Merge branch 'main' into howto-constraints

.github/workflows/actionlint.yml

@@ -0,0 +1,18 @@
+name: Actionlint
+
+on:
+  pull_request:
+    paths:
+      - '.github/**'
+
+jobs:
+  actionlint:
+    name: Action lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Check workflow files
+        run: |
+          bash <(curl https://raw.githubusercontent.com/rhysd/actionlint/main/scripts/download-actionlint.bash)
+          ./actionlint -color -ignore SC2129
+        shell: bash

.github/workflows/build_and_deploy.yml

@@ -106,15 +106,22 @@ jobs:
 
       - name: get directory name
         # if this is a tag, use the tag name as the directory name else dev
+        env:
+          REF: ${{ github.ref }}
         run: |
-          if [[ "${{ github.ref }}" == "refs/tags/"* ]]; then
-            echo "branch_name=${{ github.ref_name }}" >> $GITHUB_ENV
+          TAG="${GITHUB_REF/refs\/tags\/v/}"
+          VER="${TAG/a*/}"  # remove alpha identifier
+          VER="${VER/b*/}"  # remove beta identifier
+          VER="${VER/rc*/}"  # remove rc identifier
+
+          if [[ "$REF" == "refs/tags/v"* ]]; then
+            echo "branch_name=$VER" >> "$GITHUB_ENV"
           else
-            echo "branch_name=dev" >> $GITHUB_ENV
+            echo "branch_name=dev" >> "$GITHUB_ENV"
           fi
 
       - name: Deploy Docs
-        if: github.event_name == 'push' && (startsWith(github.ref, 'refs/tags/v') || startsWith(github.ref, 'refs/heads/main'))
+        if: (github.event_name == 'push' || github.event_name == 'workflow_dispatch') && (startsWith(github.ref, 'refs/tags/v') || startsWith(github.ref, 'refs/heads/main'))
         uses: peaceiris/actions-gh-pages@v3
         with:
           deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}

Makefile

@@ -28,7 +28,7 @@ prep-docs:
 	python $(docs_dir)/_scripts/prep_docs.py
 
 docs-build: prep-docs
-	NAPARI_CONFIG="" NAPARI_APPLICATION_IPY_INTERACTIVE=0 sphinx-build -M html docs/ docs/_build -D sphinx_gallery_conf.examples_dirs=$(GALLERY_PATH) $(SPHINXOPTS)
+	NAPARI_CONFIG="" NAPARI_APPLICATION_IPY_INTERACTIVE=0 sphinx-build -M html docs/ docs/_build  -WT --keep-going -D sphinx_gallery_conf.examples_dirs=$(GALLERY_PATH) $(SPHINXOPTS)
 
 docs-xvfb: prep-docs
 	NAPARI_CONFIG="" NAPARI_APPLICATION_IPY_INTERACTIVE=0 xvfb-run --auto-servernum sphinx-build -M html docs/ docs/_build -D sphinx_gallery_conf.examples_dirs=$(GALLERY_PATH) $(SPHINXOPTS)

docs/_static/version_switcher.json

@@ -5,11 +5,16 @@
 		"url": "https://napari.org/dev/"
 	},
 	{
-		"name": "stable (0.5.0)",
-		"version": "0.5.0",
+		"name": "stable (0.5.1)",
+		"version": "0.5.1",
 		"preferred": true,
 		"url": "https://napari.org/stable/"
 	},
+	{
+		"name": "0.5.0",
+		"version": "0.5.0",
+		"url": "https://napari.org/0.5.0/"
+	},
 	{
 		"name": "0.4.19",
 		"version": "0.4.19",

docs/_toc.yml

@@ -11,6 +11,7 @@ subtrees:
           entries:
           - file: tutorials/fundamentals/quick_start
           - file: tutorials/fundamentals/installation
+          - file: tutorials/fundamentals/installation_bundle_conda
           - file: tutorials/fundamentals/getting_started
           - file: tutorials/fundamentals/viewer
           - file: guides/layers
@@ -180,6 +181,7 @@ subtrees:
       - file: release/index
         subtrees:
         - entries:
+          - file: release/release_0_5_1
           - file: release/release_0_5_0
           - file: release/release_0_4_19
           - file: release/release_0_4_18

docs/community/meeting_schedule.md

@@ -51,7 +51,8 @@ If you are using napari or interested in how napari could be used in your work,
         var modal = document.getElementById("eventDetailBackground");
         modal.style.display = "block";
         var eventTitle = eventObj.title.charAt(0).toUpperCase() + eventObj.title.slice(1);
-        document.getElementById("details").innerHTML = '<b>' + eventTitle + '</b>' + '<br>' + eventObj.extendedProps.description;
+        var eventLocation = eventObj.extendedProps.location;
+        document.getElementById("details").innerHTML = '<b>' + eventTitle + '</b>' + '<br>' + eventObj.extendedProps.description + '<br>' + '<b>Location: </b>' + '<a href='+eventLocation+'>'+eventLocation+'</a>';
         // When the user clicks on <span> (x), close the modal
         span.onclick = function() {
           modal.style.display = "none";

docs/conf.py

@@ -126,6 +126,8 @@
         # The analytics script that is served by Plausible
         "plausible_analytics_url": "https://plausible.io/js/plausible.js",
     },
+    "footer_start": ["napari-footer-links"],
+    "footer_end": ["napari-copyright"],
 }
 
 html_context = {
@@ -229,7 +231,7 @@ def get_supported_python_versions(project_name):
 
 panels_add_bootstrap_css = False
 pygments_style = 'solarized-dark'
-suppress_warnings = ['myst.header', 'etoc.toctree']
+suppress_warnings = ['myst.header', 'etoc.toctree', 'config.cache']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -324,6 +326,7 @@ def add_google_calendar_secrets(app, docname, source):
     if docname == 'community/meeting_schedule':
         source[0] = source[0].replace('{API_KEY}', GOOGLE_CALENDAR_API_KEY)
 
+
 class FilterSphinxWarnings(logging.Filter):
     """Filter 'duplicate object description' warnings.
 
@@ -349,16 +352,19 @@ def filter(self, record: logging.LogRecord) -> bool:
             return False
         return True
 
+
 def qt_docstrings(app, what, name, obj, options, lines):
     """Only show first line of Qt threading docstrings.
 
     Avoids syntax errors since the Qt threading docstrings are written in
     Markdown, and injected into rst docstring automatically.
     """
-    if "WorkerBase" in name:
+    ignore_list = ["WorkerBase", "FunctionWorker", "GeneratorWorker"]
+    if any([f in name for f in ignore_list]):
         if len(lines) > 0:
             del lines[1:]
 
+
 def setup(app):
     """Set up docs build.
 

docs/developers/coredev/packaging.md

@@ -26,7 +26,7 @@ This is all automated by the `conda-forge` infrastructure (see [previous example
 We only need to check that the metadata in the recipe has been adjusted for the new release.
 Pay special attention to the runtime dependencies and version strings!
 
-> We keep a copy of the feedstock's recipe in the `napari/packaging` repo, which is updated manually whenever a change to `setup.cfg` is detected.
+> We keep a copy of the feedstock's recipe in the `napari/packaging` repo, which is updated manually whenever a change to `pyproject.toml` is detected.
 > Check the file `conda-recipe/meta.yaml` and make sure its `outputs` contents are synced to the `napari-feedstock` copy.
 
 Once the conda-forge CI is passing and the PR is approved and merged, the final packages will be built on the default branch and uploaded to the `conda-forge` channel.
@@ -36,6 +36,22 @@ Due to the staging steps and CDN synchronization delays, the conda packages can
 Check {doc}`release` for more details about the conda-forge release process and maintenance tasks.
 ```
 
+#### conda packaging split
+
+We provide three different outputs in the conda package recipe:
+
+- `napari-base`: This is the package that ships the actual source and data. The runtime
+  requirements only include the basic functionality. This package is recommended as a
+  dependency for plugins and other projects. Most end users will prefer the `napari`
+  package, below, but this one may be useful for those wanting a more minimal
+  environment.
+- `napari`: This output is what most users want. It depends on `napari-base`, and adds optional yet
+  recommended dependencies for (performant) GUI usage, like the plugin manager or numba. Note that
+  the Qt backend is _not_ included.
+- `napari-menu`: Depends on `napari`, and ships the menuinst JSON file, in case you want a desktop
+  shortcut to start the application easily. This is included as part of the bundled installers for
+  convenience.
+
 ### conda packages in the `napari` channel
 
 The `napari` project also has a `napari` channel in anaconda.org.

docs/release/release_0_5_1.md

@@ -0,0 +1,114 @@
+# napari 0.5.1
+
+*Thursday, Jul 25, 2024*
+
+We're happy to announce the release of napari 0.5.1!
+
+napari is a fast, interactive, multi-dimensional image viewer for Python.
+It's designed for exploring, annotating, and analyzing multi-dimensional
+images. It's built on Qt (for the GUI), VisPy (for performant GPU-based
+rendering), and the scientific Python stack (NumPy, SciPy, and friends).
+
+For more information, examples, and documentation, please visit our website:
+https://napari.org/
+
+## Highlights
+
+napari 0.5.1 is a bugfix release hot on the heels of
+[napari 0.5.0](release_0_5_0). It fixes a critical bug with creating viewers
+multiple times within a single IPython/Jupyter session
+([#7106](https://github.com/napari/napari/pull/7106)), as well as regressions
+with viewing multiscale 3D time series
+([#7103](https://github.com/napari/napari/pull/7103)) and with converting image
+layers to labels layers ([#7095](https://github.com/napari/napari/pull/7095)).
+
+It also fixes a bug with NumPy 2 support
+([#7104](https://github.com/napari/napari/pull/7104)) and our storing of layer
+axis info when using the `channel_axis` keyword argument for images
+([#7089](https://github.com/napari/napari/pull/7089)).
+
+Read on for the full list of changes since the last version from just two weeks
+ago!
+
+## Improvements
+
+- [enh] add an `add_plane` convenience method to ClippingPlaneList ([#6921](https://github.com/napari/napari/pull/6921))
+- Cleanup _image_key_bindings ([#7116](https://github.com/napari/napari/pull/7116))
+- Add napari-plugin-manager to optional info list ([#7117](https://github.com/napari/napari/pull/7117))
+
+## Bug Fixes
+
+- Move the _is_created assignment to the top ([#5078](https://github.com/napari/napari/pull/5078))
+- [Bugfix] Fix logic in setting settings using env vars. ([#6669](https://github.com/napari/napari/pull/6669))
+- Fix handling of units and axis_labels in add_image ([#7089](https://github.com/napari/napari/pull/7089))
+- Fix label conversion with proj mode ([#7095](https://github.com/napari/napari/pull/7095))
+- Account for displayed dimensions in multiscale translate adjustment ([#7103](https://github.com/napari/napari/pull/7103))
+- fix call of np.clip in _update_thumbnail ([#7104](https://github.com/napari/napari/pull/7104))
+- Always add `Empty` context key, even if `action` is already registered ([#7106](https://github.com/napari/napari/pull/7106))
+- fix condition of adding asterix, when save reader of path ([#7112](https://github.com/napari/napari/pull/7112))
+- Normalize path when searching for a plugin to open file ([#7127](https://github.com/napari/napari/pull/7127))
+
+## Documentation
+
+- Add link to partners in README.md ([#7069](https://github.com/napari/napari/pull/7069))
+- Restore README image ([#7098](https://github.com/napari/napari/pull/7098))
+- Update docs constraints files for new napari-sphinx-theme release ([#7111](https://github.com/napari/napari/pull/7111))
+- Update release notes for 0.5.1 with new PRs ([docs#466](https://github.com/napari/docs/pull/466))
+- Update Bundled App Installation Instructions ([docs#74](https://github.com/napari/docs/pull/74))
+- Update Makefile to be consistent ([docs#448](https://github.com/napari/docs/pull/448))
+- Use plausible configuration by the PyData Sphinx Theme ([docs#453](https://github.com/napari/docs/pull/453))
+- More fixes to contributing documentation guide ([docs#454](https://github.com/napari/docs/pull/454))
+- Add location field to community calendar ([docs#455](https://github.com/napari/docs/pull/455))
+- Fix footer items ([docs#456](https://github.com/napari/docs/pull/456))
+- Add docs about the new `napari-base` structure ([docs#457](https://github.com/napari/docs/pull/457))
+- Add draft 0.5.1 release notes ([docs#464](https://github.com/napari/docs/pull/464))
+- Update draft warning on 0.5.1 release notes ([docs#465](https://github.com/napari/docs/pull/465))
+- Update release notes for 0.5.1 with new PRs ([docs#466](https://github.com/napari/docs/pull/466))
+
+## Other Pull Requests
+
+- Remove ready to merge on update of constraints PR ([#6984](https://github.com/napari/napari/pull/6984))
+- Update `app-model`, `coverage`, `dask`, `fsspec`, `hypothesis`, `imageio`, `ipython`, `jsonschema`, `matplotlib`, `napari-svg`, `numpy`, `pillow`, `pint`, `pydantic`, `pyqt5`, `pyqt6`, `pytest`, `scipy`, `tifffile` ([#7045](https://github.com/napari/napari/pull/7045))
+- Add actionlint on CI ([#7049](https://github.com/napari/napari/pull/7049))
+- fix: set `target_commitish` for commit sha to fix benchmarks ([#7091](https://github.com/napari/napari/pull/7091))
+- Use `viewer.layers` instead of  `_layers.model().sourceModel()._root` for dummy context creation ([#7109](https://github.com/napari/napari/pull/7109))
+- Limit setuptools vesion for minimum requirements test ([#7110](https://github.com/napari/napari/pull/7110))
+- [Maint] Update dockerfile for xpra source change ([#7115](https://github.com/napari/napari/pull/7115))
+- Fix pinning packages workflow by remove special pinning from macOS and add special for Windows ([#7119](https://github.com/napari/napari/pull/7119))
+- Trigger docs deployment on tagged commit ([#7122](https://github.com/napari/napari/pull/7122))
+- Update version switcher to include 0.5.0 ([docs#452](https://github.com/napari/docs/pull/452))
+- deploy docs on manual trigger ([docs#462](https://github.com/napari/docs/pull/462))
+- Add actionlint to prevent GHA workflow errors ([docs#463](https://github.com/napari/docs/pull/463))
+
+
+## 9 authors added to this release (alphabetical)
+
+(+) denotes first-time contributors 🥳
+
+- [danieldegroot2](https://github.com/napari/napari/commits?author=danieldegroot2) - @danieldegroot2 +
+- [Draga Doncila Pop](https://github.com/napari/napari/commits?author=DragaDoncila) - @DragaDoncila
+- [Grzegorz Bokota](https://github.com/napari/napari/commits?author=Czaki) - @Czaki
+- [jaime rodriguez-guerra](https://github.com/napari/napari/commits?author=jaimergp) ([docs](https://github.com/napari/docs/commits?author=jaimergp))  - @jaimergp
+- [Juan Nunez-Iglesias](https://github.com/napari/napari/commits?author=jni) ([docs](https://github.com/napari/docs/commits?author=jni))  - @jni
+- [Lorenzo Gaifas](https://github.com/napari/napari/commits?author=brisvag) - @brisvag
+- [Markus Stabrin](https://github.com/napari/napari/commits?author=mstabrin) - @mstabrin
+- [Melissa Weber Mendonça](https://github.com/napari/napari/commits?author=melissawm) ([docs](https://github.com/napari/docs/commits?author=melissawm))  - @melissawm
+- [Peter Sobolewski](https://github.com/napari/napari/commits?author=psobolewskiPhD) - @psobolewskiPhD
+
+
+## 11 reviewers added to this release (alphabetical)
+
+(+) denotes first-time contributors 🥳
+
+- [andrew sweet](https://github.com/napari/docs/commits?author=andy-sweet) - @andy-sweet
+- [Draga Doncila Pop](https://github.com/napari/napari/commits?author=DragaDoncila) - @DragaDoncila
+- [Genevieve Buckley](https://github.com/napari/docs/commits?author=GenevieveBuckley) - @GenevieveBuckley
+- [Grzegorz Bokota](https://github.com/napari/napari/commits?author=Czaki) - @Czaki
+- [jaime rodriguez-guerra](https://github.com/napari/napari/commits?author=jaimergp) ([docs](https://github.com/napari/docs/commits?author=jaimergp))  - @jaimergp
+- [Juan Nunez-Iglesias](https://github.com/napari/napari/commits?author=jni) ([docs](https://github.com/napari/docs/commits?author=jni))  - @jni
+- [Lorenzo Gaifas](https://github.com/napari/napari/commits?author=brisvag) - @brisvag
+- [Lucy Liu](https://github.com/napari/docs/commits?author=lucyleeow) - @lucyleeow
+- [Melissa Weber Mendonça](https://github.com/napari/napari/commits?author=melissawm) ([docs](https://github.com/napari/docs/commits?author=melissawm))  - @melissawm
+- [Peter Sobolewski](https://github.com/napari/napari/commits?author=psobolewskiPhD) - @psobolewskiPhD
+- [Wouter-Michiel Vierdag](https://github.com/napari/docs/commits?author=melonora) - @melonora
+

docs/tutorials/fundamentals/installation.md

@@ -237,19 +237,14 @@ process described above working. The bundled app version of napari is the same
 version that you can get through the above described processes, and can still be
 extended with napari plugins installed directly via the app.
 
-```{important}
-Note that the bundled app is still
-in active development, and may not be very stable. We strongly recommend
-[installing as a Python package instead](install-python-package).
-```
-
 To access the cross platform bundles you can visit our [release
 page](https://github.com/napari/napari/releases) and scroll to the release you
 are interested in. For example, the bundles for napari {{ napari_version }} can be
 accessed {{ '[here](https://github.com/napari/napari/releases/tag/vNAPARI_VER)'.replace('NAPARI_VER', napari_version) }}.
 To get to the download link, just scroll all the way to bottom of the page and
 expand the `Assets` section. You can then download the appropriate file for your platform.
 
+Check {doc}`installation_bundle_conda` for more detailed instructions.
 
 <!-- #endregion -->