  push:
+    branches:
+      - main
+    tags:
+      - 'v*'
   pull_request:
     branches:
       - main
@@ -20,21 +30,23 @@ jobs:
       - name: Clone docs repo
         uses: actions/checkout@v4
         with:
+          # place in '/home/runner/work/docs/docs/docs'
           path: docs  # place in a named directory
 
       - name: Clone main repo
         uses: actions/checkout@v4
         with:
+          # place in '/home/runner/work/docs/docs/napari'
           path: napari  # place in a named directory
           repository: napari/napari
           # ensure version metadata is proper
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
           cache-dependency-path: |
-            napari/setup.cfg
+            napari/pyproject.toml
             docs/requirements.txt
 
       - uses: tlambert03/setup-qt-libs@v1
@@ -51,13 +63,21 @@ jobs:
           python -c 'import napari; print(napari.__version__)'
           python -c 'import napari.layers; print(napari.layers.__doc__)'
 
+      - name: Create fallback videos
+        run: |
+          sudo apt-get update && sudo apt-get install -y ffmpeg
+          cd docs
+          make fallback-videos
+
       - name: Build Docs
         uses: aganders3/headless-gui@v2
         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:
+          # Runs in '/home/runner/work/docs/docs/docs'
+          # Built HTML pages in '/home/runner/work/docs/docs/docs/docs/_build/html'
           run:  make -C docs docs
           # skipping setup stops the action from running the default (tiling) window manager
           # the window manager is not necessary for docs builds at this time and it was causing
@@ -66,7 +86,40 @@ jobs:
           linux-teardown: "echo 'skip teardown'"
 
       - name: Upload artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
+        with:
+          name: html
+          path: docs/docs/_build/html/
+
+  deploy:
+    name: Download & Deploy Artifact
+    needs: build-and-upload
+    runs-on: ubuntu-latest
+    # Working directory: '/home/runner/work/docs/docs'
+    steps:
+      - name: Download artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: html
+          # Downloads to '/home/runner/work/docs/docs/html'
+          path: html
+
+      - name: get directory name
+        # if this is a tag, use the tag name as the directory name else dev
+        run: |
+          if [[ "${{ github.ref }}" == "refs/tags/"* ]]; then
+            echo "branch_name=${{ github.ref_name }}" >> $GITHUB_ENV
+          else
+            echo "branch_name=dev" >> $GITHUB_ENV
+          fi
+
+      - name: Deploy Docs
+        if: github.event_name == 'push' && (startsWith(github.ref, 'refs/tags/v') || startsWith(github.ref, 'refs/heads/main'))
+        uses: peaceiris/actions-gh-pages@v3
         with:
-          name: docs
-          path: docs/docs/_build
+          deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
+          external_repository: napari/napari.github.io
+          publish_dir: ./html
+          publish_branch: gh-pages
+          destination_dir: ${{ env.branch_name }}
+          cname: napari.org
diff --git a/.github/workflows/circleci.yml b/.github/workflows/circleci.yml
@@ -19,6 +19,6 @@ jobs:
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           api-token: ${{ secrets.CIRCLECI_TOKEN }}
-          artifact-path: 0/docs/docs/_build/index.html
+          artifact-path: 0/docs/docs/_build/html/index.html
           circleci-jobs: build-docs
           job-title: Check the rendered docs here!
diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml
diff --git a/.github/workflows/edit_pr_description.yml b/.github/workflows/edit_pr_description.yml
@@ -0,0 +1,16 @@
+name: Remove html In PR description
+on:
+  # see https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#pull_request_target
+  pull_request_target:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - edited
+permissions:
+  pull-requests: write
+
+jobs:
+  remove_comment:
+    name: Remove html comments.
+    uses: napari/napari/.github/workflows/edit_pr_description.yml@main
diff --git a/.github/workflows/remove_ready_to_merge.yml b/.github/workflows/remove_ready_to_merge.yml
@@ -0,0 +1,15 @@
+name: Remove "ready to merge" label
+
+on:
+  pull_request_target:
+    types: [closed]
+  workflow_call:
+
+
+permissions:
+  pull-requests: write
+
+jobs:
+  remove_label:
+    name: Remove ready to merge label
+    uses: napari/napari/.github/workflows/remove_ready_to_merge.yml@main
diff --git a/.gitignore b/.gitignore
@@ -154,3 +154,6 @@ docs/sg_execution_times.rst
 # come from npe2 docs
 docs/plugins/_npe2_*.md
 npe2/
+
+# autogenerated fallback videos
+docs/_static/images/*.mp4
diff --git a/Makefile b/Makefile
@@ -27,10 +27,10 @@ prep-docs:
 	python $(docs_dir)/_scripts/prep_docs.py
 
 docs-build: prep-docs
-	NAPARI_CONFIG="" NAPARI_APPLICATION_IPY_INTERACTIVE=0 sphinx-build -b html docs/ docs/_build -D sphinx_gallery_conf.examples_dirs=$(GALLERY_PATH) $(SPHINXOPTS)
+	NAPARI_CONFIG="" NAPARI_APPLICATION_IPY_INTERACTIVE=0 sphinx-build -M html docs/ docs/_build -D sphinx_gallery_conf.examples_dirs=$(GALLERY_PATH) $(SPHINXOPTS)
 
 docs-xvfb: prep-docs
-	NAPARI_CONFIG="" NAPARI_APPLICATION_IPY_INTERACTIVE=0 xvfb-run --auto-servernum sphinx-build -b html docs/ docs/_build -D sphinx_gallery_conf.examples_dirs=$(GALLERY_PATH) $(SPHINXOPTS)
+	NAPARI_CONFIG="" NAPARI_APPLICATION_IPY_INTERACTIVE=0 xvfb-run --auto-servernum sphinx-build -M html docs/ docs/_build -D sphinx_gallery_conf.examples_dirs=$(GALLERY_PATH) $(SPHINXOPTS)
 
 docs: clean docs-install docs-build
 
@@ -55,7 +55,19 @@ html-live: prep-docs
 		$(SPHINXOPTS)
 
 html-noplot: clean prep-docs
-	NAPARI_APPLICATION_IPY_INTERACTIVE=0 sphinx-build -D plot_gallery=0 -b html docs/ docs/_build -D sphinx_gallery_conf.examples_dirs=$(GALLERY_PATH) $(SPHINXOPTS)
+	NAPARI_APPLICATION_IPY_INTERACTIVE=0 sphinx-build -M html docs/ docs/_build -D plot_gallery=0 -D sphinx_gallery_conf.examples_dirs=$(GALLERY_PATH) $(SPHINXOPTS)
 
 linkcheck-files:
 	NAPARI_APPLICATION_IPY_INTERACTIVE=0 sphinx-build -b linkcheck -D plot_gallery=0 --color docs/ docs/_build ${FILES} -D sphinx_gallery_conf.examples_dirs=$(GALLERY_PATH) $(SPHINXOPTS)
+
+fallback-videos:
+	for video in $(basename $(wildcard docs/_static/images/*.webm)); do \
+		if [ -a $$video.mp4 ]; then \
+			echo "skipping $$video.mp4"; \
+			continue; \
+		fi; \
+		ffmpeg -i $$video.webm -vf "scale=trunc(iw/2)*2:trunc(ih/2)*2" -c:v libx264 -preset slow -crf 22 -c:a aac -b:a 128k -strict -2 -y $$video.mp4; \
+	done
+
+fallback-videos-clean:
+	rm -f docs/_static/images/*.mp4
diff --git a/docs/_static/images/LLSM.png b/docs/_static/images/LLSM.png
diff --git a/docs/images/LLSM.webm → docs/_static/images/LLSM.webm b/docs/images/LLSM.webm → docs/_static/images/LLSM.webm
diff --git a/docs/_static/images/brain_surface.png b/docs/_static/images/brain_surface.png
diff --git a/docs/images/brain_surface.webm → docs/_static/images/brain_surface.webm b/docs/images/brain_surface.webm → docs/_static/images/brain_surface.webm
diff --git a/docs/_static/images/dask1.png b/docs/_static/images/dask1.png
diff --git a/docs/tutorials/assets/tutorials/dask1.webm → docs/_static/images/dask1.webm b/docs/tutorials/assets/tutorials/dask1.webm → docs/_static/images/dask1.webm
diff --git a/docs/_static/images/dask2.png b/docs/_static/images/dask2.png
diff --git a/docs/tutorials/assets/tutorials/dask2.webm → docs/_static/images/dask2.webm b/docs/tutorials/assets/tutorials/dask2.webm → docs/_static/images/dask2.webm
diff --git a/docs/_static/images/delete_label.png b/docs/_static/images/delete_label.png
diff --git a/docs/images/delete_label.webm → docs/_static/images/delete_label.webm b/docs/images/delete_label.webm → docs/_static/images/delete_label.webm
diff --git a/docs/_static/images/draw_component.png b/docs/_static/images/draw_component.png
diff --git a/docs/images/draw_component.webm → docs/_static/images/draw_component.webm b/docs/images/draw_component.webm → docs/_static/images/draw_component.webm
diff --git a/docs/_static/images/editing_points.png b/docs/_static/images/editing_points.png
diff --git a/docs/images/editing_points.webm → docs/_static/images/editing_points.webm b/docs/images/editing_points.webm → docs/_static/images/editing_points.webm
diff --git a/docs/_static/images/editing_shapes.png b/docs/_static/images/editing_shapes.png
diff --git a/docs/images/editing_shapes.webm → docs/_static/images/editing_shapes.webm b/docs/images/editing_shapes.webm → docs/_static/images/editing_shapes.webm
diff --git a/docs/_static/images/manual_label.png b/docs/_static/images/manual_label.png
diff --git a/docs/images/manual_label.webm → docs/_static/images/manual_label.webm b/docs/images/manual_label.webm → docs/_static/images/manual_label.webm
diff --git a/docs/_static/images/merge_labels.png b/docs/_static/images/merge_labels.png
diff --git a/docs/images/merge_labels.webm → docs/_static/images/merge_labels.webm b/docs/images/merge_labels.webm → docs/_static/images/merge_labels.webm
diff --git a/docs/_static/images/mitosis.png b/docs/_static/images/mitosis.png
diff --git a/docs/guides/images/mitosis.webm → docs/_static/images/mitosis.webm b/docs/guides/images/mitosis.webm → docs/_static/images/mitosis.webm
diff --git a/docs/_static/images/nD_shapes.png b/docs/_static/images/nD_shapes.png
diff --git a/docs/images/nD_shapes.webm → docs/_static/images/nD_shapes.webm b/docs/images/nD_shapes.webm → docs/_static/images/nD_shapes.webm
diff --git a/docs/_static/images/nD_vectors.png b/docs/_static/images/nD_vectors.png
diff --git a/docs/images/nD_vectors.webm → docs/_static/images/nD_vectors.webm b/docs/images/nD_vectors.webm → docs/_static/images/nD_vectors.webm
diff --git a/docs/_static/images/pathology.png b/docs/_static/images/pathology.png
diff --git a/docs/images/pathology.webm → docs/_static/images/pathology.webm b/docs/images/pathology.webm → docs/_static/images/pathology.webm
diff --git a/docs/_static/images/point_annotator_demo.png b/docs/_static/images/point_annotator_demo.png
diff --git a/...ssets/tutorials/point_annotator_demo.webm → .../_static/images/point_annotator_demo.webm b/...ssets/tutorials/point_annotator_demo.webm → .../_static/images/point_annotator_demo.webm
diff --git a/docs/_static/images/scaling.png b/docs/_static/images/scaling.png
diff --git a/docs/guides/images/scaling.webm → docs/_static/images/scaling.webm b/docs/guides/images/scaling.webm → docs/_static/images/scaling.webm
diff --git a/docs/_static/images/shape_resizing.png b/docs/_static/images/shape_resizing.png
diff --git a/docs/images/shape_resizing.webm → docs/_static/images/shape_resizing.webm b/docs/images/shape_resizing.webm → docs/_static/images/shape_resizing.webm
diff --git a/docs/_static/images/shape_vertex_editing.png b/docs/_static/images/shape_vertex_editing.png
diff --git a/docs/_static/images/shape_vertex_editing.webm b/docs/_static/images/shape_vertex_editing.webm
diff --git a/docs/_static/images/smFISH.png b/docs/_static/images/smFISH.png
diff --git a/docs/images/smFISH.webm → docs/_static/images/smFISH.webm b/docs/images/smFISH.webm → docs/_static/images/smFISH.webm
diff --git a/docs/_static/images/split_label.png b/docs/_static/images/split_label.png
diff --git a/docs/images/split_label.webm → docs/_static/images/split_label.webm b/docs/images/split_label.webm → docs/_static/images/split_label.webm
diff --git a/docs/_static/images/tracks_3d_t.png b/docs/_static/images/tracks_3d_t.png
diff --git a/docs/images/tracks_3d_t.webm → docs/_static/images/tracks_3d_t.webm b/docs/images/tracks_3d_t.webm → docs/_static/images/tracks_3d_t.webm
diff --git a/docs/_static/images/tracks_color_by.png b/docs/_static/images/tracks_color_by.png
diff --git a/docs/images/tracks_color_by.webm → docs/_static/images/tracks_color_by.webm b/docs/images/tracks_color_by.webm → docs/_static/images/tracks_color_by.webm
diff --git a/docs/_static/images/tracks_isbi.png b/docs/_static/images/tracks_isbi.png
diff --git a/...torials/assets/tutorials/tracks_isbi.webm → docs/_static/images/tracks_isbi.webm b/...torials/assets/tutorials/tracks_isbi.webm → docs/_static/images/tracks_isbi.webm
diff --git a/docs/_static/images/tracks_simple_demo.png b/docs/_static/images/tracks_simple_demo.png
diff --git a/docs/images/tracks_simple_demo.webm → docs/_static/images/tracks_simple_demo.webm b/docs/images/tracks_simple_demo.webm → docs/_static/images/tracks_simple_demo.webm
diff --git a/docs/_static/images/tracks_tail_length.png b/docs/_static/images/tracks_tail_length.png
diff --git a/docs/images/tracks_tail_length.webm → docs/_static/images/tracks_tail_length.webm b/docs/images/tracks_tail_length.webm → docs/_static/images/tracks_tail_length.webm
diff --git a/docs/_static/images/tracks_tail_width.png b/docs/_static/images/tracks_tail_width.png
diff --git a/docs/images/tracks_tail_width.webm → docs/_static/images/tracks_tail_width.webm b/docs/images/tracks_tail_width.webm → docs/_static/images/tracks_tail_width.webm
diff --git a/docs/_static/images/tribolium.mp4 b/docs/_static/images/tribolium.mp4
diff --git a/docs/_static/images/viewer_pan_zoom.png b/docs/_static/images/viewer_pan_zoom.png
diff --git a/...als/assets/tutorials/viewer_pan_zoom.webm → docs/_static/images/viewer_pan_zoom.webm b/...als/assets/tutorials/viewer_pan_zoom.webm → docs/_static/images/viewer_pan_zoom.webm
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
@@ -5,9 +5,10 @@
 .. autoclass:: {{ objname }}
    :members:
    :show-inheritance:
-   {% if objname != "progress" %}
-      :inherited-members:
-   {% endif %}
+   {#- These classes inherit docstrings from the raw qt source, which generates rst syntax errors when building the docs #}
+   {% if objname not in ["progress", "cancelable_progress"] -%}
+   :inherited-members:
+   {%- endif %}
 
    {% block methods %}
 

diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -163,6 +163,7 @@ subtrees:
           - file: developers/architecture/dir_organization
           - file: developers/architecture/napari_models
           - file: developers/architecture/app_model
+          - file: developers/architecture/magicgui_type_reg
       - file: naps/index
         subtrees:
         - maxdepth: 1

diff --git a/docs/api/modules.rst b/docs/api/modules.rst
@@ -13,6 +13,7 @@ For the average user's workflows.
    napari.types
    napari.utils
    napari.window
+   napari.utils.transforms
 
 .. rubric:: Advanced
 

diff --git a/docs/community/team.md b/docs/community/team.md
@@ -59,6 +59,6 @@ Read more about napari’s [mission and values](https://napari.org/community/mis
     - The CZI Imaging Tech Team, through an effort led by Justin Kiggins, has created [napari-hub.org](https://www.napari-hub.org/), a site to make discovering and sharing napari plugins easier.
     - CZI has launched a [grant program](https://chanzuckerberg.com/rfa/napari-plugin-grants/) to help accelerate the napari plugin developer community.
 
-The current representative of the Insitutional and Funding Partner Advisory Council on the napari steering council is Nicholas Sofroniew.
+The current representative of the Insitutional and Funding Partner Advisory Council on the napari steering council is Kyle I. S. Harrington.
 
 If you or your organization are interested in also supporting the napari project and becoming an Institutional and Funding Partner, please email the napari steering council at `[email protected]`.