fix check for SIRIUS annotation #93
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| name: Build executable for Windows | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| workflow_dispatch: | |
| jobs: | |
| build-openms: | |
| runs-on: windows-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: OpenMS/OpenMS | |
| ref: develop | |
| path: 'OpenMS' | |
| - name: Install Qt | |
| uses: jurplel/install-qt-action@v3 | |
| with: | |
| version: '5.15.2' # 5.12.7 is broken https://bugreports.qt.io/browse/QTBUG-81715, > 5.15.2 is not available on official archives (https://github.com/miurahr/aqtinstall/issues/636) | |
| host: 'windows' # default: win64_msvc2017_64 | |
| target: 'desktop' | |
| install-deps: 'true' | |
| cache: 'false' | |
| aqtversion: '==3.1.*' | |
| # https://github.com/marketplace/actions/visual-studio-shell | |
| - name: Set up Visual Studio shell | |
| uses: egor-tensin/vs-shell@v2 | |
| with: | |
| arch: x64 | |
| - name: Setup build tools | |
| shell: bash | |
| run: | | |
| choco install ccache ninja cmake | |
| ## GH CLI "SHOULD BE" installed. Sometimes I had to manually install nonetheless. Super weird. | |
| # https://github.com/actions/runner-images/blob/main/images/win/scripts/Installers/Install-GitHub-CLI.ps1 | |
| echo "C:/Program Files (x86)/GitHub CLI" >> $GITHUB_PATH | |
| - name: Extract branch/PR infos | |
| shell: bash | |
| run: | | |
| cd OpenMS | |
| RUN_NAME_LOCAL=$(echo ${GITHUB_REF#refs/heads/} | tr / -) | |
| echo "RUN_NAME=${RUN_NAME_LOCAL}" >> $GITHUB_ENV | |
| echo "BASE_REF=$(gh pr view --json baseRefName -q .baseRefName || echo ${RUN_NAME_LOCAL})" >> $GITHUB_ENV | |
| id: extract_branch | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Cache contrib | |
| id: cache-contrib-win | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ github.workspace }}/OpenMS/contrib | |
| key: ${{ runner.os }}-contrib3 | |
| - name: Load contrib build | |
| if: steps.cache-contrib-win.outputs.cache-hit != 'true' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| cd OpenMS/contrib | |
| # Download the file using the URL fetched from GitHub | |
| gh release download -R OpenMS/contrib --pattern 'contrib_build-Windows.tar.gz' | |
| # Extract the archive | |
| 7z x -so contrib_build-Windows.tar.gz | 7z x -si -ttar | |
| rm contrib_build-Windows.tar.gz | |
| ls | |
| - name: Setup ccache cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: .ccache | |
| key: ${{ runner.os }}-ccache-${{ env.RUN_NAME }}-${{ github.run_number }} | |
| # Restoring: From current branch, otherwise from base branch, otherwise from any branch. | |
| restore-keys: | | |
| ${{ runner.os }}-ccache-${{ env.RUN_NAME }} | |
| ${{ runner.os }}-ccache-${{ env.BASE_REF }} | |
| ${{ runner.os }}-ccache- | |
| - name: Add THIRDPARTY | |
| shell: bash | |
| run: | | |
| # initialize THIRDPARTY | |
| cd OpenMS | |
| git submodule update --init THIRDPARTY | |
| cd .. | |
| # add third-party binaries to PATH | |
| # use flat THIRDPARTY structure | |
| mkdir -p _thirdparty | |
| cp -R OpenMS/THIRDPARTY/Windows/64bit/* _thirdparty/ | |
| cp -R OpenMS/THIRDPARTY/All/* _thirdparty/ | |
| # add third-party binaries to PATH | |
| for thirdpartytool in ${{ github.workspace }}/_thirdparty/* | |
| do | |
| echo $thirdpartytool >> $GITHUB_PATH | |
| done | |
| - name: Build Windows | |
| shell: bash | |
| run: | | |
| mkdir $GITHUB_WORKSPACE/OpenMS/bld/ | |
| ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake | |
| env: | |
| #OS_PREFIX_PATH: "${{ env.Qt5_DIR }}/lib/cmake;${{ env.Qt5_DIR }}" | |
| CONTRIB_BUILD_DIRECTORY: "${{ github.workspace }}/OpenMS/contrib" | |
| CI_PROVIDER: "GitHub-Actions" | |
| CMAKE_GENERATOR: "Ninja" | |
| SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" | |
| BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}" | |
| ENABLE_STYLE_TESTING: "OFF" | |
| ENABLE_TOPP_TESTING: "ON" | |
| ENABLE_CLASS_TESTING: "ON" | |
| WITH_GUI: "ON" | |
| ADDRESS_SANITIZER: "Off" | |
| BUILD_TYPE: "Release" | |
| OPENMP: "Off" | |
| USE_STATIC_BOOST: "On" | |
| # BUILD_FLAGS: "-p:CL_MPCount=2" # For VS Generator and MSBuild | |
| BUILD_FLAGS: "-j2" # Ninja will otherwise use all cores (doesn't go well in GHA) | |
| CMAKE_CCACHE_EXE: "ccache" | |
| CCACHE_BASEDIR: ${{ github.workspace }} | |
| CCACHE_DIR: ${{ github.workspace }}/.ccache | |
| CCACHE_COMPRESS: true | |
| CCACHE_COMPRESSLEVEL: 12 | |
| CCACHE_MAXSIZE: 400M | |
| - name: Test Windows | |
| shell: bash | |
| run: $LAUNCHER ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake | |
| env: | |
| LAUNCHER: "" | |
| SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" | |
| CI_PROVIDER: "GitHub-Actions" | |
| BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}" | |
| - name: Upload TOPP tools as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: OpenMS-bin | |
| path: OpenMS/bld/bin | |
| - name: Upload share as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: OpenMS-share | |
| path: OpenMS/share | |
| build-executable: | |
| runs-on: windows-latest | |
| needs: build-openms | |
| env: | |
| PYTHON_VERSION: 3.11.0 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Download TOPP tools as artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: OpenMS-bin | |
| path: openms-bin | |
| - name: Download share as artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: OpenMS-share | |
| path: share | |
| - name: Setup python embeddable version | |
| run: | | |
| mkdir python-${{ env.PYTHON_VERSION }} | |
| curl -O https://www.python.org/ftp/python/${{ env.PYTHON_VERSION }}/python-${{ env.PYTHON_VERSION }}-embed-amd64.zip | |
| unzip python-${{ env.PYTHON_VERSION }}-embed-amd64.zip -d python-${{ env.PYTHON_VERSION }} | |
| rm python-${{ env.PYTHON_VERSION }}-embed-amd64.zip | |
| - name: Install pip | |
| run: | | |
| curl -O https://bootstrap.pypa.io/get-pip.py | |
| ./python-${{ env.PYTHON_VERSION }}/python get-pip.py --no-warn-script-location | |
| rm get-pip.py | |
| - name: Uncomment 'import site' in python311._pth file | |
| run: | | |
| sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python311._pth | |
| - name: Install Required Packages | |
| run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements.txt --no-warn-script-location | |
| - name: Create run_app.bat file | |
| run: | | |
| echo '@echo off' > UmetaFlow.bat | |
| echo '.\\python-${{ env.PYTHON_VERSION }}\\python -m streamlit run Home.py local' >> UmetaFlow.bat | |
| - name: Download and extract SIRIUS | |
| run: | | |
| curl -L -O https://github.com/sirius-ms/sirius/releases/download/v5.8.6/sirius-5.8.6-win64.zip | |
| unzip sirius-5.8.6-win64.zip | |
| - name: Create All-in-one executable folder | |
| run: | | |
| mkdir streamlit_exe | |
| mv python-${{ env.PYTHON_VERSION }} streamlit_exe | |
| mv UmetaFlow.bat streamlit_exe | |
| cp -r src streamlit_exe | |
| cp -r pages streamlit_exe | |
| cp -r assets streamlit_exe | |
| cp -r example-data streamlit_exe | |
| cp -r .streamlit streamlit_exe | |
| cp -r openms-bin streamlit_exe/bin | |
| cp -r share streamlit_exe/share | |
| cp -r sirius streamlit_exe/sirius | |
| cp Home.py streamlit_exe | |
| - name: Delete OpenMS bin artifact | |
| uses: geekyeggo/delete-artifact@v5 | |
| with: | |
| name: OpenMS-bin | |
| - name: Delete OpenMS share artifact | |
| uses: geekyeggo/delete-artifact@v5 | |
| with: | |
| name: OpenMS-share | |
| - name: Compress streamlit_exe folder to UmetaFlow-App.zip | |
| run: | | |
| 7z a UmetaFlow-App.zip ./streamlit_exe/* -r | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: UmetaFlow-App | |
| path: UmetaFlow-App.zip | |