WIP: Implement Pydra code-generators

.github/workflows/package-pydra.yml

@@ -0,0 +1,173 @@
+#This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+# For deployment, it will be necessary to create a PyPI API token and store it as a secret
+# https://docs.github.com/en/actions/reference/encrypted-secrets
+
+name: Pydra
+
+on:
+  push:
+    branches: [ master ]
+    tags: [ '*' ]
+  pull_request:
+    branches:
+      - master
+      - dev
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    env:
+      CFLAGS: -Werror
+      QT_SELECT: qt6
+      SCCACHE_GHA_ENABLED: "true"
+      SCCACHE_CACHE_SIZE: "2G"
+
+    steps:
+      - uses: actions/checkout@v1
+        with:
+          submodules: true
+
+      - name: Determine MRtrix3 version
+        run: echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV
+
+      - name: install dependencies
+        run: |
+           sudo apt-get update
+           sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
+
+      - name: Run sccache-cache
+        uses: mozilla-actions/[email protected]
+
+      - name: Get CMake
+        uses: lukka/get-cmake@latest
+        with:
+          cmakeVersion: '3.16.3'
+
+      - name: Print CMake version
+        run: cmake --version
+
+      - name: configure
+        run: >
+          cmake
+          -B build
+          -G Ninja
+          -D CMAKE_BUILD_TYPE=Release
+          -D MRTRIX_BUILD_TESTS=ON
+          -D MRTRIX_STL_DEBUGGING=ON
+          -D MRTRIX_WARNINGS_AS_ERRORS=ON
+          -D CMAKE_C_COMPILER=clang
+          -D CMAKE_CXX_COMPILER=clang++
+          -D CMAKE_INSTALL_PREFIX=$(pwd)/install
+
+      - name: Build Mrtrix
+        run: cmake --build build
+
+      - name: Install Mrtrix
+        run: cmake --install build
+
+      - name: Set PATH Variable
+        run: echo "PATH=$PATH:$(pwd)/install/bin" >> $GITHUB_ENV
+
+      - name: Set LD_LIBRARY_PATH Variable
+        run: echo "LD_LIBRARY_PATH=$(pwd)/install/lib" >> $GITHUB_ENV
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+
+      - name: Install Python build dependencies
+        run: |
+          python -m pip install --upgrade pip
+
+      - name: Clone Pydra-MRtrix3 package
+        run: git clone https://github.com/nipype/pydra-mrtrix3.git pydra
+
+      - name: Install pydra-auto-gen requirements
+        run: |
+          pip install -e ./pydra/fileformats-medimage-mrtrix3
+          pip install -e ./pydra/fileformats-medimage-mrtrix3-extras
+          pip install -e ./pydra[dev]
+
+      - name: Generate task specifications
+        run: >
+          ./pydra/generate.py
+          $(pwd)/install/bin
+          $(pwd)/pydra/src
+          $MRTRIX3_VERSION
+          --log-errors
+          --latest
+
+      - name: Upload MRtrix3 install
+        uses: actions/upload-artifact@v2
+        with:
+          name: MRtrix3
+          path: mrtrix3/install
+
+      - name: Upload auto-gen pydra
+        uses: actions/upload-artifact@v2
+        with:
+          name: AutoGen
+          path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION
+
+      - name: Write version file
+        run: echo $MRTRIX3_VERSION > mrtrix3_version.txt
+
+      - name: Upload version file
+        uses: actions/upload-artifact@v2
+        with:
+          name: VersionFile
+          path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION
+
+  test:
+    needs: [build]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8, 3.11]
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+
+    - name: Download version file
+      uses: actions/download-artifact@v2
+      with:
+        name: VersionFile
+        path: mrtrix3_version.txt
+
+    - name: Extract Mrtrix version
+      run: echo "MRTRIX3_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV  
+
+    - uses: actions/checkout@v2
+    - name: Install Minconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-activate-base: true
+        activate-environment: ""
+    - name: Install MRtrix via Conda
+      run: |
+        conda install -c mrtrix3 mrtrix3
+        mrconvert --version
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+    - name: Install task package
+      run: |
+        pip install pydra/fileformats-medimage-mrtrix pydra/fileformats-medimage-mrtrix-extras '.[test]'
+        python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+    - name: Test with pytest
+      run: |
+        pytest -sv --doctest-modules pydra/tasks/mrtrix3 \
+            --cov pydra.tasks.mrtrix3 --cov-report xml
+    - uses: codecov/codecov-action@v1
+      if: ${{ always() }}
+

.gitignore

@@ -11,12 +11,22 @@
 *.img
 *.hdr
 *.rste
-/python/lib/mrtrix3/_version.py
+*.venv
+config
+build.*
+/configure.log
+/build.log
+/core/version.cpp
+/src/exec_version.cpp
+/src/project_version.h
+/lib/mrtrix3/_version.py
+/test/src/project_version.h
 /scripts/mrtrix_bash_completion
 /dev/
 /compiled_docs/
 /.vscode/
 .cproject
+.DS_store
 .idea
 .project
 .settings
@@ -32,4 +42,12 @@
 .check_syntax.tmp
 .check_syntax2.tmp
 build/
-CMakeLists.txt.user
+CMakeLists.txt.user
+*.venv
+__pycache__
+.DS_Store
+_version.py
+/interfaces/pydra/src/pydra/tasks/mrtrix3/v3_0
+/interfaces/pydra/**/dist/**
+.pytest_cache
+

cmd/amp2response.cpp

@@ -57,7 +57,7 @@ void usage() {
   ARGUMENTS
     + Argument ("amps", "the amplitudes image").type_image_in()
     + Argument ("mask", "the mask containing the voxels from which to estimate the response function").type_image_in()
-    + Argument ("directions", "a 4D image containing the estimated fibre directions").type_image_in()
+    + Argument ("directions_image", "a 4D image containing the estimated fibre directions").type_image_in()
     + Argument ("response", "the output zonal spherical harmonic coefficients").type_file_out();
 
   OPTIONS