Update scalafmt-core to 3.9.1

.git-blame-ignore-revs

@@ -3,3 +3,6 @@
 
 # Scala Steward: Reformat with scalafmt 3.6.0
 df858b0ea7cc4743ec9c78cee1486ad91de1dbd4
+
+# Scala Steward: Reformat with scalafmt 3.9.1
+ff891b2389314643c4c2107e589623266729573b

.scalafmt.conf

@@ -13,5 +13,5 @@ optIn.breakChainOnFirstMethodDot = false
 align.openParenDefnSite          = false
 project.git                      = true
 assumeStandardLibraryStripMargin = true
-version                          = 3.6.1
+version                          = 3.9.1
 runner.dialect                   = scala213

modules/common/src/main/scala/de/proteinevolution/common/models/ConstantsV2.scala

@@ -57,10 +57,10 @@ class ConstantsV2 @Inject() (config: Configuration) {
 
   // Job deletion settings
   /** Sweeps at this time after server start */
-  final val jobDeletionDelay: FiniteDuration = 10 minutes
+  final val jobDeletionDelay: FiniteDuration = 10.minutes
 
   /** Sweeps in this interval */
-  final val jobDeletionInterval: FiniteDuration = 3 hours
+  final val jobDeletionInterval: FiniteDuration = 3.hours
 
   /** all jobs of registered users that are older than the given number are permanently deleted everywhere */
   final val jobDeletionRegistered: Int = 90
@@ -73,10 +73,10 @@ class ConstantsV2 @Inject() (config: Configuration) {
 
   // User Deletion settings
   /** Sweeps at this time after server start */
-  final val userDeletionDelay: FiniteDuration = 70 minutes
+  final val userDeletionDelay: FiniteDuration = 70.minutes
 
   /** Sweeps in this interval */
-  final val userDeletionInterval: FiniteDuration = 3 hours
+  final val userDeletionInterval: FiniteDuration = 3.hours
 
   /** Sending an eMail to the user this many days before the deletion */
   final val userDeletionWarning: Int = 14 // days
@@ -89,7 +89,7 @@ class ConstantsV2 @Inject() (config: Configuration) {
 
   // qstat long polling in order to detect zombie jobs, not used for cluster load calc anymore
   /** Interval of the qstat requests */
-  final val pollingInterval: FiniteDuration = 5 minutes
+  final val pollingInterval: FiniteDuration = 5.minutes
 
   /** The marker for 100% load capacity */
   final val loadPercentageMarker: Int = 32 // Jobs

modules/jobs/src/main/scala/de/proteinevolution/jobs/actors/JobActor.scala

@@ -75,7 +75,7 @@ class JobActor @Inject() (
   @volatile private var currentJobLogs: Map[String, JobEventLog]                = Map.empty[String, JobEventLog]
   @volatile private var currentExecutionContexts: Map[String, ExecutionContext] = Map.empty[String, ExecutionContext]
 
-  private val fetchLatestInterval = 500 millis
+  private val fetchLatestInterval = 500.millis
   private val Tick: Cancellable = {
     // scheduler should use the system dispatcher
     context.system.scheduler.scheduleWithFixedDelay(Duration.Zero, fetchLatestInterval, self, UpdateLog)(

modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/ResultsController.scala

@@ -71,8 +71,9 @@ final class ResultsController @Inject() (
             // access allowed to job
             (for {
               json <- EitherT.liftF(resultFiles.getResults(jobID))
-              r <- EitherT
-                .fromEither[Future](json.hcursor.downField(resultField.getOrElse("alignment")).as[AlignmentResult])
+              r <- EitherT.fromEither[Future](
+                json.hcursor.downField(resultField.getOrElse("alignment")).as[AlignmentResult]
+              )
             } yield r).value.map {
               case Right(r) =>
                 val l = r.alignment.length

modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/SubmissionController.scala

@@ -63,8 +63,10 @@ class SubmissionController @Inject() (
             case None => BadRequest
             case Some(obj) =>
               if (obj.contains("isPublic")) {
-                jobActorAccess
-                  .sendToJobActor(jobID, SetJobPublic(jobID, obj("isPublic").get.asBoolean.getOrElse(false)))
+                jobActorAccess.sendToJobActor(
+                  jobID,
+                  SetJobPublic(jobID, obj("isPublic").get.asBoolean.getOrElse(false))
+                )
               }
               Ok
           }

modules/statistics/src/main/scala/de/proteinevolution/statistics/UserStatistic.scala

@@ -0,0 +1 @@
+

modules/tools/src/main/scala/de/proteinevolution/tools/parameters/ParamAccess.scala

@@ -93,14 +93,12 @@ class ParamAccess @Inject() (tel: TEL) {
     case "COSINE_PERCENTILE_CUTOFF" => select("cosine_percentile_cutoff", default = Some("70"))
     case "ALIGNMENT_CUTOFF"         => select("alignment_cutoff", default = Some("0.30"))
     case "WIN_LEN"                  => select("win_len", default = Some("15"))
-    case "MERGE_HITS" => select("merge_hits", default = Some("1"))
-    case "PLM_ALN_MODE" => select("plm_aln_mode", default = Some("loc"))
-    case "SPAN" => select("span", default = Some("25"))
-    case "SIGMA_FACTOR" => select("sigma_factor", default = Some("2"))
-    case "BFACTOR" => select("bfactor", default = Some("2"))
-    case "PLM_GAP_EXT" => select("plm_gap_ext", default = Some("0.5"))
-
-
+    case "MERGE_HITS"               => select("merge_hits", default = Some("1"))
+    case "PLM_ALN_MODE"             => select("plm_aln_mode", default = Some("loc"))
+    case "SPAN"                     => select("span", default = Some("25"))
+    case "SIGMA_FACTOR"             => select("sigma_factor", default = Some("2"))
+    case "BFACTOR"                  => select("bfactor", default = Some("2"))
+    case "PLM_GAP_EXT"              => select("plm_gap_ext", default = Some("0.5"))
 
     // HHpred
     case "TWOTEXTALIGNMENT" =>