WIP: Implement Pydra code-generators

.flake8

@@ -0,0 +1,10 @@
+
+[flake8]
+doctests = True
+exclude =
+    **/__init__.py
+max-line-length = 88
+select = C,E,F,W,B,B950
+extend-ignore = E203,E501,E129,E111,E303,E211,E201,E114,E261,E262,E226,E302,E121
+per-file-ignores =
+    setup.py:F401

.github/workflows/package-pydra.yml

@@ -0,0 +1,243 @@
+#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:
+
+  generate-pydra:
+
+    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)" >> $GITHUB_ENV
+
+      - name: install dependencies
+        run: |
+           sudo apt-get update
+           sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
+
+      - name: Run sccache-cache
+        uses: mozilla-actions/sccache-action@v0.0.3
+
+      - name: Get CMake
+        uses: lukka/get-cmake@latest
+        with:
+          cmakeVersion: '3.16.3'
+
+      - name: Print CMake version
+        run: cmake --version
+
+      - name: configure
+        run: >
+          cmake
+          -B build
+          -G Ninja
+          -D CMAKE_BUILD_TYPE=Release
+          -D MRTRIX_BUILD_TESTS=ON
+          -D MRTRIX_STL_DEBUGGING=ON
+          -D MRTRIX_WARNINGS_AS_ERRORS=ON
+          -D CMAKE_C_COMPILER=clang
+          -D CMAKE_CXX_COMPILER=clang++
+          -D CMAKE_INSTALL_PREFIX=$(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: Install pydra-auto-gen requirements
+        run: |
+          pip install -e interfaces/pydra/fileformats-medimage-mrtrix3
+          pip install -e interfaces/pydra/fileformats-medimage-mrtrix3-extras
+          pip install -e interfaces/pydra/src
+          pip install -r interfaces/pydra/requirements.txt          
+
+      - name: Generate task specifications
+        run: >
+          ./interfaces/pydra/generate.py
+          $(pwd)/install/bin
+          $(pwd)/interfaces/pydra/src
+          $MRTRIX3_VERSION
+          --log-errors
+          --latest
+
+      - name: Upload auto-gen pydra
+        uses: actions/upload-artifact@v2
+        with:
+          name: AutoGen
+          path: interfaces/pydra/src/pydra/tasks/mrtrix3/v3_0
+
+  devcheck:
+    needs: [generate-pydra]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8, 3.11]  # Check oldest and newest versions
+        pip-flags: ['', '--editable']
+        pydra:
+        - 'pydra'
+        - '--editable git+https://github.com/nipype/pydra.git#egg=pydra'
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Download auto-gen pydra
+      uses: actions/download-artifact@v2
+      with:
+        name: AutoGen
+        path: interfaces/pydra/src/pydra/tasks/mrtrix3/v3_0
+
+    - 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 Pydra
+      run: |
+        pip install ${{ matrix.pydra }}
+        python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+
+    - name: Install task package
+      run: |
+        pip install ${{ matrix.pip-flags }} "interfaces/pydra/fileformats-medimage-mrtrix3"
+        pip install ${{ matrix.pip-flags }} "interfaces/pydra/src[dev]"
+        python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        python -c "import pydra.tasks.mrtrix3.v3_0"
+        python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+
+  # test:
+  #   needs: [generate]
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     matrix:
+  #       python-version: [3.8, 3.11]
+  #   defaults:
+  #     run:
+  #       shell: bash -l {0}
+  #   steps:
+  #   - 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 interfaces/pydra/fileformats-medimage-mrtrix interfaces/pydra/fileformats-medimage-mrtrix-extras 'interfaces/pydra/src[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 interfaces/src/pydra/tasks/mrtrix3 \
+  #           --cov pydra.tasks.mrtrix3 --cov-report xml
+  #   - uses: codecov/codecov-action@v1
+  #     if: ${{ always() }}
+
+
+  deploy:
+    needs: [devcheck] # , test]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11]
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Download auto-gen pydra
+      uses: actions/download-artifact@v2
+      with:
+        name: AutoGen
+        path: interfaces/pydra/src/pydra/tasks/mrtrix3/v3_0
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install build tools
+      run: python -m pip install --upgrade pip twine build
+
+    - name: Build source and wheel distributions
+      working-directory: ./interfaces/pydra/src
+      run: python -m build
+
+    - name: Check distributions
+      run: twine check interfaces/pydra/src/dist/*
+
+    - name: Upload sdist
+      uses: actions/upload-artifact@v2
+      with:
+        name: SDist
+        path: interfaces/pydra/src/dist/*.tar.gz
+
+    # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
+    # Secrets are not accessible in the if: condition [0], so set an output variable [1]
+    # [0] https://github.community/t/16928
+    # [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter
+    - name: Check for PyPI token on tag
+      id: deployable
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      env:
+        PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
+      run: if [ -n "$PYPI_API_TOKEN" ]; then echo ::set-output name=DEPLOY::true; fi
+
+    - name: Upload to PyPI
+      if: steps.deployable.outputs.DEPLOY
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
+        packages-dir: interfaces/pydra/src/dist/

.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

@@ -52,7 +52,7 @@ 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