Merge branch 'master' into virtual-remote-datasets

Author: frcroth

CHANGELOG.released.md

@@ -7,6 +7,12 @@ 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).
 
+## [25.06.1](https://github.com/scalableminds/webknossos/releases/tag/25.06.1) - 2025-06-03
+[Commits](https://github.com/scalableminds/webknossos/compare/25.06.0...25.06.1)
+
+### Fixed
+- Fixed viewing the results of volume annotation tasks in compound view. [#8668](https://github.com/scalableminds/webknossos/pull/8668)
+
 ## [25.06.0](https://github.com/scalableminds/webknossos/releases/tag/25.06.0) - 2025-05-26
 [Commits](https://github.com/scalableminds/webknossos/compare/25.05.1...25.06.0)
 
@@ -22,7 +28,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Added the possibility for super users to retry manually cancelled jobs from the jobs list. [#8629](https://github.com/scalableminds/webknossos/pull/8629)
 
 ### Changed
-- Remove `data.maybe` dependency and replaced with regular Typescript types. [#8563](https://github.com/scalableminds/webknossos/pull/8563)
+- Removed `data.maybe` dependency and replaced with regular Typescript types. [#8563](https://github.com/scalableminds/webknossos/pull/8563)
 - Updated `View Modes` documentation page with links for mouse and keyboard shortcuts. [#8582](https://github.com/scalableminds/webknossos/pull/8582)
 - Renamed the button to view the compound annotation of all tasks of a tasktype to be more descriptive. [#8565](https://github.com/scalableminds/webknossos/pull/8565)
 - Replaced fixed threshold of 40 meshes by a dynamic limit based on the number of triangles in the mesh for the "Create Animation" job. [#8588](https://github.com/scalableminds/webknossos/pull/8588)

CHANGELOG.unreleased.md

@@ -8,16 +8,19 @@ 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/25.06.0...HEAD)
+[Commits](https://github.com/scalableminds/webknossos/compare/25.06.1...HEAD)
 
 ### Added
+- 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)
+- Meshes are now reloaded using their previous opacity value. [#8622](https://github.com/scalableminds/webknossos/pull/8622)
 
 ### Changed
 
 ### Fixed
 - Improved efficiency of saving bounding box related changes. [#8492](https://github.com/scalableminds/webknossos/pull/8492)
-- Fixed regression which caused the import of trees (also of agglomerate skeletons) to crash if the annotation was not empty. [#8656](https://github.com/scalableminds/webknossos/pull/8656)
 - 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 activating a mapping got stuck when a dataset was opened in "view" mode. [#8687](https://github.com/scalableminds/webknossos/pull/8687)
 
 ### Removed
 

MIGRATIONS.released.md

@@ -6,6 +6,12 @@ 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).
 
+## [25.06.1](https://github.com/scalableminds/webknossos/releases/tag/25.06.1) - 2025-06-03
+[Commits](https://github.com/scalableminds/webknossos/compare/25.06.0...25.06.1)
+
+### Postgres Evolutions:
+None.
+
 ## [25.06.0](https://github.com/scalableminds/webknossos/releases/tag/25.06.0) - 2025-05-26
 [Commits](https://github.com/scalableminds/webknossos/compare/25.05.1...25.06.0)
 

MIGRATIONS.unreleased.md

@@ -6,8 +6,9 @@ This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 
 ## Unreleased
-[Commits](https://github.com/scalableminds/webknossos/compare/25.06.0...HEAD)
+[Commits](https://github.com/scalableminds/webknossos/compare/25.06.1...HEAD)
 
-### Postgres Evolutions:
+- 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. [#8686](https://github.com/scalableminds/webknossos/pull/8686)
 
+### Postgres Evolutions:
 - [134-dataset-layer-attachments.sql](conf/evolutions/134-dataset-layer-attachments.sql)

conf/application.conf

@@ -66,12 +66,12 @@ play {
 pekko.actor.default-dispatcher {
   # We use a compromise for our thread pool configuration
   # Parts of our api are async, so they should not need many threads,
-  # but some parts are also blocking (file io, gcs, s3 access), causing new requests
+  # but some parts are also blocking (some file io, gcs access), causing new requests
   # to wait despite idle cpu, if there are too few threads
   fork-join-executor {
-    parallelism-factor = 5.0 # Thread count = ceil(available processors * factor)
+    parallelism-factor = 10.0 # Thread count = ceil(available processors * factor)
     parallelism-min = 8 # Min number of threads to cap factor-based parallelism number to
-    parallelism-max = 300 # Max number of threads to cap factor-based parallelism number to
+    parallelism-max = 1000 # Max number of threads to cap factor-based parallelism number to
   }
 }
 

frontend/javascripts/admin/rest_api.ts

@@ -1,6 +1,6 @@
 import dayjs from "dayjs";
 import { V3 } from "libs/mjs";
-import type { RequestOptions } from "libs/request";
+import type { RequestOptions, RequestOptionsWithData } from "libs/request";
 import Request from "libs/request";
 import type { Message } from "libs/toast";
 import Toast from "libs/toast";
@@ -90,6 +90,7 @@ import type {
   MappingType,
   NumberLike,
   PartialDatasetConfiguration,
+  SaveQueueEntry,
   StoreAnnotation,
   TraceOrViewCommand,
   UserConfiguration,
@@ -2398,3 +2399,12 @@ export function requestVerificationMail() {
     method: "POST",
   });
 }
+
+export function sendSaveRequestWithToken(
+  urlWithoutToken: string,
+  data: RequestOptionsWithData<Array<SaveQueueEntry>>,
+): Promise<void> {
+  // Ideally, this function should be refactored further so that it generates the
+  // correct urlWithoutToken itself.
+  return doWithToken((token) => Request.sendJSONReceiveJSON(`${urlWithoutToken}${token}`, data));
+}

frontend/javascripts/components/color_picker.tsx

@@ -1,7 +1,7 @@
 import { InputNumber, Popover } from "antd";
 import useThrottledCallback from "beautiful-react-hooks/useThrottledCallback";
 import * as Utils from "libs/utils";
-import { useRef, useState } from "react";
+import { useEffect, useRef, useState } from "react";
 import type { CSSProperties } from "react";
 import { HexColorInput, HexColorPicker, type RgbaColor, RgbaColorPicker } from "react-colorful";
 import type { Vector3, Vector4 } from "viewer/constants";
@@ -36,14 +36,20 @@ const ThrottledColorPicker = ({
 }) => {
   const [value, localSetValue] = useState(color);
   const throttledSetValue = useThrottledCallback(onChange, [onChange], 20);
+
+  // Sync local state when external color prop changes
+  useEffect(() => {
+    localSetValue(color);
+  }, [color]);
+
   const setValue = (newValue: string) => {
     localSetValue(newValue);
     throttledSetValue(newValue);
   };
   return (
     <div style={{ marginRight: 10 }}>
       <HexColorPicker color={value} onChange={setValue} />
-      <HexColorInput color={color} onChange={setValue} style={inputStyle} />
+      <HexColorInput color={value} onChange={setValue} style={inputStyle} />
     </div>
   );
 };
@@ -90,6 +96,12 @@ const ThrottledRGBAColorPicker = ({
 }) => {
   const [value, localSetValue] = useState(color);
   const throttledSetValue = useThrottledCallback(onChangeColor, [onChangeColor, value], 20);
+
+  // Sync local state when external color prop changes
+  useEffect(() => {
+    localSetValue(color);
+  }, [color]);
+
   const setValue = (newValue: RgbaColor) => {
     localSetValue(newValue);
     throttledSetValue(newValue);

frontend/javascripts/libs/utils.ts

@@ -1303,3 +1303,11 @@ export function getPhraseFromCamelCaseString(stringInCamelCase: string): string
     .map((word) => capitalize(word.replace(/(^|\s)td/, "$13D")))
     .join(" ");
 }
+
+export function areSetsEqual<T>(setA: Set<T>, setB: Set<T>) {
+  if (setA.size !== setB.size) return false;
+  for (const val of setA) {
+    if (!setB.has(val)) return false;
+  }
+  return true;
+}

frontend/javascripts/test/api/api_skeleton_latest.spec.ts

@@ -8,10 +8,9 @@ import { vi, describe, it, expect, beforeEach } from "vitest";
 import type { Vector3 } from "viewer/constants";
 import { enforceSkeletonTracing } from "viewer/model/accessors/skeletontracing_accessor";
 
-// All the mocking is done in the helpers file, so it can be reused for both skeleton and volume API
 describe("API Skeleton", () => {
   beforeEach<WebknossosTestContext>(async (context) => {
-    await setupWebknossosForTesting(context, "skeleton");
+    await setupWebknossosForTesting(context, "skeleton", { dontDispatchWkReady: true });
   });
 
   it<WebknossosTestContext>("getActiveNodeId should get the active node id", ({ api }) => {

frontend/javascripts/test/api/api_volume_latest.spec.ts

@@ -7,7 +7,6 @@ import {
 } from "../fixtures/volumetracing_server_objects";
 import { AnnotationTool } from "viewer/model/accessors/tool_accessor";
 
-// All the mocking is done in the helpers file, so it can be reused for both skeleton and volume API
 describe("API Volume", () => {
   beforeEach<WebknossosTestContext>(async (context) => {
     await setupWebknossosForTesting(context, "volume");