fix bug in MS1 annotation #77
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| name: Build executable for Windows | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| jobs: | |
| build-openms: | |
| runs-on: windows-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: OpenMS/OpenMS | |
| ref: develop # take latest develop due to changes to SiriusAdapter | |
| 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' | |
| run: | | |
| cd OpenMS/contrib | |
| curl -o contribbld.tar.gz https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/windows/x64/msvc-14.2/contrib_build.tar.gz | |
| tar -xzf contribbld.tar.gz | |
| rm contribbld.tar.gz | |
| - 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@v3 | |
| with: | |
| name: OpenMS-bin | |
| path: OpenMS/bld/bin | |
| - name: Upload share as artifact | |
| uses: actions/upload-artifact@v3 | |
| 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@v3 | |
| - name: Download TOPP tools as artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: OpenMS-bin | |
| path: openms-bin | |
| - name: Download share as artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: OpenMS-share | |
| path: share | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| - name: Setup virtual environment | |
| shell: cmd | |
| run: | | |
| python -m venv myenv | |
| call myenv\Scripts\activate.bat | |
| pip install -r requirements.txt | |
| pip install pyinstaller | |
| - name: Write function to cli.py | |
| shell: bash | |
| run: | | |
| head -n -2 D:/a/streamlit-template/streamlit-template/myenv/Lib/site-packages/streamlit/web/cli.py > temp_cli.py | |
| cat << EOF >> temp_cli.py | |
| def _main_run_clExplicit(file, command_line, args=[], flag_options=[]): | |
| main._is_running_with_streamlit = True | |
| bootstrap.run(file, command_line, args, flag_options) | |
| if __name__ == "__main__": | |
| main() | |
| EOF | |
| mv temp_cli.py D:/a/streamlit-template/streamlit-template/myenv/Lib/site-packages/streamlit/web/cli.py | |
| - name: Compile app with pyinstaller | |
| shell: cmd | |
| run: | | |
| call myenv\Scripts\activate.bat | |
| pyinstaller --onefile --additional-hooks-dir ./hooks run_app.py --clean | |
| - name: Copy everything to dist directory | |
| run: | | |
| cp -r .streamlit dist/.streamlit | |
| cp -r pages dist/pages | |
| cp -r src dist/src | |
| cp -r assets dist/assets | |
| cp -r example-data dist/example-data | |
| cp -r openms-bin dist/bin | |
| cp -r share dist/share | |
| cp Home.py dist/ | |
| - name: Modify .spec file | |
| shell: bash | |
| run: | | |
| cp run_app_temp.spec run_app.spec | |
| - name: Make executable | |
| shell: cmd | |
| run: | | |
| call myenv\Scripts\activate.bat | |
| pyinstaller run_app.spec --clean | |
| - name: Delete OpenMS bin artifact | |
| uses: geekyeggo/delete-artifact@v2 | |
| with: | |
| name: OpenMS-bin | |
| - name: Delete OpenMS share artifact | |
| uses: geekyeggo/delete-artifact@v2 | |
| with: | |
| name: OpenMS-share | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: UmetaFlow-App | |
| path: dist |