remove j4ml dependency

.github/dependabot.yml

@@ -18,11 +18,8 @@ updates:
     commit-message:
       prefix: "build(deps)"
     ignore:
-      - dependency-name: "org.jlab:groot" # since version numbers are not in order
-      - dependency-name: "net.objecthunter:exp4j" # pinned for dependency convergence
-      - dependency-name: "org.ejml:ejml-simple" # pinned for dependency convergence
-      - dependency-name: "org.apache.commons:commons-lang3" # pinned for dependency convergence
-      - dependency-name: "org.slf4j:slf4j-api" # pinned for dependency convergence
+      - dependency-name: "org.jlab:groot" # since clasweb version numbers are not in order
+      - dependency-name: "org.ejml:ejml-simple" # see https://github.com/JeffersonLab/coatjava/pull/636
       - dependency-name: "org.openjfx:javafx-base"
         versions: [">= 24"] # version 24 requires JAVA_VERSION 22+
       - dependency-name: "org.openjfx:javafx-graphics"

.github/workflows/ci.yml

@@ -23,7 +23,7 @@ env:
   RCDB_CONNECTION: 'sqlite:///${{ github.workspace }}/coatjava/etc/data/sqlite/rcdb.sqlite'
   nthreads: 1
   # Maven 3.9+ reads MAVEN_ARGS automatically, including inside build-coatjava.sh:
-  #   --no-snapshot-updates : don't re-check remote repos (j4ml) for newer SNAPSHOTs;
+  #   --no-snapshot-updates : don't re-check remote repos for newer SNAPSHOTs;
   #                           use whatever `warm_maven_cache` resolved
   #   retryHandler.count    : built-in HTTP retries for transient 403/429/5xx
   MAVEN_ARGS: --no-snapshot-updates -Daether.connector.http.retryHandler.count=5

CODEOWNERS

@@ -79,7 +79,6 @@ reconstruction/ft/ @raffaelladevita
 reconstruction/htcc/ @raffaelladevita @baltzell @zieglerv
 reconstruction/ltcc/ @raffaelladevita @baltzell @zieglerv @sly2j
 reconstruction/mc/ @baltzell @rafopar
-reconstruction/mltn/ @gavalian
 reconstruction/postproc/ @baltzell
 reconstruction/raster/ @raffaelladevita @N-Plx
 reconstruction/recoil/ @silvianic

Makefile

@@ -21,4 +21,7 @@ clean:
 clara:
 	$(BUILD) --clara $(THREADS)
 
+test:
+	$(BUILD) --unittests $(THREADS)
+
 all: clara

build-coatjava.sh

@@ -403,14 +403,8 @@ install_jars() {
 for pom in $(find reconstruction -name pom.xml); do
   install_jars $pom $prefix_dir/lib/services
 done
-for pom in $(find common-tools -name pom.xml); do
-  if [[ "$pom" =~ coat-libs ]]; then
-    install_jars $pom $prefix_dir/lib/clas 'coat-libs-*.jar'
-  # else # FIXME, consumers may be need these after https://github.com/JeffersonLab/coatjava/pull/632 ; alternatively add needed deps to `coat-libs`
-  #   install_jars $pom $prefix_dir/lib/services
-  fi
-done
-
+install_jars common-tools/djl-runtime/pom.xml $prefix_dir/lib/services
+install_jars common-tools/coat-libs/pom.xml   $prefix_dir/lib/clas 'coat-libs-*.jar'
 echo "installed coatjava to: $prefix_dir"
 
 # install clara

common-tools/coat-libs/pom.xml

@@ -26,16 +26,6 @@
       <artifactId>et</artifactId>
     </dependency>
 
-    <dependency>
-      <groupId>j4ml</groupId>
-      <artifactId>j4ml-neuroph</artifactId>
-    </dependency>
-
-    <dependency>
-      <groupId>j4ml</groupId>
-      <artifactId>j4ml-clas12</artifactId>
-    </dependency>
-
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-io</artifactId>

common-tools/djl-runtime/pom.xml

@@ -0,0 +1,116 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <!--
+    this POM installs `ai.djl` runtime dependencies to our prefix classpath;
+    this includes its transitive dependencies, e.g. `gson` and `slf4j`
+  -->
+
+  <artifactId>djl-runtime</artifactId>
+  <packaging>pom</packaging>
+
+  <parent>
+    <groupId>org.jlab.clas</groupId>
+    <artifactId>common-tools</artifactId>
+    <version>14.2.3-SNAPSHOT</version>
+  </parent>
+
+  <properties>
+    <!-- Native PyTorch classifier; overridden per-OS by the profiles below -->
+    <djl.pytorch.classifier>linux-x86_64</djl.pytorch.classifier>
+  </properties>
+
+  <profiles>
+    <!-- Linux x86_64 is the default via the property above; this profile exists only to make the choice explicit/overridable -->
+    <profile>
+      <id>djl-linux-x86_64</id>
+      <activation>
+        <os>
+          <family>unix</family>
+          <name>Linux</name>
+          <arch>amd64</arch>
+        </os>
+      </activation>
+      <properties>
+        <djl.pytorch.classifier>linux-x86_64</djl.pytorch.classifier>
+      </properties>
+    </profile>
+    <profile>
+      <id>djl-osx-aarch64</id>
+      <activation>
+        <os>
+          <family>mac</family>
+          <arch>aarch64</arch>
+        </os>
+      </activation>
+      <properties>
+        <djl.pytorch.classifier>osx-aarch64</djl.pytorch.classifier>
+      </properties>
+    </profile>
+    <profile>
+      <id>djl-win-x86_64</id>
+      <activation>
+        <os>
+          <family>windows</family>
+          <arch>amd64</arch>
+        </os>
+      </activation>
+      <properties>
+        <djl.pytorch.classifier>win-x86_64</djl.pytorch.classifier>
+      </properties>
+    </profile>
+  </profiles>
+
+  <dependencies>
+    <dependency>
+      <groupId>ai.djl</groupId>
+      <artifactId>api</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>ai.djl</groupId>
+      <artifactId>model-zoo</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>ai.djl.pytorch</groupId>
+      <artifactId>pytorch-model-zoo</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>ai.djl.pytorch</groupId>
+      <artifactId>pytorch-engine</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>ai.djl.pytorch</groupId>
+      <artifactId>pytorch-native-cpu</artifactId>
+      <classifier>${djl.pytorch.classifier}</classifier>
+    </dependency>
+    <dependency>
+      <groupId>ai.djl.pytorch</groupId>
+      <artifactId>pytorch-jni</artifactId>
+    </dependency>
+  </dependencies>
+
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-dependency-plugin</artifactId>
+        <version>3.11.0</version>
+        <executions>
+          <execution>
+            <id>copy-djl-runtime</id>
+            <phase>package</phase>
+            <goals>
+              <goal>copy-dependencies</goal>
+            </goals>
+            <configuration>
+              <outputDirectory>${project.build.directory}/lib/services</outputDirectory>
+              <includeScope>runtime</includeScope>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+
+</project>

common-tools/pom.xml

@@ -29,6 +29,7 @@
     <module>clara-io</module>
     <module>clas-tracking</module>
     <module>clas-decay-tools</module>
+    <module>djl-runtime</module>
     <module>coat-libs</module>
   </modules>
 

etc/services/kpp.yaml

@@ -1,10 +1,17 @@
-io-services:
-  reader:
-    class: org.jlab.io.clara.Clas12Reader
-    name: Clas12Reader
-  writer:
-    class: org.jlab.io.clara.Clas12Writer
-    name: Clas12Writer
+configuration:
+  services:
+    MAGFIELDS:
+      magfieldSolenoidMap: Symm_solenoid_r601_phi1_z1201_13June2018.dat
+      magfieldTorusMap: Full_torus_r251_phi181_z251_25Jan2021.dat
+    DCCR:
+      rawBankGroup: "NODENOISE"
+    DCHTAI:
+      outputBankPrefix: "AI"
+    DCTAI:
+      outputBankPrefix: "AI"
+    EBTAI:
+      outputBankPrefix: "RECAI"
+
 services:
   - class: org.jlab.clas.reco.DecoderEngine
     name: DECO
@@ -20,18 +27,16 @@ services:
     name: FTEB
   - class: org.jlab.service.raster.RasterEngine
     name: RASTER
-# DC clustering: nominal algoritm, filled the cluster bank for ai and conventional tracking
+  - class: org.jlab.service.ai.DCDenoiseEngine
+    name: DCDN    
   - class: org.jlab.service.dc.DCHBClustering
     name: DCCR
-# This is where the AI plugin would go.  THe AI code reads the HB clusters.  
-  - class: org.jlab.service.mltn.MLTDEngine
-    name: MLTD
-# DC using clustering: regular HB tracking
+  - class: org.jlab.service.ai.DCClsComboEngine
+    name: DCCC
   - class: org.jlab.service.dc.DCHBPostClusterConv
     name: DCHB
-# DC using clustering on AI hits: NN assisted HB tracking
-  - class: org.jlab.service.dc.DCHBPostClusterAI
-    name: DCHAI
+  - class: org.jlab.service.dc.DCHBTrackingAI
+    name: DCHTAI
   - class: org.jlab.service.ftof.FTOFHBEngine
     name: FTOFHB
   - class: org.jlab.service.ec.ECEngine
@@ -72,36 +77,18 @@ services:
     name: RICH
   - class: org.jlab.service.rtpc.RTPCEngine
     name: RTPC
+  - class: org.jlab.rec.service.vtx.VTXEngine
+    name: VTX
   - class: org.jlab.calibration.service.CalibBanksEngine
     name: CALIB
-configuration:
-  services:
-    MAGFIELDS:
-      magfieldSolenoidMap: Symm_solenoid_r601_phi1_z1201_13June2018.dat
-      magfieldTorusMap: Symm_torus_r2501_phi16_z251_24Apr2018.dat
-# examples of yaml settings for magfields 
-#      magfieldSolenoidShift: "0.0"
-#      magfieldTorusXShift: "0.0"
-#      magfieldTorusYShift: "0.0"
-#      magfieldTorusZShift: "0.0"
-# examples of yaml settings for DC services 
-#    DCRC:
-#      dcGeometryVariation: rga_spring2018
-#      dcT2DFunc: "Polynomial"
-#      dcWireDistortion: "true"
-# example of how to set variation and timestamp for a service, uncomment to use
-#    EBTB:
-#      variation: default
-#      timestamp: 08/22/2018
-    DCCR:
-      dcT2DFunc: "Exponential"  
-    DCHB:
-      dcT2DFunc: "Exponential"  
-    DCHAI:
-      dcT2DFunc: "Exponential"  
-    DCTB:
-      dcT2DFunc: "Exponential"  
-    DCTAI:
-      dcT2DFunc: "Exponential"  
+
+io-services:
+  reader:
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
+  writer:
+    class: org.jlab.io.clara.Clas12Writer
+    name: Clas12Writer
+
 mime-types:
   - binary/data-hipo