merge master

Author: knollengewaechs

.github/workflows/build_test_deploy.yml

@@ -263,44 +263,58 @@ jobs:
         run: docker compose --file .github/docker-compose.yml down --volumes --remove-orphans
 
       - uses: docker/login-action@v3
+        if: ${{ github.actor != 'dependabot[bot]' &&
+          (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository) }}
         with:
           username: ${{ secrets.DOCKER_USER }}
           password: ${{ secrets.DOCKER_PASS }}
 
       - name: Push webknossos image
-        if: ${{ ! startsWith(github.ref, 'refs/tags/') }}
+        if: ${{ ! startsWith(github.ref, 'refs/tags/') &&
+          github.actor != 'dependabot[bot]' &&
+          (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository) }}
         uses: ./.github/actions/retry
         with:
           run: docker push "scalableminds/webknossos:${{ env.DOCKER_TAG }}"
           retries: 5
           retry_delay_seconds: 10
       - name: Push normalized webknossos image
+        if: ${{ github.actor != 'dependabot[bot]' &&
+          (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository) }}
         uses: ./.github/actions/retry
         with:
           run: docker push "scalableminds/webknossos:${{ env.NORMALIZED_BRANCH }}"
           retries: 5
           retry_delay_seconds: 10
       - name: Push webknossos-datastore image
-        if: ${{ ! startsWith(github.ref, 'refs/tags/') }}
+        if: ${{ ! startsWith(github.ref, 'refs/tags/') &&
+          github.actor != 'dependabot[bot]' &&
+          (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository) }}
         uses: ./.github/actions/retry
         with:
           run: docker push "scalableminds/webknossos-datastore:${{ env.DOCKER_TAG }}"
           retries: 5
           retry_delay_seconds: 10
       - name: Push normalized webknossos-datastore image
+        if: ${{ github.actor != 'dependabot[bot]' &&
+          (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository) }}
         uses: ./.github/actions/retry
         with:
           run: docker push "scalableminds/webknossos-datastore:${{ env.NORMALIZED_BRANCH }}"
           retries: 5
           retry_delay_seconds: 10
       - name: Push webknossos-tracingstore image
-        if: ${{ ! startsWith(github.ref, 'refs/tags/') }}
+        if: ${{ ! startsWith(github.ref, 'refs/tags/') &&
+          github.actor != 'dependabot[bot]' &&
+          (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository) }}
         uses: ./.github/actions/retry
         with:
           run: docker push "scalableminds/webknossos-tracingstore:${{ env.DOCKER_TAG }}"
           retries: 5
           retry_delay_seconds: 10
       - name: Push normalized webknossos-tracingstore image
+        if: ${{ github.actor != 'dependabot[bot]' &&
+          (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository) }}
         uses: ./.github/actions/retry
         with:
           run: docker push "scalableminds/webknossos-tracingstore:${{ env.NORMALIZED_BRANCH }}"

.github/workflows/nightly.yml

@@ -53,7 +53,7 @@ jobs:
 
       - name: Refresh datasets
         run: |
-          curl -X POST --fail https://${{ env.SUBDOMAIN }}.webknossos.xyz/data/triggers/checkInboxBlocking?token=${{ secrets.WK_AUTH_TOKEN }}
+          curl -X POST --fail https://${{ env.SUBDOMAIN }}.webknossos.xyz/data/triggers/checkInboxBlocking?token=${{ secrets.WK_DEV_AUTH_TOKEN }}
 
       - name: Run screenshot tests
         run: |
@@ -62,7 +62,7 @@ jobs:
           yarn test-screenshot
         env:
           URL: https://${{ env.SUBDOMAIN }}.webknossos.xyz/
-          WK_AUTH_TOKEN: ${{ secrets.WK_AUTH_TOKEN }}
+          WK_AUTH_TOKEN: ${{ secrets.WK_DEV_AUTH_TOKEN }}
           BROWSERSTACK_USERNAME: ${{ secrets.BROWSERSTACK_USERNAME }}
           BROWSERSTACK_ACCESS_KEY: ${{ secrets.BROWSERSTACK_ACCESS_KEY }}
 

.github/workflows/wkorg-nightly.yaml

@@ -28,7 +28,7 @@ jobs:
           yarn test-wkorg-screenshot
         env:
           URL: https://webknossos.org/
-          WK_AUTH_TOKEN: ${{ secrets.WK_AUTH_TOKEN }}
+          WK_AUTH_TOKEN: ${{ secrets.WK_ORG_AUTH_TOKEN }}
           BROWSERSTACK_USERNAME: ${{ secrets.BROWSERSTACK_USERNAME }}
           BROWSERSTACK_ACCESS_KEY : ${{ secrets.BROWSERSTACK_ACCESS_KEY }}
 
@@ -57,4 +57,4 @@ jobs:
             --data-raw '[{"position":[2752,4320,1728],"additionalCoordinates":[],"mag":[1,1,1],"cubeSize":32,"fourBit":false}]' \
             'https://data-humerus.webknossos.org/data/datasets/scalable_minds/l4dense_motta_et_al_demo/layers/segmentation/data?token=' \
             | grep -q "content-encoding: gzip"
-          echo Success.
+          echo Success.

CHANGELOG.released.md

@@ -7,6 +7,77 @@ 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).
 
+## [25.07.1](https://github.com/scalableminds/webknossos/releases/tag/25.07.1) - 2025-07-11
+[Commits](https://github.com/scalableminds/webknossos/compare/25.07.0...25.07.1)
+
+### Highlights
+- When you are viewing an annotation and another user changes that annotation, these changes will be automatically shown. For some changes (e.g., when adding a new annotation layer), you will still need to reload the page, but most of the time WEBKNOSSOS will update the annotation automatically. [#8648](https://github.com/scalableminds/webknossos/pull/8648)
+
+### Added
+- Segment index files can now also be read from the new zarr3-based format, and from remote object storage. [#8711](https://github.com/scalableminds/webknossos/pull/8711)
+- Connectomes can now also be read from the new zarr3-based format, and from remote object storage. [#8717](https://github.com/scalableminds/webknossos/pull/8717)
+
+### Changed
+- Compound annotations (merged views of finished task annotations) now show the task bounding boxes. [#8735](https://github.com/scalableminds/webknossos/pull/8735)
+- Adapted zarr mesh loading to skip segments missing in the meshfile. This was already the case for the hdf5 variant. [#8771](https://github.com/scalableminds/webknossos/pull/8771)
+- Users of organizations with a trial pricing plan can now join other organizations as guests. [#8772](https://github.com/scalableminds/webknossos/pull/8772)
+
+### Fixed
+- Fixed a bug where segment index files for segmentation layers with no mag1 would be read incorrectly. [#8711](https://github.com/scalableminds/webknossos/pull/8711)
+- Fixed a bug where authentication tokens would sometimes expire too soon. [#8738](https://github.com/scalableminds/webknossos/pull/8738)
+- Fixed a bug where duplicating a compound annotation would fail if it has volume annotation layers. [#8743](https://github.com/scalableminds/webknossos/pull/8743)
+- Fixed that compound (merged) views of tasks, projects and task types would sometimes show outdated annotation data, leaving out the data from recently finished tasks annotations. [#8756](https://github.com/scalableminds/webknossos/pull/8756)
+- Fixed a bug where dataset layer attachments with absolute paths would not get loaded unless the paths are specified with file:// scheme. [#8761](https://github.com/scalableminds/webknossos/pull/8761)
+- Fixed that WEBKNOSSOS would crash directly if the communication with the server was interrupted while using the proofreading tool. [#8767](https://github.com/scalableminds/webknossos/pull/8767)
+- Fixed a bug where WEBKNOSSOS would show an error toast for volume annotations that have no fallback segmentation layer. [#8768](https://github.com/scalableminds/webknossos/pull/8768)
+- Fixed broken node selection in 3d viewport when continuous drawing was enabled in skeleton tool. [#8769](https://github.com/scalableminds/webknossos/pull/8769)
+- Fixed layer linking to support non-WKW layers. [#8773](https://github.com/scalableminds/webknossos/pull/8773)
+
+## [25.07.0](https://github.com/scalableminds/webknossos/releases/tag/25.07.0) - 2025-07-01
+[Commits](https://github.com/scalableminds/webknossos/compare/25.06.2...25.07.0)
+
+### Highlights
+- Added the ability to duplicate trees in skeleton annotations. Users can create a copy of any tree (including all nodes, edges, and properties) via the context menu in the skeleton tab. [#8662](https://github.com/scalableminds/webknossos/pull/8662)
+- Added a new Account Settings page for managing user preferences, passwords and authentication methods. [#8672](https://github.com/scalableminds/webknossos/pull/8672)
+- Improved efficiency of saving bounding box related annotation changes. [#8492](https://github.com/scalableminds/webknossos/pull/8492)
+
+### Added
+- In shared annotations with multiple authors, some changes are now stored per user. This means that other users won’t see all those changes if their own diverge. This includes the current position and zoom, visibilities of trees, bounding boxes, and segments (as specified with the checkboxes in the lists), as well as which groups are expanded in the lists. The annotation owner’s user state is used as a fallback for users who haven’t explicitly changed these values themselves. [#8542](https://github.com/scalableminds/webknossos/pull/8542)
+- Meshes are now reloaded using their previous opacity value. [#8622](https://github.com/scalableminds/webknossos/pull/8622)
+- Agglomerate Mappings can now also be read from the new zarr3-based format, and from remote object storage. [#8633](https://github.com/scalableminds/webknossos/pull/8633)
+- Added the ability to duplicate trees in skeleton annotations. Users can create a copy of any tree (including all nodes, edges, and properties) via the context menu in the skeleton tab. [#8662](https://github.com/scalableminds/webknossos/pull/8662)
+- Added a new Account Settings page for managing user preferences, passwords and authentication methods. [#8672](https://github.com/scalableminds/webknossos/pull/8672)
+- Precomputed Meshes can now also be read from the new zarr3-based format, and from remote object storage. [#8682](https://github.com/scalableminds/webknossos/pull/8682)
+- Added Zstandard support for N5 [#8703](https://github.com/scalableminds/webknossos/pull/8703)
+- WKW datasets can now also have custom paths in their datasource-properties.json. [#8725](https://github.com/scalableminds/webknossos/pull/8725)
+
+### Changed
+- The datasource-properties.json as exposed in zarr streaming routes and volume annotation download now includes an explicit “path” attribute for every mag. The supplied path is relative to the location of the datasource-properties.json itself, e.g. `./color/2-2-1`. [#8518](https://github.com/scalableminds/webknossos/pull/8518)
+- When creating an annotation from the dataset view mode, and more than one segmentation layer is visible or multiple segmentation layers are invisible but available, a selection modal now appears allowing users to choose which segmentation layer to use for the newly created volume annotation. Per default, annotations are still based on the visible segmentation layer. [#8677](https://github.com/scalableminds/webknossos/pull/8677)
+- Updated the UI for the organizations settings page. [#8679](https://github.com/scalableminds/webknossos/pull/8679)
+- Changed the process for adding changelog and migration guide items to avoid merge conflicts. Instead of editing the "*.unreleased.md" files, developers should run `python3 tools/create-changelog-entry.py`. This will create a md file within `unreleased_changes` with the number of the current pull request. The file will contain the correct format with dummy values for the changelog and migration guide. The developer should adapt the template and commit it. When bundling a release, these changelog files will be read and written into the released changelog/migration guide. [#8698](https://github.com/scalableminds/webknossos/pull/8698)
+- The HTTP API of tracing store and data store endpoints now also support versioning for better compatibility across webknossos-libs python clients. [#8705](https://github.com/scalableminds/webknossos/pull/8705)
+- Replaced withRouter HOC with useHistory hook for several components. [#8721](https://github.com/scalableminds/webknossos/pull/8721)
+
+### Fixed
+- Improved efficiency of saving bounding box related annotation changes. [#8492](https://github.com/scalableminds/webknossos/pull/8492)
+- When deleting a dataset, its caches are cleared, so that if a new dataset by the same name is uploaded afterwards, only new data is loaded. [#8638](https://github.com/scalableminds/webknossos/pull/8638)
+- Fixed a race condition when starting proofreading with a split action. [#8676](https://github.com/scalableminds/webknossos/pull/8676)
+- Fixed that the healthcheck for a dedicated tracing store would fail sometimes. [#8683](https://github.com/scalableminds/webknossos/pull/8683)
+- Fixed that activating a mapping got stuck when a dataset was opened in "view" mode. [#8687](https://github.com/scalableminds/webknossos/pull/8687)
+- Fixed the contrast of the WelcomeToast buttons. Updated `antd` to version `5.22`. [#8688](https://github.com/scalableminds/webknossos/pull/8688)
+- Fixed a regression that led to incorrect behavior when trying to jump to the last branchpoint even though no branchpoint existed. [#8695](https://github.com/scalableminds/webknossos/pull/8695)
+- Fixed the sandbox mode for annotations. [#8702](https://github.com/scalableminds/webknossos/pull/8702)
+- Fixed the nightly screenshot tests. [#8702](https://github.com/scalableminds/webknossos/pull/8702)
+- Fixed that one could not scroll to the last item in the segments and trees tab. [#8709](https://github.com/scalableminds/webknossos/pull/8709)
+- Fixed that WEBKNOSSOS could crash when mappings were requested for a volume layer that is not based on another segmentation layer. [#8710](https://github.com/scalableminds/webknossos/pull/8710)
+- Fixed a crash when an ad-hoc mesh could not be loaded for some reason. [#8716](https://github.com/scalableminds/webknossos/pull/8716)
+- Fixed a bug where the checks on relative paths were too strict when editing dataset settings. [#8720](https://github.com/scalableminds/webknossos/pull/8720)
+- Fixed a bug when loading mesh files for segmentation layer without fallback data. Such layer cannot have mesh files. [#8726](https://github.com/scalableminds/webknossos/pull/8726)
+- Fixed reading chunks from arrays where the whole shard is missing (should return fill_value) [#8727](https://github.com/scalableminds/webknossos/pull/8727)
+- Fixed fetching mesh files in view only mode. Bug introduced by #8726 [#8728](https://github.com/scalableminds/webknossos/pull/8728)
+- Fixed that on dataset upload the storage usage would get scanned even if it is disabled in config for that particular data store server. [#8733](https://github.com/scalableminds/webknossos/pull/8733)
+
 ## [25.06.2](https://github.com/scalableminds/webknossos/releases/tag/25.06.2) - 2025-06-17
 [Commits](https://github.com/scalableminds/webknossos/compare/25.06.1...25.06.2)
 

MIGRATIONS.released.md

@@ -6,6 +6,21 @@ 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).
 
+## [25.07.1](https://github.com/scalableminds/webknossos/releases/tag/25.07.1) - 2025-07-11
+[Commits](https://github.com/scalableminds/webknossos/compare/25.07.0...25.07.1)
+
+### Postgres Evolutions
+None.
+
+## [25.07.0](https://github.com/scalableminds/webknossos/releases/tag/25.07.0) - 2025-07-01
+[Commits](https://github.com/scalableminds/webknossos/compare/25.06.2...25.07.0)
+
+- The default thread pool size was increased from 5 to 10 times the number of available CPUs (capped at 1000). Note that wk may need slightly more memory because of this.
+
+### Postgres Evolutions
+- [134-dataset-layer-attachments.sql](conf/evolutions/134-dataset-layer-attachments.sql)
+- [135-neuroglancer-attachment.sql](conf/evolutions/135-neuroglancer-attachment.sql)
+
 ## [25.06.2](https://github.com/scalableminds/webknossos/releases/tag/25.06.2) - 2025-06-17
 [Commits](https://github.com/scalableminds/webknossos/compare/25.06.1...25.06.2)
 

app/RequestHandler.scala

@@ -1,4 +1,4 @@
-import com.scalableminds.util.mvc.{CspHeaders, ExtendedController}
+import com.scalableminds.util.mvc.{ApiVersioning, CspHeaders, ExtendedController}
 import com.typesafe.scalalogging.LazyLogging
 import controllers.{Assets, SitemapController, AboutPageRedirectController}
 
@@ -9,7 +9,7 @@ import play.api.mvc.{Handler, InjectedController, RequestHeader}
 import play.api.routing.Router
 import play.core.WebCommands
 import play.filters.csp.CSPConfig
-import utils.{ApiVersioning, WkConf}
+import utils.WkConf
 
 import scala.concurrent.ExecutionContext
 

app/Startup.scala

@@ -8,7 +8,7 @@ import mail.{Mailer, MailerConfig}
 import models.annotation.AnnotationDAO
 import models.dataset.ThumbnailCachingService
 import models.user.InviteService
-import net.liftweb.common.{Failure, Full}
+import com.scalableminds.util.tools.{Failure, Full}
 import org.apache.http.client.utils.URIBuilder
 import play.api.inject.ApplicationLifecycle
 import security.WkSilhouetteEnvironment

app/controllers/AnalyticsController.scala

@@ -6,16 +6,15 @@ import play.api.libs.json.JsObject
 import play.api.mvc.{Action, PlayBodyParsers}
 import play.silhouette.api.Silhouette
 import security.WkEnv
-import utils.{ApiVersioning, WkConf}
+import utils.WkConf
 
 import javax.inject.Inject
 import scala.concurrent.ExecutionContext
 
 class AnalyticsController @Inject()(analyticsService: AnalyticsService, conf: WkConf, sil: Silhouette[WkEnv])(
     implicit ec: ExecutionContext,
     bodyParsers: PlayBodyParsers)
-    extends Controller
-    with ApiVersioning {
+    extends Controller {
 
   def ingestAnalyticsEvents: Action[AnalyticsEventsIngestJson] = Action.async(validateJson[AnalyticsEventsIngestJson]) {
     implicit request =>