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tclosetclose
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moved auto-gen GH action job into separate workflow
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‎.github/workflows/auto-gen.yaml‎

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#This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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# For deployment, it will be necessary to create a PyPI API token and store it as a secret
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# https://docs.github.com/en/actions/reference/encrypted-secrets
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name: CI/CD
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on:
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workflow_dispatch: # Trigger this workflow manually or via a repository dispatch event
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repository_dispatch:
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types: [auto-gen]
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env:
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MRTRIX_HOME: /opt/mrtrix3
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MRTRIX_INSTALL: /opt/mrtrix3/install
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MRTRIX_VERSION: 3.1.0
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SUBPKG_NAME: v3_1
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jobs:
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generate:
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runs-on: ubuntu-latest
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env:
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CFLAGS: -Werror
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QT_SELECT: qt6
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SCCACHE_GHA_ENABLED: "true"
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SCCACHE_CACHE_SIZE: "2G"
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steps:
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- uses: actions/checkout@v3
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with:
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submodules: true
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- name: Set Git User
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# checkout@v2 adds a header that makes branch protection report errors
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# because the Github action bot is not a collaborator on the repo
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run: |
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git config --global user.email "[email protected]"
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git config --global user.name "Dummy User"
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- name: Unset header
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# checkout@v2 adds a header that makes branch protection report errors
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# because the Github action bot is not a collaborator on the repo
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run: git config --local --unset http.https://github.com/.extraheader
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- name: Fetch tags
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run: git fetch --prune --unshallow
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- name: Create auto-gen tag
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run: git tag -a old-auto-gen -m "Old point of auto-generation"
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- name: Checkout auto-gen branch
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run: git checkout auto-gen
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- name: install dependencies
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run: |
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sudo apt-get update
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sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
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- name: Run sccache-cache
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uses: mozilla-actions/[email protected]
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- name: Get CMake
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uses: lukka/get-cmake@latest
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with:
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cmakeVersion: '3.16.3'
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- name: Print CMake version
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run: cmake --version
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- name: Clone latest MRtrix and switch to latest tag
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run: |
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mkdir $MRTRIX_HOME
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sudo chown -R $USER $MRTRIX_HOME
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git clone https://github.com/tclose/mrtrix3.git $MRTRIX_HOME/src
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cd $MRTRIX_HOME/src
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git checkout print-pydra-dev
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git tag -a $MRTRIX_VERSION -m"Tag used to create a pydra-task-mrtrix3 release"
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git describe --abbrev=0
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# echo "MRTRIX_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV
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# git checkout $MRTRIX_VERSION
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- name: configure
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run: |
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cd $MRTRIX_HOME/src
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cmake \
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-B build \
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-G Ninja \
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-D CMAKE_BUILD_TYPE=Release \
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-D MRTRIX_BUILD_TESTS=ON \
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-D MRTRIX_STL_DEBUGGING=ON \
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-D MRTRIX_WARNINGS_AS_ERRORS=ON \
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-D CMAKE_C_COMPILER=clang \
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-D CMAKE_CXX_COMPILER=clang++ \
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-D CMAKE_INSTALL_PREFIX=$MRTRIX_INSTALL
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- name: Build Mrtrix
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run: |
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cd $MRTRIX_HOME/src
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cmake --build build
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- name: Install Mrtrix
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run: |
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cd $MRTRIX_HOME/src
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cmake --install build
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- name: Set PATH Variable
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run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV
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- name: Set LD_LIBRARY_PATH Variable
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run: echo "LD_LIBRARY_PATH=$MRTRIX_INSTALL/lib" >> $GITHUB_ENV
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- name: Change back to the root directory
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run: cd ..
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- name: Set up Python
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uses: actions/setup-python@v5
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- name: Install Python build dependencies
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run: |
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python -m pip install --upgrade pip
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- name: Install pydra-auto-gen requirements
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run: >
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pip install
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-e related-packages/fileformats
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-e related-packages/fileformats-extras
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-e .[dev,test]
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- name: Install development Pydra
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run: pip install --no-deps git+https://github.com/nipype/pydra.git@develop
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- name: Generate task specifications
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run: >
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./generate.py
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$MRTRIX_INSTALL/bin
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$(pwd)
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$MRTRIX_VERSION
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--raise-errors
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--latest
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- name: Commit changes to auto-gen branch
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run: |
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git add .
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git commit -m "Refresh of auto-generated task specifications"
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git push
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- name: Rebase main on auto-gen
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run: |
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git checkout main
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git checkout -b main-rebase
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git rebase old-auto-gen --onto auto-gen
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- name: Create pull request
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uses: peter-evans/create-pull-request@v4
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with:
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branch: main-rebase
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title: 'Rebase main on auto-gen'
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body: 'This PR rebases the main branch on the auto-gen branch to include the latest Nipype to Pydra conversions.'
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base: main
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commit-message: 'Rebase main on auto-gen'
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labels: auto-gen

‎.github/workflows/ci-cd.yml‎ renamed to ‎.github/workflows/ci-cd.yaml‎

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jobs:
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generate:
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runs-on: ubuntu-latest
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env:
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CFLAGS: -Werror
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QT_SELECT: qt6
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SCCACHE_GHA_ENABLED: "true"
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SCCACHE_CACHE_SIZE: "2G"
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: true
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- name: Set Git User
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# checkout@v2 adds a header that makes branch protection report errors
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# because the Github action bot is not a collaborator on the repo
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run: |
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git config --global user.email "[email protected]"
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git config --global user.name "Dummy User"
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- name: Unset header
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# checkout@v2 adds a header that makes branch protection report errors
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# because the Github action bot is not a collaborator on the repo
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run: git config --local --unset http.https://github.com/.extraheader
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- name: Fetch tags
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run: git fetch --prune --unshallow
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- name: install dependencies
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run: |
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sudo apt-get update
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sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
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- name: Run sccache-cache
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uses: mozilla-actions/[email protected]
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- name: Get CMake
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uses: lukka/get-cmake@latest
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with:
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cmakeVersion: '3.16.3'
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- name: Print CMake version
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run: cmake --version
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- name: Clone latest MRtrix and switch to latest tag
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run: |
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mkdir $MRTRIX_HOME
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sudo chown -R $USER $MRTRIX_HOME
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git clone https://github.com/tclose/mrtrix3.git $MRTRIX_HOME/src
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cd $MRTRIX_HOME/src
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git checkout pydra-usage-new-syntax
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git tag -a $MRTRIX_VERSION -m"Tag used to create a pydra-mrtrix3 release"
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git describe --abbrev=0
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# echo "MRTRIX_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV
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# git checkout $MRTRIX_VERSION
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- name: configure
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run: |
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cd $MRTRIX_HOME/src
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cmake \
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-B build \
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-G Ninja \
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-D CMAKE_BUILD_TYPE=Release \
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-D MRTRIX_BUILD_TESTS=ON \
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-D MRTRIX_STL_DEBUGGING=ON \
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-D MRTRIX_WARNINGS_AS_ERRORS=ON \
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-D CMAKE_C_COMPILER=clang \
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-D CMAKE_CXX_COMPILER=clang++ \
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-D CMAKE_INSTALL_PREFIX=$MRTRIX_INSTALL
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- name: Build Mrtrix
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run: |
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cd $MRTRIX_HOME/src
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cmake --build build
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- name: Install Mrtrix
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run: |
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cd $MRTRIX_HOME/src
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cmake --install build
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- name: Set PATH Variable
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run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV
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- name: Set LD_LIBRARY_PATH Variable
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run: echo "LD_LIBRARY_PATH=$MRTRIX_INSTALL/lib" >> $GITHUB_ENV
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- name: Change back to the root directory
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run: cd ..
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- name: Set up Python
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uses: actions/setup-python@v2
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- name: Install Python build dependencies
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run: |
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python -m pip install --upgrade pip
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- name: Install pydra-auto-gen requirements
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run: >
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pip install
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-e related-packages/fileformats
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-e related-packages/fileformats-extras
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-e .[dev,test]
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- name: Install development Pydra
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run: pip install --no-deps git+https://github.com/nipype/pydra.git@develop
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- name: Generate task specifications
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run: >
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./generate.py
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$MRTRIX_INSTALL/bin
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$(pwd)
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$MRTRIX_VERSION
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--raise-errors
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--latest
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- name: Upload MRtrix3 install
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uses: actions/upload-artifact@v4
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with:
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name: MRtrix3
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path: ${{ env.MRTRIX_INSTALL}}
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- name: Upload auto-gen pydra
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uses: actions/upload-artifact@v4
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with:
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name: AutoGen
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path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
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- name: Write version file
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run: echo $MRTRIX_VERSION > mrtrix3_version.txt
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- name: Upload version file
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uses: actions/upload-artifact@v4
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with:
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name: VersionFile
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path: mrtrix3_version.txt
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test:
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needs: [generate]
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runs-on: ubuntu-latest
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strategy:
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matrix:

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