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Merge pull request #60 from DataAnalyticsEngineering/FANS-v0.4.0
Release v0.4.0
2 parents 158ddd1 + 055e4c7 commit 1bb7470

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‎.gitattributes‎

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# SCM syntax highlighting & preventing 3-way merges
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pixi.lock merge=binary linguist-language=YAML linguist-generated=true

‎.github/dependabot.yml‎

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# To get started with Dependabot version updates, you'll need to specify which
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# package ecosystems to update and where the package manifests are located.
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# Please see the documentation for all configuration options:
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# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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# Check for updates to GitHub Actions every week
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interval: "weekly"

‎.github/pull_request_template.md‎

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<!-- Add a short description of your contribution here. Skip this if the title is self-explanatory -->
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Checklist:
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- [ ] I made sure that the CI passed before I ask for a review.
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- [ ] I added a summary of the changes (compared to the last release) in the `CHANGELOG.md`.
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- [ ] If necessary, I made changes to the documentation and/or added new content.
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- [ ] I will remember to squash-and-merge, providing a useful summary of the changes of this PR.

‎.github/workflows/build_and_test.yaml‎

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strategy:
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fail-fast: false
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matrix:
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UBUNTU_VERSION: [noble, jammy, focal]
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UBUNTU_VERSION: [noble, jammy]
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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: Set up pixi
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uses: prefix-dev/setup-pixi@v0.8.8
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- name: Generate build directory
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run: mkdir -p ${{ env.FANS_BUILD_DIR }}
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- name: Tests
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working-directory: ${{ env.FANS_BUILD_DIR }}
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run: su -c "ctest" ${{ env.FANS_MPI_USER }}
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run: |
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su -c "ctest" ${{ env.FANS_MPI_USER }}
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- uses: actions/upload-artifact@v4
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if: failure()
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with:
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name: ${{ format('Ubuntu {0}', matrix.UBUNTU_VERSION) }} CTest logs
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path: ${{ env.FANS_BUILD_DIR }}/Testing/Temporary/LastTest.log
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# ────────────────────────────────────────────────────────────────
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# Pytest checks
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# ────────────────────────────────────────────────────────────────
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- name: Install Pixi Python deps
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run: |
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pixi --version
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pixi install
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- name: Run pytest checks on HDF5 output
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run: pixi run test
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- uses: actions/upload-artifact@v4
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if: failure()
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with:
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name: ${{ format('Ubuntu {0}', matrix.UBUNTU_VERSION) }} PyTest logs
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path: |
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**/pytest*.xml
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**/.pytest_cache

‎.github/workflows/build_and_test_mac.yaml‎

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name: Build and test macOS 15
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# Builds FANS for macOS 15 on Apple Silicon CPU and runs the tests.
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on:
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push:
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branches:
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- main
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- develop
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pull_request:
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workflow_dispatch:
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concurrency:
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group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: ${{github.event_name == 'pull_request'}}
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jobs:
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build-macos:
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name: macOS 15
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runs-on: macos-15
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env:
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FANS_BUILD_DIR: build
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strategy:
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fail-fast: false
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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: Install FANS dependencies
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run: |
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brew install gnu-time cmake gcc@14
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brew install open-mpi --build-from-source --cc=gcc-14
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brew install hdf5-mpi --build-from-source --cc=gcc-14
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brew install fftw eigen
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- name: Set up pixi
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uses: prefix-dev/setup-pixi@v0.8.8
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- name: Generate build directory
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run: mkdir -p ${{ env.FANS_BUILD_DIR }}
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- name: Configure
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working-directory: ${{ env.FANS_BUILD_DIR }}
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env:
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CC: gcc-14
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CXX: g++-14
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MPICC: mpicc
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MPICXX: mpicxx
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run: |
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cmake --version
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cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_EXPORT_COMPILE_COMMANDS=ON ..
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- uses: actions/upload-artifact@v4
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if: failure()
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with:
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name: macOS 15 CMakeCache
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path: ${{ env.FANS_BUILD_DIR }}/CMakeCache.txt
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- uses: actions/upload-artifact@v4
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if: failure()
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with:
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name: macOS 15 CMakeLogs
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path: '${{ env.FANS_BUILD_DIR }}/CMakeFiles/*.log'
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- uses: actions/upload-artifact@v4
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if: failure()
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with:
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name: macOS 15 CompileCommands
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path: ${{ env.FANS_BUILD_DIR }}/compile_commands.json
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- name: Compile
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working-directory: ${{ env.FANS_BUILD_DIR }}
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run:
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cmake --build . -j $(nproc) || cmake --build . -j1
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- name: Tests
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working-directory: ${{ env.FANS_BUILD_DIR }}
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env:
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CTEST_OUTPUT_ON_FAILURE: 1
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run: ctest
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- uses: actions/upload-artifact@v4
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if: failure()
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with:
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name: macOS 15 CTest logs
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path: ${{ env.FANS_BUILD_DIR }}/Testing/Temporary/LastTest.log
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# ────────────────────────────────────────────────────────────────
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# Pytest checks
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# ────────────────────────────────────────────────────────────────
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- name: Install Pixi Python deps
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run: |
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pixi --version
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pixi install
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- name: Run pytest checks on HDF5 output
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run: pixi run test
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- uses: actions/upload-artifact@v4
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if: failure()
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with:
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name: ${{ format('Ubuntu {0}', matrix.UBUNTU_VERSION) }} PyTest logs
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path: |
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**/pytest*.xml
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**/.pytest_cache

‎.github/workflows/docker.yaml‎

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build-and-push:
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strategy:
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matrix:
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ubuntu-version: [noble, jammy, focal]
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ubuntu-version: [noble, jammy]
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runs-on: ubuntu-latest
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‎.github/workflows/test_pyfans.yaml‎

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name: Test PyFans
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on:
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push:
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branches:
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- main
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- develop
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pull_request:
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branches:
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- "*"
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jobs:
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test-pyfans:
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runs-on: ubuntu-latest
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container: unistuttgartdae/fans-ci:noble
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defaults:
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run:
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shell: "bash --login -eo pipefail {0}"
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env:
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FANS_BUILD_DIR: build
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FANS_MPI_USER: fans
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Generate build directory
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run: mkdir -p ${{ env.FANS_BUILD_DIR }}
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- name: Install dependencies
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run: |
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apt update
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apt install -y wget python3-venv
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- name: Install preCICE
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run: |
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wget https://github.com/precice/precice/releases/download/v3.2.0/libprecice3_3.2.0_noble.deb
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apt install -y ./libprecice3_3.2.0_noble.deb
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- name: Install the Micro Manager
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run: |
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python3 -m venv .venv
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. .venv/bin/activate
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pip install micro-manager-precice
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- name: Configure
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working-directory: ${{ env.FANS_BUILD_DIR }}
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run: |
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cmake .. -DFANS_LIBRARY_FOR_MICRO_MANAGER=ON
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make
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- name: Run a dummy macro-micro coupling test
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run: |
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. .venv/bin/activate
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cd test/test_pyfans
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python3 macro-cube.py & micro-manager-precice micro-manager-config.json

‎.gitignore‎

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**/scratch/
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# Test microstructure files
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!sphere.h5
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!sphere32.h5
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# Test input files
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!test_LinearElastic.json
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!test_LinearThermal.json
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!test_PseudoPlastic.json
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!test_J2Plasticity.json
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!test_MixedBCs.json
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# pixi environments
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.pixi
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*.egg-info

‎CHANGELOG.md‎

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# FANS Changelog
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## v0.4.0
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- Support compilaion on MacOS X via conda-forge https://github.com/DataAnalyticsEngineering/FANS/pull/59
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- Add support for macroscale mixed stress-strain boundary conditions https://github.com/DataAnalyticsEngineering/FANS/pull/58
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- Add grain boundary diffusion material model for polycrystals https://github.com/DataAnalyticsEngineering/FANS/pull/52
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- Add a pixi environment for the FANS_dashboard and some tests https://github.com/DataAnalyticsEngineering/FANS/pull/55
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- Remove MPI initialization from pyFANS and add an integration test for it https://github.com/DataAnalyticsEngineering/FANS/pull/46
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- Native support for MacOS https://github.com/DataAnalyticsEngineering/FANS/pull/25
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- Remove Ubuntu 20.04 from testing and Docker support https://github.com/DataAnalyticsEngineering/FANS/pull/51
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- Add support for `--version` command line argument for checking the version of FANS
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- Modify way to provide micro structure in JSON input https://github.com/DataAnalyticsEngineering/FANS/pull/43
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- Add conda package for FANS https://github.com/DataAnalyticsEngineering/FANS/pull/39
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- Introduce system for checking compiler flags: `avx2` & `fma` https://github.com/DataAnalyticsEngineering/FANS/pull/34
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- Add `results_prefix` field in the JSON input https://github.com/DataAnalyticsEngineering/FANS/pull/36
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- Build FANS as a library to be coupled to a macro-scale simulation via preCICE and the Micro Manager https://github.com/DataAnalyticsEngineering/FANS/pull/23
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## v0.3.0
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- Added Linear thermal and mechanical triclinic material models https://github.com/DataAnalyticsEngineering/FANS/pull/32

‎CMakeLists.txt‎

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cmake_minimum_required(VERSION 3.0...3.28)
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cmake_minimum_required(VERSION 3.21)
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# ##############################################################################
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# GENERAL SETTINGS
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# ##############################################################################
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project(FANS
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VERSION 0.3.0
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VERSION 0.4.0
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LANGUAGES C CXX
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)
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# with -fno-implicit-templates I get linker errors when using std:: stuff
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# TODO: should be developer specific, by using e.g. CMake Presets
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set(CMAKE_CXX_FLAGS "-fmax-errors=1 -O3")
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")
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set(CMAKE_PREFIX_PATH $ENV{CMAKE_PREFIX_PATH})
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# IPO
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set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
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# From https://stackoverflow.com/questions/73248130/how-to-avoid-the-removal-of-the-rpath-during-cmake-install-step
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# Set RPATH to be relative and honor user overrides, whether at the command line or FetchContent
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set(RPATH_BASE "$ORIGIN")
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if(APPLE)
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set(RPATH_BASE "@loader_path")
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else()
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set(RPATH_BASE "$ORIGIN")
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endif()
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file(RELATIVE_PATH REL_PATH_LIB
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"/${CMAKE_INSTALL_BINDIR}/"
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"/${CMAKE_INSTALL_LIBDIR}/")
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find_package(Eigen3 REQUIRED)
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find_package(OpenMP REQUIRED)
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find_package(MPI REQUIRED)
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find_package(FFTW3 REQUIRED COMPONENTS DOUBLE MPI)
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option(FANS_LIBRARY_FOR_MICRO_MANAGER "Building FANS as a library to be used by the Micro Manager." OFF)
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if (FANS_LIBRARY_FOR_MICRO_MANAGER)
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include(FetchContent)
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FetchContent_Declare(
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pybind11 GIT_REPOSITORY https://github.com/pybind/pybind11.git
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GIT_TAG v2.12.0
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)
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FetchContent_MakeAvailable(pybind11)
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endif()
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# ##############################################################################
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# TARGETS
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# ##############################################################################
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add_library(FANS::FANS ALIAS FANS_FANS)
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if (CMAKE_SYSTEM_PROCESSOR MATCHES "arm|aarch64")
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target_compile_options(FANS_FANS PUBLIC -march=armv8-a+simd+fp+crypto)
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elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64")
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target_compile_options(FANS_FANS PUBLIC -mavx2 -mfma)
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endif ()
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COMMENT "Create a symlink for FANS executable to ${CMAKE_CURRENT_SOURCE_DIR}/test/"
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)
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if (FANS_LIBRARY_FOR_MICRO_MANAGER)
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add_subdirectory(pyfans)
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endif ()
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# ##############################################################################
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# HEADERS
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# ##############################################################################
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include/solverFP.h
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include/solver.h
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include/setup.h
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include/mixedBCs.h
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include/material_models/LinearThermal.h
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include/material_models/GBDiffusion.h
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include/material_models/LinearElastic.h
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include/material_models/PseudoPlastic.h
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include/material_models/J2Plasticity.h
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)
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# version.h is generated and added to the build include directory
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configure_file(
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"${PROJECT_SOURCE_DIR}/include/version.h.in"
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"${PROJECT_BINARY_DIR}/include/version.h" @ONLY
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)
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target_include_directories(FANS_main PRIVATE "${PROJECT_BINARY_DIR}/include")
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# ##############################################################################
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# SOURCES
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# ##############################################################################
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target_link_libraries(FANS_FANS PUBLIC Eigen3::Eigen)
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target_link_libraries(FANS_FANS PUBLIC OpenMP::OpenMP_CXX)
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target_link_libraries(FANS_main PRIVATE FANS::FANS)
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# ##############################################################################

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