Add pytorch-lightning to GATK conda env, temporarily disable jacoco i…

…n build.gradle
broadinstitute · Sep 27, 2024 · 9e8c3da · 9e8c3da
1 parent 22902a1
commit 9e8c3da
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Showing 3 changed files with 38 additions and 36 deletions.
diff --git a/build.gradle b/build.gradle
@@ -11,7 +11,7 @@ plugins {
  id "application" // provides installDist
  id 'maven-publish'
  id 'signing'
- id "jacoco"
+// id "jacoco"
  id "de.undercouch.download" version "5.4.0" //used for downloading GSA lib
  id "com.github.johnrengelman.shadow" version "8.1.1" //used to build the shadow and sparkJars
  id "com.github.ben-manes.versions" version "0.12.0" //used for identifying dependencies that need updating
@@ -625,18 +625,19 @@ task bundle(type: Zip) {
  }
 }
 
-jacocoTestReport {
- dependsOn test
-
- group = "Reporting"
- description = "Generate Jacoco coverage reports after running tests."
- getAdditionalSourceDirs().from(sourceSets.main.allJava.srcDirs)
-
- reports {
- xml.required = true
- html.required = true
- }
-}
+//jacocoTestReport {
+// dependsOn test
+//
+// group = "Reporting"
+// description = "Generate Jacoco coverage reports after running tests."
+// getAdditionalSourceDirs().from(sourceSets.main.allJava.srcDirs)
+//
+// reports {
+// xml.required = true
+// html.required = true
+// }
+//}
+//}
 
 task condaStandardEnvironmentDefinition(type: Copy) {
  from "scripts"

diff --git a/scripts/docker/dockertest.gradle b/scripts/docker/dockertest.gradle
@@ -8,7 +8,7 @@ buildscript {
 
 plugins {
  id "java" // set up default java compile and test tasks
- id "jacoco"
+// id "jacoco"
 }
 
 repositories {
@@ -113,9 +113,9 @@ def getJVMArgs(runtimeAddOpens, testAddOpens) {
 
 test {
  jvmArgs = getJVMArgs(runtimeAddOpens, testAddOpens)
- jacoco {
- jvmArgs = getJVMArgs(runtimeAddOpens, testAddOpens)
- }
+// jacoco {
+// jvmArgs = getJVMArgs(runtimeAddOpens, testAddOpens)
+// }
 }
 
 task testOnPackagedReleaseJar(type: Test){
@@ -153,22 +153,22 @@ task testOnPackagedReleaseJar(type: Test){
 
 // Task intended to collect coverage data from testOnPackagedReleaseJar executed inside the docker image
 // the classpath for these tests is set at execution time for testOnPackagedReleaseJar
-task jacocoTestReportOnPackagedReleaseJar(type: JacocoReport) {
- String sourceFiles = "$System.env.SOURCE_DIR"
- String testClassesUnpacked = "$System.env.CP_DIR"
-
- dependsOn testOnPackagedReleaseJar
- executionData testOnPackagedReleaseJar
- additionalSourceDirs.setFrom(sourceSets.main.allJava.srcDirs)
-
- sourceDirectories.setFrom(sourceFiles)
- classDirectories.setFrom(testClassesUnpacked)
-
- group = "Reporting"
- description = "Generate Jacoco coverage reports after running tests inside the docker image."
-
- reports {
- xml.required = true
- html.required = true
- }
-}
+//task jacocoTestReportOnPackagedReleaseJar(type: JacocoReport) {
+// String sourceFiles = "$System.env.SOURCE_DIR"
+// String testClassesUnpacked = "$System.env.CP_DIR"
+//
+// dependsOn testOnPackagedReleaseJar
+// executionData testOnPackagedReleaseJar
+// additionalSourceDirs.setFrom(sourceSets.main.allJava.srcDirs)
+//
+// sourceDirectories.setFrom(sourceFiles)
+// classDirectories.setFrom(testClassesUnpacked)
+//
+// group = "Reporting"
+// description = "Generate Jacoco coverage reports after running tests inside the docker image."
+//
+// reports {
+// xml.required = true
+// html.required = true
+// }
+//}
diff --git a/scripts/gatkcondaenv.yml.template b/scripts/gatkcondaenv.yml.template
@@ -30,6 +30,7 @@ dependencies:
 - conda-forge::scipy=1.11.4
 - conda-forge::h5py=3.10.0
 - conda-forge::pytorch=2.1.0=*mkl*100
+- conda-forge::pytorch-lightning=2.4.0 # supports Pytorch >= 2.1 and <= 2.4
 - conda-forge::scikit-learn=1.3.2
 - conda-forge::matplotlib=3.8.2
 - conda-forge::pandas=2.1.3