merge with dev (update to Kotlin 1.9.0)

# Conflicts:
#	numass-data-proto/src/gen/kotlin/ru/inr/mass/data/proto/Point.kt
#	numass-workspace/src/main/kotlin/ru/inr/mass/scripts/fit.kt

build.gradle.kts

@@ -13,12 +13,12 @@ allprojects {
     }
 
     group = "ru.inr.mass"
-    version = "0.1.4-dev-1"
+    version = "0.1.4-dev-2"
 }
 
-val dataforgeVersion by extra("0.6.0-dev-15")
+val dataforgeVersion by extra("0.6.2")
 val tablesVersion: String by extra("0.2.0-dev-3")
-val kmathVersion by extra("0.3.1-dev-9")
+val kmathVersion by extra("0.3.1")
 val visionForgeVersion: String by rootProject.extra("0.3.0-dev-6")
 
 

gradle.properties

@@ -5,12 +5,11 @@
 
 kotlin.code.style=official
 kotlin.mpp.stability.nowarn=true
-
-kotlin.jupyter.add.scanner=false
+kotlin.js.compiler=ir
 
 org.gradle.configureondemand=true
 org.gradle.parallel=true
 org.gradle.jvmargs=-XX:MaxMetaspaceSize=1G
 
-toolsVersion=0.13.3-kotlin-1.7.20
-compose.version=1.2.2
+toolsVersion=0.14.10-kotlin-1.9.0
+compose.version=1.5.1

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.6-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.3-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

numass-analysis/build.gradle.kts

@@ -8,7 +8,9 @@ val dataforgeVersion: String by rootProject.extra
 val kmathVersion: String by rootProject.extra
 val tablesVersion: String by rootProject.extra
 
-kotlin.sourceSets {
+kscience {
+    jvm()
+    js()
     commonMain {
         dependencies {
             api(projects.numass.numassDataModel)

numass-data-model/build.gradle.kts

@@ -6,7 +6,11 @@ plugins {
 
 val dataforgeVersion: String by rootProject.extra
 
-kotlin.sourceSets {
+kscience{
+    jvm()
+    js()
+    useSerialization()
+
     commonMain {
         dependencies {
             api("space.kscience:dataforge-context:$dataforgeVersion")
@@ -14,15 +18,14 @@ kotlin.sourceSets {
             api("org.jetbrains.kotlinx:kotlinx-datetime:${space.kscience.gradle.KScienceVersions.dateTimeVersion}")
         }
     }
-    jvmMain{
+}
+
+kotlin.sourceSets{
+    getByName("jvmMain"){
         dependencies{
             api("ch.qos.logback:logback-classic:1.2.3")
         }
     }
 }
 
-kscience{
-    useSerialization()
-}
-
 

numass-data-proto/build.gradle.kts

@@ -1,6 +1,6 @@
 plugins {
     id("space.kscience.gradle.jvm")
-    id("com.squareup.wire") version "4.4.1"
+    id("com.squareup.wire") version "4.9.1"
     `maven-publish`
 }
 

numass-data-proto/src/gen/kotlin/ru/inr/mass/data/proto/Point.kt

@@ -8,9 +8,9 @@ import com.squareup.wire.ProtoAdapter
 import com.squareup.wire.ProtoReader
 import com.squareup.wire.ProtoWriter
 import com.squareup.wire.ReverseProtoWriter
-import com.squareup.wire.Syntax
 import com.squareup.wire.Syntax.PROTO_3
 import com.squareup.wire.WireField
+import com.squareup.wire.`internal`.JvmField
 import com.squareup.wire.`internal`.immutableCopyOf
 import com.squareup.wire.`internal`.redactElements
 import kotlin.Any
@@ -22,9 +22,7 @@ import kotlin.Int
 import kotlin.Long
 import kotlin.Nothing
 import kotlin.String
-import kotlin.Unit
 import kotlin.collections.List
-import kotlin.jvm.JvmField
 import okio.ByteString
 
 public class Point(
@@ -38,6 +36,7 @@ public class Point(
     tag = 1,
     adapter = "ru.inr.mass.data.proto.Point${'$'}Channel#ADAPTER",
     label = WireField.Label.REPEATED,
+    schemaIndex = 0,
   )
   public val channels: List<Channel> = immutableCopyOf("channels", channels)
 
@@ -45,10 +44,10 @@ public class Point(
     message = "Shouldn't be used in Kotlin",
     level = DeprecationLevel.HIDDEN,
   )
-  public override fun newBuilder(): Nothing = throw
+  override fun newBuilder(): Nothing = throw
       AssertionError("Builders are deprecated and only available in a javaInterop build; see https://square.github.io/wire/wire_compiler/#kotlin")
 
-  public override fun equals(other: Any?): Boolean {
+  override fun equals(other: Any?): Boolean {
     if (other === this) return true
     if (other !is Point) return false
     if (unknownFields != other.unknownFields) return false
@@ -56,7 +55,7 @@ public class Point(
     return true
   }
 
-  public override fun hashCode(): Int {
+  override fun hashCode(): Int {
     var result = super.hashCode
     if (result == 0) {
       result = unknownFields.hashCode()
@@ -66,7 +65,7 @@ public class Point(
     return result
   }
 
-  public override fun toString(): String {
+  override fun toString(): String {
     val result = mutableListOf<String>()
     if (channels.isNotEmpty()) result += """channels=$channels"""
     return result.joinToString(prefix = "Point{", separator = ", ", postfix = "}")
@@ -85,23 +84,23 @@ public class Point(
       null, 
       "numass-proto.proto"
     ) {
-      public override fun encodedSize(`value`: Point): Int {
+      override fun encodedSize(`value`: Point): Int {
         var size = value.unknownFields.size
         size += Channel.ADAPTER.asRepeated().encodedSizeWithTag(1, value.channels)
         return size
       }
 
-      public override fun encode(writer: ProtoWriter, `value`: Point): Unit {
+      override fun encode(writer: ProtoWriter, `value`: Point) {
         Channel.ADAPTER.asRepeated().encodeWithTag(writer, 1, value.channels)
         writer.writeBytes(value.unknownFields)
       }
 
-      public override fun encode(writer: ReverseProtoWriter, `value`: Point): Unit {
+      override fun encode(writer: ReverseProtoWriter, `value`: Point) {
         writer.writeBytes(value.unknownFields)
         Channel.ADAPTER.asRepeated().encodeWithTag(writer, 1, value.channels)
       }
 
-      public override fun decode(reader: ProtoReader): Point {
+      override fun decode(reader: ProtoReader): Point {
         val channels = mutableListOf<Channel>()
         val unknownFields = reader.forEachTag { tag ->
           when (tag) {
@@ -115,7 +114,7 @@ public class Point(
         )
       }
 
-      public override fun redact(`value`: Point): Point = value.copy(
+      override fun redact(`value`: Point): Point = value.copy(
         channels = value.channels.redactElements(Channel.ADAPTER),
         unknownFields = ByteString.EMPTY
       )
@@ -135,6 +134,7 @@ public class Point(
       tag = 1,
       adapter = "com.squareup.wire.ProtoAdapter#UINT64",
       label = WireField.Label.OMIT_IDENTITY,
+      schemaIndex = 0,
     )
     public val id: Long = 0L,
     blocks: List<Block> = emptyList(),
@@ -147,6 +147,7 @@ public class Point(
       tag = 2,
       adapter = "ru.inr.mass.data.proto.Point${'$'}Channel${'$'}Block#ADAPTER",
       label = WireField.Label.REPEATED,
+      schemaIndex = 1,
     )
     public val blocks: List<Block> = immutableCopyOf("blocks", blocks)
 
@@ -154,10 +155,10 @@ public class Point(
       message = "Shouldn't be used in Kotlin",
       level = DeprecationLevel.HIDDEN,
     )
-    public override fun newBuilder(): Nothing = throw
+    override fun newBuilder(): Nothing = throw
         AssertionError("Builders are deprecated and only available in a javaInterop build; see https://square.github.io/wire/wire_compiler/#kotlin")
 
-    public override fun equals(other: Any?): Boolean {
+    override fun equals(other: Any?): Boolean {
       if (other === this) return true
       if (other !is Channel) return false
       if (unknownFields != other.unknownFields) return false
@@ -166,7 +167,7 @@ public class Point(
       return true
     }
 
-    public override fun hashCode(): Int {
+    override fun hashCode(): Int {
       var result = super.hashCode
       if (result == 0) {
         result = unknownFields.hashCode()
@@ -177,7 +178,7 @@ public class Point(
       return result
     }
 
-    public override fun toString(): String {
+    override fun toString(): String {
       val result = mutableListOf<String>()
       result += """id=$id"""
       if (blocks.isNotEmpty()) result += """blocks=$blocks"""
@@ -200,26 +201,26 @@ public class Point(
         null, 
         "numass-proto.proto"
       ) {
-        public override fun encodedSize(`value`: Channel): Int {
+        override fun encodedSize(`value`: Channel): Int {
           var size = value.unknownFields.size
           if (value.id != 0L) size += ProtoAdapter.UINT64.encodedSizeWithTag(1, value.id)
           size += Block.ADAPTER.asRepeated().encodedSizeWithTag(2, value.blocks)
           return size
         }
 
-        public override fun encode(writer: ProtoWriter, `value`: Channel): Unit {
+        override fun encode(writer: ProtoWriter, `value`: Channel) {
           if (value.id != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.id)
           Block.ADAPTER.asRepeated().encodeWithTag(writer, 2, value.blocks)
           writer.writeBytes(value.unknownFields)
         }
 
-        public override fun encode(writer: ReverseProtoWriter, `value`: Channel): Unit {
+        override fun encode(writer: ReverseProtoWriter, `value`: Channel) {
           writer.writeBytes(value.unknownFields)
           Block.ADAPTER.asRepeated().encodeWithTag(writer, 2, value.blocks)
           if (value.id != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.id)
         }
 
-        public override fun decode(reader: ProtoReader): Channel {
+        override fun decode(reader: ProtoReader): Channel {
           var id: Long = 0L
           val blocks = mutableListOf<Block>()
           val unknownFields = reader.forEachTag { tag ->
@@ -236,7 +237,7 @@ public class Point(
           )
         }
 
-        public override fun redact(`value`: Channel): Channel = value.copy(
+        override fun redact(`value`: Channel): Channel = value.copy(
           blocks = value.blocks.redactElements(Block.ADAPTER),
           unknownFields = ByteString.EMPTY
         )
@@ -256,6 +257,7 @@ public class Point(
         tag = 1,
         adapter = "com.squareup.wire.ProtoAdapter#UINT64",
         label = WireField.Label.OMIT_IDENTITY,
+        schemaIndex = 0,
       )
       public val time: Long = 0L,
       frames: List<Frame> = emptyList(),
@@ -266,6 +268,7 @@ public class Point(
         tag = 3,
         adapter = "ru.inr.mass.data.proto.Point${'$'}Channel${'$'}Block${'$'}Events#ADAPTER",
         label = WireField.Label.OMIT_IDENTITY,
+        schemaIndex = 2,
       )
       public val events: Events? = null,
       /**
@@ -275,6 +278,7 @@ public class Point(
         tag = 4,
         adapter = "com.squareup.wire.ProtoAdapter#UINT64",
         label = WireField.Label.OMIT_IDENTITY,
+        schemaIndex = 3,
       )
       public val length: Long = 0L,
       /**
@@ -285,6 +289,7 @@ public class Point(
         adapter = "com.squareup.wire.ProtoAdapter#UINT64",
         label = WireField.Label.OMIT_IDENTITY,
         jsonName = "binSize",
+        schemaIndex = 4,
       )
       public val bin_size: Long = 0L,
       unknownFields: ByteString = ByteString.EMPTY,
@@ -296,6 +301,7 @@ public class Point(
         tag = 2,
         adapter = "ru.inr.mass.data.proto.Point${'$'}Channel${'$'}Block${'$'}Frame#ADAPTER",
         label = WireField.Label.REPEATED,
+        schemaIndex = 1,
       )
       public val frames: List<Frame> = immutableCopyOf("frames", frames)
 
@@ -303,10 +309,10 @@ public class Point(
         message = "Shouldn't be used in Kotlin",
         level = DeprecationLevel.HIDDEN,
       )
-      public override fun newBuilder(): Nothing = throw
+      override fun newBuilder(): Nothing = throw
           AssertionError("Builders are deprecated and only available in a javaInterop build; see https://square.github.io/wire/wire_compiler/#kotlin")
 
-      public override fun equals(other: Any?): Boolean {
+      override fun equals(other: Any?): Boolean {
         if (other === this) return true
         if (other !is Block) return false
         if (unknownFields != other.unknownFields) return false
@@ -318,7 +324,7 @@ public class Point(
         return true
       }
 
-      public override fun hashCode(): Int {
+      override fun hashCode(): Int {
         var result = super.hashCode
         if (result == 0) {
           result = unknownFields.hashCode()
@@ -332,7 +338,7 @@ public class Point(
         return result
       }
 
-      public override fun toString(): String {
+      override fun toString(): String {
         val result = mutableListOf<String>()
         result += """time=$time"""
         if (frames.isNotEmpty()) result += """frames=$frames"""
@@ -361,7 +367,7 @@ public class Point(
           null, 
           "numass-proto.proto"
         ) {
-          public override fun encodedSize(`value`: Block): Int {
+          override fun encodedSize(`value`: Block): Int {
             var size = value.unknownFields.size
             if (value.time != 0L) size += ProtoAdapter.UINT64.encodedSizeWithTag(1, value.time)
             size += Frame.ADAPTER.asRepeated().encodedSizeWithTag(2, value.frames)
@@ -372,7 +378,7 @@ public class Point(
             return size
           }
 
-          public override fun encode(writer: ProtoWriter, `value`: Block): Unit {
+          override fun encode(writer: ProtoWriter, `value`: Block) {
             if (value.time != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.time)
             Frame.ADAPTER.asRepeated().encodeWithTag(writer, 2, value.frames)
             if (value.events != null) Events.ADAPTER.encodeWithTag(writer, 3, value.events)
@@ -381,7 +387,7 @@ public class Point(
             writer.writeBytes(value.unknownFields)
           }
 
-          public override fun encode(writer: ReverseProtoWriter, `value`: Block): Unit {
+          override fun encode(writer: ReverseProtoWriter, `value`: Block) {
             writer.writeBytes(value.unknownFields)
             if (value.bin_size != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 5, value.bin_size)
             if (value.length != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 4, value.length)
@@ -390,7 +396,7 @@ public class Point(
             if (value.time != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.time)
           }
 
-          public override fun decode(reader: ProtoReader): Block {
+          override fun decode(reader: ProtoReader): Block {
             var time: Long = 0L
             val frames = mutableListOf<Frame>()
             var events: Events? = null
@@ -416,7 +422,7 @@ public class Point(
             )
           }
 
-          public override fun redact(`value`: Block): Block = value.copy(
+          override fun redact(`value`: Block): Block = value.copy(
             frames = value.frames.redactElements(Frame.ADAPTER),
             events = value.events?.let(Events.ADAPTER::redact),
             unknownFields = ByteString.EMPTY
@@ -437,6 +443,7 @@ public class Point(
           tag = 1,
           adapter = "com.squareup.wire.ProtoAdapter#UINT64",
           label = WireField.Label.OMIT_IDENTITY,
+          schemaIndex = 0,
         )
         public val time: Long = 0L,
         /**
@@ -447,6 +454,7 @@ public class Point(
           adapter = "com.squareup.wire.ProtoAdapter#BYTES",
           label = WireField.Label.OMIT_IDENTITY,
           declaredName = "data",
+          schemaIndex = 1,
         )
         public val data_: ByteString = ByteString.EMPTY,
         unknownFields: ByteString = ByteString.EMPTY,
@@ -455,10 +463,10 @@ public class Point(
           message = "Shouldn't be used in Kotlin",
           level = DeprecationLevel.HIDDEN,
         )
-        public override fun newBuilder(): Nothing = throw
+        override fun newBuilder(): Nothing = throw
             AssertionError("Builders are deprecated and only available in a javaInterop build; see https://square.github.io/wire/wire_compiler/#kotlin")
 
-        public override fun equals(other: Any?): Boolean {
+        override fun equals(other: Any?): Boolean {
           if (other === this) return true
           if (other !is Frame) return false
           if (unknownFields != other.unknownFields) return false
@@ -467,7 +475,7 @@ public class Point(
           return true
         }
 
-        public override fun hashCode(): Int {
+        override fun hashCode(): Int {
           var result = super.hashCode
           if (result == 0) {
             result = unknownFields.hashCode()
@@ -478,7 +486,7 @@ public class Point(
           return result
         }
 
-        public override fun toString(): String {
+        override fun toString(): String {
           val result = mutableListOf<String>()
           result += """time=$time"""
           result += """data_=$data_"""
@@ -501,7 +509,7 @@ public class Point(
             null, 
             "numass-proto.proto"
           ) {
-            public override fun encodedSize(`value`: Frame): Int {
+            override fun encodedSize(`value`: Frame): Int {
               var size = value.unknownFields.size
               if (value.time != 0L) size += ProtoAdapter.UINT64.encodedSizeWithTag(1, value.time)
               if (value.data_ != ByteString.EMPTY) size += ProtoAdapter.BYTES.encodedSizeWithTag(2,
@@ -509,21 +517,21 @@ public class Point(
               return size
             }
 
-            public override fun encode(writer: ProtoWriter, `value`: Frame): Unit {
+            override fun encode(writer: ProtoWriter, `value`: Frame) {
               if (value.time != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.time)
               if (value.data_ != ByteString.EMPTY) ProtoAdapter.BYTES.encodeWithTag(writer, 2,
                   value.data_)
               writer.writeBytes(value.unknownFields)
             }
 
-            public override fun encode(writer: ReverseProtoWriter, `value`: Frame): Unit {
+            override fun encode(writer: ReverseProtoWriter, `value`: Frame) {
               writer.writeBytes(value.unknownFields)
               if (value.data_ != ByteString.EMPTY) ProtoAdapter.BYTES.encodeWithTag(writer, 2,
                   value.data_)
               if (value.time != 0L) ProtoAdapter.UINT64.encodeWithTag(writer, 1, value.time)
             }
 
-            public override fun decode(reader: ProtoReader): Frame {
+            override fun decode(reader: ProtoReader): Frame {
               var time: Long = 0L
               var data_: ByteString = ByteString.EMPTY
               val unknownFields = reader.forEachTag { tag ->
@@ -540,7 +548,7 @@ public class Point(
               )
             }
 
-            public override fun redact(`value`: Frame): Frame = value.copy(
+            override fun redact(`value`: Frame): Frame = value.copy(
               unknownFields = ByteString.EMPTY
             )
           }
@@ -566,6 +574,7 @@ public class Point(
           tag = 1,
           adapter = "com.squareup.wire.ProtoAdapter#UINT64",
           label = WireField.Label.PACKED,
+          schemaIndex = 0,
         )
         public val times: List<Long> = immutableCopyOf("times", times)
 
@@ -576,6 +585,7 @@ public class Point(
           tag = 2,
           adapter = "com.squareup.wire.ProtoAdapter#UINT64",
           label = WireField.Label.PACKED,
+          schemaIndex = 1,
         )
         public val amplitudes: List<Long> = immutableCopyOf("amplitudes", amplitudes)
 
@@ -583,10 +593,10 @@ public class Point(
           message = "Shouldn't be used in Kotlin",
           level = DeprecationLevel.HIDDEN,
         )
-        public override fun newBuilder(): Nothing = throw
+        override fun newBuilder(): Nothing = throw
             AssertionError("Builders are deprecated and only available in a javaInterop build; see https://square.github.io/wire/wire_compiler/#kotlin")
 
-        public override fun equals(other: Any?): Boolean {
+        override fun equals(other: Any?): Boolean {
           if (other === this) return true
           if (other !is Events) return false
           if (unknownFields != other.unknownFields) return false
@@ -595,7 +605,7 @@ public class Point(
           return true
         }
 
-        public override fun hashCode(): Int {
+        override fun hashCode(): Int {
           var result = super.hashCode
           if (result == 0) {
             result = unknownFields.hashCode()
@@ -606,7 +616,7 @@ public class Point(
           return result
         }
 
-        public override fun toString(): String {
+        override fun toString(): String {
           val result = mutableListOf<String>()
           if (times.isNotEmpty()) result += """times=$times"""
           if (amplitudes.isNotEmpty()) result += """amplitudes=$amplitudes"""
@@ -629,43 +639,61 @@ public class Point(
             null, 
             "numass-proto.proto"
           ) {
-            public override fun encodedSize(`value`: Events): Int {
+            override fun encodedSize(`value`: Events): Int {
               var size = value.unknownFields.size
               size += ProtoAdapter.UINT64.asPacked().encodedSizeWithTag(1, value.times)
               size += ProtoAdapter.UINT64.asPacked().encodedSizeWithTag(2, value.amplitudes)
               return size
             }
 
-            public override fun encode(writer: ProtoWriter, `value`: Events): Unit {
+            override fun encode(writer: ProtoWriter, `value`: Events) {
               ProtoAdapter.UINT64.asPacked().encodeWithTag(writer, 1, value.times)
               ProtoAdapter.UINT64.asPacked().encodeWithTag(writer, 2, value.amplitudes)
               writer.writeBytes(value.unknownFields)
             }
 
-            public override fun encode(writer: ReverseProtoWriter, `value`: Events): Unit {
+            override fun encode(writer: ReverseProtoWriter, `value`: Events) {
               writer.writeBytes(value.unknownFields)
               ProtoAdapter.UINT64.asPacked().encodeWithTag(writer, 2, value.amplitudes)
               ProtoAdapter.UINT64.asPacked().encodeWithTag(writer, 1, value.times)
             }
 
-            public override fun decode(reader: ProtoReader): Events {
-              val times = mutableListOf<Long>()
-              val amplitudes = mutableListOf<Long>()
+            override fun decode(reader: ProtoReader): Events {
+              var times: MutableList<Long>? = null
+              var amplitudes: MutableList<Long>? = null
               val unknownFields = reader.forEachTag { tag ->
                 when (tag) {
-                  1 -> times.add(ProtoAdapter.UINT64.decode(reader))
-                  2 -> amplitudes.add(ProtoAdapter.UINT64.decode(reader))
+                  1 -> {
+                    if (times == null) {
+                      val minimumByteSize = 1
+                      val initialCapacity = (reader.nextFieldMinLengthInBytes() / minimumByteSize)
+                        .coerceAtMost(Int.MAX_VALUE.toLong())
+                        .toInt()
+                      times = ArrayList(initialCapacity)
+                    }
+                    times!!.add(ProtoAdapter.UINT64.decode(reader))
+                  }
+                  2 -> {
+                    if (amplitudes == null) {
+                      val minimumByteSize = 1
+                      val initialCapacity = (reader.nextFieldMinLengthInBytes() / minimumByteSize)
+                        .coerceAtMost(Int.MAX_VALUE.toLong())
+                        .toInt()
+                      amplitudes = ArrayList(initialCapacity)
+                    }
+                    amplitudes!!.add(ProtoAdapter.UINT64.decode(reader))
+                  }
                   else -> reader.readUnknownField(tag)
                 }
               }
               return Events(
-                times = times,
-                amplitudes = amplitudes,
+                times = times ?: listOf(),
+                amplitudes = amplitudes ?: listOf(),
                 unknownFields = unknownFields
               )
             }
 
-            public override fun redact(`value`: Events): Events = value.copy(
+            override fun redact(`value`: Events): Events = value.copy(
               unknownFields = ByteString.EMPTY
             )
           }

numass-data-proto/src/main/kotlin/ru/inr/mass/data/proto/NumassProtoPlugin.kt

@@ -20,7 +20,6 @@ import java.nio.file.Path
 import kotlin.io.path.exists
 import kotlin.io.path.isDirectory
 import kotlin.io.path.relativeTo
-import kotlin.reflect.KClass
 
 public class NumassProtoPlugin : AbstractPlugin() {
     public val io: IOPlugin by require(IOPlugin)
@@ -35,7 +34,6 @@ public class NumassProtoPlugin : AbstractPlugin() {
     public companion object : PluginFactory<NumassProtoPlugin> {
         override fun build(context: Context, meta: Meta): NumassProtoPlugin = NumassProtoPlugin()
         override val tag: PluginTag = PluginTag("numass-proto", group = "ru.inr.mass")
-        override val type: KClass<out NumassProtoPlugin> = NumassProtoPlugin::class
     }
 }
 

numass-data-proto/src/main/kotlin/ru/inr/mass/data/proto/TaggedNumassEnvelopeFormat.kt

@@ -39,24 +39,8 @@ public class TaggedNumassEnvelopeFormat(private val io: IOPlugin) : EnvelopeForm
         writeRawString(END_SEQUENCE)
     }
 
-    override fun writeEnvelope(
-        output: Output,
-        envelope: Envelope,
-        metaFormatFactory: MetaFormatFactory,
-        formatMeta: Meta,
-    ) {
+    override fun writeObject(output: Output, obj: Envelope) {
         error("Don't write legacy formats")
-//        val metaFormat = metaFormatFactory.invoke(formatMeta, io.context)
-//        val metaBytes = metaFormat.toBinary(envelope.meta)
-//        val actualSize: ULong = (envelope.data?.size ?: 0).toULong()
-//        val tag = Tag(metaFormatFactory.key, metaBytes.size.toUInt() + 2u, actualSize)
-//        output.writeBinary(tag.toBinary())
-//        output.writeBinary(metaBytes)
-//        output.writeRawString("\r\n")
-//        envelope.data?.let {
-//            output.writeBinary(it)
-//        }
-//        output.flush()
     }
 
     /**
@@ -68,31 +52,30 @@ public class TaggedNumassEnvelopeFormat(private val io: IOPlugin) : EnvelopeForm
     override fun readObject(input: Input): Envelope {
         val tag = input.readTag()
 
-        val metaFormat = io.resolveMetaFormat(tag.metaFormatKey)
-            ?: error("Meta format with key ${tag.metaFormatKey} not found")
+        val metaFormat = io.resolveMetaFormat(tag.metaFormatKey) ?: JsonMetaFormat
 
         val meta: Meta = metaFormat.readObjectFrom(input.readBinary(tag.metaSize.toInt()))
 
         val data = input.readBinary(tag.dataSize.toInt())
 
-        return SimpleEnvelope(meta, data)
-    }
-
-    override fun readPartial(input: Input): PartialEnvelope {
-        val tag = input.readTag()
-
-        val metaFormat = if (tag.metaFormatKey == 1.toShort()) {
-            JsonMetaFormat
-        } else {
-            io.resolveMetaFormat(tag.metaFormatKey)
-                ?: error("Meta format with key ${tag.metaFormatKey} not found")
-        }
-
-        val meta: Meta = metaFormat.readObjectFrom(input.readBinary(tag.metaSize.toInt()))
-
-
-        return PartialEnvelope(meta, 30 + tag.metaSize.toInt(), tag.dataSize)
+        return Envelope(meta, data)
     }
+//
+//    override fun readPartial(input: Input): PartialEnvelope {
+//        val tag = input.readTag()
+//
+//        val metaFormat = if (tag.metaFormatKey == 1.toShort()) {
+//            JsonMetaFormat
+//        } else {
+//            io.resolveMetaFormat(tag.metaFormatKey)
+//                ?: error("Meta format with key ${tag.metaFormatKey} not found")
+//        }
+//
+//        val meta: Meta = metaFormat.readObjectFrom(input.readBinary(tag.metaSize.toInt()))
+//
+//
+//        return PartialEnvelope(meta, 30 + tag.metaSize.toInt(), tag.dataSize)
+//    }
 
     private data class Tag(
         val metaFormatKey: Short,
@@ -149,23 +132,11 @@ public class TaggedNumassEnvelopeFormat(private val io: IOPlugin) : EnvelopeForm
 
         private val default by lazy { invoke() }
 
-        override fun readPartial(input: Input): PartialEnvelope =
-            default.run { readPartial(input) }
-
-        override fun writeEnvelope(
-            output: Output,
-            envelope: Envelope,
-            metaFormatFactory: MetaFormatFactory,
-            formatMeta: Meta,
-        ): Unit = default.run {
-            writeEnvelope(
-                output,
-                envelope,
-                metaFormatFactory,
-                formatMeta
-            )
+        override fun writeObject(output: Output, obj: Envelope) {
+            error("Don't write legacy formats")
         }
 
+
         override fun readObject(input: Input): Envelope = default.readObject(input)
     }
 }

numass-data-server/build.gradle.kts

@@ -8,62 +8,41 @@ val visionForgeVersion: String by rootProject.extra
 
 val production: Boolean by rootProject.extra(true)
 
-kotlin {
-    js(IR) {
-        browser {
-            webpackTask {
-                this.outputFileName = "js/numass-web.js"
-            }
-        }
-        binaries.executable()
+
+kscience {
+    fullStack("js/numass-web.js")
+
+    useSerialization {
+        json()
     }
 
-    sourceSets {
+    useContextReceivers()
+    useKtor()
+
     commonMain {
         dependencies {
             implementation(project(":numass-data-model"))
             implementation("space.kscience:visionforge-core:$visionForgeVersion")
             implementation("space.kscience:visionforge-plotly:$visionForgeVersion")
-                implementation(compose.runtime)
         }
     }
-        jvmMain {
+}
+
+kotlin{
+    sourceSets{
+        getByName("jvmMain"){
             dependencies{
+                implementation(compose.runtime)
                 implementation(project(":numass-data-proto"))
-                implementation("io.ktor:ktor-server-cio:2.1.3")
-                implementation("io.ktor:ktor-server-html-builder-jvm:2.1.3")
+                implementation("io.ktor:ktor-server-cio")
+                implementation("io.ktor:ktor-server-html-builder")
                 implementation("space.kscience:visionforge-plotly:$visionForgeVersion")
             }
         }
-        jsMain{
+        getByName("jsMain"){
             dependencies{
-                implementation(compose.web.core)
-            }
-        }
-
-    }
-}
-
-afterEvaluate {
-    val distributionTask = if (production) {
-        tasks.getByName("jsBrowserDistribution")
-    } else {
-        tasks.getByName("jsBrowserDevelopmentExecutableDistribution")
-    }
-
-    tasks.getByName<ProcessResources>("jvmProcessResources") {
-        dependsOn(distributionTask)
-        from(distributionTask)
-        include("**/*.js")
-        if (production) {
-            include("**/*.map")
+                implementation(compose.html.core)
             }
         }
     }
-
-kscience {
-    useSerialization {
-        json()
-    }
-    withContextReceivers()
 }

numass-data-server/src/commonMain/kotlin/ru/inr/mass/data/server/NumassCommonPlugin.kt

@@ -9,7 +9,6 @@ import space.kscience.dataforge.context.PluginTag
 import space.kscience.dataforge.meta.Meta
 import space.kscience.visionforge.Vision
 import space.kscience.visionforge.VisionPlugin
-import kotlin.reflect.KClass
 
 public class NumassCommonPlugin(meta: Meta = Meta.EMPTY) : VisionPlugin(meta) {
     override val tag: PluginTag get() = Companion.tag
@@ -18,7 +17,6 @@ public class NumassCommonPlugin(meta: Meta = Meta.EMPTY) : VisionPlugin(meta) {
 
     public companion object : PluginFactory<NumassCommonPlugin> {
         override val tag: PluginTag = PluginTag("numass.common", "ru.inr.mass")
-        override val type: KClass<NumassCommonPlugin> = NumassCommonPlugin::class
 
         override fun build(context: Context, meta: Meta): NumassCommonPlugin = NumassCommonPlugin()
 

numass-data-server/src/jsMain/kotlin/ru/inr/mass/data/server/NumassJsPlugin.kt

@@ -18,7 +18,6 @@ import space.kscience.visionforge.ElementVisionRenderer
 import space.kscience.visionforge.Vision
 import space.kscience.visionforge.VisionClient
 import space.kscience.visionforge.plotly.PlotlyPlugin
-import kotlin.reflect.KClass
 
 public class NumassJsPlugin : AbstractPlugin(), ElementVisionRenderer {
     public val client: VisionClient by require(VisionClient)
@@ -83,8 +82,6 @@ public class NumassJsPlugin : AbstractPlugin(), ElementVisionRenderer {
 
     public companion object : PluginFactory<NumassJsPlugin> {
         override val tag: PluginTag = PluginTag("numass.js", "ru.inr.mass")
-        override val type: KClass<NumassJsPlugin> = NumassJsPlugin::class
-
         override fun build(context: Context, meta: Meta): NumassJsPlugin = NumassJsPlugin()
 
     }

numass-model/build.gradle.kts

@@ -7,7 +7,9 @@ plugins {
 val dataforgeVersion: String by rootProject.extra
 val kmathVersion: String by rootProject.extra
 
-kotlin.sourceSets {
+kscience{
+    jvm()
+    js()
     commonMain {
         dependencies {
             api("space.kscience:dataforge-context:$dataforgeVersion")
@@ -15,7 +17,10 @@ kotlin.sourceSets {
             api("space.kscience:kmath-functions:$kmathVersion")
         }
     }
-    jvmMain {
+}
+
+kotlin.sourceSets{
+    getByName("jvmMain"){
         dependencies {
             api("space.kscience:kmath-commons:$kmathVersion")
             api("ch.qos.logback:logback-classic:1.2.3")

numass-model/src/commonMain/kotlin/ru/inr/mass/models/FSS.kt

@@ -15,10 +15,10 @@
  */
 package ru.inr.mass.models
 
+import space.kscience.kmath.UnstableKMathAPI
 import space.kscience.kmath.data.ColumnarData
 import space.kscience.kmath.expressions.Symbol
 import space.kscience.kmath.expressions.symbol
-import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.structures.Buffer
 
 

numass-model/src/commonMain/kotlin/ru/inr/mass/models/NBkgSpectrum.kt

@@ -33,7 +33,7 @@ public class NBkgSpectrum(public val source: Spectrum) : DifferentiableSpectrum
         symbols.isEmpty() -> this
         symbols.size == 1 -> when (symbols.first()) {
             norm -> Spectrum { x, arguments -> source(x, arguments) }
-            bkg -> Spectrum { x, _ -> 1.0 }
+            bkg -> Spectrum { _, _ -> 1.0 }
             else -> (source as? DifferentiableSpectrum)?.derivativeOrNull(symbols)?.let { NBkgSpectrum(it) }
         }
         else -> null

numass-workspace/build.gradle.kts

@@ -2,6 +2,7 @@ plugins {
     id("space.kscience.gradle.jvm")
     id("com.github.johnrengelman.shadow") version "7.1.2"
     `maven-publish`
+//    application
 }
 
 kotlin {
@@ -9,7 +10,7 @@ kotlin {
 }
 
 val dataforgeVersion: String by rootProject.extra
-val visionForgeVersion: String by rootProject.extra
+val plotlyKtVersion = "0.6.0"
 val kmathVersion: String by rootProject.extra
 val tablesVersion: String by rootProject.extra
 
@@ -21,9 +22,15 @@ dependencies {
 
     implementation("space.kscience:kmath-jupyter:$kmathVersion")
     implementation("space.kscience:tables-kt:$tablesVersion")
-    implementation("space.kscience:visionforge-plotly:$visionForgeVersion")
+    implementation("space.kscience:plotlykt-core:$plotlyKtVersion")
+
+    implementation("com.github.ajalt.clikt:clikt:4.2.1")
 }
 
 kscience{
     jupyterLibrary("ru.inr.mass.notebook.NumassJupyter")
 }
+
+//application {
+//    mainClass.set("ru.inr.mass.scripts.Spectrum_serverKt")
+//}

numass-workspace/src/main/kotlin/ru/inr/mass/scripts/fit.kt

@@ -3,12 +3,12 @@ package ru.inr.mass.scripts
 import ru.inr.mass.models.*
 import ru.inr.mass.workspace.buffer
 import ru.inr.mass.workspace.fitWith
+import space.kscience.kmath.UnstableKMathAPI
 import space.kscience.kmath.data.XYColumnarData
 import space.kscience.kmath.data.XYErrorColumnarData
 import space.kscience.kmath.data.indices
 import space.kscience.kmath.expressions.Symbol
 import space.kscience.kmath.expressions.derivative
-import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.operations.asSequence
 import space.kscience.kmath.optimization.*
 import space.kscience.kmath.real.step
@@ -18,6 +18,7 @@ import space.kscience.plotly.models.ScatterMode
 import java.io.File
 import kotlin.math.pow
 
+@OptIn(UnstableKMathAPI::class)
 fun parse(filename: String): XYErrorColumnarData<Double, Double, Double> {
     val x: MutableList<Double> = mutableListOf()
     val y: MutableList<Double> = mutableListOf()
@@ -37,8 +38,12 @@ fun parse(filename: String): XYErrorColumnarData<Double, Double, Double> {
     )
 }
 
-@OptIn(UnstableKMathAPI::class)
+//@OptIn(UnstableKMathAPI::class)
+@UnstableKMathAPI
 suspend fun main() {
+
+//    val fitParams = FitParams().main(args);
+
     val spectrum: NBkgSpectrum = SterileNeutrinoSpectrum(
 //        fss = FSS.default,
           transmission = NumassTransmission(NumassTransmission.trapFunction),
@@ -64,7 +69,7 @@ suspend fun main() {
 //
 //    val strategy = (12000.0..19000.0 step 100.0).asSequence().associateWith { timePerPoint }
 
-    val data = parse("/home/sabina/Numass/Fit/Data/03.10.2023")
+    val data = parse("/home/chernov/projects/notebooks/manual-fit/06.10.2023")
 
     val fit: XYFit = data.fitWith(
         optimizer = QowOptimizer,
@@ -74,7 +79,7 @@ suspend fun main() {
         OptimizationIterations(20)
     )
 
-    //println("Chi squared/dof: ${fit.chiSquaredOrNull}/${fit.dof}")
+    println(fit.resultPoint)
 
     Plotly.page {
         plot {
@@ -92,7 +97,7 @@ suspend fun main() {
                 mode = ScatterMode.lines
                 x.buffer = 12000.0..18600.0 step 50.0
                 y.numbers = x.doubles.map { spectrum(it, args + fit.resultPoint) }
-                File("/home/sabina/Numass/Fit/trap1").printWriter().use { out ->
+                File("/home/chernov/projects/notebooks/manual-fit/04.10.2023-fit").printWriter().use { out ->
                     y.numbers.forEach {
                         out.println(it)
                     }

numass-workspace/src/main/kotlin/ru/inr/mass/scripts/get-spectrum.kt

@@ -0,0 +1,44 @@
+package ru.inr.mass.scripts
+
+import kotlinx.coroutines.Dispatchers
+import kotlinx.coroutines.async
+import kotlinx.coroutines.runBlocking
+import ru.inr.mass.models.*
+import space.kscience.kmath.expressions.Symbol
+import space.kscience.kmath.operations.toTypedArray
+import space.kscience.kmath.real.plus
+import space.kscience.kmath.real.step
+
+fun main(args: Array<String>) {
+    val cli = args.map { it.toDouble() }
+
+    val args: Map<Symbol, Double> = mapOf(
+        NBkgSpectrum.norm to cli[0],
+        NBkgSpectrum.bkg to cli[1],
+        NumassBeta.mnu2 to cli[2],
+        NumassBeta.e0 to cli[3],
+        NumassBeta.msterile2 to cli[4],
+        NumassBeta.u2 to cli[5],
+        NumassTransmission.thickness to cli[6],
+        NumassTransmission.trap to cli[7]
+    )
+
+    runBlocking(Dispatchers.Default) {
+        val range = (12000.0..16000.0 step 50.0).toTypedArray()
+            .plus((16100.0..18600.0 step 100.0).toTypedArray());
+
+        val handles = range.map {
+
+            async(Dispatchers.Default) {
+                val spectrum: NBkgSpectrum = SterileNeutrinoSpectrum(
+                    transmission = NumassTransmission(NumassTransmission.trapFunction),
+                ).withNBkg()
+
+                val res = spectrum.invoke(it, args)
+                return@async res
+            }
+        }
+        val out = handles.map { it.await() }
+        println(out.joinToString("\n"))
+    }
+}

numass-workspace/src/main/kotlin/ru/inr/mass/workspace/NumassWorkspacePlugin.kt

@@ -18,7 +18,6 @@ import space.kscience.dataforge.workspace.WorkspacePlugin
 import space.kscience.dataforge.workspace.pipeFrom
 import space.kscience.dataforge.workspace.task
 import space.kscience.tables.Table
-import kotlin.reflect.KClass
 
 class NumassWorkspacePlugin : WorkspacePlugin() {
     override val tag: PluginTag get() = Companion.tag
@@ -128,7 +127,6 @@ class NumassWorkspacePlugin : WorkspacePlugin() {
 
     companion object : PluginFactory<NumassWorkspacePlugin> {
         override val tag: PluginTag = PluginTag("numass", "ru.mipt.npm")
-        override val type: KClass<out NumassWorkspacePlugin> = NumassWorkspacePlugin::class
         override fun build(context: Context, meta: Meta): NumassWorkspacePlugin = NumassWorkspacePlugin()
     }
 }

numass-workspace/src/main/kotlin/ru/inr/mass/workspace/dataUtils.kt

@@ -3,13 +3,13 @@
 package ru.inr.mass.workspace
 
 import ru.inr.mass.models.Spectrum
+import space.kscience.kmath.UnstableKMathAPI
 import space.kscience.kmath.data.XYColumnarData
 import space.kscience.kmath.data.XYErrorColumnarData
 import space.kscience.kmath.expressions.DifferentiableExpression
 import space.kscience.kmath.expressions.Symbol
 import space.kscience.kmath.misc.FeatureSet
 import space.kscience.kmath.misc.Loggable
-import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.optimization.*
 import space.kscience.kmath.random.RandomGenerator
 import space.kscience.kmath.samplers.PoissonSampler

numass-workspace/src/main/kotlin/ru/inr/mass/workspace/plots.kt

@@ -12,9 +12,9 @@ import ru.inr.mass.data.proto.HVData
 import ru.inr.mass.data.proto.NumassDirectorySet
 import space.kscience.dataforge.meta.asValue
 import space.kscience.dataforge.meta.double
+import space.kscience.kmath.UnstableKMathAPI
 import space.kscience.kmath.domains.center
 import space.kscience.kmath.histogram.Histogram1D
-import space.kscience.kmath.misc.UnstableKMathAPI
 import space.kscience.kmath.operations.asIterable
 import space.kscience.kmath.structures.Buffer
 import space.kscience.kmath.structures.DoubleBuffer

settings.gradle.kts

@@ -1,7 +1,6 @@
 rootProject.name = "numass"
 
 enableFeaturePreview("TYPESAFE_PROJECT_ACCESSORS")
-enableFeaturePreview("VERSION_CATALOGS")
 
 pluginManagement {