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Merge branch 'main' into readme_vtk
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‎.github/actions/test-macos/action.yml‎

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name: 'Test macOS'
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description: 'Run tests on macOS with all dependencies'
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runs:
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using: 'composite'
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steps:
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- name: Install macOS dependencies
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shell: bash
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run: |
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brew reinstall -v gcc
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brew install -v vtk openblas lapack mesa open-mpi qt
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brew install lcov
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sudo ln -s /usr/local/opt/qt5/mkspecs /usr/local/mkspecs
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sudo ln -s /usr/local/opt/qt5/plugins /usr/local/plugins
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- name: Install Miniconda
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shell: bash
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run: |
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curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
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bash Miniconda3-latest-MacOSX-x86_64.sh -b -p $HOME/miniconda
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echo "$HOME/miniconda/bin" >> $GITHUB_PATH
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- name: Build svZeroDSolver
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shell: bash
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run: |
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git clone https://github.com/SimVascular/svZeroDSolver.git
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cd svZeroDSolver
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mkdir build
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cd build
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cmake ..
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make -j2
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- name: Build svMultiPhysics
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shell: bash
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run: |
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mkdir build
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cd build
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cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON ..
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make -j2
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- name: Install test dependencies
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shell: bash
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run: |
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conda create -n svmultiphysics python=3.9
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conda run -n svmultiphysics pip install pytest pytest-cov pytest-mock numpy meshio pandas
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- name: Run integration tests
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shell: bash
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run: |
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git lfs pull
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cd tests
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conda run -n svmultiphysics pytest -rPv --durations=0
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- name: Run unit tests
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shell: bash
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run: |
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cd build/svMultiPhysics-build/Source/solver
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ctest --verbose

‎.github/actions/test-ubuntu/action.yml‎

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name: 'Test Ubuntu'
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description: 'Run tests on Ubuntu with coverage reporting'
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inputs:
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codecov-token:
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description: 'Codecov token for uploading coverage reports'
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required: false
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default: ''
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runs:
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using: 'composite'
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steps:
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- name: Build svZeroDSolver
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shell: bash
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run: |
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conda init
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source /conda/etc/profile.d/conda.sh
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conda activate svmultiphysics
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git clone https://github.com/SimVascular/svZeroDSolver.git
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cd svZeroDSolver
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mkdir build
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cd build
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cmake ..
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make -j2
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- name: Build svMultiPhysics
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shell: bash
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run: |
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if [ -d "build" ]; then
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rm -rf "build"
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fi
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mkdir build
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cd build
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cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON -DSV_USE_TRILINOS:BOOL=ON ..
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make -j2
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cd ..
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- name: Build svMultiPhysics (PETSc)
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shell: bash
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run: |
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if [ -d "build-petsc" ]; then
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rm -rf "build-petsc"
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fi
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mkdir build-petsc
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cd build-petsc
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cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON -DSV_PETSC_DIR:STRING=/petsc ..
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make -j2
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cd ..
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- name: Run integration tests
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shell: bash
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run: |
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git config --global --add safe.directory /__w/svMultiPhysics/svMultiPhysics
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git lfs pull
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cd tests
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conda run -n svmultiphysics pytest -rPv --durations=0
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- name: Run unit tests
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shell: bash
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run: |
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cd build/svMultiPhysics-build/Source/solver
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ctest --verbose
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- name: Generate code coverage
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shell: bash
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run: |
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cd build/svMultiPhysics-build
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make coverage
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- name: Save coverage report
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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: build/svMultiPhysics-build/coverage
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v5
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env:
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CODECOV_TOKEN: ${{ inputs.codecov-token }}

‎.github/workflows/test_macos.yml‎

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‎.github/workflows/test_ubuntu.yml‎

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‎.github/workflows/tests.yml‎

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name: Tests
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on:
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pull_request:
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push:
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jobs:
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# Check if there are any changes to important code files
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check-for-changes:
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name: Check for relevant changes
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runs-on: ubuntu-latest
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outputs:
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run_full_tests: ${{ steps.set-outputs.outputs.run_full_tests }}
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Check for relevant file changes
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uses: dorny/paths-filter@v3
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id: filter
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with:
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base: ${{ github.event.pull_request.base.sha || github.event.before }}
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filters: |
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relevant:
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- 'Code/**'
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- 'tests/**'
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- '.github/**'
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- name: Set test execution flag
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id: set-outputs
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run: |
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if [ "${{ steps.filter.outputs.relevant }}" = "true" ]; then
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echo "run_full_tests=true" >> "$GITHUB_OUTPUT"
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else
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echo "run_full_tests=false" >> "$GITHUB_OUTPUT"
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fi
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# Run Ubuntu tests when relevant changes detected
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test-ubuntu:
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name: Test Ubuntu
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runs-on: ubuntu-latest
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container: simvascular/libraries:ubuntu22
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needs: check-for-changes
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if: ${{ needs.check-for-changes.outputs.run_full_tests == 'true' }}
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Run Ubuntu tests
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uses: ./.github/actions/test-ubuntu
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with:
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codecov-token: ${{ secrets.CODECOV_TOKEN }}
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# Run macOS tests when relevant changes detected
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test-macos:
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name: Test macOS
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runs-on: macos-latest
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needs: check-for-changes
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if: ${{ needs.check-for-changes.outputs.run_full_tests == 'true' }}
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Run macOS tests
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uses: ./.github/actions/test-macos
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# Single coordinating job for branch protection rules
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# This job succeeds if:
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# 1. Tests are skipped (no relevant changes) OR
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# 2. All tests pass (both Ubuntu and macOS)
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# This job fails only if tests actually fail
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all-tests:
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name: All Tests
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runs-on: ubuntu-latest
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needs: [check-for-changes, test-ubuntu, test-macos]
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if: always()
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steps:
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- name: Determine results of tests
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run: |
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# If tests were skipped, the job should succeed
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if [ "${{ needs.check-for-changes.outputs.run_full_tests }}" = "false" ]; then
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echo "✅ Tests were skipped - no relevant changes detected"
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exit 0
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fi
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# If tests were supposed to run, check if they passed
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if [ "${{ needs.check-for-changes.outputs.run_full_tests }}" = "true" ]; then
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if [ "${{ needs.test-ubuntu.result }}" = "success" ] && [ "${{ needs.test-macos.result }}" = "success" ]; then
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echo "✅ All tests passed successfully"
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exit 0
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else
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echo "❌ One or more tests failed"
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echo "Ubuntu test result: ${{ needs.test-ubuntu.result }}"
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echo "macOS test result: ${{ needs.test-macos.result }}"
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exit 1
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fi
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fi

‎Code/Source/solver/read_files.cpp‎

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@@ -1935,10 +1935,9 @@ void read_fourier_coeff_values_file(const std::string& file_name, bcType& lBc)
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values.push_back(value);
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}
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int num_vals = values.size();
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for (int i = 0; i < values.size(); i++) {
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lBc.gt.r(i,j) = values[i];
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lBc.gt.i(i,j) = values[i+num_vals];
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for (int i = 0; i < lBc.gt.d; i++) {
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lBc.gt.r(i,j) = values[i];
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lBc.gt.i(i,j) = values[i + lBc.gt.d];
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}
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j += 1;
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values.push_back(value);
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}
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int num_vals = values.size();
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for (int i = 0; i < values.size(); i++) {
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lBf.bt.r(i,j) = values[i];
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lBf.bt.i(i,j) = values[i+num_vals];
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for (int i = 0; i < lBf.bt.d; i++) {
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lBf.bt.r(i,j) = values[i];
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lBf.bt.i(i,j) = values[i + lBf.bt.d];
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}
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j += 1;

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