feat(solver): graph decomposition for cluster-by-cluster solving (phase 3)

Add a Python decomposition layer using NetworkX that partitions the
constraint graph into biconnected components (rigid clusters), orders
them via a block-cut tree, and solves each cluster independently.
Articulation-point bodies propagate as boundary conditions between
clusters.

New module kindred_solver/decompose.py:
- DOF table mapping BaseJointKind to residual counts
- Constraint graph construction (nx.MultiGraph)
- Biconnected component detection + articulation points
- Block-cut tree solve ordering (root-first from grounded cluster)
- Cluster-by-cluster solver with boundary body fix/unfix cycling
- Pebble game integration for per-cluster rigidity classification

Changes to existing modules:
- params.py: add unfix() for boundary body cycling
- solver.py: extract _monolithic_solve(), add decomposition branch
  for assemblies with >= 8 free bodies

Performance: for k clusters of ~n/k params each, total cost drops
from O(n^3) to O(n^3/k^2).

220 tests passing (up from 207).

.gitea/workflows/ci.yaml

@@ -1,65 +0,0 @@
-name: CI
-
-on:
-  push:
-    branches: [main]
-  pull_request:
-    branches: [main]
-
-jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-
-      - name: Install dependencies
-        run: |
-          pip install ruff mypy
-          pip install -e ".[dev]" || pip install ruff mypy numpy
-
-      - name: Ruff check
-        run: ruff check solver/ freecad/ tests/ scripts/
-
-      - name: Ruff format check
-        run: ruff format --check solver/ freecad/ tests/ scripts/
-
-  type-check:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-
-      - name: Install dependencies
-        run: |
-          pip install mypy numpy
-          pip install torch --index-url https://download.pytorch.org/whl/cpu
-          pip install torch-geometric
-          pip install -e ".[dev]"
-
-      - name: Mypy
-        run: mypy solver/ freecad/
-
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-
-      - name: Install dependencies
-        run: |
-          pip install torch --index-url https://download.pytorch.org/whl/cpu
-          pip install torch-geometric
-          pip install -e ".[train,dev]"
-
-      - name: Run tests
-        run: pytest tests/ freecad/tests/ -v --tb=short

GNN/.gitea/workflows/ci.yaml

@@ -0,0 +1,209 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+    inputs:
+      run_datagen:
+        description: "Run dataset generation"
+        required: false
+        type: boolean
+        default: false
+      num_assemblies:
+        description: "Number of assemblies to generate"
+        required: false
+        type: string
+        default: "100000"
+      num_workers:
+        description: "Parallel workers for datagen"
+        required: false
+        type: string
+        default: "4"
+
+env:
+  PIP_CACHE_DIR: /tmp/pip-cache-solver
+  TORCH_INDEX: https://download.pytorch.org/whl/cpu
+  VIRTUAL_ENV: /tmp/solver-venv
+
+jobs:
+  # ---------------------------------------------------------------------------
+  # Lint — fast, no torch required
+  # ---------------------------------------------------------------------------
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      PATH: /tmp/solver-venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+    steps:
+      - name: Trust internal CA
+        run: |
+          curl -sk https://ipa.kindred.internal/ipa/config/ca.crt \
+            -o /usr/local/share/ca-certificates/kindred-internal.crt
+          update-ca-certificates
+
+      - name: Checkout
+        uses: https://github.com/actions/checkout@v4
+
+      - name: Set up venv
+        run: python3 -m venv $VIRTUAL_ENV
+
+      - name: Install lint tools
+        run: pip install --cache-dir $PIP_CACHE_DIR ruff
+
+      - name: Ruff check
+        run: ruff check solver/ freecad/ tests/ scripts/
+
+      - name: Ruff format check
+        run: ruff format --check solver/ freecad/ tests/ scripts/
+
+  # ---------------------------------------------------------------------------
+  # Type check
+  # ---------------------------------------------------------------------------
+  type-check:
+    runs-on: ubuntu-latest
+    env:
+      PATH: /tmp/solver-venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+    steps:
+      - name: Trust internal CA
+        run: |
+          curl -sk https://ipa.kindred.internal/ipa/config/ca.crt \
+            -o /usr/local/share/ca-certificates/kindred-internal.crt
+          update-ca-certificates
+
+      - name: Checkout
+        uses: https://github.com/actions/checkout@v4
+
+      - name: Set up venv
+        run: python3 -m venv $VIRTUAL_ENV
+
+      - name: Install dependencies
+        run: |
+          pip install --cache-dir $PIP_CACHE_DIR \
+            mypy numpy scipy \
+            torch --index-url $TORCH_INDEX
+          pip install --cache-dir $PIP_CACHE_DIR torch-geometric
+          pip install --cache-dir $PIP_CACHE_DIR -e ".[dev]"
+
+      - name: Mypy
+        run: mypy solver/ freecad/
+
+  # ---------------------------------------------------------------------------
+  # Tests
+  # ---------------------------------------------------------------------------
+  test:
+    runs-on: ubuntu-latest
+    env:
+      PATH: /tmp/solver-venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+    steps:
+      - name: Trust internal CA
+        run: |
+          curl -sk https://ipa.kindred.internal/ipa/config/ca.crt \
+            -o /usr/local/share/ca-certificates/kindred-internal.crt
+          update-ca-certificates
+
+      - name: Checkout
+        uses: https://github.com/actions/checkout@v4
+
+      - name: Set up venv
+        run: python3 -m venv $VIRTUAL_ENV
+
+      - name: Install dependencies
+        run: |
+          pip install --cache-dir $PIP_CACHE_DIR \
+            torch --index-url $TORCH_INDEX
+          pip install --cache-dir $PIP_CACHE_DIR torch-geometric
+          pip install --cache-dir $PIP_CACHE_DIR -e ".[train,dev]"
+
+      - name: Run tests
+        run: pytest tests/ freecad/tests/ -v --tb=short
+
+  # ---------------------------------------------------------------------------
+  # Dataset generation — manual trigger or on main push
+  # ---------------------------------------------------------------------------
+  datagen:
+    runs-on: ubuntu-latest
+    if: >-
+      (github.event_name == 'workflow_dispatch' && inputs.run_datagen == true) ||
+      (github.event_name == 'push' && github.ref == 'refs/heads/main')
+    needs: [test]
+    env:
+      PATH: /tmp/solver-venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+    steps:
+      - name: Trust internal CA
+        run: |
+          curl -sk https://ipa.kindred.internal/ipa/config/ca.crt \
+            -o /usr/local/share/ca-certificates/kindred-internal.crt
+          update-ca-certificates
+
+      - name: Checkout
+        uses: https://github.com/actions/checkout@v4
+
+      - name: Set up venv
+        run: python3 -m venv $VIRTUAL_ENV
+
+      - name: Install dependencies
+        run: |
+          pip install --cache-dir $PIP_CACHE_DIR \
+            torch --index-url $TORCH_INDEX
+          pip install --cache-dir $PIP_CACHE_DIR torch-geometric
+          pip install --cache-dir $PIP_CACHE_DIR -e ".[train]"
+
+      - name: Restore datagen checkpoint
+        id: datagen-cache
+        uses: https://github.com/actions/cache/restore@v4
+        with:
+          path: data/synthetic
+          key: datagen-${{ github.sha }}
+          restore-keys: |
+            datagen-
+
+      - name: Generate dataset
+        run: |
+          NUM=${INPUTS_NUM_ASSEMBLIES:-100000}
+          WORKERS=${INPUTS_NUM_WORKERS:-4}
+          echo "Generating ${NUM} assemblies with ${WORKERS} workers"
+          python3 scripts/generate_synthetic.py \
+            --num-assemblies "${NUM}" \
+            --num-workers "${WORKERS}" \
+            --output-dir data/synthetic
+        env:
+          INPUTS_NUM_ASSEMBLIES: ${{ inputs.num_assemblies }}
+          INPUTS_NUM_WORKERS: ${{ inputs.num_workers }}
+
+      - name: Save datagen checkpoint
+        if: always()
+        uses: https://github.com/actions/cache/save@v4
+        with:
+          path: data/synthetic
+          key: datagen-${{ github.sha }}
+
+      - name: Upload dataset
+        uses: https://github.com/actions/upload-artifact@v3
+        with:
+          name: synthetic-dataset
+          path: |
+            data/synthetic/index.json
+            data/synthetic/stats.json
+            data/synthetic/shards/
+          retention-days: 90
+
+      - name: Print summary
+        if: always()
+        run: |
+          echo "=== Dataset Generation Results ==="
+          if [ -f data/synthetic/stats.json ]; then
+            python3 -c "
+          import json
+          with open('data/synthetic/stats.json') as f:
+              s = json.load(f)
+          print(f'Total examples: {s[\"total_examples\"]}')
+          print(f'Classification: {json.dumps(s[\"classification_distribution\"], indent=2)}')
+          print(f'Rigid: {s[\"rigidity\"][\"rigid_fraction\"]*100:.1f}%')
+          print(f'Degeneracy: {s[\"geometric_degeneracy\"][\"fraction_with_degeneracy\"]*100:.1f}%')
+          "
+          else
+            echo "stats.json not found — generation may have failed"
+            ls -la data/synthetic/ 2>/dev/null || echo "output dir missing"
+          fi