Minor upgrades for backend dependencies, scala, sbt, run codespell (#7922)

fm3 · MichaelBuessemeyer · web-flow · commit 9f2eb107862a · 2024-07-17T10:53:14.000+02:00
* Minor upgrades for backend dependencies, run codespell

* changelog

* bump scala and sbt

---------

Co-authored-by: MichaelBuessemeyer &lt;39529669+MichaelBuessemeyer@users.noreply.github.com&gt;
diff --git a/.codespellrc b/.codespellrc
@@ -1,6 +1,6 @@
 [codespell]
 # Ref: https://github.com/codespell-project/codespell#using-a-config-file
-skip = *.svg,*.sublime-workspace,*.lock,.codespellrc,./util/target/,./binaryData,./node_modules,./pg,./project/target,./target,./webknossos-datastore/target,./webknossos-jni/target,./webknossos-tracingstore/target,./util/target,./coverage,./public-test,./tools/proxy/node_modules,./docs/publications.md
+skip = *.svg,*.sublime-workspace,*.lock,.codespellrc,./util/target/,./binaryData,./node_modules,./pg,./project/target,./target,./webknossos-datastore/target,./webknossos-jni/target,./webknossos-tracingstore/target,./util/target,./coverage,./public-test,./tools/proxy/node_modules,./docs/publications.md,./public/bundle
 # some names and camelCased variables etc
 ignore-regex = \b([a-z]+[A-Z][a-zA-Z]*|H Mattern|Manuel|Nat Commun)\b
 ignore-words-list = lod,nd,ue
diff --git a/CHANGELOG.released.md b/CHANGELOG.released.md
@@ -15,7 +15,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Added the ability to change the unit of the dataset voxel size to any supported unit of the [ome/ngff standard](https://github.com/ome/ngff/blob/39605eec64ceff481bb3a98f0adeaa330ab1ef26/latest/index.bs#L192). This allows users to upload and work with low-resolution datasets with a different base unit than nanometer. [#7783](https://github.com/scalableminds/webknossos/pull/7783)
 
 ### Added
-- Added that proofreading merge actions reuse custom names of segments. A merge action now combines the potenial existing custom names of both segments and a split-action copies the custom name to the split-off segment. [#7877](https://github.com/scalableminds/webknossos/pull/7877)
+- Added that proofreading merge actions reuse custom names of segments. A merge action now combines the potential existing custom names of both segments and a split-action copies the custom name to the split-off segment. [#7877](https://github.com/scalableminds/webknossos/pull/7877)
 - Added the option to set a default mapping for a dataset in the dataset view configuration. The default mapping is loaded when the dataset is opened and the user / url does not configure something else. [#7858](https://github.com/scalableminds/webknossos/pull/7858)
 - Uploading an annotation into a dataset that it was not created for now also works if the dataset is in a different organization. [#7816](https://github.com/scalableminds/webknossos/pull/7816)
 - When downloading + reuploading an annotation that is based on a segmentation layer with active mapping, that mapping is now still selected after the reupload. [#7822](https://github.com/scalableminds/webknossos/pull/7822)
@@ -36,7 +36,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed a bug that prevented saving new dataset settings. [#7903](https://github.com/scalableminds/webknossos/pull/7903)
 - Fixed that on large screens the login forms were not horizontally centered. [#7909](https://github.com/scalableminds/webknossos/pull/7909)
 - Fixed a bug where brushing on a fallback segmentation with active mapping and with segment index file would lead to failed saves. [#7833](https://github.com/scalableminds/webknossos/pull/7833)
-- Fixed a bug where the "Hide Meshes" / "Show Meshes" options of the context menu for segment groups were not available although at leas one mesh was set to visible / invisible. [#7890](https://github.com/scalableminds/webknossos/pull/7890)
+- Fixed a bug where the "Hide Meshes" / "Show Meshes" options of the context menu for segment groups were not available although at least one mesh was set to visible / invisible. [#7890](https://github.com/scalableminds/webknossos/pull/7890)
 - Fixed a bug where sometimes old mismatching javascript code would be served after upgrades. [#7854](https://github.com/scalableminds/webknossos/pull/7854)
 - Fixed a bug where dataset uploads of zipped tiff data via the UI would be rejected. [#7856](https://github.com/scalableminds/webknossos/pull/7856)
 - Fixed a bug with incorrect validation of layer names in the animation modal. [#7882](https://github.com/scalableminds/webknossos/pull/7882)
diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -14,6 +14,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Added the option to move a bounding box via dragging while pressing ctrl / meta. [#7892](https://github.com/scalableminds/webknossos/pull/7892)
 - Added route `/import?url=<url_to_datasource>` to automatically import and view remote datasets. [#7844](https://github.com/scalableminds/webknossos/pull/7844)
 - The context menu that is opened upon right-clicking a segment in the dataview port now contains the segment's name. [#7920](https://github.com/scalableminds/webknossos/pull/7920) 
+- Upgraded backend dependencies for improved performance and stability. [#7922](https://github.com/scalableminds/webknossos/pull/7922)
 
 ### Changed
 - The warning about a mismatch between the scale of a pre-computed mesh and the dataset scale's factor now also considers all supported mags of the active segmentation layer. This reduces the false posive rate regarding this warning. [#7921](https://github.com/scalableminds/webknossos/pull/7921/)
diff --git a/build.sbt b/build.sbt
@@ -1,8 +1,8 @@
 import sbt._
 
 ThisBuild / version := "wk"
-ThisBuild / scalaVersion := "2.13.11"
-ThisBuild / scapegoatVersion := "2.1.2"
+ThisBuild / scalaVersion := "2.13.14"
+ThisBuild / scapegoatVersion := "2.1.6"
 val failOnWarning = if (sys.props.contains("failOnWarning")) Seq("-Xfatal-warnings") else Seq()
 ThisBuild / scalacOptions ++= Seq(
   "-release:11",
diff --git a/frontend/javascripts/navbar.tsx b/frontend/javascripts/navbar.tsx
@@ -483,7 +483,7 @@ function NotificationIcon({
     sendAnalyticsEvent("open_whats_new_view");
 
     if (window.Olvy) {
-      // Setting the target lazily, to finally let olvy  load the whats new modal as it should be shown now.
+      // Setting the target lazily, to finally let olvy load the “what’s new” modal, as it should be shown now.
       window.Olvy.config.target = "#unused-olvy-target";
       window.Olvy.show();
     }
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
@@ -2,14 +2,14 @@ import play.sbt.PlayImport.{filters, _}
 import sbt._
 
 object Dependencies {
-  private val silhouetteVersion = "10.0.0"
+  private val silhouetteVersion = "10.0.1"
   private val brotliVersion = "1.16.0"
   private val scalapbVersion = scalapb.compiler.Version.scalapbVersion
   private val grpcVersion = scalapb.compiler.Version.grpcJavaVersion
 
   val utilDependencies: Seq[ModuleID] = Seq(
     // Play Web Framework. import play
-    "org.playframework" %% "play" % "3.0.3",
+    "org.playframework" %% "play" % "3.0.4",
     // Play’s JSON serialization. import play.api.libs.json
     "com.typesafe.play" %% "play-json" % "2.10.5",
     // Sending emails. import org.apache.commons.mail
@@ -96,7 +96,7 @@ object Dependencies {
     // Makes txw2 write self-closing tags in xml (which we want). Not imported.
     "org.codehaus.woodstox" % "wstx-asl" % "4.0.6",
     // Json Web Tokens (used for OIDC Auth). import pdi.jwt
-    "com.github.jwt-scala" %% "jwt-play-json" % "10.0.0",
+    "com.github.jwt-scala" %% "jwt-play-json" % "10.0.1",
     // SQL Queries. import slick
     "com.typesafe.slick" %% "slick" % "3.5.0",
     // SQL Queries connection pool. not imported.
diff --git a/project/build.properties b/project/build.properties
@@ -1 +1 @@
-sbt.version=1.9.6
+sbt.version=1.10.1
diff --git a/util/src/main/scala/com/scalableminds/util/cache/LRUConcurrentCache.scala b/util/src/main/scala/com/scalableminds/util/cache/LRUConcurrentCache.scala
@@ -7,7 +7,7 @@ trait LRUConcurrentCache[K, V] {
 
   private val cache = new java.util.LinkedHashMap[K, V]() {
     override def removeEldestEntry(eldest: java.util.Map.Entry[K, V]): Boolean =
-      if (size > maxEntries) {
+      if (this.size > maxEntries) {
         onElementRemoval(eldest.getKey, eldest.getValue)
         true
       } else {
diff --git a/util/src/main/scala/com/scalableminds/util/tools/Fox.scala b/util/src/main/scala/com/scalableminds/util/tools/Fox.scala
@@ -351,20 +351,18 @@ class Fox[+A](val futureBox: Future[Box[A]])(implicit ec: ExecutionContext) {
     }).flatMap(identity)
 
   /**
-    *
-    *  Awaits the future and opens the box. Do not use this in production code (therefore marked as Deprecated)!
+    *  Awaits the future and opens the box.
     */
-  @Deprecated
+  @deprecated(message = "Do not use this in production code", since = "forever")
   def get(justification: String, awaitTimeout: FiniteDuration = 10 seconds): A = {
     val box = await(justification, awaitTimeout)
     box.openOrThrowException(justification)
   }
 
   /**
-    *
-    * Awaits the future and returns the box. Should not be used in production code (therefore marked as Deprecated).
+    * Awaits the future and returns the box.
     */
-  @Deprecated
+  @deprecated(message = "Do not use this in production code", since = "forever")
   def await(justification: String, awaitTimeout: FiniteDuration = 10 seconds): Box[A] =
     Await.result(futureBox, awaitTimeout)
 
diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/models/datasource/DataSource.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/models/datasource/DataSource.scala
@@ -5,8 +5,6 @@ import com.scalableminds.webknossos.datastore.models.datasource.DatasetViewConfi
 import com.scalableminds.webknossos.datastore.models.datasource.inbox.GenericInboxDataSource
 import play.api.libs.json._
 
-import scala.annotation.nowarn
-
 package object datasource {
 
   // here team is not (yet) renamed to organization to avoid migrating all jsons
@@ -54,7 +52,6 @@ package object datasource {
   }
 
   object GenericDataSource {
-    @nowarn // Suppress unused warning. The passed Format[T] is expanded to more than what is really used. It can not be omitted, though.
     implicit def dataSourceFormat[T <: DataLayerLike](implicit fmt: Format[T]): Format[GenericDataSource[T]] =
       Json.format[GenericDataSource[T]]
 

Original file line number	Diff line number	Diff line change
`@@ -483,7 +483,7 @@ function NotificationIcon({`
`483`	`483`	`sendAnalyticsEvent("open_whats_new_view");`
`484`	`484`
`485`	`485`	`if (window.Olvy) {`
`486`		`- // Setting the target lazily, to finally let olvy load the whats new modal as it should be shown now.`
	`486`	`+ // Setting the target lazily, to finally let olvy load the “what’s new” modal, as it should be shown now.`
`487`	`487`	`window.Olvy.config.target = "#unused-olvy-target";`
`488`	`488`	`window.Olvy.show();`
`489`	`489`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-sbt.version=1.9.6`
	`1`	`+sbt.version=1.10.1`