release 5.8.5 #474
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| name: Build and Publish | |
| on: | |
| push: | |
| branches: | |
| - stable | |
| - master | |
| paths-ignore: | |
| - '**/README.md' | |
| - 'sirius_doc/**/*' | |
| jobs: | |
| # distCLI: | |
| # strategy: | |
| # matrix: | |
| # os: [ ubuntu-latest, windows-latest, macos-latest ] | |
| # runs-on: ${{ matrix.os }} | |
| # env: | |
| # GENERIC_INSTALLER_CERTIFICATE: ${{ secrets.GENERIC_INSTALLER_CERTIFICATE }} | |
| # MACOS_APP_IDENTITY_ID: ${{ secrets.MACOS_APP_IDENTITY_ID }} | |
| # MACOS_IDENTITY_ID: ${{ secrets.MACOS_IDENTITY_ID }} | |
| # MACOS_APPLE_ID: ${{ secrets.MACOS_APPLE_ID }} | |
| # MACOS_APPLE_ID_PW: ${{ secrets.MACOS_APPLE_ID_PW }} | |
| # MACOS_TEAM_ID : ${{ secrets.MACOS_TEAM_ID }} | |
| # SIRIUS_USER: ${{ secrets.SIRIUS_USER }} | |
| # SIRIUS_PW: ${{ secrets.SIRIUS_PW }} | |
| # # LINUX_INSTALLER_CERTIFICATE_FILE: ${{ steps.generic_codesign_cert.outputs.filePath }} | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # - name: Set up Zulu JDK | |
| # uses: actions/setup-java@v1 | |
| # with: | |
| # java-version: '17' # The JDK version to make available on the path. | |
| # java-package: jdk # (jre, jdk, or jdk+fx) - defaults to jdk | |
| # architecture: x64 # (x64 or x86) - defaults to x64 | |
| # - name: Load Build properties | |
| # uses: Reedyuk/[email protected] | |
| # id: sirius_version | |
| # with: | |
| # path: './sirius_cli/src/main/resources/sirius_frontend.build.properties' | |
| # property: 'de.unijena.bioinf.siriusFrontend.version' | |
| # | |
| # - if: ${{ (matrix.os == 'macos-latest') && (env.MACOS_APP_IDENTITY_ID != '') }} | |
| # name: Import Apple APP Code-signing ID and p12 | |
| # uses: apple-actions/import-codesign-certs@v1 | |
| # with: | |
| # keychain-password: ${{ secrets.MACOS_TMP_KEYCHAIN_PWD }} | |
| # p12-file-base64: ${{ secrets.MACOS_APP_CERTIFICATE }} | |
| # p12-password: ${{ secrets.MACOS_APP_CERTIFICATE_PWD }} | |
| # | |
| # - if: ${{ (matrix.os == 'macos-latest') && (env.MACOS_IDENTITY_ID != '') }} | |
| # name: Import Apple Installer Code-signing ID and p12 | |
| # uses: apple-actions/import-codesign-certs@v1 | |
| # with: | |
| # create-keychain: false | |
| # keychain-password: ${{ secrets.MACOS_TMP_KEYCHAIN_PWD }} | |
| # p12-file-base64: ${{ secrets.MACOS_CERTIFICATE }} | |
| # p12-password: ${{ secrets.MACOS_CERTIFICATE_PWD }} | |
| # | |
| # - if: matrix.os == 'macos-latest' | |
| # name: Check Identities | |
| # run: /usr/bin/security find-identity | |
| # | |
| # - if: ${{ (matrix.os == 'windows-latest' || matrix.os == 'ubuntu-latest') && (env.GENERIC_INSTALLER_CERTIFICATE != '') }} | |
| # name: Load generic installer codesign cert | |
| # id: generic_codesign_cert | |
| # uses: timheuer/[email protected] | |
| # with: | |
| # fileName: 'generic_installer_cert.p12' | |
| # encodedString: ${{ env.GENERIC_INSTALLER_CERTIFICATE }} | |
| # | |
| # - name: Gradle Build | |
| # uses: eskatos/gradle-command-action@v1 | |
| # env: | |
| # WIN_INSTALLER_CERTIFICATE_FILE: ${{ steps.generic_codesign_cert.outputs.filePath }} | |
| # with: | |
| # gradle-version: 7.6 | |
| # build-root-directory: sirius_dist/sirius_cli_single_os | |
| # arguments: clean publishSiriusPublicationToMavenLocal -P "build.sirius.native.openjfx.exclude=true" -P "build.sirius.starter.jdk.include=true" -P "de.unijena.bioinf.build.MACOS_TEAM_ID=${{ secrets.MACOS_TEAM_ID }}" -P "de.unijena.bioinf.build.MACOS_APP_IDENTITY_ID=${{ secrets.MACOS_APP_IDENTITY_ID }}" -P "de.unijena.bioinf.build.MACOS_IDENTITY_ID=${{ secrets.MACOS_IDENTITY_ID }}" -P "de.unijena.bioinf.build.MACOS_APPLE_ID=${{ secrets.MACOS_APPLE_ID }}" -P "de.unijena.bioinf.build.MACOS_APPLE_ID_PW=${{ secrets.MACOS_APPLE_ID_PW }}" -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_FILE=${{ steps.generic_codesign_cert.outputs.filePath }}" -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_PW=${{ secrets.GENERIC_INSTALLER_CERTIFICATE_PW }}" -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_TIMESTAMP_URL=${{ secrets.GENERIC_INSTALLER_CERTIFICATE_TIMESTAMP_URL }}" | |
| # | |
| # - name: Sirius Run | |
| # run: | | |
| # TEMP_DIR="$(cd "$(dirname "sirius_cli/src/test/temp_results")"; pwd -P)/$(basename "sirius_cli/src/test/temp_results")" | |
| # mkdir "${TEMP_DIR}" "${TEMP_DIR}/mgf_temp_output" "${TEMP_DIR}/mgf_temp_summary" "${TEMP_DIR}/ms_temp_output" "${TEMP_DIR}/ms_temp_summary" "${TEMP_DIR}/txt_temp_output" "${TEMP_DIR}/txt_temp_summary" | |
| # DEMO_DIR="$(cd "$(dirname "sirius_doc/manual/demo-data")"; pwd -P)/$(basename "sirius_doc/manual/demo-data")" | |
| # MGF_DATA="${DEMO_DIR}/mgf/laudanosine.mgf" | |
| # MS_DATA="${DEMO_DIR}/ms/Bicuculline.ms" | |
| # TXT_DATA_1="${DEMO_DIR}/txt/chelidonine_ms.txt" | |
| # TXT_DATA_2="${DEMO_DIR}/txt/chelidonine_msms1.txt,${DEMO_DIR}/txt/chelidonine_msms2.txt" | |
| # MGF_OUTPUT="${TEMP_DIR}/mgf_temp_output" | |
| # MGF_SUMMARY="${TEMP_DIR}/mgf_temp_summary" | |
| # MS_OUTPUT="${TEMP_DIR}/ms_temp_output" | |
| # MS_SUMMARY="${TEMP_DIR}/ms_temp_summary" | |
| # TXT_OUTPUT="${TEMP_DIR}/txt_temp_output" | |
| # TXT_SUMMARY="${TEMP_DIR}/txt_temp_summary" | |
| # case "$OSTYPE" in | |
| # darwin*) SIRIUS="./sirius_dist/sirius_cli_single_os/build/distributions/sirius.app/Contents/MacOS/sirius" ;; | |
| # linux*) SIRIUS="./sirius_dist/sirius_cli_single_os/build/distributions/sirius/bin/sirius" ;; | |
| # msys*) SIRIUS="./sirius_dist/sirius_cli_single_os/build/distributions/sirius/sirius.exe" ;; | |
| # *) echo "Error: Could not find OS."; exit 1 ;; | |
| # esac | |
| # ${SIRIUS} login --user-env SIRIUS_USER --password-env SIRIUS_PW | |
| # ${SIRIUS} --input ${MGF_DATA} --output ${MGF_OUTPUT} formula -p orbitrap fingerprint structure compound-classes write-summaries --output ${MGF_SUMMARY} | |
| # ${SIRIUS} -1 ${TXT_DATA_1} -2 ${TXT_DATA_2} -z 354.134704589844 -o ${TXT_OUTPUT} formula -p orbitrap write-summaries --output ${TXT_SUMMARY} | |
| # ${SIRIUS} -o ${MS_OUTPUT} -i ${MS_DATA} --ignore-formula formula -p orbitrap -c 5 fingerprint structure compound-classes write-summaries --output ${MS_SUMMARY} | |
| # shell: bash | |
| # | |
| # - name: Sirius MGF Test | |
| # run: | | |
| # RESULTS="sirius_cli/src/test/temp_results/" | |
| # OUTPUT="${RESULTS}mgf_temp_output/1_laudanosine_FEATURE_1/" | |
| # SUMMARY="${RESULTS}mgf_temp_summary/1_laudanosine_FEATURE_1/" | |
| # CANOPUS="${OUTPUT}canopus/" | |
| # CANOPUS_NPC="${OUTPUT}canopus_npc/" | |
| # FINGERPRINTS="${OUTPUT}fingerprints/" | |
| # FINGER_ID="${OUTPUT}fingerid/" | |
| # DIRS=(${SUMMARY} ${OUTPUT} ${CANOPUS} ${CANOPUS_NPC} ${FINGERPRINTS} ${FINGER_ID}) | |
| # for DIR in "${DIRS[@]}" ; do | |
| # if [ -d "${DIR}" ]; then | |
| # echo "Found result directory ${DIR}..." | |
| # if [ "$(ls -A ${DIR})" ]; then | |
| # echo "${DIR} is not empty." | |
| # else | |
| # echo "Error: ${DIR} is empty." | |
| # exit 1 | |
| # fi | |
| # else | |
| # echo "Error: result directory ${DIR} not found." | |
| # exit 1 | |
| # fi | |
| # done | |
| # shell: bash | |
| # | |
| # - name: Sirius MS Test | |
| # run: | | |
| # RESULTS="sirius_cli/src/test/temp_results/" | |
| # OUTPUT="${RESULTS}ms_temp_output/1_Bicuculline_Bicuculline/" | |
| # SUMMARY="${RESULTS}ms_temp_summary/1_Bicuculline_Bicuculline/" | |
| # CANOPUS="${OUTPUT}canopus/" | |
| # CANOPUS_NPC="${OUTPUT}canopus_npc/" | |
| # FINGERPRINTS="${OUTPUT}fingerprints/" | |
| # FINGER_ID="${OUTPUT}fingerid/" | |
| # echo "${FINGER_ID}" | |
| # DIRS=(${SUMMARY} ${OUTPUT} ${CANOPUS} ${CANOPUS_NPC} ${FINGERPRINTS} ${FINGER_ID}) | |
| # echo "${DIRS}" | |
| # for DIR in "${DIRS[@]}" ; do | |
| # if [ -d "${DIR}" ]; then | |
| # echo "Found result directory ${DIR}..." | |
| # if [ "$(ls -A ${DIR})" ]; then | |
| # echo "${DIR} is not empty." | |
| # else | |
| # echo "Error: ${DIR} is empty." | |
| # exit 1 | |
| # fi | |
| # else | |
| # echo "Error: result directory ${DIR} not found." | |
| # exit 1 | |
| # fi | |
| # done | |
| # shell: bash | |
| # | |
| # - name: Sirius TXT Test | |
| # run: | | |
| # RESULTS="sirius_cli/src/test/temp_results/" | |
| # SUMMARY="${RESULTS}txt_temp_summary/1_unknown_/" | |
| # if [ -d "${SUMMARY}" ]; then | |
| # echo "Found result directory ${SUMMARY}..." | |
| # if [ "$(ls -A ${SUMMARY})" ]; then | |
| # echo "${SUMMARY} is not empty." | |
| # else | |
| # echo "Error: ${SUMMARY} is empty." | |
| # exit 1 | |
| # fi | |
| # else | |
| # echo "Error: result directory ${SUMMARY} not found." | |
| # exit 1 | |
| # fi | |
| # shell: bash | |
| # | |
| # - name: Sirius Run Cleanup | |
| # run: | | |
| # rm -r sirius_cli/src/test/temp_results | |
| # | |
| # - name: Upload Distributions | |
| # uses: actions/upload-artifact@v2 | |
| # with: | |
| # retention-days: 1 | |
| # name: "sirius-${{ steps.sirius_version.outputs.value }}-${{ runner.os }}-x86-64-headless" | |
| # path: | | |
| # ~/.m2/repository/de/unijena/bioinf/ms/sirius/${{ steps.sirius_version.outputs.value }}/*.zip | |
| # ~/.m2/repository/de/unijena/bioinf/ms/sirius/${{ steps.sirius_version.outputs.value }}/*.msi | |
| # ~/.m2/repository/de/unijena/bioinf/ms/sirius/${{ steps.sirius_version.outputs.value }}/*.pkg | |
| # ~/.m2/repository/de/unijena/bioinf/ms/sirius/${{ steps.sirius_version.outputs.value }}/*.deb | |
| # ~/.m2/repository/de/unijena/bioinf/ms/sirius/${{ steps.sirius_version.outputs.value }}/*.sha256 | |
| distGUI: | |
| strategy: | |
| matrix: | |
| os: [ ubuntu-latest, windows-latest, macos-latest ] | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| GENERIC_INSTALLER_CERTIFICATE: ${{ secrets.GENERIC_INSTALLER_CERTIFICATE }} | |
| MACOS_APP_IDENTITY_ID: ${{ secrets.MACOS_APP_IDENTITY_ID }} | |
| MACOS_IDENTITY_ID: ${{ secrets.MACOS_IDENTITY_ID }} | |
| MACOS_APPLE_ID: ${{ secrets.MACOS_APPLE_ID }} | |
| MACOS_APPLE_ID_PW: ${{ secrets.MACOS_APPLE_ID_PW }} | |
| MACOS_TEAM_ID : ${{ secrets.MACOS_TEAM_ID }} | |
| SIRIUS_USER: ${{ secrets.SIRIUS_USER }} | |
| SIRIUS_PW: ${{ secrets.SIRIUS_PW }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Zulu JDK-FX | |
| uses: actions/setup-java@v1 | |
| with: | |
| java-version: '17' # The JDK version to make available on the path. | |
| java-package: jdk # (jre, jdk, or jdk+fx) - defaults to jdk | |
| architecture: x64 # (x64 or x86) - defaults to x64 | |
| - name: Load Build properties | |
| uses: Reedyuk/[email protected] | |
| id: sirius_version | |
| with: | |
| path: './sirius_cli/src/main/resources/sirius_frontend.build.properties' | |
| property: 'de.unijena.bioinf.siriusFrontend.version' | |
| - if: ${{ (matrix.os == 'macos-latest') && (env.MACOS_APP_IDENTITY_ID != '') }} | |
| name: Import Apple APP Code-signing ID and p12 | |
| uses: apple-actions/import-codesign-certs@v1 | |
| with: | |
| keychain-password: ${{ secrets.MACOS_TMP_KEYCHAIN_PWD }} | |
| p12-file-base64: ${{ secrets.MACOS_APP_CERTIFICATE }} | |
| p12-password: ${{ secrets.MACOS_APP_CERTIFICATE_PWD }} | |
| - if: ${{ (matrix.os == 'macos-latest') && (env.MACOS_IDENTITY_ID != '') }} | |
| name: Import Apple Installer Code-signing ID and p12 | |
| uses: apple-actions/import-codesign-certs@v1 | |
| with: | |
| create-keychain: false | |
| keychain-password: ${{ secrets.MACOS_TMP_KEYCHAIN_PWD }} | |
| p12-file-base64: ${{ secrets.MACOS_CERTIFICATE }} | |
| p12-password: ${{ secrets.MACOS_CERTIFICATE_PWD }} | |
| - if: matrix.os == 'macos-latest' | |
| name: Check Identities | |
| run: /usr/bin/security find-identity | |
| - if: ${{ (matrix.os == 'windows-latest' || matrix.os == 'ubuntu-latest') && (env.GENERIC_INSTALLER_CERTIFICATE != '') }} | |
| name: Load generic installer codesign cert | |
| id: generic_codesign_cert | |
| uses: timheuer/[email protected] | |
| with: | |
| fileName: 'generic_installer_cert.p12' | |
| encodedString: ${{ env.GENERIC_INSTALLER_CERTIFICATE }} | |
| - name: Gradle Build | |
| uses: eskatos/gradle-command-action@v1 | |
| env: | |
| WIN_INSTALLER_CERTIFICATE_FILE: ${{ steps.generic_codesign_cert.outputs.filePath }} | |
| with: | |
| gradle-version: 7.6 | |
| build-root-directory: sirius_dist/sirius_gui_dist | |
| arguments: clean publishSiriusPublicationToMavenLocal -P "build.sirius.native.openjfx.exclude=true" -P "build.sirius.starter.jdk.include=true" -P "de.unijena.bioinf.build.MACOS_TEAM_ID=${{ secrets.MACOS_TEAM_ID }}" -P "de.unijena.bioinf.build.MACOS_APP_IDENTITY_ID=${{ secrets.MACOS_APP_IDENTITY_ID }}" -P "de.unijena.bioinf.build.MACOS_IDENTITY_ID=${{ secrets.MACOS_IDENTITY_ID }}" -P "de.unijena.bioinf.build.MACOS_APPLE_ID=${{ secrets.MACOS_APPLE_ID }}" -P "de.unijena.bioinf.build.MACOS_APPLE_ID_PW=${{ secrets.MACOS_APPLE_ID_PW }}" -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_FILE=${{ steps.generic_codesign_cert.outputs.filePath }}" -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_PW=${{ secrets.GENERIC_INSTALLER_CERTIFICATE_PW }}" -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_TIMESTAMP_URL=${{ secrets.GENERIC_INSTALLER_CERTIFICATE_TIMESTAMP_URL }}" | |
| - name: Sirius Run | |
| run: | | |
| TEMP_DIR="$(cd "$(dirname "sirius_cli/src/test/temp_results")"; pwd -P)/$(basename "sirius_cli/src/test/temp_results")" | |
| mkdir "${TEMP_DIR}" "${TEMP_DIR}/mgf_temp_output" "${TEMP_DIR}/mgf_temp_summary" "${TEMP_DIR}/ms_temp_output" "${TEMP_DIR}/ms_temp_summary" "${TEMP_DIR}/txt_temp_output" "${TEMP_DIR}/txt_temp_summary" | |
| DEMO_DIR="$(cd "$(dirname "sirius_doc/manual/demo-data")"; pwd -P)/$(basename "sirius_doc/manual/demo-data")" | |
| MGF_DATA="${DEMO_DIR}/mgf/laudanosine.mgf" | |
| MS_DATA="${DEMO_DIR}/ms/Bicuculline.ms" | |
| TXT_DATA_1="${DEMO_DIR}/txt/chelidonine_ms.txt" | |
| TXT_DATA_2="${DEMO_DIR}/txt/chelidonine_msms1.txt,${DEMO_DIR}/txt/chelidonine_msms2.txt" | |
| MGF_OUTPUT="${TEMP_DIR}/mgf_temp_output" | |
| MGF_SUMMARY="${TEMP_DIR}/mgf_temp_summary" | |
| MS_OUTPUT="${TEMP_DIR}/ms_temp_output" | |
| MS_SUMMARY="${TEMP_DIR}/ms_temp_summary" | |
| TXT_OUTPUT="${TEMP_DIR}/txt_temp_output" | |
| TXT_SUMMARY="${TEMP_DIR}/txt_temp_summary" | |
| case "$OSTYPE" in | |
| darwin*) SIRIUS="./sirius_dist/sirius_gui_dist/build/distributions/sirius.app/Contents/MacOS/sirius" ;; | |
| linux*) SIRIUS="./sirius_dist/sirius_gui_dist/build/distributions/sirius/bin/sirius" ;; | |
| msys*) SIRIUS="./sirius_dist/sirius_gui_dist/build/distributions/sirius/sirius.exe" ;; | |
| *) echo "Error: Could not find OS."; exit 1 ;; | |
| esac | |
| ${SIRIUS} login --user-env SIRIUS_USER --password-env SIRIUS_PW | |
| ${SIRIUS} --input ${MGF_DATA} --output ${MGF_OUTPUT} formula -p orbitrap fingerprint structure compound-classes write-summaries --output ${MGF_SUMMARY} | |
| ${SIRIUS} -1 ${TXT_DATA_1} -2 ${TXT_DATA_2} -z 354.134704589844 -o ${TXT_OUTPUT} formula -p orbitrap write-summaries --output ${TXT_SUMMARY} | |
| ${SIRIUS} -o ${MS_OUTPUT} -i ${MS_DATA} --ignore-formula formula -p orbitrap -c 5 fingerprint structure compound-classes write-summaries --output ${MS_SUMMARY} | |
| shell: bash | |
| - name: Sirius MGF Test | |
| run: | | |
| RESULTS="sirius_cli/src/test/temp_results/" | |
| OUTPUT="${RESULTS}mgf_temp_output/1_laudanosine_FEATURE_1/" | |
| SUMMARY="${RESULTS}mgf_temp_summary/1_laudanosine_FEATURE_1/" | |
| CANOPUS="${OUTPUT}canopus/" | |
| CANOPUS_NPC="${OUTPUT}canopus_npc/" | |
| FINGERPRINTS="${OUTPUT}fingerprints/" | |
| FINGER_ID="${OUTPUT}fingerid/" | |
| DIRS=(${SUMMARY} ${OUTPUT} ${CANOPUS} ${CANOPUS_NPC} ${FINGERPRINTS} ${FINGER_ID}) | |
| for DIR in "${DIRS[@]}" ; do | |
| if [ -d "${DIR}" ]; then | |
| echo "Found result directory ${DIR}..." | |
| if [ "$(ls -A ${DIR})" ]; then | |
| echo "${DIR} is not empty." | |
| else | |
| echo "Error: ${DIR} is empty." | |
| exit 1 | |
| fi | |
| else | |
| echo "Error: result directory ${DIR} not found." | |
| exit 1 | |
| fi | |
| done | |
| shell: bash | |
| - name: Sirius MS Test | |
| run: | | |
| RESULTS="sirius_cli/src/test/temp_results/" | |
| OUTPUT="${RESULTS}ms_temp_output/1_Bicuculline_Bicuculline/" | |
| SUMMARY="${RESULTS}ms_temp_summary/1_Bicuculline_Bicuculline/" | |
| CANOPUS="${OUTPUT}canopus/" | |
| CANOPUS_NPC="${OUTPUT}canopus_npc/" | |
| FINGERPRINTS="${OUTPUT}fingerprints/" | |
| FINGER_ID="${OUTPUT}fingerid/" | |
| echo "${FINGER_ID}" | |
| DIRS=(${SUMMARY} ${OUTPUT} ${CANOPUS} ${CANOPUS_NPC} ${FINGERPRINTS} ${FINGER_ID}) | |
| echo "${DIRS}" | |
| for DIR in "${DIRS[@]}" ; do | |
| if [ -d "${DIR}" ]; then | |
| echo "Found result directory ${DIR}..." | |
| if [ "$(ls -A ${DIR})" ]; then | |
| echo "${DIR} is not empty." | |
| else | |
| echo "Error: ${DIR} is empty." | |
| exit 1 | |
| fi | |
| else | |
| echo "Error: result directory ${DIR} not found." | |
| exit 1 | |
| fi | |
| done | |
| shell: bash | |
| - name: Sirius TXT Test | |
| run: | | |
| RESULTS="sirius_cli/src/test/temp_results/" | |
| SUMMARY="${RESULTS}txt_temp_summary/1_unknown_/" | |
| if [ -d "${SUMMARY}" ]; then | |
| echo "Found result directory ${SUMMARY}..." | |
| if [ "$(ls -A ${SUMMARY})" ]; then | |
| echo "${SUMMARY} is not empty." | |
| else | |
| echo "Error: ${SUMMARY} is empty." | |
| exit 1 | |
| fi | |
| else | |
| echo "Error: result directory ${SUMMARY} not found." | |
| exit 1 | |
| fi | |
| shell: bash | |
| - name: Sirius Run Cleanup | |
| run: | | |
| rm -r sirius_cli/src/test/temp_results | |
| - name: Upload Distributions | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| retention-days: 1 | |
| name: "sirius-${{ steps.sirius_version.outputs.value }}-${{ runner.os }}-x86-64" | |
| path: | | |
| ~/.m2/repository/de/unijena/bioinf/ms/sirius/${{ steps.sirius_version.outputs.value }}/*.zip | |
| ~/.m2/repository/de/unijena/bioinf/ms/sirius/${{ steps.sirius_version.outputs.value }}/*.msi | |
| ~/.m2/repository/de/unijena/bioinf/ms/sirius/${{ steps.sirius_version.outputs.value }}/*.pkg | |
| ~/.m2/repository/de/unijena/bioinf/ms/sirius/${{ steps.sirius_version.outputs.value }}/*.deb | |
| ~/.m2/repository/de/unijena/bioinf/ms/sirius/${{ steps.sirius_version.outputs.value }}/*.sha256 | |
| dockergen: | |
| needs: [ distGUI ] | |
| uses: ./.github/workflows/dockergen.yaml | |
| secrets: inherit | |
| release: | |
| needs: [distGUI] | |
| # needs: [ distCLI, distGUI] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Inject slug/short variables | |
| uses: rlespinasse/[email protected] | |
| - name: Load Build properties | |
| uses: Reedyuk/[email protected] | |
| id: sirius_version | |
| with: | |
| path: './sirius_cli/src/main/resources/sirius_frontend.build.properties' | |
| property: 'de.unijena.bioinf.siriusFrontend.version' | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| path: sirius_dist/build/tmp/artifacts/ | |
| - name: Display downloaded artifact files | |
| run: ls -lah | |
| working-directory: sirius_dist/build/tmp/artifacts/ | |
| - uses: ncipollo/release-action@v1 | |
| with: | |
| artifacts: "sirius_dist/build/tmp/artifacts/*/*" | |
| body: | | |
| ### Prebuilt SIRIUS releases for all supported platforms. | |
| Installers provided by [Bright Giant](https://github.com/bright-giant/sirius/releases/) are identical to the ones provided by the [Böckerlab](https://github.com/boecker-lab/sirius/releases) but are digitally signed which eases installation on Windows and MacOS. | |
| Package names are made up as follows: `<App Name>-<Version>-<Operating System>-<Flavor>.<PackageType>`. Package types are either generic `.zip` archives or operating system specific installers (e.g. `.pkg` or `.msi`). The flavors describe builds with different features: | |
| * no _Flavor_ suffix represents for the standard SIRIUS package that contains the Graphical User Interface (GUI) and the Command Line Tool (CLI) | |
| * `headless` represents a command line only version that does not contain GUI relevant packages. It is smaller and does not need any GUI libraries installed on the users system (good for servers). | |
| * `service` like standard but additionally contains the experimental _service mode_ of SIRIUS which allows to start SIRIUS as a background service that can be queried form scripting languages or as part of workflows. See the [online documentation](https://boecker-lab.github.io/docs.sirius.github.io/quick-start/#background-service---generic-sirius-api) for details. | |
| Changelog can be found [here](https://boecker-lab.github.io/docs.sirius.github.io/changelog/). | |
| name: "SIRIUS v${{ steps.sirius_version.outputs.value }}" | |
| tag: "v${{ steps.sirius_version.outputs.value }}" | |
| prerelease: ${{ endsWith(steps.sirius_version.outputs.value, '-SNAPSHOT') }} | |
| allowUpdates: ${{ endsWith(steps.sirius_version.outputs.value, '-SNAPSHOT') }} | |
| draft: ${{ env.GITHUB_REF_SLUG == 'stable' && 'false' || 'true' }} | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| trigger-client-api-build: | |
| needs: [ release ] | |
| runs-on: ubuntu-latest | |
| env: | |
| CLIENT_API_REPO_URL: ${{ secrets.CLIENT_API_REPO_URL }} | |
| CLIENT_API_REPO_TOKEN: ${{ secrets.CLIENT_API_REPO_TOKEN }} | |
| steps: | |
| - if: ${{ (env.CLIENT_API_REPO_URL != '') && (env.CLIENT_API_REPO_TOKEN != '') }} | |
| name: Trigger Actions on sirius-client-openAPI | |
| run: curl -X POST -H "Authorization:Bearer ${{ secrets.CLIENT_API_REPO_TOKEN }}" -H "Accept:application/vnd.github.v3+json" ${{ secrets.CLIENT_API_REPO_URL }} -d '{"ref":"master"}' |