upgrade backend dependencies; run codespell

.codespellrc

@@ -3,4 +3,4 @@
 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,./tools/migration-unified-annotation-versioning/venv,./tools/migration-unified-annotation-versioning/*.json
 # 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,DoubleClick
+ignore-words-list = lod,nd,ue,DoubleClick,InOut

build.sbt

@@ -2,7 +2,7 @@ import sbt._
 
 ThisBuild / version := "wk"
 ThisBuild / scalaVersion := "2.13.16"
-ThisBuild / scapegoatVersion := "3.1.8"
+ThisBuild / scapegoatVersion := "3.1.9"
 val failOnWarning = if (sys.props.contains("failOnWarning")) Seq("-Xfatal-warnings") else Seq()
 ThisBuild / scalacOptions ++= Seq(
   "-release:11",

frontend/javascripts/test/sagas/volumetracing/volumetracing_saga_integration_1.spec.ts

@@ -1,5 +1,5 @@
 /*
- * Also have a look at the sibiling module volumetracing_saga_integration_2.spec.ts.
+ * Also have a look at the sibling module volumetracing_saga_integration_2.spec.ts.
  * The tests are split into two modules to allow for isolated parallelization and thus
  * increased performance.
  */

frontend/javascripts/viewer/controller/mesh_helpers.ts

@@ -22,7 +22,7 @@ export class VertexSegmentMapping {
    * E.g., one query allows to go from a vertex index ("position", named
    * like the BufferAttribute "position") to
    * the unmapped segment id of the geometry that belongs to the vertex.
-   * Similarily, one can obtain the range that covers all vertices
+   * Similarly, one can obtain the range that covers all vertices
    * that belong to a certain unmapped segment id.
    * Other queries allow a similar mapping between vertex index ("position")
    * and unmapped segment id.

project/Dependencies.scala

@@ -2,20 +2,21 @@ import play.sbt.PlayImport.{filters, _}
 import sbt._
 
 object Dependencies {
-  private val silhouetteVersion = "10.0.1"
-  private val brotliVersion = "1.17.0"
+  private val silhouetteVersion = "10.0.3"
+  private val brotliVersion = "1.18.0"
+  private val slickVersion = "3.5.2"
   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" % "3.0.7",
     // Play’s JSON serialization. import play.api.libs.json
-    "com.typesafe.play" %% "play-json" % "2.10.5",
+    "org.playframework" %% "play-json" % "3.0.4",
     // Sending emails. import org.apache.commons.mail
-    "org.apache.commons" % "commons-email" % "1.5",
+    "org.apache.commons" % "commons-email" % "1.6.0",
     // File utils. import org.apache.commons.io
-    "commons-io" % "commons-io" % "2.17.0",
+    "commons-io" % "commons-io" % "2.19.0",
     // HashCodeBuilder. import org.apache.commons.lang3
     "org.apache.commons" % "commons-lang3" % "3.17.0",
     // Box/Tryo. import net.liftweb
@@ -42,7 +43,7 @@ object Dependencies {
     // Protocol buffer GRPC health check for FossilDB. import io.grpc
     "io.grpc" % "grpc-services" % grpcVersion,
     // Streaming JSON parsing. import com.google.gson
-    "com.google.code.gson" % "gson" % "2.10.1",
+    "com.google.code.gson" % "gson" % "2.13.1",
     // Play WS Http client, used for RPC calls. import play.api.libs.ws
     ws,
     // Dependency Injection. import javax.inject.Inject
@@ -56,15 +57,15 @@ object Dependencies {
     // MultiArray (ndarray) handles. import ucar
     "edu.ucar" % "cdm-core" % "5.4.2",
     // Amazon S3 cloud storage client. import software.amazon.awssdk
-    "software.amazon.awssdk" % "s3" % "2.26.21",
+    "software.amazon.awssdk" % "s3" % "2.31.50",
     // Google cloud storage client. import com.google.cloud.storage, import com.google.auth.oauth2
-    "com.google.cloud" % "google-cloud-storage" % "2.43.1",
+    "com.google.cloud" % "google-cloud-storage" % "2.52.3",
     // Blosc compression. import org.blosc
     "org.lasersonlab" % "jblosc" % "1.0.1",
     // Zstd compression. import org.apache.commons.compress
     "org.apache.commons" % "commons-compress" % "1.27.1",
     // Zstd compression native bindings. not imported
-    "com.github.luben" % "zstd-jni" % "1.5.5-5",
+    "com.github.luben" % "zstd-jni" % "1.5.7-3",
     // Brotli compression. import com.aayushatharva.brotli4j
     "com.aayushatharva.brotli4j" % "brotli4j" % brotliVersion,
     // Brotli compression native bindings. not imported
@@ -82,7 +83,7 @@ object Dependencies {
 
   val webknossosDependencies: Seq[ModuleID] = Seq(
     // Base64, Hashing. import org.apache.commons.codec
-    "commons-codec" % "commons-codec" % "1.17.0",
+    "commons-codec" % "commons-codec" % "1.18.0",
     // End-to-end tests, backend unit tests. import org.scalatestplus.play
     "org.scalatestplus.play" %% "scalatestplus-play" % "7.0.1" % "test",
     // Authenticated requests. import play.silhouette
@@ -94,17 +95,17 @@ object Dependencies {
     // Writing XML. import com.sun.xml.txw2
     "org.glassfish.jaxb" % "txw2" % "4.0.5",
     // Makes txw2 write self-closing tags in xml (which we want). Not imported.
-    "org.codehaus.woodstox" % "wstx-asl" % "4.0.6",
+    "com.fasterxml.woodstox" % "woodstox-core" % "7.1.0",
     // Json Web Tokens (used for OIDC Auth). import pdi.jwt
-    "com.github.jwt-scala" %% "jwt-play-json" % "10.0.1",
+    "com.github.jwt-scala" %% "jwt-play-json" % "10.0.4",
     // SQL Queries. import slick
-    "com.typesafe.slick" %% "slick" % "3.5.2",
+    "com.typesafe.slick" %% "slick" % slickVersion,
     // SQL Queries connection pool. not imported.
-    "com.typesafe.slick" %% "slick-hikaricp" % "3.5.2",
+    "com.typesafe.slick" %% "slick-hikaricp" % slickVersion,
     // SQL Queries class generation. Started with runner as slick.codegen.SourceCodeGenerator
-    "com.typesafe.slick" %% "slick-codegen" % "3.5.2",
+    "com.typesafe.slick" %% "slick-codegen" % slickVersion,
     // SQL Queries postgres specifics. not imported.
-    "org.postgresql" % "postgresql" % "42.7.4"
+    "org.postgresql" % "postgresql" % "42.7.5"
   )
 
   val dependencyOverrides: Seq[ModuleID] = Seq(

project/build.properties

@@ -1 +1 @@
-sbt.version=1.10.11
+sbt.version=1.11.0

project/plugins.sbt

@@ -2,7 +2,7 @@
 addSbtPlugin("org.playframework" % "sbt-plugin" % "3.0.7")
 
 // buildinfo routes
-addSbtPlugin("com.eed3si9n" % "sbt-buildinfo" % "0.13.0")
+addSbtPlugin("com.eed3si9n" % "sbt-buildinfo" % "0.13.1")
 
 // protocol buffers
 addSbtPlugin("com.thesamet" % "sbt-protoc" % "1.0.7")
@@ -11,7 +11,7 @@ addSbtPlugin("com.thesamet" % "sbt-protoc" % "1.0.7")
 addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.5.4")
 
 // scala linter
-addSbtPlugin("com.sksamuel.scapegoat" %% "sbt-scapegoat" % "1.2.12")
+addSbtPlugin("com.sksamuel.scapegoat" %% "sbt-scapegoat" % "1.2.13")
 
 // check dependencies against published vulnerabilities with sbt dependencyCheck
 addSbtPlugin("net.vonbuchholtz" % "sbt-dependency-check" % "5.1.0")

util/src/main/scala/com/scalableminds/util/tools/TristateOptionJsonHelper.scala

@@ -5,7 +5,7 @@ import play.api.libs.json.JsonConfiguration.Aux
 import play.api.libs.json._
 
 // Allows a case class json format that distinguishes between absent keys and keys with the value null
-// See TristateJsonTestSuite for a usage example. The Some(None) defualt must by set for the case class
+// See TristateJsonTestSuite for a usage example. The Some(None) default must by set for the case class
 trait TristateOptionJsonHelper {
 
   implicit protected def optionFormat[T: Format]: Format[Option[T]] = new Format[Option[T]] {