Release notes v0.6.5

docs/release/release_0_6_5.md

@@ -3,7 +3,6 @@
 
 *Fri, Sep 26, 2025*
 
-
 We're happy to announce the release of napari 0.6.5!
 napari is a fast, interactive, multi-dimensional image viewer for Python.
 It's designed for browsing, annotating, and analyzing large multi-dimensional
@@ -13,29 +12,66 @@ rendering), and the scientific Python stack (numpy, scipy).
 For more information, examples, and documentation, please visit our website,
 https://napari.org.
 
+napari follows [EffVer (Intended Effort Versioning)](https://effver.org/); this is a **Meso** release containing awesome new features, but some effort may be needed when updating previous projects to use this version.
+
 ## Highlights
 
-- Add colormap overlay ([#7832](https://github.com/napari/napari/pull/7832))
-- add option to define startup script in settings ([#8188](https://github.com/napari/napari/pull/8188))
-- Multilayer features table ([#8189](https://github.com/napari/napari/pull/8189))
-- Add a tasks manager status for plugins actions and napari processes ([#8211](https://github.com/napari/napari/pull/8211))
+### Define a startup script for custom launch behaviour
+Do you have a code snippet that you always find yourself running after you launch napari? No more! You can now put this code in a script and set its path in the new `startup script` setting ([#8188](https://github.com/napari/napari/pull/8188)), and it will be executed every time napari opens. It's just a python script, so sky's the limit :) We found it particularly useful for adding custom colormaps, setting up the scale bar *just right*, or automatically launching our favourite plugin on startup.
+
+![Screenshot of the application settings menu highlighting the field for the startup script path](https://github.com/user-attachments/assets/7b0e5e5c-252b-45a0-ae76-aac88e488cbc)
+
+### Automatically tiled overlays and ColorBar overlay
+Canvas overlays such as `scale_bar`, `text_overlay`, and `colorbar` overlay are now automatically tiling ([#7836](https://github.com/napari/napari/pull/7836)), preventing annoying overlap and making them easier to use without having to manage positioning. Wait, `colorbar` overlay you said? You heard it right! This is a new overlay ([#7832](https://github.com/napari/napari/pull/7832))that shows a color bar legend, and it works with any layer which uses a colormap. All of this works seamlessly with multiple overlays and even grid mode:
+
+```py
+import napari
+
+viewer = napari.Viewer()
+
+# enable grid with stride 2 to get layers split two-by-two
+viewer.grid.enabled = True
+viewer.grid.stride = 2
+
+# set the scale bar to gridded mode so it appears in each grid box
+viewer.scale_bar.visible = True
+viewer.scale_bar.gridded = True
+
+layers = viewer.open_sample('napari', 'lily')
+
+# enable color bars
+for layer in layers:
+    layer.colorbar.visible = True
+```
+
+![Image depicting the napari viewer in grid mode with scale bars and color bars enabled](https://github.com/user-attachments/assets/622b2d36-11a7-4c55-9550-c82ddebc2fda)
+
+### Task manager will now try to prevent losing unfinished work
+We added a new task manager ([#8211](https://github.com/napari/napari/pull/8211)) which automatically registers any running `thread_worker`, showing a confirmation dialog if you attempt to close napari while a task is running.
+
+### New `remove()` and `pop()` methods for Points and Shapes
+Points and Shapes can now be easily removed, not just added :P ([#8031](https://github.com/napari/napari/pull/8031) and [#8072](https://github.com/napari/napari/pull/8072)).
+
+### A new and updated guide on napari Preferences
+Our documentation on the napari Preferences has received a major overhaul! [Check it out here](https://napari.org/stable/guides/preferences.html#preferences)!
+
+TODO: does this link work?
+
 - Migrate non-user extras to dependency-groups ([#8227](https://github.com/napari/napari/pull/8227))
+- [maint] Drop alpha mentions ([#8288](https://github.com/napari/napari/pull/8288))
 - Auto generate release index with highlights and timeline ([docs#838](https://github.com/napari/docs/pull/838))
 
 ## New Features
 
-- Feature: labels layer with a closed predefined set of named labels + combobox selection ([#5875](https://github.com/napari/napari/pull/5875))
+- Add color bar overlay ([#7832](https://github.com/napari/napari/pull/7832))
 - Tiling canvas overlays ([#7836](https://github.com/napari/napari/pull/7836))
-- Use information about units when calculate scale of layers when render ([#7889](https://github.com/napari/napari/pull/7889))
-- Add hot-reload for the devs ([#8007](https://github.com/napari/napari/pull/8007))
-- Cursor overlay ([#8017](https://github.com/napari/napari/pull/8017))
+- Add `pop()` for `Points` and `Shapes` ([#8072](https://github.com/napari/napari/pull/8072))
 - add option to define startup script in settings ([#8188](https://github.com/napari/napari/pull/8188))
-- Multilayer features table ([#8189](https://github.com/napari/napari/pull/8189))
+- use `Selection` class in shapes layer ([#8297](https://github.com/napari/napari/pull/8297))
 
 ## Improvements
 
-- [Update] Added `remove` and `remove_selected` in Shapes and Points ([#8031](https://github.com/napari/napari/pull/8031))
-- Add Features using Features Table widget ([#8093](https://github.com/napari/napari/pull/8093))
+- Add `remove()` in Shapes and Points ([#8031](https://github.com/napari/napari/pull/8031))
 - Example from SciPy 2025 tutorial; image warping ([#8111](https://github.com/napari/napari/pull/8111))
 - Add a tasks manager status for plugins actions and napari processes ([#8211](https://github.com/napari/napari/pull/8211))
 - Use single settings path for all `uv tool run` ([#8250](https://github.com/napari/napari/pull/8250))
@@ -46,23 +82,23 @@ https://napari.org.
 ## Bug Fixes
 
 - Layer controls widgets refactor ([#7355](https://github.com/napari/napari/pull/7355))
-- Set the dimensions of the label equal to the maximum value of the layers world ([#8098](https://github.com/napari/napari/pull/8098))
+- Fix effect of scaling when converting shapes to labels ([#8098](https://github.com/napari/napari/pull/8098))
 - Fix disappearing points ([#8223](https://github.com/napari/napari/pull/8223))
 - Fix shape position by using a stable algorithm for sorting z_position ([#8232](https://github.com/napari/napari/pull/8232))
 - Remove console print action shortcut to prevent collision with command palette shortcut ([#8233](https://github.com/napari/napari/pull/8233))
 - Do not update thumbnail on Labels empty slice ([#8251](https://github.com/napari/napari/pull/8251))
+- Handle affine layer metadata when splitting RGB images ([#8256](https://github.com/napari/napari/pull/8256))
 - fix slice_from_axis to wrap zarr in dask to keep lazy behavior ([#8260](https://github.com/napari/napari/pull/8260))
 - Add menu-xdg to XPRA containers ([#8263](https://github.com/napari/napari/pull/8263))
 - Check for zarr in `images_to_stack` and use da.stack instead of np.stack ([#8267](https://github.com/napari/napari/pull/8267))
 - Better handling of remote zarr ([#8268](https://github.com/napari/napari/pull/8268))
-
-## API Changes
-
-- Expose force_sync context manager ([#7908](https://github.com/napari/napari/pull/7908))
+- Use custom logger formatting to most of argument to string ([#8305](https://github.com/napari/napari/pull/8305))
 
 ## Documentation
 
 - Use EffVer ([#8243](https://github.com/napari/napari/pull/8243))
+- Use shared workflows for build docs ([#8308](https://github.com/napari/napari/pull/8308))
+- Bump napari-sphinx-theme in deps and constraints ([#8315](https://github.com/napari/napari/pull/8315))
 - Add funding information to the home page ([docs#818](https://github.com/napari/docs/pull/818))
 - Update version switcher for 0.6.4 ([docs#826](https://github.com/napari/docs/pull/826))
 - Fix version switcher URL to prevent problems with unversioned pages ([docs#827](https://github.com/napari/docs/pull/827))
@@ -71,14 +107,15 @@ https://napari.org.
 - Fix @jaimergp's last name ([docs#835](https://github.com/napari/docs/pull/835))
 - Auto generate release index with highlights and timeline ([docs#838](https://github.com/napari/docs/pull/838))
 - Add EffVer to release guide and link to checklist template ([docs#839](https://github.com/napari/docs/pull/839))
+- Enable dark mode for website ([docs#840](https://github.com/napari/docs/pull/840))
+- Add draft of 0.6.5 release notes ([docs#845](https://github.com/napari/docs/pull/845))
+- Add documentation for startup script. ([docs#846](https://github.com/napari/docs/pull/846))
+- Add some info about running python scripts via cli ([docs#847](https://github.com/napari/docs/pull/847))
+- Add note about workers registration as tasks and close confirmation dialog when closing napari GUI via close button ([docs#851](https://github.com/napari/docs/pull/851))
+- Release notes v0.6.5 ([docs#853](https://github.com/napari/docs/pull/853))
 
 ## Other Pull Requests
 
-- Add codespell support (config, workflow to detect/not fix) and make it fix few typos ([#7619](https://github.com/napari/napari/pull/7619))
-- Clipping planes control widget ([#7993](https://github.com/napari/napari/pull/7993))
-- Add cell tracking example ([#8051](https://github.com/napari/napari/pull/8051))
-- [Update] Added `pop` for `Points` and `Shapes` ([#8072](https://github.com/napari/napari/pull/8072))
-- Welcome widget as an overlay ([#8117](https://github.com/napari/napari/pull/8117))
 - Improve workflow naming by prefixing triage- doc- make- ([#8159](https://github.com/napari/napari/pull/8159))
 - Move the test that requires `make_napari_viewer` from `test_qt_viewer` ([#8176](https://github.com/napari/napari/pull/8176))
 - Bump `superqt` min version ([#8212](https://github.com/napari/napari/pull/8212))
@@ -101,50 +138,56 @@ https://napari.org.
 - [maint] Revert back to windows-2022 for windows runners ([#8265](https://github.com/napari/napari/pull/8265))
 - Update `dask`, `hypothesis`, `pydantic`, `qtconsole`, `scipy`, `tifffile` ([#8270](https://github.com/napari/napari/pull/8270))
 - Add napari to trove classifiers to populate builtins on napari hub ([#8277](https://github.com/napari/napari/pull/8277))
-- [maint] Drop alpha mentions ([#8288](https://github.com/napari/napari/pull/8288))
 - Add release checklist template ([#8295](https://github.com/napari/napari/pull/8295))
 - Update `coverage`, `dask`, `hypothesis`, `lxml`, `numpy`, `psutil`, `tensorstore`, `tifffile` ([#8296](https://github.com/napari/napari/pull/8296))
 - Move Jaime Rodríguez-Guerra to core-team section of CITATION.cff ([#8298](https://github.com/napari/napari/pull/8298))
+- Do not use verbose mode for headless test ([#8300](https://github.com/napari/napari/pull/8300))
+- Migrate macos-13 to macos-15-intel runner ([#8301](https://github.com/napari/napari/pull/8301))
+- Update `remove_ready_to_merge` so it only sweeps on pushed and crons ([#8302](https://github.com/napari/napari/pull/8302))
+- [maint] Revert docs constraints changes from #8270 ([#8307](https://github.com/napari/napari/pull/8307))
+- Fix constraints generation  ([#8309](https://github.com/napari/napari/pull/8309))
+- CI: Fix `github.rest.issues.removeLabel` call ([#8311](https://github.com/napari/napari/pull/8311))
 - Add pooch cache for build docs ([docs#830](https://github.com/napari/docs/pull/830))
 - ci(dependabot): bump the github-actions group with 3 updates ([docs#831](https://github.com/napari/docs/pull/831))
+- add docs/release/index.md to gitignore ([docs#843](https://github.com/napari/docs/pull/843))
 - Add Jaime Rodríguez-Guerra to core-team ([docs#844](https://github.com/napari/docs/pull/844))
+- Bump python to 3.12 for build docs workflows ([docs#848](https://github.com/napari/docs/pull/848))
+- Use shared workflow for build docs ([docs#850](https://github.com/napari/docs/pull/850))
 
 
-## 9 authors added to this release (alphabetical)
+## 12 authors added to this release (alphabetical)
 
 (+) denotes first-time contributors 🥳
 
-- [Daniel Althviz Moré](https://github.com/napari/napari/commits?author=dalthviz) - @dalthviz
+- [Daniel Althviz Moré](https://github.com/napari/napari/commits?author=dalthviz) ([docs](https://github.com/napari/docs/commits?author=dalthviz))  - @dalthviz
 - [Grzegorz Bokota](https://github.com/napari/napari/commits?author=Czaki) ([docs](https://github.com/napari/docs/commits?author=Czaki))  - @Czaki
 - [Jaime Rodríguez-Guerra](https://github.com/napari/napari/commits?author=jaimergp) ([docs](https://github.com/napari/docs/commits?author=jaimergp))  - @jaimergp
+- [Johannes Soltwedel](https://github.com/napari/napari/commits?author=jo-mueller) - @jo-mueller
 - [Juan Nunez-Iglesias](https://github.com/napari/docs/commits?author=jni) - @jni
 - [Kanai Potts](https://github.com/napari/napari/commits?author=8bitbiscuit) - @8bitbiscuit
-- [Lorenzo Gaifas](https://github.com/napari/napari/commits?author=brisvag) - @brisvag
+- [Lorenzo Gaifas](https://github.com/napari/napari/commits?author=brisvag) ([docs](https://github.com/napari/docs/commits?author=brisvag))  - @brisvag
 - [Melissa Weber Mendonça](https://github.com/napari/docs/commits?author=melissawm) - @melissawm
 - [Peter Sobolewski](https://github.com/napari/napari/commits?author=psobolewskiPhD) ([docs](https://github.com/napari/docs/commits?author=psobolewskiPhD))  - @psobolewskiPhD
+- [Rahul Kumar](https://github.com/napari/napari/commits?author=rahul713rk) - @rahul713rk
+- [rwkozar](https://github.com/napari/napari/commits?author=rwkozar) - @rwkozar
 - [Tim Monko](https://github.com/napari/napari/commits?author=TimMonko) ([docs](https://github.com/napari/docs/commits?author=TimMonko))  - @TimMonko
 
-
-## 18 reviewers added to this release (alphabetical)
+## 15 reviewers added to this release (alphabetical)
 
 (+) denotes first-time contributors 🥳
 
 - [Andrew Sweet](https://github.com/napari/docs/commits?author=andy-sweet) - @andy-sweet
 - [Carol Willing](https://github.com/napari/docs/commits?author=willingc) - @willingc
-- [Daniel Althviz Moré](https://github.com/napari/napari/commits?author=dalthviz) - @dalthviz
+- [Daniel Althviz Moré](https://github.com/napari/napari/commits?author=dalthviz) ([docs](https://github.com/napari/docs/commits?author=dalthviz))  - @dalthviz
 - [Davis Bennett](https://github.com/napari/docs/commits?author=d-v-b) - @d-v-b
 - [Draga Doncila Pop](https://github.com/napari/docs/commits?author=DragaDoncila) - @DragaDoncila
 - [Grzegorz Bokota](https://github.com/napari/napari/commits?author=Czaki) ([docs](https://github.com/napari/docs/commits?author=Czaki))  - @Czaki
 - [Jaime Rodríguez-Guerra](https://github.com/napari/napari/commits?author=jaimergp) ([docs](https://github.com/napari/docs/commits?author=jaimergp))  - @jaimergp
-- [Johannes Soltwedel](https://github.com/napari/docs/commits?author=jo-mueller) - @jo-mueller
+- [Johannes Soltwedel](https://github.com/napari/napari/commits?author=jo-mueller) - @jo-mueller
 - [Juan Nunez-Iglesias](https://github.com/napari/docs/commits?author=jni) - @jni
-- [Lorenzo Gaifas](https://github.com/napari/napari/commits?author=brisvag) - @brisvag
-- [Marcelo Zoccoler](https://github.com/napari/docs/commits?author=zoccoler) - @zoccoler
+- [Lorenzo Gaifas](https://github.com/napari/napari/commits?author=brisvag) ([docs](https://github.com/napari/docs/commits?author=brisvag))  - @brisvag
 - [Melissa Weber Mendonça](https://github.com/napari/docs/commits?author=melissawm) - @melissawm
 - [Peter Sobolewski](https://github.com/napari/napari/commits?author=psobolewskiPhD) ([docs](https://github.com/napari/docs/commits?author=psobolewskiPhD))  - @psobolewskiPhD
-- [Rahul Kumar](https://github.com/napari/docs/commits?author=rahul713rk) - @rahul713rk
-- [rwkozar](https://github.com/napari/docs/commits?author=rwkozar) - @rwkozar
-- [Sesan](https://github.com/napari/docs/commits?author=Olusesan) - @Olusesan
+- [Rahul Kumar](https://github.com/napari/napari/commits?author=rahul713rk) - @rahul713rk
+- [rwkozar](https://github.com/napari/napari/commits?author=rwkozar) - @rwkozar
 - [Tim Monko](https://github.com/napari/napari/commits?author=TimMonko) ([docs](https://github.com/napari/docs/commits?author=TimMonko))  - @TimMonko
-- [Yaroslav Halchenko](https://github.com/napari/docs/commits?author=yarikoptic) - @yarikoptic
-