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Adding Github actions as an alternative to travis. (#1572)
* Adding Github actions as an alternative to travis. * This runs the same tests as travis does using github actions. * This currently doesn't upload artifacts to artifactory.
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‎.github/workflows/tests.yml‎

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# This is a github actions workflow which runs htsjdk tests and spotbugs.
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name: Build and Test
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on:
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push:
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branches: [master]
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pull_request:
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workflow_dispatch:
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jobs:
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test:
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env:
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HTSJDK_SAMTOOLS_BIN: /usr/bin/samtools
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runs-on: ubuntu-latest
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strategy:
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matrix:
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java: [ 8, 11 ]
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experimental: [false]
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# include:
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# - java: 17
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# experimental: true
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fail-fast: false
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continue-on-error: ${{ matrix.experimental }}
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name: Java ${{ matrix.Java }} build and test
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steps:
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- uses: actions/checkout@v2
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- name: Set up java ${{ matrix.Java }}
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uses: actions/setup-java@v2
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with:
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java-version: ${{ matrix.Java }}
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distribution: 'adopt'
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cache: gradle
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- name: Grant execute permission for gradlew
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run: chmod +x gradlew
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- name: Compile with Gradle
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run: ./gradlew compileJava
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- name: Install Samtools
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run: scripts/install-samtools.sh
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- name: Start the htsget server
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run: scripts/htsget-scripts/start-htsget-test-server.sh
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- name: Run tests
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run: ./gradlew test jacocoTestReport
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- name: Upload to codecov
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run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash)
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- name: Upload test results
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if: always()
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uses: actions/upload-artifact@v2
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with:
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name: test-results-${{ matrix.Java }}
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path: build/reports/tests
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testExternalApis:
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continue-on-error: true
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runs-on: ubuntu-latest
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name: Tests that require external APIs
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steps:
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- uses: actions/checkout@v2
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- name: Set up java 8
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uses: actions/setup-java@v2
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with:
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java-version: '8'
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distribution: 'adopt'
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cache: gradle
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- name: Grant execute permission for gradlew
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run: chmod +x gradlew
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- name: Compile with Gradle
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run: ./gradlew compileJava
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- name: Run tests
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run: ./gradlew testFTP jacocoTestReport
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- name: Upload to codecov
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run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash)
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- name: Upload test results
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if: always()
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uses: actions/upload-artifact@v2
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with:
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name: test-results-external-apis
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path: build/reports/tests
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testFTP:
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continue-on-error: true
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runs-on: ubuntu-latest
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name: FTP tests
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steps:
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- uses: actions/checkout@v2
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- name: Set up java 8
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uses: actions/setup-java@v2
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with:
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java-version: '8'
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distribution: 'adopt'
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cache: gradle
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- name: Grant execute permission for gradlew
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run: chmod +x gradlew
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- name: Compile with Gradle
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run: ./gradlew compileJava
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- name: Run tests
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run: ./gradlew testFTP jacocoTestReport
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- name: Upload to codecov
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run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash)
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- name: Upload test results
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if: always()
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uses: actions/upload-artifact@v2
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with:
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name: test-results-ftp
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path: build/reports/tests
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spotBugs:
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runs-on: ubuntu-latest
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name: SpotBugs
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steps:
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- uses: actions/checkout@v2
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- name: Set up java 8
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uses: actions/setup-java@v2
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with:
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java-version: '8'
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distribution: 'adopt'
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cache: gradle
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- name: Grant execute permission for gradlew
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run: chmod +x gradlew
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- name: Compile with Gradle
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run: ./gradlew spotBugsMain spotBugsTest
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- name: Upload spotBugs Report
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if: failure()
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uses: actions/upload-artifact@v2
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with:
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name: spotBugs-Report
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path: build/reports/spotbugs
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‎README.md‎

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[![Coverage Status](https://codecov.io/gh/samtools/htsjdk/branch/master/graph/badge.svg)](https://codecov.io/gh/samtools/htsjdk)
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[![Build Status](https://travis-ci.org/samtools/htsjdk.svg?branch=master)](https://travis-ci.org/samtools/htsjdk)
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[![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)
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[![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)
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[![License](http://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/samtools/htsjdk)
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[![Language](http://img.shields.io/badge/language-java-brightgreen.svg)](https://www.java.com/)

‎scripts/htsget-scripts/start-htsget-test-server.sh‎

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#!/bin/sh
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set -e
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set -v
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DOCKER_NAME='ga4gh/htsget-refserver'
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SERVER_VERSION='1.4.1'
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DOCKER_COORDINATE=${DOCKER_NAME}:${SERVER_VERSION}
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WORKING_DIR=/home/travis/build/samtools/htsjdk
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CONTAINER_NAME="htsget-test-server"
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docker pull ${DOCKER_COORDINATE}
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docker container run -d --name htsget-server -p 3000:3000 --env HTSGET_PORT=3000 --env HTSGET_HOST=http://127.0.0.1:3000 \
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-v $WORKING_DIR/src/test/resources/htsjdk/samtools/BAMFileIndexTest/:/data \
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-v $WORKING_DIR/scripts/htsget-scripts:/data/scripts \
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#Remove the container if it already exists
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docker rm -f ${CONTAINER_NAME} || true
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#Run the container set port mapping and mount in the data
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docker container run -d --name ${CONTAINER_NAME} -p 3000:3000 --env HTSGET_PORT=3000 --env HTSGET_HOST=http://127.0.0.1:3000 \
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-v ${PWD}/src/test/resources/htsjdk/samtools/BAMFileIndexTest/:/data \
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-v ${PWD}/scripts/htsget-scripts:/data/scripts \
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${DOCKER_COORDINATE} \
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./htsget-refserver -config /data/scripts/htsget_config.json
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#give it a second(s) to start
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sleep 2
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#List containers
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docker container ls -a
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curl http://localhost:3000
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#Check that we can connect
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curl http://localhost:3000/reads/service-info

‎src/test/java/htsjdk/tribble/IntervalList/IntervalListCodecTest.java‎

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@Test(dataProvider = "TribbleDecodeData")
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public void testTribbleDecodeCompressed(final File file) throws IOException {
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// compress 'file' to bgzf
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File tmpGz = File.createTempFile("htsjdk.", FileExtensions.COMPRESSED_INTERVAL_LIST, IOUtil.getDefaultTmpDir());
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File tmpGz = File.createTempFile("htsjdk.", FileExtensions.COMPRESSED_INTERVAL_LIST);
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try(BlockCompressedOutputStream bgz = new BlockCompressedOutputStream(tmpGz);
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FileInputStream fis = new FileInputStream(file)) {
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IOUtil.copyStream(fis,bgz);

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