ENH: AnatomyTaxonomy, USD pipeline hardening, tutorials + docs

.agents/.gitignore

@@ -1 +1,2 @@
 settings.local.json
+.nicc*

.github/workflows/README.md

@@ -10,7 +10,7 @@ Runs on every push and pull request to main branches. Includes:
 
 - **unit-tests**: Cross-platform unit tests
   - Runs on Ubuntu and Windows
-  - Python 3.10, 3.11, and 3.12
+  - Python 3.11 and 3.12
   - Uses PyTorch CPU version to avoid GPU dependencies
   - Excludes slow tests and tests requiring external data
   - Generates coverage reports
@@ -83,7 +83,7 @@ The workflows use multiple caching layers to speed up builds:
 
 ### Important: GPU Tests Are Disabled by Default
 
-⚠️ **GPU tests do NOT run automatically** to prevent jobs from waiting indefinitely in the queue when no runner is available.
+**GPU tests do NOT run automatically** to prevent jobs from waiting indefinitely in the queue when no runner is available.
 
 To run GPU tests, you must either:
 1. **Manually trigger the workflow**: Go to Actions > CI > Run workflow

.github/workflows/ci.yml

@@ -30,7 +30,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.11', '3.12']
 
     steps:
     - name: Checkout code
@@ -79,7 +79,9 @@ jobs:
           libxrender1 \
           libxext6 \
           libxrandr2 \
-          libxi6
+          libxi6 \
+          xvfb \
+          libosmesa6
         sudo apt-get clean
         sudo rm -rf /var/lib/apt/lists/*
 
@@ -99,13 +101,20 @@ jobs:
       run: |
         pip list
 
-    - name: Run unit tests (fast, no external data)
+    - name: Run unit tests (fast, no external data) - Ubuntu
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        xvfb-run -a --server-args="-screen 0 1024x768x24" \
+          pytest tests/ -v -m "not slow and not requires_data and not experiment" --cov=physiomotion4d --cov-report=xml --cov-report=term --cov-report=html
+
+    - name: Run unit tests (fast, no external data) - Windows
+      if: matrix.os == 'windows-latest'
       run: |
         pytest tests/ -v -m "not slow and not requires_data and not experiment" --cov=physiomotion4d --cov-report=xml --cov-report=term --cov-report=html
 
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10'
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -115,7 +124,7 @@ jobs:
 
     - name: Upload coverage artifacts
       uses: actions/upload-artifact@v4
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10'
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
       with:
         name: coverage-report-unit-tests
         path: htmlcov/
@@ -148,10 +157,10 @@ jobs:
         echo "Disk space after cleanup:"
         df -h
 
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
         cache: 'pip'
         cache-dependency-path: pyproject.toml
 
@@ -185,7 +194,9 @@ jobs:
           libxrender1 \
           libxext6 \
           libxrandr2 \
-          libxi6
+          libxi6 \
+          xvfb \
+          libosmesa6
         sudo apt-get clean
         sudo rm -rf /var/lib/apt/lists/*
 
@@ -218,17 +229,20 @@ jobs:
 
     - name: Run USD conversion tests
       run: |
-        pytest tests/test_convert_vtk_to_usd_polymesh.py -v -m "not slow" --cov=physiomotion4d --cov-append --cov-report=xml
+        xvfb-run -a --server-args="-screen 0 1024x768x24" \
+          pytest tests/test_convert_vtk_to_usd_polymesh.py -v -m "not slow" --cov=physiomotion4d --cov-append --cov-report=xml
       continue-on-error: true
 
     - name: Run USD utility tests
       run: |
-        pytest tests/test_usd_merge.py tests/test_usd_time_preservation.py -v --cov=physiomotion4d --cov-append --cov-report=xml
+        xvfb-run -a --server-args="-screen 0 1024x768x24" \
+          pytest tests/test_usd_merge.py tests/test_usd_time_preservation.py -v --cov=physiomotion4d --cov-append --cov-report=xml
       continue-on-error: true
 
     - name: Run all integration tests
       run: |
-        pytest tests/ -v -m "not slow and not experiment and not requires_gpu"
+        xvfb-run -a --server-args="-screen 0 1024x768x24" \
+          pytest tests/ -v -m "not slow and not experiment and not requires_gpu"
       continue-on-error: true
 
     - name: Upload coverage to Codecov
@@ -345,10 +359,10 @@ jobs:
       with:
         lfs: true
 
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.11"
         cache: 'pip'
 
     - name: Install dev dependencies

.github/workflows/release.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Install build tools
         run: |

CLAUDE.md

@@ -36,7 +36,7 @@ py -m pytest tests/ --ignore=tests/test_segment_chest_total_segmentator.py \
 # With coverage
 py -m pytest tests/ --cov=src/physiomotion4d --cov-report=html
 
-# Experiment notebook tests (very slow, opt-in)
+# Experiment script tests (very slow, opt-in)
 py -m pytest tests/ --run-experiments
 
 # Create missing baselines