Jaxley Integration

.github/workflows/build-wheels.yml

@@ -179,9 +179,64 @@ jobs:
         run: |
           python -c "from myogen.simulator.neuron.populations import AlphaMN__Pool; print('NEURON components OK')"
 
+  test_wheels_jaxley_only:
+    name: Test wheel WITHOUT NEURON/MPI (Jaxley-only install)
+    needs: [build_wheels]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+    steps:
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Download wheels
+        uses: actions/download-artifact@v7
+        with:
+          name: wheels-ubuntu-latest
+          path: dist/
+
+      # Deliberately DO NOT install NEURON, mpi4py, or system MPI. This proves the
+      # default (Jaxley-only) install works with none of the NEURON stack present.
+      - name: Install wheel (core deps only)
+        run: |
+          python -m pip install --upgrade pip
+          # dist/ holds both cp312 and cp313 wheels; install only the one matching
+          # this runner's Python so pip doesn't reject the other ABI.
+          tag="cp$(echo '${{ matrix.python-version }}' | tr -d .)"
+          pip install dist/*"${tag}-${tag}"*.whl
+
+      - name: Verify NEURON is absent
+        run: |
+          python -c "
+          try:
+              import neuron
+              raise SystemExit('FAIL: neuron is installed; this job must run without it')
+          except ImportError:
+              print('OK: NEURON runtime is not installed')
+          "
+
+      - name: Import MyoGen without NEURON
+        run: |
+          python -c "import myogen; print('import myogen OK')"
+          python -c "import myogen.simulator as s; print('import myogen.simulator OK; HillModel <-', s.HillModel.__module__)"
+          python -c "from myogen.simulator.jaxley import run_jax, value_and_grad_run, surface_emg_jax; print('differentiable API OK')"
+
+      - name: Build real NERLab motor neurons on the Jaxley backend
+        run: |
+          python -c "
+          import numpy as np
+          from myogen.simulator.jaxley.populations import AlphaMN__Pool
+          pool = AlphaMN__Pool(recruitment_thresholds__array=np.array([0.1, 0.3, 0.6]), mode='active')
+          assert len(pool) == 3, len(pool)
+          print('Jaxley-only install verified:', len(pool), 'NERLab MNs built, no NEURON present')
+          "
+
   publish:
     name: Publish to PyPI
-    needs: [build_wheels, build_sdist, test_wheels]
+    needs: [build_wheels, build_sdist, test_wheels, test_wheels_jaxley_only]
     runs-on: ubuntu-latest
     if: github.event_name == 'release' || (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v'))
     permissions:

.github/workflows/docs.yml

@@ -34,8 +34,11 @@ jobs:
         with:
           enable-cache: true
 
-      - name: Sync project + docs/nwb extras
-        run: uv sync --locked --group docs --extra nwb
+      - name: Sync project + docs/nwb/neuron extras
+        # NEURON is now an optional extra (Jaxley is the default backend). The docs
+        # build needs it: `poe setup_myogen` compiles NMODL, and mkdocstrings imports
+        # the NEURON injection utilities (api/io-and-neuron.md) to document them.
+        run: uv sync --locked --group docs --extra nwb --extra neuron
 
       - name: Compile NMODL mechanisms
         run: uv run poe setup_myogen

.github/workflows/tests.yml

@@ -46,9 +46,11 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install uv
 
-      - name: Install project with dev group
+      - name: Install project with dev group + optional NEURON backend
+        # NEURON is now an optional extra (Jaxley is the default backend), so the
+        # test suite must opt into it to exercise the NEURON-backed tests.
         run: |
-          uv sync --locked --group dev
+          uv sync --locked --group dev --extra neuron
 
       - name: Compile NEURON mechanisms
         run: uv run poe setup_myogen

.gitignore

@@ -1,4 +1,7 @@
 ### Python template
+# macOS Finder metadata
+.DS_Store
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -212,3 +215,26 @@ notes/
 /artifacts/
 /.runtime-deps/
 /graphify-out/
+
+# Local working artifacts kept out of the public history
+docs/session_notes/*
+!docs/session_notes/2026-06-02_jaxley_nerlab_architecture_migration.md
+# Evidence: only the final full runs are versioned; exploratory/intermediate
+# runs stay local (git add -A must not re-add them).
+experiments/twin/evidence/*
+!experiments/twin/evidence/pic_grid_full_20261018_132043.json
+!experiments/twin/evidence/val_comparison_bac411989ee8d42b_20261018_124637.json
+!experiments/twin/evidence/val_comparison_ef1bd7e84b9abd03_20261018_124343.json
+!experiments/twin/evidence/deliverable_b_full_binned_20261018_123116.json
+!experiments/twin/evidence/deliverable_c_full_binned_20261018_131156.json
+!experiments/twin/evidence/g4_descent_full_20261018_180008.json
+!experiments/twin/evidence/g5_basin_full_20261018_191021.json
+!experiments/twin/evidence/r2a_profiles_full_20261018_134617.json
+!experiments/twin/evidence/sensitivity_checks_20261013_112432.json
+!experiments/twin/evidence/gradient_repair_x64_20261018_154132.json
+docs/DIGITAL_TWIN_ROADMAP.md
+debug_*.py
+diag_*.py
+README-old.md
+Figure_1.pdf
+Figure_1_preview.jpg