Merge pull request #1 from aylward/transfer

ENH: Initial commit to transfer files

Author: aylward

.flake8

@@ -0,0 +1,16 @@
+[flake8]
+max-line-length = 88
+extend-ignore = E203, E501, W503
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    .eggs,
+    *.egg-info,
+    .venv,
+    venv,
+    .mypy_cache,
+    .pytest_cache
+per-file-ignores =
+    __init__.py:F401

.github/workflows/docs.yml

@@ -0,0 +1,54 @@
+name: Documentation
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  release:
+    types: [published]
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+      
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+        
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install uv
+        uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
+        uv pip install --system -e ".[docs]"
+        
+    - name: Build documentation
+      run: |
+        cd docs
+        make html
+        
+    - name: Check for warnings
+      run: |
+        cd docs
+        make html SPHINXOPTS="-W --keep-going"
+        
+    - name: Upload documentation artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: documentation
+        path: docs/_build/html/
+        
+    - name: Deploy to GitHub Pages (main branch only)
+      if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs/_build/html
+        cname: physiomotion4d.readthedocs.io  # Optional: if using custom domain
+

.github/workflows/tests.yml

@@ -0,0 +1,128 @@
+name: Tests
+
+# Test organization:
+# - Unit tests: Run on all PRs and pushes, no external data required
+# - Integration tests with data: Run on PRs, download and cache test data
+# - GPU tests (segmentation): Excluded from CI (requires CUDA), run locally
+#
+# Test markers:
+# - requires_data: Tests that need external data downloads
+# - slow: Tests that are computationally intensive or require GPU
+
+on:
+  pull_request:
+    branches: [ main ]
+  push:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .
+        pip install pytest pytest-cov
+
+    - name: Run unit tests (no data required)
+      run: |
+        pytest tests/ -v -m "not requires_data and not slow" --cov=src/physiomotion4d --cov-report=xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10'
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        fail_ci_if_error: false
+
+  test-with-data:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request'
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .
+        pip install pytest pytest-cov
+
+    - name: Cache test data
+      uses: actions/cache@v4
+      with:
+        path: |
+          tests/data/
+          tests/results/
+        key: test-data-${{ hashFiles('tests/test_*.py') }}-v2
+        restore-keys: |
+          test-data-
+
+    - name: Run data download tests
+      run: |
+        pytest tests/test_download_heart_data.py -v --cov=src/physiomotion4d --cov-report=xml
+      continue-on-error: true
+
+    - name: Run data conversion tests
+      run: |
+        pytest tests/test_convert_nrrd_4d_to_3d.py -v --cov=src/physiomotion4d --cov-append --cov-report=xml
+      continue-on-error: true
+
+    - name: Run contour tools tests
+      run: |
+        pytest tests/test_contour_tools.py -v -m "not slow" --cov=src/physiomotion4d --cov-append --cov-report=xml
+      continue-on-error: true
+
+    - name: Run USD conversion tests
+      run: |
+        pytest tests/test_convert_vtk_4d_to_usd_polymesh.py -v -m "not slow" --cov=src/physiomotion4d --cov-append --cov-report=xml
+      continue-on-error: true
+
+    - name: Run existing USD tests
+      run: |
+        pytest tests/test_usd_merge.py tests/test_usd_time_preservation.py -v --cov=src/physiomotion4d --cov-append --cov-report=xml
+      continue-on-error: true
+
+    - name: Upload coverage
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        flags: integration-tests
+        fail_ci_if_error: false
+
+  # Note: Slow and GPU-dependent tests are excluded from CI
+  # These tests should be run locally:
+  # - tests/test_register_images_ants.py (slow, computationally intensive)
+  # - tests/test_register_images_icon.py (requires CUDA for ICON)
+  # - tests/test_transform_tools.py (depends on slow registration tests)
+  # - tests/test_segment_chest_total_segmentator.py (requires CUDA for TotalSegmentator)
+  # - tests/test_segment_chest_vista_3d.py (requires CUDA for VISTA-3D)
+  #
+  # To run slow/GPU tests locally:
+  # pytest tests/ -v -m "slow"  # Run all slow tests
+  # pytest tests/test_register_images_ants.py -v -s
+  # pytest tests/test_register_images_icon.py -v -s
+  # pytest tests/test_transform_tools.py -v -s
+  # pytest tests/test_segment_chest_total_segmentator.py -v -s
+  # pytest tests/test_segment_chest_vista_3d.py -v -s

.gitignore

@@ -0,0 +1,44 @@
+# Project files
+.claude
+.coverage
+coverage.xml
+*~
+venv*
+.venv
+build
+*.egg-info
+*.log
+__pycache__
+_version.py
+htmlcov
+
+# Network weights
+network_weights
+
+# Data files
+*.gz
+*.mha
+*.mhd
+*.zip
+*.nii
+*.tfm
+*.vtp
+*.vtk
+*.vtu
+*.usd
+*.usda
+*.usdc
+*.nrrd
+
+# Archive and Output Directories
+archive
+old
+output
+save
+results*
+
+# Test data and outputs
+tests/data/
+tests/results/
+tests/baseline_staging/
+test_output.txt

.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+# Example pre-commit configuration for PhysioMotion4D
+# Copy to .pre-commit-config.yaml to enable pre-commit hooks
+
+repos:
+  # Code formatting
+  - repo: https://github.com/psf/black
+    rev: 24.1.1
+    hooks:
+      - id: black
+        args: [--line-length=88]
+
+  # Import sorting
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: [--profile=black, --line-length=88]
+
+  # Linting
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        args: [--max-line-length=88]
+
+  # Local tests
+  - repo: local
+    hooks:
+      - id: test-heart-ct-cli
+        name: Test Heart CT CLI Pipeline
+        entry: pytest tests/test_process_heart_gated_ct_cli.py -v
+        language: system
+        pass_filenames: false
+        always_run: false
+        files: ^(src/physiomotion4d/|cli/process_heart_gated_ct.py)
+        stages: [pre-commit]
+
+      - id: fast-unit-tests
+        name: Run Fast Unit Tests
+        entry: pytest tests/ -m "not slow" -v
+        language: system
+        pass_filenames: false
+        always_run: false
+        files: ^(src/physiomotion4d/|tests/)
+        stages: [pre-push]

.readthedocs.yaml

@@ -0,0 +1,37 @@
+# Read the Docs configuration file for PhysioMotion4D
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+  jobs:
+    post_create_environment:
+      # Install uv for faster dependency installation
+      - pip install uv
+    post_install:
+      # Install torch with CUDA support (CPU version for docs build)
+      - uv pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
+
+# Sphinx configuration
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: false
+
+# Python configuration
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+# Formats to build (PDF, ePub, HTML)
+formats:
+  - pdf
+  - epub
+

.vscode/settings.json

@@ -0,0 +1,52 @@
+{
+  // Python formatting
+  "python.formatting.provider": "black",
+  "python.formatting.blackArgs": [
+    "--line-length=88"
+  ],
+  // Editor settings
+  "editor.rulers": [
+    88
+  ],
+  "editor.wordWrapColumn": 88,
+  // Python linting
+  "python.linting.enabled": true,
+  "python.linting.flake8Enabled": true,
+  "python.linting.flake8Args": [
+    "--max-line-length=88"
+  ],
+  "python.linting.pylintEnabled": true,
+  "python.linting.pylintArgs": [
+    "--max-line-length=88"
+  ],
+  // Format on save
+  "editor.formatOnSave": true,
+  "editor.formatOnPaste": false,
+  // Python-specific editor settings
+  "[python]": {
+    "editor.rulers": [
+      88
+    ],
+    "editor.tabSize": 4,
+    "editor.insertSpaces": true,
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+      "source.organizeImports": "explicit"
+    }
+  },
+  // isort settings
+  "isort.args": [
+    "--profile",
+    "black",
+    "--line-length",
+    "88"
+  ],
+  // Pylance diagnostic settings for Jupyter notebooks
+  "python.analysis.diagnosticSeverityOverrides": {
+    "reportUndefinedVariable": "warning",
+    "reportMissingImports": "warning"
+  },
+  "jupyter.pylanceHandlesNotebooks": true,
+  "python.analysis.typeCheckingMode": "basic",
+  "ruff.configuration": ""
+}