Merge branch 'master' into 5596-link-for-bare-repository

build.gradle

@@ -109,8 +109,8 @@ allprojects {
 
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:2.4.0'
-        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.23"
-        groovyDoc "org.apache.groovy:groovy-ant:4.0.23"
+        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.24"
+        groovyDoc "org.apache.groovy:groovy-ant:4.0.24"
     }
 
     test {

docs/reference/process.md

@@ -1078,11 +1078,11 @@ The following options are available:
 : *Can be specified multiple times*
 : Mounts a [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `ConfigMap` are exposed in that path.
 
-`csi: '<name>', mountPath: '</absolute/path>'`
+`csi: '<config>', mountPath: '</absolute/path>'`
 : :::{versionadded} 22.11.0-edge
   :::
 : *Can be specified multiple times*
-: Mounts a [CSI ephemeral volume](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#csi-ephemeral-volumes) by name to the given path.
+: Mounts a [CSI ephemeral volume](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#csi-ephemeral-volumes) with the given configuration to the given path.
 
 `emptyDir: <config>, mountPath: '</absolute/path>'`
 : :::{versionadded} 22.11.0-edge

modules/nextflow/build.gradle

@@ -21,11 +21,11 @@ dependencies {
     api(project(':nf-commons'))
     api(project(':nf-httpfs'))
     api "org.apache.groovy:groovy:4.0.24"
-    api "org.apache.groovy:groovy-nio:4.0.23"
-    api "org.apache.groovy:groovy-xml:4.0.23"
-    api "org.apache.groovy:groovy-json:4.0.23"
-    api "org.apache.groovy:groovy-templates:4.0.23"
-    api "org.apache.groovy:groovy-yaml:4.0.23"
+    api "org.apache.groovy:groovy-nio:4.0.24"
+    api "org.apache.groovy:groovy-xml:4.0.24"
+    api "org.apache.groovy:groovy-json:4.0.24"
+    api "org.apache.groovy:groovy-templates:4.0.24"
+    api "org.apache.groovy:groovy-yaml:4.0.24"
     api "org.slf4j:jcl-over-slf4j:2.0.7"
     api "org.slf4j:jul-to-slf4j:2.0.7"
     api "org.slf4j:log4j-over-slf4j:2.0.7"
@@ -39,7 +39,7 @@ dependencies {
     api "com.beust:jcommander:1.35"
     api("com.esotericsoftware.kryo:kryo:2.24.0") { exclude group: 'com.esotericsoftware.minlog', module: 'minlog' }
     api('org.iq80.leveldb:leveldb:0.12')
-    api('org.eclipse.jgit:org.eclipse.jgit:6.10.0.202406032230-r')
+    api('org.eclipse.jgit:org.eclipse.jgit:7.1.0.202411261347-r')
     api ('javax.activation:activation:1.1.1')
     api ('javax.mail:mail:1.4.7')
     api ('org.yaml:snakeyaml:2.2')
@@ -53,7 +53,7 @@ dependencies {
     testImplementation 'org.subethamail:subethasmtp:3.1.7'
 
     // test configuration
-    testFixturesApi ("org.apache.groovy:groovy-test:4.0.23") { exclude group: 'org.apache.groovy' }
+    testFixturesApi ("org.apache.groovy:groovy-test:4.0.24") { exclude group: 'org.apache.groovy' }
     testFixturesApi ("org.objenesis:objenesis:3.4")
     testFixturesApi ("net.bytebuddy:byte-buddy:1.14.17")
     testFixturesApi ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy' }

modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy

@@ -833,7 +833,7 @@ class AssetManager {
 
     protected Map refToMap(Ref ref, Map<String,Ref> remote) {
         final entry = new HashMap(2)
-        final peel = git.getRepository().peel(ref)
+        final peel = git.getRepository().getRefDatabase().peel(ref)
         final objId = peel.getPeeledObjectId() ?: peel.getObjectId()
         // the branch or tag name
         entry.name = shortenRefName(ref.name)
@@ -867,7 +867,7 @@ class AssetManager {
         result << (name == current ? '*' : ' ')
 
         if( level ) {
-            def peel = git.getRepository().peel(ref)
+            def peel = git.getRepository().getRefDatabase().peel(ref)
             def obj = peel.getPeeledObjectId() ?: peel.getObjectId()
             result << ' '
             result << formatObjectId(obj, level == 1)

modules/nextflow/src/main/groovy/nextflow/scm/AzureRepositoryProvider.groovy

@@ -35,13 +35,15 @@ final class AzureRepositoryProvider extends RepositoryProvider {
 
     private String user
     private String repo
+    private String urlPath;
     private String continuationToken
 
     AzureRepositoryProvider(String project, ProviderConfig config=null) {
         /*
         Azure repo format follows Organization/Project/Repository where Project can be optional
         If Project is not present then Repository is used as Project (and also as Repository)
          */
+        this.urlPath = project
         def tokens = project.tokenize('/')
         this.repo = tokens.removeLast()
         if( tokens.size() == 1){
@@ -164,7 +166,7 @@ final class AzureRepositoryProvider extends RepositoryProvider {
     /** {@inheritDoc} */
     @Override
     String getRepositoryUrl() {
-        "${config.server}/$project"
+        "${config.server}/${urlPath}"
     }
 
     /** {@inheritDoc} */

modules/nextflow/src/main/resources/nextflow/executor/command-trace.txt

@@ -114,26 +114,28 @@ nxf_mem_watch() {
     done
 
     ## result struct: pid %mem vmem rss peak_vmem peak_rss
-    echo "%mem=${nxf_stat_ret[1]}"      >> $trace_file
-    echo "vmem=${nxf_stat_ret[2]}"      >> $trace_file
-    echo "rss=${nxf_stat_ret[3]}"       >> $trace_file
-    echo "peak_vmem=${nxf_stat_ret[4]}" >> $trace_file
-    echo "peak_rss=${nxf_stat_ret[5]}"  >> $trace_file
-    echo "vol_ctxt=${nxf_stat_ret[6]}"  >> $trace_file
-    echo "inv_ctxt=${nxf_stat_ret[7]}"  >> $trace_file
+    printf "%s\n" \
+        "%mem=${nxf_stat_ret[1]}" \
+        "vmem=${nxf_stat_ret[2]}" \
+        "rss=${nxf_stat_ret[3]}" \
+        "peak_vmem=${nxf_stat_ret[4]}" \
+        "peak_rss=${nxf_stat_ret[5]}" \
+        "vol_ctxt=${nxf_stat_ret[6]}" \
+        "inv_ctxt=${nxf_stat_ret[7]}" >> "$trace_file" || >&2 echo "Error: Failed to append to file: $trace_file"
 }
 
 nxf_write_trace() {
-    echo "nextflow.trace/v2"           > $trace_file
-    echo "realtime=$wall_time"         >> $trace_file
-    echo "%cpu=$ucpu"                  >> $trace_file
-    echo "cpu_model=$cpu_model"        >> $trace_file
-    echo "rchar=${io_stat1[0]}"        >> $trace_file
-    echo "wchar=${io_stat1[1]}"        >> $trace_file
-    echo "syscr=${io_stat1[2]}"        >> $trace_file
-    echo "syscw=${io_stat1[3]}"        >> $trace_file
-    echo "read_bytes=${io_stat1[4]}"   >> $trace_file
-    echo "write_bytes=${io_stat1[5]}"  >> $trace_file
+    printf "%s\n" \
+        "nextflow.trace/v2" \
+        "realtime=$wall_time" \
+        "%cpu=$ucpu" \
+        "cpu_model=$cpu_model" \
+        "rchar=${io_stat1[0]}" \
+        "wchar=${io_stat1[1]}" \
+        "syscr=${io_stat1[2]}" \
+        "syscw=${io_stat1[3]}" \
+        "read_bytes=${io_stat1[4]}" \
+        "write_bytes=${io_stat1[5]}" > "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
 }
 
 nxf_trace_mac() {
@@ -199,16 +201,17 @@ nxf_trace_linux() {
     local wall_time=$((end_millis-start_millis))
     [ $NXF_DEBUG = 1 ] && echo "+++ STATS %CPU=$ucpu TIME=$wall_time I/O=${io_stat1[*]}"
 
-    echo "nextflow.trace/v2"           > $trace_file
-    echo "realtime=$wall_time"         >> $trace_file
-    echo "%cpu=$ucpu"                  >> $trace_file
-    echo "cpu_model=$cpu_model"        >> $trace_file
-    echo "rchar=${io_stat1[0]}"        >> $trace_file
-    echo "wchar=${io_stat1[1]}"        >> $trace_file
-    echo "syscr=${io_stat1[2]}"        >> $trace_file
-    echo "syscw=${io_stat1[3]}"        >> $trace_file
-    echo "read_bytes=${io_stat1[4]}"   >> $trace_file
-    echo "write_bytes=${io_stat1[5]}"  >> $trace_file
+    printf "%s\n" \
+        "nextflow.trace/v2" \
+        "realtime=$wall_time" \
+        "%cpu=$ucpu" \
+        "cpu_model=$cpu_model" \
+        "rchar=${io_stat1[0]}" \
+        "wchar=${io_stat1[1]}" \
+        "syscr=${io_stat1[2]}" \
+        "syscw=${io_stat1[3]}" \
+        "read_bytes=${io_stat1[4]}" \
+        "write_bytes=${io_stat1[5]}" > "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
 
     ## join nxf_mem_watch
     [ -e /proc/$mem_proc ] && eval "echo 'DONE' >&$mem_fd" || true

modules/nextflow/src/test/groovy/nextflow/scm/AzureRepositoryProviderTest.groovy

@@ -80,7 +80,7 @@ class AzureRepositoryProviderTest extends Specification {
         def obj = new ProviderConfig('azurerepos', config.providers.azurerepos as ConfigObject)
 
         expect:
-        new AzureRepositoryProvider('ORGANIZATION/PROJECT/hello', obj).getRepositoryUrl() == 'https://dev.azure.com/ORGANIZATION/PROJECT'
+        new AzureRepositoryProvider('ORGANIZATION/PROJECT/hello', obj).getRepositoryUrl() == 'https://dev.azure.com/ORGANIZATION/PROJECT/hello'
 
     }
 

modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt

@@ -98,26 +98,28 @@ nxf_mem_watch() {
         count=$((count+1))
     done
 
-    echo "%mem=${nxf_stat_ret[1]}"      >> $trace_file
-    echo "vmem=${nxf_stat_ret[2]}"      >> $trace_file
-    echo "rss=${nxf_stat_ret[3]}"       >> $trace_file
-    echo "peak_vmem=${nxf_stat_ret[4]}" >> $trace_file
-    echo "peak_rss=${nxf_stat_ret[5]}"  >> $trace_file
-    echo "vol_ctxt=${nxf_stat_ret[6]}"  >> $trace_file
-    echo "inv_ctxt=${nxf_stat_ret[7]}"  >> $trace_file
+    printf "%s\n" \
+        "%mem=${nxf_stat_ret[1]}" \
+        "vmem=${nxf_stat_ret[2]}" \
+        "rss=${nxf_stat_ret[3]}" \
+        "peak_vmem=${nxf_stat_ret[4]}" \
+        "peak_rss=${nxf_stat_ret[5]}" \
+        "vol_ctxt=${nxf_stat_ret[6]}" \
+        "inv_ctxt=${nxf_stat_ret[7]}" >> "$trace_file" || >&2 echo "Error: Failed to append to file: $trace_file"
 }
 
 nxf_write_trace() {
-    echo "nextflow.trace/v2"           > $trace_file
-    echo "realtime=$wall_time"         >> $trace_file
-    echo "%cpu=$ucpu"                  >> $trace_file
-    echo "cpu_model=$cpu_model"        >> $trace_file
-    echo "rchar=${io_stat1[0]}"        >> $trace_file
-    echo "wchar=${io_stat1[1]}"        >> $trace_file
-    echo "syscr=${io_stat1[2]}"        >> $trace_file
-    echo "syscw=${io_stat1[3]}"        >> $trace_file
-    echo "read_bytes=${io_stat1[4]}"   >> $trace_file
-    echo "write_bytes=${io_stat1[5]}"  >> $trace_file
+    printf "%s\n" \
+        "nextflow.trace/v2" \
+        "realtime=$wall_time" \
+        "%cpu=$ucpu" \
+        "cpu_model=$cpu_model" \
+        "rchar=${io_stat1[0]}" \
+        "wchar=${io_stat1[1]}" \
+        "syscr=${io_stat1[2]}" \
+        "syscw=${io_stat1[3]}" \
+        "read_bytes=${io_stat1[4]}" \
+        "write_bytes=${io_stat1[5]}" > "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
 }
 
 nxf_trace_mac() {
@@ -173,16 +175,17 @@ nxf_trace_linux() {
     local wall_time=$((end_millis-start_millis))
     [ $NXF_DEBUG = 1 ] && echo "+++ STATS %CPU=$ucpu TIME=$wall_time I/O=${io_stat1[*]}"
 
-    echo "nextflow.trace/v2"           > $trace_file
-    echo "realtime=$wall_time"         >> $trace_file
-    echo "%cpu=$ucpu"                  >> $trace_file
-    echo "cpu_model=$cpu_model"        >> $trace_file
-    echo "rchar=${io_stat1[0]}"        >> $trace_file
-    echo "wchar=${io_stat1[1]}"        >> $trace_file
-    echo "syscr=${io_stat1[2]}"        >> $trace_file
-    echo "syscw=${io_stat1[3]}"        >> $trace_file
-    echo "read_bytes=${io_stat1[4]}"   >> $trace_file
-    echo "write_bytes=${io_stat1[5]}"  >> $trace_file
+    printf "%s\n" \
+        "nextflow.trace/v2" \
+        "realtime=$wall_time" \
+        "%cpu=$ucpu" \
+        "cpu_model=$cpu_model" \
+        "rchar=${io_stat1[0]}" \
+        "wchar=${io_stat1[1]}" \
+        "syscr=${io_stat1[2]}" \
+        "syscw=${io_stat1[3]}" \
+        "read_bytes=${io_stat1[4]}" \
+        "write_bytes=${io_stat1[5]}" > "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
 
     [ -e /proc/$mem_proc ] && eval "echo 'DONE' >&$mem_fd" || true
     wait $mem_proc 2>/dev/null || true

modules/nf-commons/build.gradle

@@ -27,7 +27,7 @@ sourceSets {
 dependencies {
     api "ch.qos.logback:logback-classic:1.4.14"
     api "org.apache.groovy:groovy:4.0.24"
-    api "org.apache.groovy:groovy-nio:4.0.23"
+    api "org.apache.groovy:groovy-nio:4.0.24"
     api "commons-lang:commons-lang:2.6"
     api 'com.google.guava:guava:33.0.0-jre'
     api 'org.pf4j:pf4j:3.12.0'

modules/nf-httpfs/build.gradle

@@ -31,11 +31,11 @@ dependencies {
     api project(':nf-commons')
     api "ch.qos.logback:logback-classic:1.4.14"
     api "org.apache.groovy:groovy:4.0.24"
-    api "org.apache.groovy:groovy-nio:4.0.23"
+    api "org.apache.groovy:groovy-nio:4.0.24"
     api("com.esotericsoftware.kryo:kryo:2.24.0") { exclude group: 'com.esotericsoftware.minlog', module: 'minlog' }
 
     /* testImplementation inherited from top gradle build file */
-    testImplementation "org.apache.groovy:groovy-json:4.0.23" // needed by wiremock
+    testImplementation "org.apache.groovy:groovy-json:4.0.24" // needed by wiremock
     testImplementation ('com.github.tomakehurst:wiremock:1.57') { exclude module: 'groovy-all' }
     testImplementation ('com.github.tomjankes:wiremock-groovy:0.2.0') { exclude module: 'groovy-all' }
 

plugins/nf-amazon/build.gradle

@@ -60,5 +60,5 @@ dependencies {
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }

plugins/nf-azure/build.gradle

@@ -53,5 +53,5 @@ dependencies {
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }

plugins/nf-cloudcache/build.gradle

@@ -36,6 +36,6 @@ dependencies {
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
 

plugins/nf-codecommit/build.gradle

@@ -43,5 +43,5 @@ dependencies {
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }

plugins/nf-console/build.gradle

@@ -38,13 +38,13 @@ dependencies {
     compileOnly 'org.pf4j:pf4j:3.12.0'
 
     api("org.apache.groovy:groovy-console:4.0.21-patch.2") { transitive=false }
-    api("org.apache.groovy:groovy-swing:4.0.23")  { transitive=false }
+    api("org.apache.groovy:groovy-swing:4.0.24")  { transitive=false }
     // this is required by 'groovy-console'  
     api("com.github.javaparser:javaparser-core:3.25.8")
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
 

plugins/nf-google/build.gradle

@@ -47,7 +47,7 @@ dependencies {
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
 
 test {