Release 24.04.0

CHANGELOG.released.md

@@ -7,6 +7,67 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 For upgrade instructions, please check the [migration guide](MIGRATIONS.released.md).
 
+## [24.04.0](https://github.com/scalableminds/webknossos/releases/tag/24.04.0) - 2024-03-25
+[Commits](https://github.com/scalableminds/webknossos/compare/24.02.3...24.04.0)
+
+### Highlights
+- Segment statistics are now available for ND datasets. [#7411](https://github.com/scalableminds/webknossos/pull/7411)
+- Added a new "Split from all neighboring segments" feature for the proofreading mode. [#7611](https://github.com/scalableminds/webknossos/pull/7611)
+- Added support for uploading N5 and Neuroglancer Precomputed datasets. [#7578](https://github.com/scalableminds/webknossos/pull/7578)
+
+### Added
+- Added support for storing analytics events in the Postgres. [#7594](https://github.com/scalableminds/webknossos/pull/7594) [#7609](https://github.com/scalableminds/webknossos/pull/7609)
+- Webknossos can now open ND Zarr datasets with arbitrary axis orders (not limited to `**xyz` anymore). [#7592](https://github.com/scalableminds/webknossos/pull/7592)
+- Added support for skeleton annotations within datasets that have transformed layers. The skeleton nodes will move according to the transforms when rendering a specific layer natively. Also, downloading visible trees can be done by incorporating the current transforms. However, note that the back-end export does not take transforms into account. [#7588](https://github.com/scalableminds/webknossos/pull/7588)
+- If storage scan is enabled, the measured used storage is now displayed in the dashboard’s dataset detail view. [#7677](https://github.com/scalableminds/webknossos/pull/7677)
+- Prepared support to download full stl meshes via the HTTP api. [#7587](https://github.com/scalableminds/webknossos/pull/7587)
+- You can now place segment index files with your on-disk segmentation layers, which makes segment stats available when viewing these segmentations, and also when working on volume annotations based on these segmentation layers. [#7437](https://github.com/scalableminds/webknossos/pull/7437)
+- Added an action to delete erroneous, unimported datasets directly from the dashboard. [#7448](https://github.com/scalableminds/webknossos/pull/7448)
+- Added support for `window`, `active`, `inverted` keys from the `omero` info in the NGFF metadata. [7685](https://github.com/scalableminds/webknossos/pull/7685)
+- Added getSegment function to JavaScript API. Also, createSegmentGroup returns the id of the new group now. [#7694](https://github.com/scalableminds/webknossos/pull/7694)
+- Added support for importing N5 datasets without multiscales metadata. [#7664](https://github.com/scalableminds/webknossos/pull/7664)
+
+### Changed
+- Datasets stored in WKW format are no longer loaded with memory mapping, reducing memory demands. [#7528](https://github.com/scalableminds/webknossos/pull/7528)
+- Content Security Policy (CSP) settings are now relaxed by default. To keep stricter CSP rules, add them to your specific `application.conf`. [#7589](https://github.com/scalableminds/webknossos/pull/7589)
+- The state of whether a mapping is active and what exact mapping is now locked to the annotation upon the first volume annotation action to ensure future consistent results. Moreover, while a JSON mapping is active, no volume annotation can be done. [#7549](https://github.com/scalableminds/webknossos/pull/7549)
+- WEBKNOSSOS now uses Java 21. [#7599](https://github.com/scalableminds/webknossos/pull/7599)
+- Email verification is disabled by default. To enable it, set `webKnossos.user.emailVerification.activated` to `true` in your `application.conf`. [#7620](https://github.com/scalableminds/webknossos/pull/7620) [#7621](https://github.com/scalableminds/webknossos/pull/7621)
+- Added more documentation for N5 and Neuroglancer precomputed web upload. [#7622](https://github.com/scalableminds/webknossos/pull/7622)
+- Added the config key `webKnossos.user.timeTrackingOnlyWithSignificantChanges`, which when set to `true` will only track time if the user has made significant changes to the annotation. [#7627](https://github.com/scalableminds/webknossos/pull/7627)
+- Only display UI elements to launch background jobs if the (worker) backend actually supports them. [#7591](https://github.com/scalableminds/webknossos/pull/7591)
+- If the current dataset folder in the dashboard cannot be found (e.g., because somebody else deleted it), the page navigates to the root folder automatically. [#7669](https://github.com/scalableminds/webknossos/pull/7669)
+- Voxelytics logs are now stored by organization name, rather than id, in Loki. This is in preparation of the unification of these two concepts. [#7687](https://github.com/scalableminds/webknossos/pull/7687)
+- Using a segment index file with a different data type than uint16 will now result in an error. [#7698](https://github.com/scalableminds/webknossos/pull/7698)
+- Improved performance of JSON mappings in preparation of frontend HDF5 mappings. [#7706](https://github.com/scalableminds/webknossos/pull/7706)
+
+### Fixed
+- Fixed rare SIGBUS crashes of the datastore module that were caused by memory mapping on unstable file systems. [#7528](https://github.com/scalableminds/webknossos/pull/7528)
+- Fixed loading local datasets for organizations that have spaces in their names. [#7593](https://github.com/scalableminds/webknossos/pull/7593)
+- Fixed a bug where proofreading annotations would stay black until the next server restart due to expired but cached tokens. [#7598](https://github.com/scalableminds/webknossos/pull/7598)
+- Fixed a bug where ad-hoc meshing didn't make use of a segment index, even when it existed. [#7600](https://github.com/scalableminds/webknossos/pull/7600)
+- Fixed a bug where importing remote datasets with existing datasource-properties.jsons would not properly register the remote credentials. [#7601](https://github.com/scalableminds/webknossos/pull/7601)
+- Fixed a bug in ND volume annotation downloads where the additionalAxes metadata had wrong indices. [#7592](https://github.com/scalableminds/webknossos/pull/7592)
+- Fixed a bug in proofreading aka editable mapping annotations where splitting would sometimes give the new id to the selected segment rather than to the split-off one. [#7608](https://github.com/scalableminds/webknossos/pull/7608)
+- Fixed small styling errors as a follow-up to the antd v5 upgrade. [#7612](https://github.com/scalableminds/webknossos/pull/7612)
+- Fixed that the iOS keyboard automatically showed up when moving through a dataset. [#7660](https://github.com/scalableminds/webknossos/pull/7660)
+- Fixed deprecation warnings caused by Antd \<Collapse\> components. [#7610](https://github.com/scalableminds/webknossos/pull/7610)
+- Fixed small styling error with a welcome notification for new users on webknossos.org. [#7623](https://github.com/scalableminds/webknossos/pull/7623)
+- Fixed that filtering by tags could produce false positives. [#7640](https://github.com/scalableminds/webknossos/pull/7640)
+- Fixed a slight offset when creating a node with the mouse. [#7639](https://github.com/scalableminds/webknossos/pull/7639)
+- Fixed small styling error with NML drag and drop uploading. [#7641](https://github.com/scalableminds/webknossos/pull/7641)
+- Fixed a bug where the annotation list would show teams the annotation is shared with multiple times. [#7659](https://github.com/scalableminds/webknossos/pull/7659)
+- Fixed incorrect menu position that could occur sometimes when clicking the ... button next to a segment. [#7680](https://github.com/scalableminds/webknossos/pull/7680)
+- Fixed an error in the Loki integration to support Loki 2.9+. [#7684](https://github.com/scalableminds/webknossos/pull/7684)
+- Fixed inconsistent style of antd components and odd behavior of dataset/annotation description Markdown input. [#7700](https://github.com/scalableminds/webknossos/pull/7700)
+
+### Removed
+- Removed the integration with BrainTracing user databases. [#7693](https://github.com/scalableminds/webknossos/pull/7693)
+
+### Breaking Changes
+- Updated antd UI library from version 4.24.15 to 5.13.2. Drop support for nodeJs version <18. [#7522](https://github.com/scalableminds/webknossos/pull/7522)
+
+
 ## [24.02.3](https://github.com/scalableminds/webknossos/releases/tag/24.02.3) - 2024-02-22
 [Commits](https://github.com/scalableminds/webknossos/compare/24.02.2...24.02.3)
 

CHANGELOG.unreleased.md

@@ -8,59 +8,14 @@ and this project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MIC
 For upgrade instructions, please check the [migration guide](MIGRATIONS.released.md).
 
 ## Unreleased
-[Commits](https://github.com/scalableminds/webknossos/compare/24.02.3...HEAD)
+[Commits](https://github.com/scalableminds/webknossos/compare/24.04.0...HEAD)
 
 ### Added
-- Added support for storing analytics events in the Postgres. [#7594](https://github.com/scalableminds/webknossos/pull/7594) [#7609](https://github.com/scalableminds/webknossos/pull/7609)
-- Segment statistics are now available for ND datasets. [#7411](https://github.com/scalableminds/webknossos/pull/7411)
-- Added support for uploading N5 and Neuroglancer Precomputed datasets. [#7578](https://github.com/scalableminds/webknossos/pull/7578)
-- Webknossos can now open ND Zarr datasets with arbitrary axis orders (not limited to `**xyz` anymore). [#7592](https://github.com/scalableminds/webknossos/pull/7592)
-- Added support for skeleton annotations within datasets that have transformed layers. The skeleton nodes will move according to the transforms when rendering a specific layer natively. Also, downloading visible trees can be done by incorporating the current transforms. However, note that the back-end export does not take transforms into account. [#7588](https://github.com/scalableminds/webknossos/pull/7588)
-- Added a new "Split from all neighboring segments" feature for the proofreading mode. [#7611](https://github.com/scalableminds/webknossos/pull/7611)
-- If storage scan is enabled, the measured used storage is now displayed in the dashboard’s dataset detail view. [#7677](https://github.com/scalableminds/webknossos/pull/7677)
-- Prepared support to download full stl meshes via the HTTP api. [#7587](https://github.com/scalableminds/webknossos/pull/7587)
-- You can now place segment index files with your on-disk segmentation layers, which makes segment stats available when viewing these segmentations, and also when working on volume annotations based on these segmentation layers. [#7437](https://github.com/scalableminds/webknossos/pull/7437)
-- Added an action to delete erroneous, unimported datasets directly from the dashboard. [#7448](https://github.com/scalableminds/webknossos/pull/7448)
-- Added support for `window`, `active`, `inverted` keys from the `omero` info in the NGFF metadata. [7685](https://github.com/scalableminds/webknossos/pull/7685)
-- Added getSegment function to JavaScript API. Also, createSegmentGroup returns the id of the new group now. [#7694](https://github.com/scalableminds/webknossos/pull/7694)
-- Added support for importing N5 datasets without multiscales metadata. [#7664](https://github.com/scalableminds/webknossos/pull/7664)
 
 ### Changed
-- Datasets stored in WKW format are no longer loaded with memory mapping, reducing memory demands. [#7528](https://github.com/scalableminds/webknossos/pull/7528)
-- Content Security Policy (CSP) settings are now relaxed by default. To keep stricter CSP rules, add them to your specific `application.conf`. [#7589](https://github.com/scalableminds/webknossos/pull/7589)
-- The state of whether a mapping is active and what exact mapping is now locked to the annotation upon the first volume annotation action to ensure future consistent results. Moreover, while a JSON mapping is active, no volume annotation can be done. [#7549](https://github.com/scalableminds/webknossos/pull/7549)
-- WEBKNOSSOS now uses Java 21. [#7599](https://github.com/scalableminds/webknossos/pull/7599)
-- Email verification is disabled by default. To enable it, set `webKnossos.user.emailVerification.activated` to `true` in your `application.conf`. [#7620](https://github.com/scalableminds/webknossos/pull/7620) [#7621](https://github.com/scalableminds/webknossos/pull/7621)
-- Added more documentation for N5 and Neuroglancer precomputed web upload. [#7622](https://github.com/scalableminds/webknossos/pull/7622)
-- Added the config key `webKnossos.user.timeTrackingOnlyWithSignificantChanges`, which when set to `true` will only track time if the user has made significant changes to the annotation. [#7627](https://github.com/scalableminds/webknossos/pull/7627)
-- Only display UI elements to launch background jobs if the (worker) backend actually supports them. [#7591](https://github.com/scalableminds/webknossos/pull/7591)
-- If the current dataset folder in the dashboard cannot be found (e.g., because somebody else deleted it), the page navigates to the root folder automatically. [#7669](https://github.com/scalableminds/webknossos/pull/7669)
-- Voxelytics logs are now stored by organization name, rather than id, in Loki. This is in preparation of the unification of these two concepts. [#7687](https://github.com/scalableminds/webknossos/pull/7687)
-- Using a segment index file with a different data type than uint16 will now result in an error. [#7698](https://github.com/scalableminds/webknossos/pull/7698)
-- Improved performance of JSON mappings in preparation of frontend HDF5 mappings. [#7706](https://github.com/scalableminds/webknossos/pull/7706)
 
 ### Fixed
-- Fixed rare SIGBUS crashes of the datastore module that were caused by memory mapping on unstable file systems. [#7528](https://github.com/scalableminds/webknossos/pull/7528)
-- Fixed loading local datasets for organizations that have spaces in their names. [#7593](https://github.com/scalableminds/webknossos/pull/7593)
-- Fixed a bug where proofreading annotations would stay black until the next server restart due to expired but cached tokens. [#7598](https://github.com/scalableminds/webknossos/pull/7598)
-- Fixed a bug where ad-hoc meshing didn't make use of a segment index, even when it existed. [#7600](https://github.com/scalableminds/webknossos/pull/7600)
-- Fixed a bug where importing remote datasets with existing datasource-properties.jsons would not properly register the remote credentials. [#7601](https://github.com/scalableminds/webknossos/pull/7601)
-- Fixed a bug in ND volume annotation downloads where the additionalAxes metadata had wrong indices. [#7592](https://github.com/scalableminds/webknossos/pull/7592)
-- Fixed a bug in proofreading aka editable mapping annotations where splitting would sometimes give the new id to the selected segment rather than to the split-off one. [#7608](https://github.com/scalableminds/webknossos/pull/7608)
-- Fixed small styling errors as a follow-up to the antd v5 upgrade. [#7612](https://github.com/scalableminds/webknossos/pull/7612)
-- Fixed that the iOS keyboard automatically showed up when moving through a dataset. [#7660](https://github.com/scalableminds/webknossos/pull/7660)
-- Fixed deprecation warnings caused by Antd \<Collapse\> components. [#7610](https://github.com/scalableminds/webknossos/pull/7610)
-- Fixed small styling error with a welcome notification for new users on webknossos.org. [#7623](https://github.com/scalableminds/webknossos/pull/7623)
-- Fixed that filtering by tags could produce false positives. [#7640](https://github.com/scalableminds/webknossos/pull/7640)
-- Fixed a slight offset when creating a node with the mouse. [#7639](https://github.com/scalableminds/webknossos/pull/7639)
-- Fixed small styling error with NML drag and drop uploading. [#7641](https://github.com/scalableminds/webknossos/pull/7641)
-- Fixed a bug where the annotation list would show teams the annotation is shared with multiple times. [#7659](https://github.com/scalableminds/webknossos/pull/7659)
-- Fixed incorrect menu position that could occur sometimes when clicking the ... button next to a segment. [#7680](https://github.com/scalableminds/webknossos/pull/7680)
-- Fixed an error in the Loki integration to support Loki 2.9+. [#7684](https://github.com/scalableminds/webknossos/pull/7684)
-- Fixed inconsistent style of antd components and odd behavior of dataset/annotation description Markdown input. [#7700](https://github.com/scalableminds/webknossos/pull/7700)
 
 ### Removed
-- Removed the integration with BrainTracing user databases. [#7693](https://github.com/scalableminds/webknossos/pull/7693)
 
 ### Breaking Changes
-- Updated antd UI library from version 4.24.15 to 5.13.2. Drop support for nodeJs version <18. [#7522](https://github.com/scalableminds/webknossos/pull/7522)

MIGRATIONS.released.md

@@ -6,6 +6,26 @@ See `MIGRATIONS.unreleased.md` for the changes which are not yet part of an offi
 This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 
+## [24.04.0](https://github.com/scalableminds/webknossos/releases/tag/24.04.0) - 2024-03-25
+[Commits](https://github.com/scalableminds/webknossos/compare/24.02.3...24.04.0)
+- WKW datasets can now only be read if they have a `header.wkw` file in their mag directories. If specific datasets can no longer be loaded, consider adding such a file. Backend logging should show according error message. [#7528](https://github.com/scalableminds/webknossos/pull/7528)
+- Content Security Policy (CSP) settings are now relaxed by default. To keep stricter CSP rules, add them to your specific `application.conf`. [#7589](https://github.com/scalableminds/webknossos/pull/7589)
+- The way the segment index is stored for nd-annotations has been changed ([#7411](https://github.com/scalableminds/webknossos/pull/7411)). Annotations with old segment indices should be
+archived if they do not contain relevant data. The following SQL query can be used:
+```sql
+UPDATE webknossos.annotations_ SET state = 'Finished' WHERE _id IN  (SELECT DISTINCT a._id AS nd_annotations_id FROM webknossos.annotations_ AS a INNER JOIN webknossos.datasets AS d ON a._dataset = d._id INNER JOIN webknossos.dataset_layer_additionalaxes AS dla ON d._id = dla._dataset)
+```
+- WEBKNOSSOS now uses Java 21 (up from Java 11). [#7599](https://github.com/scalableminds/webknossos/pull/7599)
+- NodeJS version 18+ is required for snapshot tests with ShadowDOM elements from Antd v5. [#7522](https://github.com/scalableminds/webknossos/pull/7522)
+- Email verification is disabled by default. To enable it, set `webKnossos.user.emailVerification.activated` to `true` in your `application.conf`. [#7620](https://github.com/scalableminds/webknossos/pull/7620) [#7621](https://github.com/scalableminds/webknossos/pull/7621)
+- New dependency draco/libdraco-dev needs to be installed when deploying without docker and for local development.
+- Config block `braintracing` is now unused and can be removed. [#7693](https://github.com/scalableminds/webknossos/pull/7693)
+
+### Postgres Evolutions:
+
+- [113-analytics-events.sql](conf/evolutions/113-analytics-events.sql)
+
+
 ## [24.02.3](https://github.com/scalableminds/webknossos/releases/tag/24.02.3) - 2024-02-22
 [Commits](https://github.com/scalableminds/webknossos/compare/24.02.2...24.02.3)
 
@@ -672,4 +692,4 @@ No migrations necessary.
 
 
 ## [18.07.0](https://github.com/scalableminds/webknossos/releases/tag/18.07.0) - 2018-07-05
-First release
+First release