Fix release signing gate; bump next version shape; refresh Maven badge; CI improvements (#1781)

* Fix release signing gate; bump next version shape; refresh Maven badge.
* CI: drop runner-wide apt upgrade, cache samtools build, modernize actions, upgrade to latest samtools
* CI: use gradle/actions/setup-gradle to cache the wrapper distribution.
* Make samtools version test a ">=" check.

Author: tfenne

.github/workflows/tests.yml

@@ -10,7 +10,8 @@ on:
 jobs:
   test:
     env:
-      HTSJDK_SAMTOOLS_BIN: /usr/bin/samtools
+      HTSJDK_SAMTOOLS_BIN: /usr/local/bin/samtools
+      SAMTOOLS_VERSION: 1.23.1
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -20,20 +21,28 @@ jobs:
     continue-on-error: ${{ matrix.experimental }}
     name: Java ${{ matrix.Java }} build and test
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # full history + tags so palantir/git-version sees the latest release tag
       - name: Set up java ${{ matrix.Java }}
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: ${{ matrix.Java }}
-          distribution: 'adopt'
-          cache: gradle
+          distribution: 'temurin'
+      - name: Set up Gradle
+        uses: gradle/actions/setup-gradle@v4
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
       - name: Compile with Gradle
         run: ./gradlew compileJava
+      - name: Cache samtools
+        id: cache-samtools
+        uses: actions/cache@v4
+        with:
+          path: /usr/local/bin/samtools
+          key: samtools-${{ env.SAMTOOLS_VERSION }}-${{ runner.os }}
       - name: Install Samtools
+        if: steps.cache-samtools.outputs.cache-hit != 'true'
         run: scripts/install-samtools.sh
       - name: Start the htsget server
         run: scripts/htsget-scripts/start-htsget-test-server.sh
@@ -50,15 +59,16 @@ jobs:
     runs-on: ubuntu-latest
     name: Tests that require external APIs
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # full history + tags so palantir/git-version sees the latest release tag
       - name: Set up java 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '17'
-          distribution: 'adopt'
-          cache: gradle
+          distribution: 'temurin'
+      - name: Set up Gradle
+        uses: gradle/actions/setup-gradle@v4
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
       - name: Compile with Gradle
@@ -75,15 +85,16 @@ jobs:
     runs-on: ubuntu-latest
     name: Java Format Check
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # full history + tags so palantir/git-version sees the latest release tag
       - name: Set up java 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '17'
-          distribution: 'adopt'
-          cache: gradle
+          distribution: 'temurin'
+      - name: Set up Gradle
+        uses: gradle/actions/setup-gradle@v4
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
       - name: Verify formatting
@@ -92,15 +103,16 @@ jobs:
     runs-on: ubuntu-latest
     name: SpotBugs
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # full history + tags so palantir/git-version sees the latest release tag
       - name: Set up java 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '17'
-          distribution: 'adopt'
-          cache: gradle
+          distribution: 'temurin'
+      - name: Set up Gradle
+        uses: gradle/actions/setup-gradle@v4
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
       - name: Compile with Gradle
@@ -111,6 +123,3 @@ jobs:
         with:
           name: spotBugs-Report
           path: build/reports/spotbugs
-
-
-

README.md

@@ -1,5 +1,5 @@
 [![Build and Test](https://github.com/samtools/htsjdk/actions/workflows/tests.yml/badge.svg?branch=master&event=push)](https://github.com/samtools/htsjdk/actions/workflows/tests.yml)
-[![Maven Central](https://maven-badges.herokuapp.com/maven-central/com.github.samtools/htsjdk/badge.svg)](http://search.maven.org/#search%7Cga%7C1%7Cg%3A%22com.github.samtools%22%20AND%20a%3A%22htsjdk%22)
+[![Maven Central](https://img.shields.io/maven-central/v/com.github.samtools/htsjdk.svg?label=Maven%20Central)](https://central.sonatype.com/artifact/com.github.samtools/htsjdk)
 [![License](http://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/samtools/htsjdk)
 [![Language](http://img.shields.io/badge/language-java-brightgreen.svg)](https://www.java.com/)
 ## A Java API for high-throughput sequencing data (HTS) formats.

build.gradle

@@ -102,7 +102,7 @@ java {
 //
 // To change the planned bump (e.g. after a release lands), update nextVersionBump
 // below and commit.
-final nextVersionBump = "x"
+final nextVersionBump = "x.x.x"
 
 final isRelease = Boolean.getBoolean("release")
 final details = versionDetails()
@@ -189,7 +189,7 @@ tasks.withType(Test).configureEach { task ->
 
     // set heap size for the test JVM(s)
     task.minHeapSize = "1G"
-    task.maxHeapSize = "12G"
+    task.maxHeapSize = "14G"
 
     task.jvmArgs '-Djava.awt.headless=true'  //this prevents awt from displaying a java icon while the tests are running
 
@@ -352,9 +352,9 @@ publishing {
 signing {
     useGpgCmd()
     sign(publishing.publications.htsjdk)
-    required = { isRelease && gradle.taskGraph.hasTask("publishAllPublicationsToCentralPortal") }
+    required = { isRelease }
     tasks.withType(Sign).configureEach {
-        onlyIf { isRelease && gradle.taskGraph.hasTask("publishAllPublicationsToCentralPortal") }
+        onlyIf { isRelease }
     }
 }
 

gradle.properties

@@ -0,0 +1 @@
+org.gradle.jvmargs=-Xmx512m -XX:MaxMetaspaceSize=256m

scripts/install-samtools.sh

@@ -1,12 +1,11 @@
 #!/bin/sh
 set -ex
-#ubuntu specific
+# ubuntu specific
 sudo apt-get update
-sudo apt-get upgrade
 sudo apt-get install -y libncurses-dev libbz2-dev liblzma-dev
 
-#install from the github tar
-export SAMTOOLS_VERSION=1.21
+# install from the github tar
+export SAMTOOLS_VERSION=1.23.1
 wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2
 tar -xjvf samtools-${SAMTOOLS_VERSION}.tar.bz2
-cd samtools-${SAMTOOLS_VERSION} && ./configure --prefix=/usr && make && sudo make install
+cd samtools-${SAMTOOLS_VERSION} && ./configure --prefix=/usr/local && make && sudo make install

src/test/java/htsjdk/utils/SamtoolsTestUtils.java

@@ -8,13 +8,46 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * Test utilities for running samtools from htsjdk tests.
  */
 public class SamtoolsTestUtils {
     private static final String SAMTOOLS_BINARY_ENV_VARIABLE = "HTSJDK_SAMTOOLS_BIN";
-    public static final String expectedSamtoolsVersion = "1.21";
+    public static final String minimumSamtoolsVersion = "1.23.1";
+
+    private static final Pattern SAMTOOLS_VERSION_PATTERN = Pattern.compile("(?m)^samtools\\s+(\\d+(?:\\.\\d+)*)");
+
+    /**
+     * Extracts the version string (e.g. "1.23.1") from the output of `samtools --version`,
+     * which begins with a line of the form {@code samtools <version>}.
+     *
+     * @return the version string, or null if no version line was found.
+     */
+    static String parseSamtoolsVersion(final String samtoolsVersionOutput) {
+        final Matcher m = SAMTOOLS_VERSION_PATTERN.matcher(samtoolsVersionOutput);
+        return m.find() ? m.group(1) : null;
+    }
+
+    /**
+     * Compares two dotted-numeric version strings (e.g. "1.23.1") component-by-component.
+     * Missing trailing components are treated as zero, so "1.23" is equal to "1.23.0".
+     */
+    static int compareVersions(final String a, final String b) {
+        final String[] aParts = a.split("\\.");
+        final String[] bParts = b.split("\\.");
+        final int len = Math.max(aParts.length, bParts.length);
+        for (int i = 0; i < len; i++) {
+            final int av = i < aParts.length ? Integer.parseInt(aParts[i]) : 0;
+            final int bv = i < bParts.length ? Integer.parseInt(bParts[i]) : 0;
+            if (av != bv) {
+                return Integer.compare(av, bv);
+            }
+        }
+        return 0;
+    }
 
     /**
      * @return true if samtools is available, otherwise false

src/test/java/htsjdk/utils/SamtoolsTestUtilsTest.java

@@ -27,10 +27,52 @@ public void testSamtoolsVersion() {
         if (!SamtoolsTestUtils.isSamtoolsAvailable()) {
             throw new SkipException("Samtools not available on local device");
         }
-        // If this test runs, but fails because version validation fails, then the local samtools version is
-        // not the one expected by the htsjdk tests
         final ProcessExecutor.ExitStatusAndOutput processStatus = SamtoolsTestUtils.executeSamToolsCommand("--version");
-        Assert.assertTrue(processStatus.stdout.contains(SamtoolsTestUtils.expectedSamtoolsVersion));
+        final String localVersion = SamtoolsTestUtils.parseSamtoolsVersion(processStatus.stdout);
+        Assert.assertNotNull(
+                localVersion,
+                "Could not parse samtools version from `samtools --version` output: " + processStatus.stdout);
+        Assert.assertTrue(
+                SamtoolsTestUtils.compareVersions(localVersion, SamtoolsTestUtils.minimumSamtoolsVersion) >= 0,
+                "Local samtools version " + localVersion + " is older than the minimum required by htsjdk tests ("
+                        + SamtoolsTestUtils.minimumSamtoolsVersion + ")");
+    }
+
+    @Test
+    public void testParseSamtoolsVersionFromTypicalOutput() {
+        final String stdout = "samtools 1.23.1\nUsing htslib 1.23.1\nCopyright (C) 2024 Genome Research Ltd.\n";
+        Assert.assertEquals(SamtoolsTestUtils.parseSamtoolsVersion(stdout), "1.23.1");
+    }
+
+    @Test
+    public void testParseSamtoolsVersionTwoComponent() {
+        Assert.assertEquals(SamtoolsTestUtils.parseSamtoolsVersion("samtools 1.21\n"), "1.21");
+    }
+
+    @Test
+    public void testParseSamtoolsVersionReturnsNullWhenAbsent() {
+        Assert.assertNull(SamtoolsTestUtils.parseSamtoolsVersion("nothing recognizable here\n"));
+    }
+
+    @Test
+    public void testCompareVersionsEqualWithImplicitZero() {
+        Assert.assertEquals(SamtoolsTestUtils.compareVersions("1.23", "1.23.0"), 0);
+    }
+
+    @Test
+    public void testCompareVersionsPatchGreater() {
+        Assert.assertTrue(SamtoolsTestUtils.compareVersions("1.23.1", "1.23") > 0);
+    }
+
+    @Test
+    public void testCompareVersionsMajorLess() {
+        Assert.assertTrue(SamtoolsTestUtils.compareVersions("1.21", "1.23.1") < 0);
+    }
+
+    @Test
+    public void testCompareVersionsNumericNotLexical() {
+        // 1.10 is greater than 1.9 numerically, even though "1.10" sorts before "1.9" lexically.
+        Assert.assertTrue(SamtoolsTestUtils.compareVersions("1.10", "1.9") > 0);
     }
 
     @Test(expectedExceptions = RuntimeException.class)