Implement Pydra code-generators

.github/workflows/clang-tidy-post.yml

@@ -0,0 +1,22 @@
+name: Post clang-tidy review comments
+
+# Runs in the base repo's context (unlike the pull_request-triggered
+# clang-tidy-review workflow, which gets a read-only GITHUB_TOKEN for PRs
+# from forks), so it has the permissions needed to post the review that
+# clang-tidy.yml generated and uploaded as an artifact.
+on:
+  workflow_run:
+    workflows: ["clang-tidy-review"]
+    types:
+      - completed
+
+jobs:
+  post-review:
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+      contents: read
+    steps:
+      - uses: ZedThree/clang-tidy-review/post@v0.21.0
+        with:
+          max_comments: 25

.github/workflows/clang-tidy-review.yml

@@ -22,6 +22,11 @@ jobs:
         apt_packages: g++,qt6-base-dev,libqt6opengl6-dev,libglvnd-dev,zlib1g-dev,libfftw3-dev,ninja-build
         config_file: .clang-tidy-review
         clang_tidy_version: 19
+        # PRs from forks get a read-only GITHUB_TOKEN, which can't post a review
+        # (see the 403 "Resource not accessible by integration" failure). Generate
+        # the review here and post it from clang-tidy-post.yml instead, which runs
+        # via workflow_run in the base repo's context and has write access.
+        split_workflow: true
 
     - uses: ZedThree/clang-tidy-review/upload@v0.21.0
       id: upload-review

.github/workflows/pydra.yml

@@ -0,0 +1,83 @@
+name: Pydra code generation
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+    branches: [ master, dev]
+    merge_group:
+      types: [checks_requested]
+      branches: [master]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  generate-pydra:
+    runs-on: ubuntu-latest
+
+    env:
+      QT_SELECT: qt6
+      SCCACHE_GHA_ENABLED: "true"
+      SCCACHE_CACHE_SIZE: "2G"
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        submodules: true
+
+    - name: Get latest version
+      run: echo "MRTRIX3_VERSION=$(git fetch --tags && 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 zlib1g-dev libfftw3-dev ninja-build python3-numpy libpng-dev
+
+    - name: Run sccache-cache
+      uses: mozilla-actions/sccache-action@v0.0.9
+
+    - name: Get CMake
+      uses: lukka/get-cmake@latest
+
+    - name: Print CMake version
+      run: cmake --version
+
+    - name: Make installation dir
+      run: |
+        sudo mkdir -p /opt/mrtrix3
+        sudo chown $USER /opt/mrtrix3
+
+    - 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=/opt/mrtrix3
+
+    - name: Build MRtrix3
+      run: cmake --build build
+
+    - name: Install MRtrix3
+      run: cmake --install build
+
+    - name: Clone pydra-tasks-mrtrix3
+      run: git clone https://github.com/nipype/pydra-tasks-mrtrix3
+
+    - name: Install pydra-tasks-mrtrix3 and fileformats packages
+      run: pip install -e ./pydra-tasks-mrtrix3[test,dev] -e ./pydra-tasks-mrtrix3/related-packages/fileformats -e ./pydra-tasks-mrtrix3/related-packages/fileformats-extras
+
+    - name: Generate Pydra task packages
+      run: python3 pydra-tasks-mrtrix3/generate.py /opt/mrtrix3/bin pydra-tasks-mrtrix3 3.1.0
+
+    - name: Test with pytest
+      run: pytest -sv pydra-tasks-mrtrix3/pydra/tasks/mrtrix3 --cov pydra.tasks.mrtrix3 --cov-report xml
+
+
+

.gitignore

@@ -17,12 +17,14 @@
 docs/**/*.md
 !docs/README.md
 /python/lib/mrtrix3/_version.py
+*.venv
 /scripts/mrtrix_bash_completion
 /dev/
 /compiled_docs/
 /.vscode/
 .claude
 .cproject
+.DS_store
 .idea
 .project
 .settings

cpp/cmd/amp2response.cpp

@@ -60,7 +60,7 @@ 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 ("fibre_directions", "a 4D image containing the estimated fibre directions").type_image_in()
     + Argument ("response", "the output zonal spherical harmonic coefficients").type_file_out();
 
   OPTIONS

cpp/cmd/peaks2amp.cpp

@@ -31,7 +31,7 @@ void usage() {
   SYNOPSIS = "Extract amplitudes from a peak directions image";
 
   ARGUMENTS
-  + Argument ("directions", "the input directions image."
+  + Argument ("fibre_directions", "the input directions image."
                             " Each volume corresponds to the x, y & z"
                             " component of each direction vector in turn.").type_image_in()
 

cpp/cmd/peaks2fixel.cpp

@@ -37,7 +37,7 @@ void usage() {
   + Fixel::format_description;
 
   ARGUMENTS
-  + Argument ("directions", "the input directions image;"
+  + Argument ("fibre_directions", "the input directions image;"
                             " each volume corresponds to the x, y & z"
                             " component of each direction vector in turn.").type_image_in()
 

cpp/cmd/sh2amp.cpp

@@ -70,7 +70,7 @@ void usage() {
 
   ARGUMENTS
     + Argument ("input", "the input spherical harmonic (SH) coefficients image").type_image_in()
-    + Argument ("directions", "the set of directions along which the SH functions will be sampled").type_file_in()
+    + Argument ("fibre_directions", "the set of directions along which the SH functions will be sampled").type_file_in()
     + Argument ("output", "the output amplitudes image").type_image_out();
 
   OPTIONS

cpp/cmd/sh2response.cpp

@@ -44,7 +44,7 @@ void usage() {
   ARGUMENTS
     + Argument ("SH", "the spherical harmonic decomposition of the diffusion-weighted images").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 direction vectors along which to estimate the response function").type_image_in()
+    + Argument ("fibre_directions", "a 4D image containing the direction vectors along which to estimate the response function").type_image_in()
     + Argument ("response", "the output axially-symmetric spherical harmonic coefficients").type_file_out();
 
   OPTIONS