From d76c5cd68974a8f27957cf633572e32ad7f27401 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Tue, 19 Dec 2023 14:03:17 -0500 Subject: [PATCH 1/3] Updating to require java 21 --- .github/workflows/cloud_tests.yml | 2 +- .github/workflows/tests.yml | 2 +- build.gradle | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/cloud_tests.yml b/.github/workflows/cloud_tests.yml index 24b32c4cc7..078a44f02c 100644 --- a/.github/workflows/cloud_tests.yml +++ b/.github/workflows/cloud_tests.yml @@ -33,7 +33,7 @@ jobs: needs: check-secrets strategy: matrix: - java: [ 17 ] + java: [ 21 ] run_barclay_tests: [true, false] experimental: [ false ] fail-fast: false diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 30fddcd431..3aaf903875 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - java: [ 17 ] + java: [ 21 ] experimental: [false] run_barclay_tests: [true, false] fail-fast: false diff --git a/build.gradle b/build.gradle index e77831db4c..f891dd10ef 100644 --- a/build.gradle +++ b/build.gradle @@ -70,7 +70,7 @@ dependencies { implementation 'org.apache.commons:commons-math3:3.6.1' implementation 'org.apache.commons:commons-collections4:4.4' implementation 'com.github.samtools:htsjdk:' + htsjdkVersion - implementation 'org.broadinstitute:barclay:5.0.0' + implementation 'org.broadinstitute:barclay:4.1.0-9-g264e876-SNAPSHOT' implementation 'org.apache.logging.log4j:log4j-api:2.20.0' implementation 'org.apache.logging.log4j:log4j-core:2.20.0' implementation 'org.openjdk.nashorn:nashorn-core:15.4' @@ -92,7 +92,7 @@ configurations.configureEach { java { toolchain { - languageVersion = JavaLanguageVersion.of(17) + languageVersion = JavaLanguageVersion.of(21) } withJavadocJar() withSourcesJar() From 184883bce79cdd5ff58b4757242a266ae67496ea Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Tue, 19 Dec 2023 14:19:56 -0500 Subject: [PATCH 2/3] fixup --- testdata/picard/util/BedToIntervalListTest/simple.bed | 1 - 1 file changed, 1 deletion(-) diff --git a/testdata/picard/util/BedToIntervalListTest/simple.bed b/testdata/picard/util/BedToIntervalListTest/simple.bed index 21389c645d..74cf130f94 100644 --- a/testdata/picard/util/BedToIntervalListTest/simple.bed +++ b/testdata/picard/util/BedToIntervalListTest/simple.bed @@ -1,3 +1,2 @@ - chr1 100 2000 chr1 3000 4000 From 3167faceb1a61f6b8d4055171d213ec93a27f2c3 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Tue, 19 Dec 2023 14:33:05 -0500 Subject: [PATCH 3/3] remove newly disallowed ; --- src/test/java/picard/util/GraphUtilsTest.java | 1 - 1 file changed, 1 deletion(-) diff --git a/src/test/java/picard/util/GraphUtilsTest.java b/src/test/java/picard/util/GraphUtilsTest.java index 47453406e4..685b8ca05f 100644 --- a/src/test/java/picard/util/GraphUtilsTest.java +++ b/src/test/java/picard/util/GraphUtilsTest.java @@ -1,6 +1,5 @@ package picard.util; -; import org.testng.annotations.Test; import java.util.Arrays;