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Arslan-SirajArslan-Siraj
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Merge pull request #22 from Arslan-Siraj/rescore
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‎.github/workflows/build-docker-images.yml‎

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name: Docker Image CI
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on:
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workflow_dispatch:
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push:
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branches: [ "main" ]
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pull_request:

‎.github/workflows/build-windows-executable-app.yaml‎

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workflow_dispatch:
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env:
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OPENMS_VERSION: 3.2.0
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OPENMS_VERSION: 3.5.0
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# Define unique GUID for UpgradeCode
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APP_UpgradeCode: "31703de0-3422-444a-a469-8df83635bd6d"
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# Define needed TOPP tools here
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TOPP_TOOLS: "OpenNuXL"
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jobs:
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build-openms:
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runs-on: windows-latest
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runs-on: windows-2022
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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with:
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repository: Arslan-Siraj/OpenMS #OpenMS/OpenMS
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ref: feature/NuXL #release/${{ env.OPENMS_VERSION }}
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repository: OpenMS/OpenMS
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ref: release/${{ env.OPENMS_VERSION }}
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path: 'OpenMS'
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- name: Install Qt
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- name: Install Qt (Windows)
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uses: jurplel/install-qt-action@v4
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with:
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version: '6.2.*' # 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)
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host: 'windows' # default: win64_msvc2017_64
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target: 'desktop'
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install-deps: 'true'
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version: '6.8.3' ## Note this version is build with win64_msvc2022_64 and should always match what we use
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arch: 'win64_msvc2022_64'
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cache: 'false'
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aqtversion: '==3.1.*'
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archives: 'qtsvg qtimageformats qtbase'
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# https://github.com/marketplace/actions/visual-studio-shell
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- name: Set up Visual Studio shell
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- name: Setup build tools
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shell: bash
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run: |
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choco install ccache ninja cmake
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choco install ccache ninja -y --no-progress
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choco install cmake --version=3.31.1 -y --no-progress --force
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## GH CLI "SHOULD BE" installed. Sometimes I had to manually install nonetheless. Super weird.
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# https://github.com/actions/runner-images/blob/main/images/win/scripts/Installers/Install-GitHub-CLI.ps1
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echo "C:/Program Files (x86)/GitHub CLI" >> $GITHUB_PATH
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rm contrib_build-Windows.tar.gz
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ls
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- name: Add contrib to PATH
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shell: bash
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run: |
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# Add contrib library path for runtime DLL resolution
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echo "${{ github.workspace }}/OpenMS/contrib/lib" >> $GITHUB_PATH
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- name: Setup ccache cache
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uses: actions/cache@v4
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with:
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# add third-party binaries to PATH
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# use flat THIRDPARTY structure
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mkdir -p _thirdparty
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cp -R OpenMS/THIRDPARTY/Windows/64bit/* _thirdparty/
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cp -R OpenMS/THIRDPARTY/Windows/x86_64/* _thirdparty/
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cp -R OpenMS/THIRDPARTY/All/* _thirdparty/
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# add third-party binaries to PATH
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for thirdpartytool in ${{ github.workspace }}/_thirdparty/*
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shell: bash
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run: |
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mkdir $GITHUB_WORKSPACE/OpenMS/bld/
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bash OpenMS/tools/ci/capture-env.sh -v $GITHUB_WORKSPACE/OpenMS/bld/CMakeCache.txt
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ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
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env:
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#OS_PREFIX_PATH: "${{ env.Qt5_DIR }}/lib/cmake;${{ env.Qt5_DIR }}"
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OPENMS_CONTRIB_LIBS: "${{ github.workspace }}/OpenMS/contrib"
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CI_PROVIDER: "GitHub-Actions"
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CMAKE_GENERATOR: "Ninja"
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ENABLE_TOPP_TESTING: "ON"
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ENABLE_CLASS_TESTING: "ON"
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WITH_GUI: "OFF"
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WITH_PARQUET: "OFF"
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ADDRESS_SANITIZER: "Off"
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BUILD_TYPE: "Release"
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OPENMP: "Off"
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CCACHE_COMPRESSLEVEL: 12
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CCACHE_MAXSIZE: 400M
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#- name: Test Windows
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# shell: bash
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# run: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
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# env:
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# SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
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# CI_PROVIDER: "GitHub-Actions"
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# BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}"
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- name: Test Windows
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shell: bash
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run: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
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env:
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SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
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CI_PROVIDER: "GitHub-Actions"
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BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}"
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#- name: Package
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# shell: bash
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# run: |
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# ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cipackage.cmake
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# env:
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# SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
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# PACKAGE_TYPE: zip
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# SEARCH_ENGINES_DIRECTORY: "${{ github.workspace }}/_thirdparty"
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# CI_PROVIDER: "GitHub-Actions"
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# CPACK_PACKAGE_FILE_NAME: "openms-package"
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- name: Package
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shell: bash
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run: |
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ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cipackage.cmake
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env:
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SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
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PACKAGE_TYPE: zip
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SEARCH_ENGINES_DIRECTORY: "${{ github.workspace }}/_thirdparty"
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CI_PROVIDER: "GitHub-Actions"
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CPACK_PACKAGE_FILE_NAME: "openms-package"
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- name: Upload package as artifact
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uses: actions/upload-artifact@v4
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#${{ github.workspace }}/OpenMS/bld/bin/*
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#${{ github.workspace }}/_thirdparty/*
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${{ github.workspace }}/OpenMS/bld/bin/OpenNuXL.exe
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${{ github.workspace }}/OpenMS/bld/bin/FileConverter.exe
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${{ github.workspace }}/OpenMS/bld/bin/PercolatorAdapter.exe
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${{ github.workspace }}/OpenMS/bld/bin/*.dll
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${{ github.workspace }}/_thirdparty/*.exe
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${{ github.workspace }}/_thirdparty/ThermoRawFileParser/**
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${{ github.workspace }}/_thirdparty/Percolator/**
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build-executable:
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runs-on: windows-latest
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runs-on: windows-2022
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needs: build-openms
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env:
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PYTHON_VERSION: 3.11.0
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PYTHON_VERSION: 3.10.0
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APP_NAME: OpenMS-NuXLApp
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steps:
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name: openms-package
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path: openms-package
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#- name: List files in openms-package
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# run: |
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# ls -R openms-package
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- name: List files in openms-package
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run: |
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ls -R openms-package
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- name: Extract bin and share from package
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run: |
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./python-${{ env.PYTHON_VERSION }}/python get-pip.py --no-warn-script-location
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rm get-pip.py
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- name: Uncomment 'import site' in python311._pth file
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- name: Uncomment 'import site' in python310._pth file
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run: |
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sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python311._pth
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sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python310._pth
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- name: Install Required Packages
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run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements.txt --no-warn-script-location

‎.github/workflows/executable.yaml‎

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name: Executable
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on:
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workflow_dispatch:
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jobs:
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build-executable:
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runs-on: windows-2022
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env:
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OPENMS_VERSION: 3.5.0
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APP_UpgradeCode: "31703de0-3422-444a-a469-8df83635bd6d"
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TOPP_TOOLS: "OpenNuXL"
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PYTHON_VERSION: 3.10.0
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APP_NAME: OpenMS-NuXLApp
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steps:
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- name: Set up Python (regular distribution)
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uses: actions/setup-python@v4
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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- name: Setup python embeddable version
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run: |
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mkdir python-${{ env.PYTHON_VERSION }}
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curl -O https://www.python.org/ftp/python/${{ env.PYTHON_VERSION }}/python-${{ env.PYTHON_VERSION }}-embed-amd64.zip
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unzip python-${{ env.PYTHON_VERSION }}-embed-amd64.zip -d python-${{ env.PYTHON_VERSION }}
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rm python-${{ env.PYTHON_VERSION }}-embed-amd64.zip
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$PYTHON_DIR="${{ runner.tool_cache }}/Python/${{ env.PYTHON_VERSION }}/x64"
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$EMBED_DIR="python-${{ env.PYTHON_VERSION }}"
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mkdir -p $EMBED_DIR/Lib/site-packages/tkinter
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mkdir -p $EMBED_DIR/tcl
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cp -r $PYTHON_DIR/Lib/tkinter/* $EMBED_DIR/Lib/site-packages/tkinter/
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cp -r $PYTHON_DIR/tcl/* $EMBED_DIR/tcl/
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cp $PYTHON_DIR/DLLs/_tkinter.pyd $EMBED_DIR/
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cp $PYTHON_DIR/DLLs/tcl86t.dll $EMBED_DIR/
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cp $PYTHON_DIR/DLLs/tk86t.dll $EMBED_DIR/
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- name: Install pip
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run: |
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curl -O https://bootstrap.pypa.io/get-pip.py
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./python-${{ env.PYTHON_VERSION }}/python get-pip.py --no-warn-script-location
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rm get-pip.py
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- name: Uncomment 'import site' in python310._pth file
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run: |
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sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python310._pth
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- name: Install Required Packages
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run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements.txt --no-warn-script-location
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- name: Set to offline deployment
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run: |
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$content = Get-Content -Raw settings.json | ConvertFrom-Json
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$content.online_deployment = $false
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$content | ConvertTo-Json -Depth 100 | Set-Content settings.json
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- name: Create .bat file
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run: |
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echo " start /min .\python-${{ env.PYTHON_VERSION }}\python -m streamlit run app.py local" > ${{ env.APP_NAME }}.bat
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- name: Create All-in-one executable folder
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run: |
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if (Test-Path -Path "streamlit_exe") {
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Remove-Item -Recurse -Force "streamlit_exe"
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}
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mkdir streamlit_exe
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mv python-${{ env.PYTHON_VERSION }} streamlit_exe
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cp -r src streamlit_exe
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cp -r content streamlit_exe
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cp -r assets streamlit_exe
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cp -r example-data streamlit_exe
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cp -r .streamlit streamlit_exe
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cp app.py streamlit_exe
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cp settings.json streamlit_exe
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cp ${{ env.APP_NAME }}.bat streamlit_exe
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- name: Generate Readme.txt
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shell: bash
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run: |
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cat <<EOF > streamlit_exe/Readme.txt
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Welcome to ${{ env.APP_NAME }} app!
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To launch the application:
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1. Navigate to the installation directory.
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2. Double-click on the file: ${{ env.APP_NAME }}.bat or ${{ env.APP_NAME }} shortcut.
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Additional Information:
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- If multiple Streamlit apps are running, you can change the port in the .streamlit/config.toml file.
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Example:
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[server]
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port = 8502
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Reach out to us:
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- Join our Discord server for support: https://discord.com/invite/4TAGhqJ7s5
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- GitHub: https://github.com/Arslan-Siraj/nuxl-app
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- Website: https://openms.de/
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Thanks for using ${{ env.APP_NAME }}!
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EOF
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# ...rest of your steps (WiX install, .wxs generation, candle/light build, zip & upload)...

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