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Add GitHub workflows back and update testing (#192)
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‎.github/codecov.yml‎

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# configuration for code coverage testing with codecov
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coverage:
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status:
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project:
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default:
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informational: true
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patch:
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default:
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informational: true
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codecov:
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token: ${{ secrets.CODECOV_TOKEN }}

‎.github/workflows/codechecks.yml‎

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# This workflow checks for compliance with the Google C++ style guide.
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name: Codechecks
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on: [push, pull_request]
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jobs:
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clang-format:
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runs-on: macos-latest
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steps:
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- uses: actions/checkout@v3
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- name: Install dependencies
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run: |
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brew install clang-format
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- name: Run clang-format
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run: |
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mkdir Release
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cd Release
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cmake ..
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make codecheck

‎.github/workflows/documentation.yml‎

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# This workflow builds and deploys the html documentation for svZeroDSolver.
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name: Documentation
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on: [push, pull_request]
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permissions:
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contents: write
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jobs:
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documentation:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Make build directory
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run: mkdir docs/build
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- name: Build doxygen documentation
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continue-on-error: false
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uses: mattnotmitt/doxygen-action@edge
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with:
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working-directory: '.'
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doxyfile-path: 'docs/Doxyfile'
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enable-latex: true
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- name: Save documentation
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uses: actions/upload-artifact@v4
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with:
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name: documentation
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path: ./docs/build/html
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- name: Deploy documentation
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if: github.ref == 'refs/heads/master'
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./docs/build/html

‎.github/workflows/gui.yml‎

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# This workflow uses Cypress for end-to-end testing of the 0D model GUI.
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name: GUI-tests
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on: [push, pull_request]
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jobs:
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cypress-run:
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest]
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fail-fast: false
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout code
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uses: actions/checkout@v3
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- name: Set up Node.js
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uses: actions/setup-node@v3
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with:
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node-version: '20'
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- name: Install dependencies
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working-directory: tests/cypress
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run: npm install
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.10' # Use the Python version compatible with your Flask app
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- name: Install Flask dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install flask
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- name: Start Flask Application
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run: |
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cd applications/svZeroDGUI
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FLASK_APP=app.py flask run --host=0.0.0.0 --port=8902 &
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env:
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FLASK_ENV: development
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- name: Run Cypress tests
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uses: cypress-io/github-action@v5
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with:
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start: npm start
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working-directory: tests/cypress

‎.github/workflows/test.yml‎

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# This workflow builds and tests svZeroDSolver. It is built and tested on
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# different versions of ubuntu and macOS.
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name: Build and test
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on: [push, pull_request]
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jobs:
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test:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-22.04, ubuntu-latest, macos-13, macos-latest, windows-latest]
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version: [13] # GCC version
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fail-fast: false
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env:
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GCC_V: ${{ matrix.version }}
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CONDA_ENV: zerod
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PYTHONPATH: ${{ github.workspace }}
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steps:
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- uses: actions/checkout@v4
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- uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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activate-environment: ${{env.CONDA_ENV}}
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python-version: "3.11.4"
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- name: Install ubuntu dependencies
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if: startsWith(matrix.os, 'ubuntu')
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run: sudo apt update && sudo apt install build-essential cmake lcov
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- name: Install dependencies to get correct version numbers (Ubuntu)
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if: startsWith(matrix.os, 'ubuntu')
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run: conda install -c conda-forge libstdcxx-ng=${GCC_V} gcc=${GCC_V}
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- name: Install dependencies to get correct version numbers (MacOS)
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if: startsWith(matrix.os, 'macos')
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run: |
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brew install gcc@${GCC_V}
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ln -s /usr/local/bin/gcc-${GCC_V} /usr/local/bin/gcc
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- name: Install dependencies for windows
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if: startsWith(matrix.os, 'windows')
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shell: pwsh
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run: |
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choco install mingw --no-progress
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conda install -y -c conda-forge cmake graphviz python-graphviz pydot
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pip install --upgrade cmake-setuptools
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- name: Install POISX-like svZeroDSolver
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if: ${{!startsWith(matrix.os, 'windows')}}
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run: conda run pip install -e ".[dev]"
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- name: Install Windows svZeroDSolver
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if: startsWith(matrix.os, 'windows')
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shell: pwsh
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run: |
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$Env:CMAKE_GENERATOR = 'MinGW Makefiles'
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Write-Host "→ Using CMAKE_GENERATOR = $Env:CMAKE_GENERATOR"
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pip install --no-build-isolation -v .[dev]
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pip show pysvzerod
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- name: Install Networkx
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run: |
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conda run pip install networkx
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- name: Test the build
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run: |
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cd tests
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conda run pytest -v --durations=0 --ignore=test_dirgraph.py
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- name: Build using CMake for POISX-like Systems
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if: ${{!startsWith(matrix.os, 'windows')}}
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run: |
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mkdir Release
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cd Release
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cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_DISTRIBUTION=ON ..
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make -j2
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- name: Build using CMake for Windows Systems
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if: startsWith(matrix.os, 'windows')
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shell: pwsh
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run: |
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mkdir Release
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cd Release
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cmake -G "MinGW Makefiles" `
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-DCMAKE_BUILD_TYPE=Release `
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-DENABLE_DISTRIBUTION=ON `
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..
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cmake --build . --parallel 2
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- name: Test interface POISX-like Systems
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if: ${{!startsWith(matrix.os, 'windows')}}
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run: |
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cd tests/test_interface
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mkdir build_tests
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cd build_tests
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cmake ../
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make -j2
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cd test_01
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./svZeroD_interface_test01 ../../../../Release ../../test_01/svzerod_3Dcoupling.json
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cd ../test_02
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./svZeroD_interface_test02 ../../../../Release ../../test_02/svzerod_tuned.json
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- name: Test interface Windows Systems
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if: startsWith(matrix.os, 'windows')
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shell: pwsh
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run: |
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cd tests/test_interface
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mkdir build_tests
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cd build_tests
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cmake -G "MinGW Makefiles" ..
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cmake --build . --parallel 2
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cd test_01
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./svZeroD_interface_test01.exe `
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../../../../Release `
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../../test_01/svzerod_3Dcoupling.json
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cd ../test_02
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./svZeroD_interface_test02 `
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../../../../Release `
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../../test_02/svzerod_tuned.json
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- name: Generate code coverage
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if: startsWith(matrix.os, 'ubuntu-22.04')
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run: |
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cd Release
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cmake -DENABLE_COVERAGE=ON ..
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make -j2
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cd ../tests
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conda run pytest -v --durations=0 --coverage --ignore=test_dirgraph.py
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cd ../Release
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make coverage
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- name: Save coverage report
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if: startsWith(matrix.os, 'ubuntu-22.04')
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uses: actions/upload-artifact@v4
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with:
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name: coverage_report
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path: Release/coverage
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- name: Upload coverage reports to Codecov
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if: startsWith(matrix.os, 'ubuntu-22.04')
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uses: codecov/codecov-action@v4
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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- name: Build installer POISX-like Systems
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if: ${{!startsWith(matrix.os, 'windows')}}
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run: |
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cd Release
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cpack
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cp distribution/svZeroDSolver_* ..
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- name: Install NSIS
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if: startsWith(matrix.os, 'windows')
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run: choco install nsis -y
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- name: Build installer Windows Systems
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if: startsWith(matrix.os, 'windows')
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shell: pwsh
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run: |
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# NSIS will be at C:\Program Files (x86)\NSIS\Bin
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echo "C:\Program Files (x86)\NSIS\Bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
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cd Release
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cpack -C Release
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Copy-Item distribution\svZeroDSolver_* -Destination ..\
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- name: Upload installer
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uses: actions/upload-artifact@v4
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with:
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name: ${{ matrix.os }} installer
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path: svZeroDSolver_*
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if-no-files-found: error

‎.github/workflows/test_visualization.yml‎

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name: Test Visualization Application
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on: [push, pull_request]
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jobs:
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test:
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest]
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fail-fast: false
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout Code
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uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.11'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r tests/requirements.txt
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- name: Install Graphviz
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update
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sudo apt-get install -y graphviz
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- name: Install Graphviz (macOS)
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if: runner.os == 'macOS'
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run: |
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brew install graphviz
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- name: Run tests
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run: |
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pytest tests/test_dirgraph.py

‎CMakeLists.txt‎

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# -----------------------------------------------------------------------------
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# Eigen is a header-only C++ template library for linear algebra.
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#
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# Tell FetchContent not to re-check for updates once Eigen is downloaded
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set(FETCHCONTENT_UPDATES_DISCONNECTED TRUE)
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FetchContent_Declare(
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Eigen
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GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
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GIT_TAG master
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GIT_TAG 3.4.0
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GIT_SHALLOW TRUE
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GIT_PROGRESS TRUE)
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‎applications/pysvzerod.cpp‎

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// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
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// SPDX-License-Identifier: BSD-3-Clause
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// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the
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// University of California, and others. SPDX-License-Identifier: BSD-3-Clause
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/**
44
* @file pysvzerod.cpp
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* @brief Python interface for svZeroDSolver
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6565
py::module_ sys = py::module_::import("sys");
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auto argv = sys.attr("argv").cast<std::vector<std::string>>();
6767
if (argv.size() != 3) {
68-
std::cout
69-
<< "Usage: svzerodsolver path/to/config.json path/to/output.csv"
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<< std::endl;
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std::cout << "Usage: svzerodsolver path/to/config.json path/to/output.csv"
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<< std::endl;
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exit(1);
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}
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std::ifstream ifs(argv[1]);

‎applications/svzerodcalibrator.cpp‎

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// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
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// SPDX-License-Identifier: BSD-3-Clause
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// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the
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// University of California, and others. SPDX-License-Identifier: BSD-3-Clause
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/**
44
* @file svzerodcalibrator.cpp
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* @brief Main routine for svZeroDCalibrator
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std::ifstream input_file(input_file_name);
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2828
if (!input_file.is_open()) {
29-
std::cerr << "[svzerodcalibrator] Error: The input file '" << input_file_name << "' cannot be opened." << std::endl;
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std::cerr << "[svzerodcalibrator] Error: The input file '"
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<< input_file_name << "' cannot be opened." << std::endl;
3031
return 1;
3132
}
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3637
try {
3738
output_config = calibrate(config);
3839
} catch (const nlohmann::json::parse_error& e) {
39-
std::cerr << "[svzerodcalibrator] Error: The input file '" << input_file_name
40-
<< "' does not have the parameters needed by the calibrate program." << std::endl;
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std::cerr
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<< "[svzerodcalibrator] Error: The input file '" << input_file_name
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<< "' does not have the parameters needed by the calibrate program."
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<< std::endl;
4144
return 1;
4245
}
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4447
// Write optimized simulation config
4548
std::ofstream out_file(output_file_name);
4649

4750
if (!out_file.is_open()) {
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std::cerr << "[svzerodcalibrator] Error: The output file '" << output_file_name << "' cannot be opened." << std::endl;
51+
std::cerr << "[svzerodcalibrator] Error: The output file '"
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<< output_file_name << "' cannot be opened." << std::endl;
4953
return 1;
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}
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