Napari

We're happy to announce the release of napari 0.4.5!
napari is a fast, interactive, multi-dimensional image viewer for Python.
It's designed for browsing, annotating, and analyzing large multi-dimensional
images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based
rendering), and the scientific Python stack (numpy, scipy).


For more information, examples, and documentation, please visit our website:
https://github.com/napari/napari

Highlights
This release is our first release using Jupyter Book to build our documentation (2187)
which can be seen at https://napari.org/docs/dev/, or
https://napari.org/docs/0.4.5/ . We'll be continuing to reorganize the
napari.org website to create a more integrate feel with documentation and tutorials living
together. You can read more about our website reorganization in (764).

We've also added exprimental support for the ability to link attribute in layers which could
be useful for synchronizing attribute values across layers, for example to
set matching contrast limits for multiple channels (2226).


New Features
- Add experimental link_layers (2226)


Improvements
- Replace evented dataclasses with pydantic evented model on viewer (2042)
- Add pydantic evented model (2127)
- UI: Add keybindings to the Paint and Pick tooltips (2184)
- Add update in-place to evented model (2197)
- Allow reader_function to return empty layer list (2206)
- Handle closing the main window via the close button and handle_exit for this case. (2215)
- More main window cleanup (2218)
- Support equality checking for arrays (or other unusual types) in EventedModel. (2232)
- Make get_stylesheet public (2241)


Bug Fixes
- Fix show/ hide plugin widgets (2173)
- Fix bug with modification of `AVAILABLE_COLORMAPS` when iterating over it (2193)
- Prevent monitor information refering to one of first issues (2214)
- Fix close procedure (2220)
- Update `napari.run`, prevent double-blocking (2225)


Documentation
- Convert docs to use Jupyter Book (2187)


API Changes
- Removed github searching for plugin discovery, instead the `Framework :: napari` classifer should be used (2228)
- Removed evented_dataclass, instead the `EventedModel` should be used (2236)
- The deprecated ``Viewer.interactive`` parameter has been removed, instead you should use ``Viewer.camera.interactive`` (2198)
- The deprecated ``Viewer.palette`` attribute has been removed. To access the palette you can get it using ``napari.utils.theme.register_theme`` dictionary using the ``viewer.theme`` as the key (2198)
- The deprecated approach of annotating a magicgui function with a return type of ``napari.layers.Layer`` has been removed. To indicate that your function returns a layer data tuple, please use a return annotation of ``napari.types.LayerDataTuple`` or ``List[napari.types.LayerDataTuple]``(2198)


Deprecations
- The `asdict` method has been renamed `dict` and is now deprecated on `Axes`, `Camera`, `Cursor`, `Dims, `GridCanvas`, `ScaleBar` (2197)


Build Tools and Support
- Use napari-console package (2118)
- Fix typo in hookspecs docs (2180)
- DOC: autoreformat all the docstrings (2186)
- Refactor a qt dims test to not use the viewer (2194)
- Move `--show-viewer` option to testsupport, add test (2208)
- Include a line on adding screenshots/animations to PRs (2219)
- Skip perfmon test on windows pyside2 CI (2223)
- Generate api file for top-level napari package (2237)
- Better plugin errors surfacing in CLI with `--plugin-info` (2244)
- Add pluginmanager fixture (2247)
- Fix API Reference link in docs (2248)
- Add missing release notes (2250)
- Update napari_plugin_tester docstring (2251)
- Remove pluginmanager fixture in favor of devtools repo (2252)


9 authors added to this release (alphabetical)

- [Gonzalo Peña-Castellanos](https://github.com/napari/napari/commits?author=goanpeca) - goanpeca
- [Grzegorz Bokota](https://github.com/napari/napari/commits?author=Czaki) - Czaki
- [Ian Hunt-Isaak](https://github.com/napari/napari/commits?author=ianhi) - ianhi
- [Jonas Windhager](https://github.com/napari/napari/commits?author=jwindhager) - jwindhager
- [Kira Evans](https://github.com/napari/napari/commits?author=kne42) - kne42
- [Matthias Bussonnier](https://github.com/napari/napari/commits?author=Carreau) - Carreau
- [Nicholas Sofroniew](https://github.com/napari/napari/commits?author=sofroniewn) - sofroniewn
- [Talley Lambert](https://github.com/napari/napari/commits?author=tlambert03) - tlambert03
- [Ziyang Liu](https://github.com/napari/napari/commits?author=ziyangczi) - ziyangczi


10 reviewers added to this release (alphabetical)

- [Gonzalo Peña-Castellanos](https://github.com/napari/napari/commits?author=goanpeca) - goanpeca
- [Grzegorz Bokota](https://github.com/napari/napari/commits?author=Czaki) - Czaki
- [Jonas Windhager](https://github.com/napari/napari/commits?author=jwindhager) - jwindhager
- [Juan Nunez-Iglesias](https://github.com/napari/napari/commits?author=jni) - jni
- [Justine Larsen](https://github.com/napari/napari/commits?author=justinelarsen) - justinelarsen
- [Kevin Yamauchi](https://github.com/napari/napari/commits?author=kevinyamauchi) - kevinyamauchi
- [Lia Prins](https://github.com/napari/napari/commits?author=liaprins-czi) - liaprins-czi
- [Matthias Bussonnier](https://github.com/napari/napari/commits?author=Carreau) - Carreau
- [Nicholas Sofroniew](https://github.com/napari/napari/commits?author=sofroniewn) - sofroniewn
- [Talley Lambert](https://github.com/napari/napari/commits?author=tlambert03) - tlambert03

We're happy to announce the release of napari 0.4.4!
napari is a fast, interactive, multi-dimensional image viewer for Python.
It's designed for browsing, annotating, and analyzing large multi-dimensional
images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based
rendering), and the scientific Python stack (numpy, scipy).


For more information, examples, and documentation, please visit our website:
https://github.com/napari/napari

Highlights
This release is a quick follow on from our `0.4.3` release and contains some
nice improvements to the GUI and analysis function hookspecs we experimentally
added in that release. We've expanded the API of the
`napari_experimental_provide_dock_widget` to accept new `magic_factory`-
decorated functions (available in magicgui 0.2.6+), or any callable that
returns one or more widgets, making it easier for developers who want to use
magicgui and not have to write their own qt widgets (2143).

We have also renamed `napari_experimental_provide_function_widget` to
`napari_experimental_provide_function` and reduced its API to receive only a
function or list of functions. napari will then take care to generate an
appropriate user interface for that function. This will make it even easier to
create analysis pipelines in napari (2158).


Improvements
- Add example code to hook documentation (2112)
- move Viewer import into method (2119)
- Support for EventedList.__setitem__ with array-like items (2120)
- Add __array__ protocol to transforms.Affine (2137)
- Relax dock_widget_hookspec to accept callable. (2143)
- Add name of system to napari sys_info (2147)
- Points layer enable interactive mode in add mode, don't add point when dragging, addresses 2146 (WIP) (2148)
- Change plugin window search from naming convention to pypi classifier (2153)
- Add compress=1 to tifffile imsave call (2157)
- Add informations on what to do on error in GUI (2165)

Documentation
- Better documentation of API changes in 0.4.4 release notes (2171)
- Add new function and dock widget hook specifications to documentation (2158)

Bug Fixes
- QtAboutKeyBindings patch (2132)
- Fix too-late registration of napari types in magicgui (2139)
- Fix magicgui.FunctionGui deprecation warning (2164)
- Fix show/ hide of plugin widgets (2173)


API Changes
- `viewer.grid_view()` has been removed, use `viewer.grid.enabled = True`
instead (2144)
- `viewer.stack_view()` has been removed, use `viewer.grid.enabled = False`
instead (2144)
- `viewer.grid_size` has been removed, use `viewer.grid.shape` instead (2144)
- `viewer.grid_stride` has been removed, use `viewer.grid.stride` instead
(2144)
- Plugins are no longer discovered by naming convention alone; to appear as an
installed plugin in napari, make sure you use the `napari.plugin`
entrypoint in your setup.py or setup.cfg. To appear as a listed plugin on
PyPI, be sure to use the `Framework :: napari` trove classifier. (2152)
- The `napari_experimental_provide_function_widget` plugin hook
specification has been removed. Plugin developers should use
`napari_experimental_provide_function` instead for functional
(layers/layer data in -> layers/layer data out) plugins, and
`napari_experimental_provide_dock_widget` for more elaborate plugins
that require custom widgets. (2158)


Deprecations
- `layer.status` is deprecated, to be removed in 0.4.6. Users should instead
use `layer.get_status(position)`. (1985)
- The position argument to `layer.get_value()` is no longer optional, and will
be required after 0.4.6. (1985)
- `layer.get_message()` is deprecated, to be removed in 0.4.6. Users should use
`layer.get_status(position)` instead. (1985)


Build Tools and Support
- Add missed doc string in `import_resources` (2113)
- Delay import of pkg_resources (2121)
- Remove duplicate entry in install_requires (2122)
- Fix typo in deprecation message (2124)
- DOC: Formatting and Typos. (2129)
- DOC: Rename Section to conform to numpydocs (Return->Returns) (2130)
- Provide `make_test_viewer` as a pytest plugin, for external use. (2131)
- Doc: fix syntax = instead of : (2141)


11 authors added to this release (alphabetical)

- [Alister Burt](https://github.com/napari/napari/commits?author=alisterburt) - alisterburt
- [Christoph Gohlke](https://github.com/napari/napari/commits?author=cgohlke) - cgohlke
- [dongyaoli10x](https://github.com/napari/napari/commits?author=dongyaoli10x) - dongyaoli10x
- [Grzegorz Bokota](https://github.com/napari/napari/commits?author=Czaki) - Czaki
- [Juan Nunez-Iglesias](https://github.com/napari/napari/commits?author=jni) - jni
- [Matthias Bussonnier](https://github.com/napari/napari/commits?author=Carreau) - Carreau
- [nhthayer](https://github.com/napari/napari/commits?author=nhthayer) - nhthayer
- [Nicholas Sofroniew](https://github.com/napari/napari/commits?author=sofroniewn) - sofroniewn
- [Robert Haase](https://github.com/napari/napari/commits?author=haesleinhuepf) - haesleinhuepf
- [Talley Lambert](https://github.com/napari/napari/commits?author=tlambert03) - tlambert03
- [Volker Hilsenstein](https://github.com/napari/napari/commits?author=VolkerH) - VolkerH


6 reviewers added to this release (alphabetical)

- [Juan Nunez-Iglesias](https://github.com/napari/napari/commits?author=jni) - jni
- [nhthayer](https://github.com/napari/napari/commits?author=nhthayer) - nhthayer
- [Nicholas Sofroniew](https://github.com/napari/napari/commits?author=sofroniewn) - sofroniewn
- [Robert Haase](https://github.com/napari/napari/commits?author=haesleinhuepf) - haesleinhuepf
- [Talley Lambert](https://github.com/napari/napari/commits?author=tlambert03) - tlambert03
- [Ziyang Liu](https://github.com/napari/napari/commits?author=ziyangczi) - ziyangczi

We're happy to announce the release of napari 0.4.3!
napari is a fast, interactive, multi-dimensional image viewer for Python.
It's designed for browsing, annotating, and analyzing large multi-dimensional
images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based
rendering), and the scientific Python stack (numpy, scipy).


For more information, examples, and documentation, please visit our website:
https://github.com/napari/napari

Highlights
In this release we've added two new analysis and GUI focused [hook specifications](https://napari.org/docs/dev/plugins/hook_specifications.html) for our plugin developers (#2080).

The first one `napari_experimental_provide_function_widget` allows you to provide a function or list of functions that we
will turn into a GUI element using using [magicgui](https://napari.org/magicgui/). This hook spec leverages the newly added and the `viewer.window.add_function_widget` method (#1856) and the newly recently released `0.2` series of magicgui which seperates out an abstract function and widget API from its Qt backend. These functions can take in and return napari layer, allowing you to
provide analysis functionality to napari without having to write GUI code.

The second one `napari_experimental_provide_dock_widget` allows you to provide a QWidget or list of QWidgets that we will instantiate with access to the napari viewer and add to the GUI. This hook spec leverages our `viewer.window.add_dock_widget` method, and allows you to provide highly customized GUI elements that could include additional plots or interactivity.

Both of these hook specs are marked as `experimental` as we're likely to evolve the API here in response to user needs, and we're excited to get early feedback from plugin developers on them.

In this release we also seperate out more of the Qt functionality from napari making it easier to run headless (2039, 2055). We also added a `napari.run` method as an alternative to using the `napari.gui_qt` context manager (2056).

We've also made good progress on our `experimental` support for an octree system for rendering large 2D multiscale images. You can try this functionality setting `NAPARI_OCTREE=1` as an environment variable. See our [asynchronous rendering guide](https://napari.org/docs/dev/events/rendering.html) for more details on how to use the octree and its current limitations.

Finally we've added our [0.4 series roadmap](https://napari.org/docs/dev/developers/ROADMAP_0_4.html) and a [retrospective on our 0.3 roadmap](https://napari.org/docs/dev/developers/ROADMAP_0_3_retrospective.html)!


New Features
- Add support for function widgets (1856)
- Gui hookspecs (2080)


Improvements
- Use evented dataclass for dims (1917)
- Add information about screen resolution (1957)
- Add asdict and update to evented dataclass (1966)
- async-30: ChunkLoader Stats (1972)
- async-31: Fix Monitor Feature Toggle (1975)
- octree: Fix float64 and check downscale ratio (1976)
- async-32: Faster Octree Rendering (1977)
- async-33: Cleanup QtPoll and Tiled Visuals (1980)
- async-34: Octree Performance (1989)
- async-35: OctreeDisplayOptions (1991)
- async-36: New OctreeChunkLoader (1992)
- async-37: Multilevel Rendering (1995)
- async-38: Better Multilevel Rendering (1997)
- async-39: Better Config and Remove Qt Code (1999)
- Improve label paint lag (2000)
- async-40: Shared Memory Resources (2004)
- async-41: Better Octree Performance (2010)
- Start magicgui apps too (2016)
- async-42: New LoaderPool and remove ChunkKey (2025)
- Two small path improvements (2030)
- Cleanup dockwidget removal (2036)
- Add a MousemapProvider (2040)
- Cleanup warnings in tests (2041)
- async-43: New LoaderPoolGroup (2049)
- Complete qt isolation (2055)
- Create QApplication on demand in viewer.Window, add napari.run function (2056)
- Remove global app logic from Window init (2065)
- async-45: Docs and Cleanup (2067)
- Better bound magicgui viewer (2100)
- reduce call of _extent_data in layer (2106)


Bug Fixes
- Fix append and remove from layerlist (1955)
- Change label tooltip checkbox (1978)
- Fix cursor size (1983)
- Fix layer removing by disconnecting each event individually (1984)
- Compatibility with magicgui v0.2.0 (1994)
- Skip rounding of numbers when comparing data slice (2017)
- Fix InitVar problem (2023)
- Fix channel_axis for affine transforms in add_image (2026)
- Fix typos in theme event and vispy camera (2034)
- Fix magicgui test funcs (2044)
- Fix magicwidget.native detection of "empty" widgets (2046)
- async-44: Fix Pixel Shift Bug (2052)
- Fix missing console widget (2063)
- Save app reference in Window init (2076)
- Add deprecated parameters for updating theme (2074)
- Coerce name before layer is added to layerlist (2087)
- Fix stale data in magicgui `*Data` parameters (2088)
- Make dock widgets non-tabbed (2096)
- Fix overly strict magic kwargs (2099)
- Undo calling pyrcc with python sys.executable (2102)


API Changes
- The ``axis`` parameter is no longer present on the ``current_step``, ``range``, or ``axis_labels`` events. Instead a single event is emitted whenever the tuple changes (1917)
- The deprecated public layer dims has been removed in 0.4.2 and the private ``layer._dims`` is now a NamedTuple (1919)
- The deprecated ``layer.shape`` arrtibute has been removed. Instead you should use the ``layer.extent.data`` and ``layer.extent.world attributes`` to get the extent of the data in data or world coordinates (1990, 2002)
- Keymap handling has been moved off the ``Viewer`` and ``Viewer.keymap_providers`` has been removed. The ``Viewer`` itself
can still provide keymappings, but no longer handles keymappings from other objects like the layers. (2003)
- Drop scale background color and axes background color. These colors are now determined by defaults or the canvas background color. (2037)
- ``event.text`` was renamed ``event.value`` for the events emitted when changing ``Viewer.status``, ``Viewer.title``,
``Viewer.help``, and ``event.item`` was renamed ``event.value`` for the event emitted when changing ``Viewer.active_layer`` (2038)


Deprecations
- The ``Viewer.interactive`` parameter has been deprecated, instead you should use ``Viewer.camera.interactive`` (2008)
- The ``Viewer.palette`` attribute has been deprecated. To access the palette you can get it using ``napari.utils.theme.register_theme`` dictionary using the ``viewer.theme`` as the key (2031)
- Annotating a magicgui function with a return type of ``napari.layers.Layer`` is deprecated. To indicate that your function returns a layer data tuple, please use a return annotation of ``napari.types.LayerDataTuple`` or ``List[napari.types.LayerDataTuple]``(2079)


Build Tools and Support
- 0.4 roadmap (1906)
- Rename artifact for nightly build releases (1971)
- Update latest tag alone with nightly build (2001)
- Only raise leaked widgets errors in tests if no other exception was raised (2043)
- Bump minimum numpy requirement to 1.16.5 (2050)
- Tox tests on github actions (2051)
- Move all requirements to extras (2054)
- Drop additional perfmon test pass (2058)
- Fix name in gha test (2059)
- Fix big sur on GHA and fix failed test template (2061)
- Update bundle.py (2064)
- Update pre-commit and add pyupgrade (2068)
- Skip perfmon test on python 3.9 on CI (2073)
- async-46: Rendering Guide and Code Comments (2078)
- Update get-tag action (2083)
- Update magicgui examples (2084)
- Add examples tests (2085)
- Skip testing examples on CI (2094)
- Fix roadmap headings in docs (2097)
- Add PR 2106 to 0.4.3 release notes (2107)
- Fix `pytest --pyargs napari` test on pip install. Add CI test (2109)


9 authors added to this release (alphabetical)

- [Alister Burt](https://github.com/napari/napari/commits?author=alisterburt) - alisterburt
- [Grzegorz Bokota](https://github.com/napari/napari/commits?author=Czaki) - Czaki
- [Heath Patterson](https://github.com/napari/napari/commits?author=NHPatterson) - NHPatterson
- [Juan Nunez-Iglesias](https://github.com/napari/napari/commits?author=jni) - jni
- [kir0ul](https://github.com/napari/napari/commits?author=kir0ul) - kir0ul
- [Kira Evans](https://github.com/napari/napari/commits?author=kne42) - kne42
- [Nicholas Sofroniew](https://github.com/napari/napari/commits?author=sofroniewn) - sofroniewn
- [Philip Winston](https://github.com/napari/napari/commits?author=pwinston) - pwinston
- [Talley Lambert](https://github.com/napari/napari/commits?author=tlambert03) - tlambert03
- [Ziyang Liu](https://github.com/napari/napari/commits?author=ziyangczi) - ziyangczi


7 reviewers added to this release (alphabetical)

- [Genevieve Buckley](https://github.com/napari/napari/commits?author=GenevieveBuckley) - GenevieveBuckley
- [Grzegorz Bokota](https://github.com/napari/napari/commits?author=Czaki) - Czaki
- [Juan Nunez-Iglesias](https://github.com/napari/napari/commits?author=jni) - jni
- [Nicholas Sofroniew](https://github.com/napari/napari/commits?author=sofroniewn) - sofroniewn
- [Philip Winston](https://github.com/napari/napari/commits?author=pwinston) - pwinston
- [Talley Lambert](https://github.com/napari/napari/commits?author=tlambert03) - tlambert03
- [Ziyang Liu](https://github.com/napari/napari/commits?author=ziyangczi) - ziyangczi