Complete Project ATO integrated SCCI research and digital engineering release

.gitattributes

@@ -1,4 +1,6 @@
 * text=auto
+.gitattributes text eol=lf
+*.yml text eol=lf
 *.py text eol=lf
 *.md text eol=lf
 *.csv text eol=lf
@@ -7,6 +9,15 @@
 *.svg text eol=lf
 *.kicad_sch text eol=lf
 *.kicad_pcb text eol=lf
+*.kicad_sym text eol=lf
+*.kicad_mod text eol=lf
+*.kicad_pro text eol=lf
+*.net text eol=lf
+*.xml text eol=lf
+*.cir text eol=lf
+*.npz binary
+**/sym-lib-table text eol=lf
+**/fp-lib-table text eol=lf
 *.step -text
 *.stl binary
 *.png binary
@@ -15,3 +26,45 @@
 *.FCStd binary
 *.mp4 binary
 *.zip binary
+*.gz binary
+# Generated geometry is reviewed through its parametric source, drawings and CAD.
+cad/stage2/*.step binary
+# Preserve KiCad's exported SVG spacing; these files are reviewed generated output.
+electronics/stage4/monitoring-cell/svg/*.svg whitespace=-blank-at-eol
+# Preserve Matplotlib's generated SVG path spacing; reviewed figures bind exact bytes.
+electronics/stage4/monitoring-study/*.svg whitespace=-blank-at-eol
+# Native exports and reviewed scientific figures retain generated path spacing.
+electronics/stage4/current-driver/svg/*.svg whitespace=-blank-at-eol
+electronics/stage4/driver-study/*.svg whitespace=-blank-at-eol
+# Reviewed observer freezes bind original bytes, including Windows JSON newlines.
+experiments/stage3/observed-state-observer/requirements-lock.txt text eol=lf
+experiments/stage3/observed-state-observer/frozen/** -text whitespace=cr-at-eol
+# This separately approved replay also binds exact protocol/source/receipt bytes.
+experiments/stage3/frozen-observer-pilot/** -text whitespace=cr-at-eol
+# Historical report embeds the exact approved review bytes, including newlines.
+provenance/stage3-closeout-review.json -text whitespace=cr-at-eol
+# Matplotlib SVG spacing is generated and visually inspected.
+# Preserve the reviewed scenario bytes bound by its review receipt.
+experiments/stage3/conditional-concept/** -text whitespace=cr-at-eol
+experiments/stage3/conditional-concept/*.svg whitespace=-blank-at-eol,cr-at-eol
+# Target binary bytes, compiler-map spacing and upstream notices are preserved.
+firmware/nrf5340/artifacts/*.elf binary
+firmware/nrf5340/artifacts/*.bin binary
+firmware/nrf5340/artifacts/ato.map text eol=lf whitespace=-blank-at-eol
+firmware/nrf5340/licenses/* text eol=lf -whitespace
+# New native exports retain their reviewed generated spacing and image bytes.
+electronics/stage4/controller-carrier/svg/*.svg whitespace=-blank-at-eol
+electronics/stage4/integrated-pcb/**/*.svg whitespace=-blank-at-eol
+electronics/stage4/integrated-pcb/firmware-profile/artifacts/*.elf binary
+electronics/stage4/integrated-pcb/firmware-profile/artifacts/*.bin binary
+electronics/stage4/integrated-pcb/firmware-profile/artifacts/ato.map text eol=lf whitespace=-blank-at-eol
+electronics/stage4/integrated-pcb/**/*.step binary
+electronics/stage4/integrated-pcb/**/*.ses whitespace=-blank-at-eol
+# Native Stage5 exchange derivatives are reviewed through CAD and drawings.
+cad/stage5/**/*.step binary
+cad/stage5/**/*.svg whitespace=-blank-at-eol
+# Keep reviewed source-hash bindings byte-stable, including final blank lines.
+cad/stage5/reference/extract_board_datums.py whitespace=-blank-at-eof
+docs/stage5/future-package-design.md whitespace=-blank-at-eof
+# Source-derived manuscript SVG path spacing is generated and visually reviewed.
+manuscript/stage6/figures/*.svg whitespace=-blank-at-eol

.github/workflows/verify-mechanics.yml

@@ -0,0 +1,21 @@
+name: Verify mechanical CAD package
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  mechanical-package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Verify exact committed artifact bytes
+        run: python scripts/verify_manifest.py
+      - name: Replay mechanical source and native-receipt checks
+        run: python scripts/verify_stage5_mechanics.py
+      - name: Preserve the integrated electronics checkpoint
+        run: python scripts/verify_integrated_pcb.py

.github/workflows/verify-pcb.yml

@@ -0,0 +1,19 @@
+name: Verify integrated PCB package
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  pcb-package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Verify exact committed artifact bytes
+        run: python scripts/verify_manifest.py
+      - name: Replay independent PCB and source-preservation checks
+        run: python scripts/verify_integrated_pcb.py

.github/workflows/verify-release.yml

@@ -0,0 +1,29 @@
+name: Verify integrated digital release
+on:
+  pull_request:
+  push:
+    tags: ['v2.*']
+  workflow_dispatch:
+
+jobs:
+  integrated-release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Install document inspection dependency
+        run: python -m pip install pypdf==6.10.0 numpy==2.3.5
+      - name: Verify exact committed Git blobs
+        run: python scripts/verify_manifest.py
+      - name: Verify manuscript, release entries and preserved sources
+        run: python scripts/verify_stage6_release.py
+      - name: Reproduce both conditional paths through the production C core
+        run: python scripts/stage6/verify_digital_path.py
+      - name: Preserve integrated electronics checkpoint
+        run: python scripts/verify_integrated_pcb.py
+      - name: Preserve mechanical source and native inspection evidence
+        run: python scripts/verify_stage5_mechanics.py

.github/workflows/verify.yml

@@ -1,16 +1,66 @@
 name: Verify digital studies
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+env:
+  OPENBLAS_NUM_THREADS: '1'
+  OMP_NUM_THREADS: '1'
+
 jobs:
-  verify:
+  audit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
       - uses: actions/setup-python@v5
         with:
           python-version: '3.12'
           cache: pip
-      - run: python -m pip install -r requirements.txt
+      - run: python -m pip install -r requirements-lock.txt
       - run: python scripts/verify_manifest.py
+      - run: python scripts/verify_stage1_specification.py
+      - run: python scripts/run_architecture_budgets.py --check
+      - run: python scripts/verify_stage2_architecture.py
+      - run: python scripts/verify_stage3_foundation.py
+      - run: python scripts/verify_stage3_continuation.py
+      - run: python scripts/verify_stage3_revision.py
+      - run: python scripts/verify_frozen_pilot_portable.py --audit-only
+      - run: python experiments/stage3/conditional-concept/study.py --check
+      - run: python electronics/stage4/monitoring-cell/verify_monitoring_cell.py
+      - run: python electronics/stage4/monitoring-study/verify_study.py
+      - run: python electronics/stage4/current-driver/verify_current_driver.py
+      - run: python electronics/stage4/driver-study/verify_study.py
+      - run: python electronics/stage4/recording-front-end/verify_recording_front_end.py
+      - run: python electronics/stage4/recording-study/verify_input_network.py
+      - run: python electronics/stage4/recording-study/input_network_study.py
+      - run: python electronics/stage4/recording-study/timing_contract.py --check
+      - run: python electronics/stage4/contact-router/verify_contact_router.py
+      - run: python electronics/stage4/routing-study/route_contract.py --check
+      - run: python electronics/stage4/routing-study/verify_parasitics.py
+      - run: python electronics/stage4/routing-study/parasitic_study.py
+      - run: python electronics/stage4/supervision/verify_supervision.py
+      - run: python electronics/stage4/supervision-study/control_study.py --check
+      - run: python electronics/stage4/supervision-study/analog_study.py
+      - run: python electronics/stage4/supervision-study/verify_analog.py
+      - run: python electronics/stage4/supervision-study/verify_integration.py
+      - run: python electronics/stage4/power/verify_power.py
+      - run: python electronics/stage4/power-study/budget_study.py
+      - run: python electronics/stage4/power-study/verify_budget.py
+      - run: python electronics/stage4/power-study/sequence_study.py --check
+      - run: python electronics/stage4/power-study/verify_integration.py
+      - run: python electronics/stage4/monitoring-transport/verify_monitoring_transport.py
+      - run: python electronics/stage4/transport-study/transport_contract.py --check
+      - run: python electronics/stage4/transport-study/verify_transport.py
+      - run: python electronics/stage4/transport-study/input_study.py
+      - run: python electronics/stage4/transport-study/verify_input.py
+      - run: python electronics/stage4/transport-study/verify_integration.py
+      - run: python firmware/nrf5340/tests/check_runtime.py
+      - run: python scripts/verify_nrf5340.py
+      - run: python scripts/verify_integrated_pcb.py
       - run: python scripts/run_studies.py
       - run: python scripts/build_firmware.py
       - run: python scripts/run_adapter.py
@@ -22,3 +72,70 @@ jobs:
         with:
           name: synthetic-study-results
           path: results/
+
+  reproduce:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - study: foundation
+            commands: |
+              python scripts/run_stage3_studies.py --check --jobs 2
+              python scripts/stage3_electrical_sweep.py --check results/stage3/electrical-sweep.json
+              python scripts/stage3_pressure_convergence_probe.py --check results/stage3/pressure-convergence-probe.json
+          - study: motor-numerics
+            commands: python scripts/stage3_motor_convergence.py --check results/stage3/numerical/motor-convergence.json.gz
+          - study: pressure-numerics
+            commands: python scripts/stage3_pressure_convergence.py --check results/stage3/numerical/pressure-convergence.json.gz --summary-check results/stage3/numerical/pressure-convergence-summary.json --jobs 2
+          - study: information
+            commands: python scripts/stage3_information_comparison.py --check --jobs 2
+          - study: response-domain
+            commands: python scripts/stage3_response_validation.py --check results/stage3/response-validation/response-domain-raw.json.gz --summary-check results/stage3/response-validation/response-domain-summary.json --jobs 2
+          - study: acquisition-cue-expert
+            commands: |
+              python scripts/stage3_acquisition_qualification.py --check results/stage3/numerical/acquisition-qualification.json.gz
+              python scripts/stage3_cue_policy_study.py --check results/stage3/cue-policy/raw.json.gz
+              python scripts/stage3_expert_validation.py --check
+          - study: teacher-revision
+            commands: |
+              python scripts/stage3_teacher_library_study.py --check
+              python scripts/stage3_resolved_teacher_study.py --check
+              python scripts/stage3_delivery_requirements.py --check
+          - study: source-revision
+            commands: python scripts/stage3_source_sensitivity.py --check results/stage3/source-sensitivity/raw.json.gz --summary-check results/stage3/source-sensitivity/summary.json
+          - study: prediction-revision
+            commands: python scripts/stage3_assisted_prediction_study.py --check results/stage3/assisted-prediction/raw.json.gz
+          - study: dynamic-response-revision
+            commands: |
+              python scripts/stage3_dynamic_response_study.py --check
+              python scripts/stage3_sparse_baseline_study.py --check results/stage3/sparse-baseline/raw.json.gz
+          - study: isolated-pilot
+            commands: python scripts/stage3_isolated_pilot_study.py --check results/stage3/isolated-pilot/raw.json.gz
+          - study: observed-state-observer
+            commands: python experiments/stage3/observed-state-observer/verify_study.py --reproduce
+          - study: frozen-observer-pilot
+            commands: python scripts/verify_frozen_pilot_portable.py --reproduce
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ (matrix.study == 'observed-state-observer' || matrix.study == 'frozen-observer-pilot') && '3.12.14' || '3.12' }}
+          cache: pip
+      - run: python -m pip install -r requirements-lock.txt
+      - run: ${{ matrix.commands }}
+
+  verify:
+    if: always()
+    needs: [audit, reproduce]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Require artifact audit and every study reproduction
+        env:
+          AUDIT_RESULT: ${{ needs.audit.result }}
+          REPRODUCTION_RESULT: ${{ needs.reproduce.result }}
+        run: |
+          test "$AUDIT_RESULT" = success
+          test "$REPRODUCTION_RESULT" = success

.gitignore

@@ -10,7 +10,12 @@ __pycache__/
 *.kicad_prl
 *.kicad_sch-bak
 *.kicad_pcb-bak
+~*.lck
 *-backups/
 tmp/
 build/
 CONTRACT.md
+# Losslessly archived populated STEP assemblies exceed GitHub's file limit.
+cad/stage5/reference/ATO_reference_assembly.step
+cad/stage5/reference/ATO_reference_exploded.step
+cad/stage5/reference/extracted/

CITATION.cff

@@ -1,15 +1,27 @@
 cff-version: 1.2.0
-message: "Please cite this digital engineering project and its primary references separately."
-title: "Project ATO: a digital engineering study of invasive spinal interfaces"
+message: "Please cite this AI-assisted digital engineering project and its primary scientific references separately."
+title: "Project ATO: integrated SCCI research and digital engineering"
 type: software
 authors:
   - family-names: Varma
     given-names: Pratham
-version: 1.0.0
-date-released: 2026-10-07
+version: 2.0.0
+date-released: 2026-10-16
+repository-code: "https://github.com/pratham-cloud-ctrl/Project-ATO"
+url: "https://github.com/pratham-cloud-ctrl/Project-ATO/releases/tag/v2.0.0"
 abstract: >-
-  An AI-assisted, entirely digital engineering proof of concept linking spinal
-  interface literature, synthetic motor-learning and physiological-control
-  studies, reference electronics, parametric CAD, and reproducible results.
-  Simulations do not establish biological or clinical effectiveness.
+  An AI-assisted, entirely digital project connecting conditional spinal-interface
+  mechanisms for expert-informed retained motor learning and selected physiological
+  feedback to computational studies, executed production control code, native
+  electronics, target-linked firmware and mechanical CAD. No original biological
+  experiment, physical execution or clinical effectiveness is claimed.
 license: LicenseRef-Proprietary
+preferred-citation:
+  type: report
+  title: "Project ATO: a conditional spinal cord-computer interface for expert-informed practice and physiological feedback"
+  authors:
+    - family-names: Varma
+      given-names: Pratham
+  version: 2.0.0
+  date-released: 2026-10-16
+  url: "https://github.com/pratham-cloud-ctrl/Project-ATO/blob/v2.0.0/output/pdf/Project_ATO_Integrated_Manuscript.pdf"