V123: typed errors, module decomposition, CI hardening, doc alignment #121

Workflow file for this run

	name: neuralSpring Rust

	on:
	push:
	branches: [main]
	paths:
	- 'src/**'
	- 'metalForge/**'
	- 'playGround/**'
	- 'Cargo.toml'
	- 'deny.toml'
	- '.github/workflows/rust.yml'
	pull_request:
	branches: [main]
	paths:
	- 'src/**'
	- 'metalForge/**'
	- 'playGround/**'
	- 'Cargo.toml'
	- 'deny.toml'

	env:
	CARGO_TERM_COLOR: always

	jobs:
	test:
	runs-on: ubuntu-latest
	timeout-minutes: 10

	steps:
	- uses: actions/checkout@v4

	# barraCuda is a standalone primal (path dep at ../barraCuda/crates/barracuda).
	- name: Checkout barraCuda (standalone math primal)
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository_owner }}/barraCuda
	path: ../barraCuda
	sparse-checkout: crates/barracuda

	- name: Install stable toolchain
	uses: dtolnay/rust-toolchain@stable
	with:
	components: clippy, rustfmt

	- name: Cache cargo
	uses: actions/cache@v4
	with:
	path: \|
	~/.cargo/bin/
	~/.cargo/registry/index/
	~/.cargo/registry/cache/
	~/.cargo/git/db/
	target/
	key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.toml') }}

	- name: Build (workspace)
	run: cargo build --workspace --all-targets

	- name: Test (workspace, lib + unit)
	run: cargo test --workspace --lib

	- name: Test (workspace, integration)
	run: cargo test --workspace --test '*'

	- name: Clippy (pedantic + nursery, all features)
	run: cargo clippy --workspace --all-targets --all-features -- -D warnings -W clippy::pedantic -W clippy::nursery

	- name: Format check (workspace)
	run: cargo fmt --all -- --check

	- name: Doc check (workspace)
	run: cargo doc --workspace --no-deps
	env:
	RUSTDOCFLAGS: "-D warnings"

	ecobin-cross-check:
	runs-on: ubuntu-latest
	timeout-minutes: 5
	needs: test

	steps:
	- uses: actions/checkout@v4

	- name: Checkout barraCuda (standalone math primal)
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository_owner }}/barraCuda
	path: ../barraCuda
	sparse-checkout: crates/barracuda

	- name: Install stable toolchain with musl target
	uses: dtolnay/rust-toolchain@stable
	with:
	targets: x86_64-unknown-linux-musl, aarch64-unknown-linux-gnu

	- name: Cache cargo
	uses: actions/cache@v4
	with:
	path: \|
	~/.cargo/bin/
	~/.cargo/registry/index/
	~/.cargo/registry/cache/
	~/.cargo/git/db/
	target/
	key: ${{ runner.os }}-cargo-musl-${{ hashFiles('Cargo.toml') }}

	- name: ecoBin musl check (zero C deps)
	run: cargo check --target x86_64-unknown-linux-musl

	- name: ecoBin ARM check (cross-compile)
	run: cargo check --target aarch64-unknown-linux-gnu

	- name: Verify no banned C sys crates
	run: \|
	if cargo tree --all-features 2>/dev/null \| grep -qE "(openssl-sys\|ring \|aws-lc-sys\|zstd-sys\|lz4-sys\|sysinfo )"; then
	echo "FAIL: Banned C sys crate detected in dependency tree"
	cargo tree --all-features \| grep -E "(openssl-sys\|ring \|aws-lc-sys\|zstd-sys\|lz4-sys\|sysinfo )"
	exit 1
	fi
	echo "PASS: No banned C sys crates"

	supply-chain:
	runs-on: ubuntu-latest
	timeout-minutes: 5
	needs: test

	steps:
	- uses: actions/checkout@v4

	- name: Checkout barraCuda (standalone math primal)
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository_owner }}/barraCuda
	path: ../barraCuda
	sparse-checkout: crates/barracuda

	- name: Install stable toolchain
	uses: dtolnay/rust-toolchain@stable

	- name: Install cargo-deny
	run: cargo install --locked cargo-deny

	- name: Cache cargo
	uses: actions/cache@v4
	with:
	path: \|
	~/.cargo/bin/
	~/.cargo/registry/index/
	~/.cargo/registry/cache/
	~/.cargo/git/db/
	target/
	key: ${{ runner.os }}-cargo-deny-${{ hashFiles('Cargo.toml') }}

	- name: Run cargo-deny (licenses, advisories, bans, sources)
	run: cargo deny check

	coverage:
	runs-on: ubuntu-latest
	timeout-minutes: 10
	needs: test

	steps:
	- uses: actions/checkout@v4

	- name: Checkout barraCuda (standalone math primal)
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository_owner }}/barraCuda
	path: ../barraCuda
	sparse-checkout: crates/barracuda

	- name: Install stable toolchain
	uses: dtolnay/rust-toolchain@stable
	with:
	components: llvm-tools-preview

	- name: Install cargo-llvm-cov
	uses: taiki-e/install-action@cargo-llvm-cov

	- name: Cache cargo
	uses: actions/cache@v4
	with:
	path: \|
	~/.cargo/bin/
	~/.cargo/registry/index/
	~/.cargo/registry/cache/
	~/.cargo/git/db/
	target/
	key: ${{ runner.os }}-cargo-cov-${{ hashFiles('Cargo.toml') }}

	- name: Collect coverage (workspace)
	run: cargo llvm-cov --workspace --lib --json --output-path coverage.json

	- name: Check coverage threshold (90%)
	run: \|
	COV=$(python3 -c "import json; d=json.load(open('coverage.json')); print(f\"{d['data'][0]['totals']['lines']['percent']:.1f}\")")
	echo "Library line coverage: ${COV}%"
	python3 -c "
	import json, sys
	d = json.load(open('coverage.json'))
	pct = d['data'][0]['totals']['lines']['percent']
	if pct < 90:
	print(f'FAIL: {pct:.1f}% < 90% target')
	sys.exit(1)
	print(f'PASS: {pct:.1f}% >= 90% target')
	"

	validate-native:
	runs-on: ubuntu-latest
	timeout-minutes: 5
	needs: test

	steps:
	- uses: actions/checkout@v4

	- name: Checkout barraCuda (standalone math primal)
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository_owner }}/barraCuda
	path: ../barraCuda
	sparse-checkout: crates/barracuda

	- name: Install stable toolchain
	uses: dtolnay/rust-toolchain@stable

	- name: Cache cargo
	uses: actions/cache@v4
	with:
	path: \|
	~/.cargo/bin/
	~/.cargo/registry/index/
	~/.cargo/registry/cache/
	~/.cargo/git/db/
	target/
	key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.toml') }}

	- name: Validate surrogate (15 checks)
	run: cargo run --bin validate_surrogate

	- name: Validate transformer (18 checks)
	run: cargo run --bin validate_transformer

	- name: Validate metrics (10 checks)
	run: cargo run --bin validate_metrics

	- name: Validate counterdiabatic (19 checks)
	run: cargo run --bin validate_counterdiabatic

	- name: Validate MODES (9 checks)
	run: cargo run --bin validate_modes

	- name: Validate eco dynamics (7 checks)
	run: cargo run --bin validate_eco_dynamics

	- name: Validate directed evolution (7 checks)
	run: cargo run --bin validate_directed_evolution

	- name: Validate HMM (17 checks)
	run: cargo run --bin validate_hmm

	- name: Validate game theory (8 checks)
	run: cargo run --bin validate_game_theory

	- name: Validate swarm robotics (7 checks)
	run: cargo run --bin validate_swarm_robotics

	- name: Validate SATé alignment (8 checks)
	run: cargo run --bin validate_sate_alignment

	- name: Validate introgression (13 checks)
	run: cargo run --bin validate_introgression

	- name: Validate regulatory network (5 checks)
	run: cargo run --bin validate_regulatory_network

	- name: Validate signal integration (8 checks)
	run: cargo run --bin validate_signal_integration

	- name: Validate spectral commutativity (8 checks)
	run: cargo run --bin validate_spectral_commutativity

	- name: Validate Anderson localization (8 checks)
	run: cargo run --bin validate_anderson_localization

	- name: Validate pangenome selection (8 checks)
	run: cargo run --bin validate_pangenome_selection

	- name: Validate meta-population (8 checks)
	run: cargo run --bin validate_meta_population

	- name: Validate LeNet-5 (22 checks)
	run: cargo run --bin validate_lenet

	- name: Validate transfer learning (11 checks)
	run: cargo run --bin validate_transfer

	- name: Validate isomorphic catalog (8 checks)
	run: cargo run --bin validate_isomorphic

	- name: Validate LSTM/GRU cell primitives
	run: cargo run --bin validate_lstm

	- name: Validate quantized inference
	run: cargo run --bin validate_quantized

	- name: Validate sequence (7 checks)
	run: cargo run --bin validate_sequence

	- name: Validate PINN (9 checks)
	run: cargo run --bin validate_pinn

	- name: Validate DeepONet (18 checks)
	run: cargo run --bin validate_deeponet

	validate-barracuda:
	runs-on: ubuntu-latest
	timeout-minutes: 5
	needs: test

	steps:
	- uses: actions/checkout@v4

	- name: Checkout barraCuda (standalone math primal)
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository_owner }}/barraCuda
	path: ../barraCuda
	sparse-checkout: crates/barracuda

	- name: Install stable toolchain
	uses: dtolnay/rust-toolchain@stable

	- name: Cache cargo
	uses: actions/cache@v4
	with:
	path: \|
	~/.cargo/bin/
	~/.cargo/registry/index/
	~/.cargo/registry/cache/
	~/.cargo/git/db/
	target/
	key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.toml') }}

	- name: Validate barracuda stats (13 checks)
	run: cargo run --bin validate_barracuda_stats

	- name: Validate barracuda linalg (17 checks)
	run: cargo run --bin validate_barracuda_linalg

	- name: Validate barracuda special (26 checks)
	run: cargo run --bin validate_barracuda_special

	- name: Validate barracuda optimize (10 checks)
	run: cargo run --bin validate_barracuda_optimize

	- name: Validate barracuda precision (12 checks)
	run: cargo run --bin validate_barracuda_precision

	- name: Validate barracuda tensor (unified WGSL + evolved ops, 86 checks)
	run: cargo run --bin validate_barracuda_tensor

	- name: Validate barracuda tensor f64 (SHADER_F64 GPU ops, 35 checks)
	run: cargo run --bin validate_barracuda_tensor_f64

	- name: Validate barracuda quantized (15 checks)
	run: cargo run --bin validate_barracuda_quantized

	- name: Validate barracuda linalg_ext (17 checks)
	run: cargo run --bin validate_barracuda_linalg_ext

	- name: Validate barracuda ml_inference (13 checks)
	run: cargo run --bin validate_barracuda_ml_inference

	- name: Validate barracuda FFT (12 checks)
	run: cargo run --bin validate_barracuda_fft

	validate-barracuda-cpu:
	runs-on: ubuntu-latest
	timeout-minutes: 5
	needs: test

	steps:
	- uses: actions/checkout@v4

	- name: Checkout barraCuda (standalone math primal)
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository_owner }}/barraCuda
	path: ../barraCuda
	sparse-checkout: crates/barracuda

	- name: Install stable toolchain
	uses: dtolnay/rust-toolchain@stable

	- name: Cache cargo
	uses: actions/cache@v4
	with:
	path: \|
	~/.cargo/bin/
	~/.cargo/registry/index/
	~/.cargo/registry/cache/
	~/.cargo/git/db/
	target/
	key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.toml') }}

	- name: Validate barracuda spectral (10 checks)
	run: cargo run --bin validate_barracuda_spectral

	- name: Validate barracuda anderson (7 checks)
	run: cargo run --bin validate_barracuda_anderson

	- name: Validate barracuda regulatory (6 checks)
	run: cargo run --bin validate_barracuda_regulatory

	- name: Validate barracuda signal (14 checks)
	run: cargo run --bin validate_barracuda_signal

	- name: Validate barracuda hmm (14 checks)
	run: cargo run --bin validate_barracuda_hmm

	- name: Validate barracuda introgression (11 checks)
	run: cargo run --bin validate_barracuda_introgression

	- name: Validate barracuda counterdiabatic (7 checks)
	run: cargo run --bin validate_barracuda_counterdiabatic

	- name: Validate barracuda modes (7 checks)
	run: cargo run --bin validate_barracuda_modes

	- name: Validate barracuda eco (6 checks)
	run: cargo run --bin validate_barracuda_eco

	- name: Validate barracuda directed (7 checks)
	run: cargo run --bin validate_barracuda_directed

	- name: Validate barracuda swarm (10 checks)
	run: cargo run --bin validate_barracuda_swarm

	- name: Validate barracuda sate (6 checks)
	run: cargo run --bin validate_barracuda_sate

	- name: Validate barracuda game (5 checks)
	run: cargo run --bin validate_barracuda_game

	- name: Validate barracuda pangenome (8 checks)
	run: cargo run --bin validate_barracuda_pangenome

	- name: Validate barracuda meta-population (8 checks)
	run: cargo run --bin validate_barracuda_meta_pop

	- name: Validate barracuda PINN (6 checks)
	run: cargo run --bin validate_barracuda_pinn

	- name: Validate barracuda DeepONet (9 checks)
	run: cargo run --bin validate_barracuda_deeponet

	- name: Validate barracuda logsumexp (5 checks)
	run: cargo run --bin validate_barracuda_logsumexp

	# Phase 3c: metalForge GPU shader validation
	- name: Validate GPU HMM forward shader (13 checks)
	run: cargo run --bin validate_gpu_hmm_forward

	- name: Validate GPU batch fitness shader (20 checks)
	run: cargo run --bin validate_gpu_batch_fitness

	- name: Validate GPU RK4 shader (8 checks)
	run: cargo run --bin validate_gpu_rk4

	# Phase 3d: Pure GPU workload + StatefulPipeline + cross-dispatch
	- name: Validate GPU StatefulPipeline (10 checks)
	run: cargo run --bin validate_gpu_stateful_pipeline

	- name: Validate GPU pure workload chain (7 checks)
	run: cargo run --bin validate_gpu_pure_workload

	- name: Validate cross-dispatch GPU vs CPU (8 checks)
	run: cargo run --bin validate_cross_dispatch

	- name: Validate GPU pangenome Jaccard (6 checks)
	run: cargo run --bin validate_gpu_pangenome

	- name: Validate GPU meta-population variance (7 checks)
	run: cargo run --bin validate_gpu_meta_pop

	- name: Validate cross-dispatch genomics (8 checks)
	run: cargo run --bin validate_cross_dispatch_genomics

	- name: Validate GPU game theory spatial payoff (5 checks)
	run: cargo run --bin validate_gpu_game_theory

	- name: Validate GPU Anderson IPR (5 checks)
	run: cargo run --bin validate_gpu_anderson

	- name: Validate GPU SATe Hamming distance (5 checks)
	run: cargo run --bin validate_gpu_sate

	- name: Validate cross-dispatch extended (12 checks)
	run: cargo run --bin validate_cross_dispatch_extended

	# Phase 3c expansion: additional GPU shader validators
	- name: Validate GPU modes pairwise_l2 (9 checks)
	run: cargo run --bin validate_gpu_modes

	- name: Validate GPU directed multi_obj_fitness (10 checks)
	run: cargo run --bin validate_gpu_directed

	- name: Validate GPU signal hill_gate (13 checks)
	run: cargo run --bin validate_gpu_signal

	- name: Validate GPU swarm nn_forward (8 checks)
	run: cargo run --bin validate_gpu_swarm

	# Phase 4b: Pure GPU end-to-end pipelines
	- name: Validate GPU pipeline HMM (5 checks)
	run: cargo run --release --bin validate_gpu_pipeline_hmm

	- name: Validate GPU pipeline ecology (5 checks)
	run: cargo run --release --bin validate_gpu_pipeline_ecology

	- name: Validate GPU pipeline spectral (5 checks)
	run: cargo run --release --bin validate_gpu_pipeline_spectral

	- name: Validate GPU pipeline genomics (5 checks)
	run: cargo run --release --bin validate_gpu_pipeline_genomics

	- name: Validate GPU pipeline modes (7 checks)
	run: cargo run --release --bin validate_gpu_pipeline_modes

	- name: Validate GPU pipeline directed (8 checks)
	run: cargo run --release --bin validate_gpu_pipeline_directed

	- name: Validate GPU pipeline signal (8 checks)
	run: cargo run --release --bin validate_gpu_pipeline_signal

	# Phase 4e: cross-dispatch expansion
	- name: Validate cross-dispatch Phase 4e (17 checks)
	run: cargo run --release --bin validate_cross_dispatch_phase4e

	# Phase 4c: GPU PRNG
	- name: Validate GPU PRNG xoshiro128ss (5 checks)
	run: cargo run --release --bin validate_gpu_prng

	# Phase 4d: ToadStool issue resolution
	- name: Validate eigh_accuracy S-12 (9 checks)
	run: cargo run --release --bin validate_eigh_accuracy
	- name: Validate MHA GPU head shaders S-03b (10 checks)
	run: cargo run --release --bin validate_mha_gpu

	# Phase 5a: BarraCUDA GPU Tensor validation
	- name: Validate BarraCUDA GPU spectral (12 checks)
	run: cargo run --release --bin validate_barracuda_gpu_spectral

	- name: Validate BarraCUDA GPU eco (20 checks)
	run: cargo run --release --bin validate_barracuda_gpu_eco

	- name: Validate BarraCUDA GPU HMM (8 checks)
	run: cargo run --release --bin validate_barracuda_gpu_hmm

	- name: Validate BarraCUDA GPU fitness (8 checks)
	run: cargo run --release --bin validate_barracuda_gpu_fitness

	- name: Validate BarraCUDA GPU neural net (8 checks)
	run: cargo run --release --bin validate_barracuda_gpu_nn

	- name: Validate BarraCUDA GPU pairwise (8 checks)
	run: cargo run --release --bin validate_barracuda_gpu_pairwise

	- name: Validate BarraCUDA GPU Anderson (8 checks)
	run: cargo run --release --bin validate_barracuda_gpu_anderson

	cross-validate:
	runs-on: ubuntu-latest
	timeout-minutes: 15
	needs: test

	steps:
	- uses: actions/checkout@v4

	- name: Checkout barraCuda (standalone math primal)
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository_owner }}/barraCuda
	path: ../barraCuda
	sparse-checkout: crates/barracuda

	- name: Set up Python 3.10
	uses: actions/setup-python@v5
	with:
	python-version: "3.10"

	- name: Install Python dependencies
	run: \|
	pip install --upgrade pip
	pip install -r control/requirements.txt
	pip install pytest

	- name: Install stable toolchain
	uses: dtolnay/rust-toolchain@stable

	- name: Cache cargo
	uses: actions/cache@v4
	with:
	path: \|
	~/.cargo/bin/
	~/.cargo/registry/index/
	~/.cargo/registry/cache/
	~/.cargo/git/db/
	target/
	key: ${{ runner.os }}-cargo-xval-${{ hashFiles('Cargo.toml') }}

	- name: Run Python unit tests
	run: python3 -m pytest tests/ -v --tb=short

	- name: Validate cross-language parity (Rust vs Python)
	run: \|
	cargo run --bin validate_surrogate
	cargo run --bin validate_transformer
	cargo run --bin validate_metrics

	benchmarks:
	runs-on: ubuntu-latest
	timeout-minutes: 5
	needs: test

	steps:
	- uses: actions/checkout@v4

	- name: Checkout barraCuda (standalone math primal)
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository_owner }}/barraCuda
	path: ../barraCuda
	sparse-checkout: crates/barracuda

	- name: Install stable toolchain
	uses: dtolnay/rust-toolchain@stable

	- name: Cache cargo
	uses: actions/cache@v4
	with:
	path: \|
	~/.cargo/bin/
	~/.cargo/registry/index/
	~/.cargo/registry/cache/
	~/.cargo/git/db/
	target/
	key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.toml') }}

	- name: Run bench_phase0pp_kernels (Rust-only, no Python)
	run: cargo run --release --bin bench_phase0pp_kernels

	- name: Run bench_gpu_kernels (WGSL shader timing)
	run: cargo run --release --bin bench_gpu_kernels

	ipc-smoke-test:
	runs-on: ubuntu-latest
	timeout-minutes: 5
	needs: test

	steps:
	- uses: actions/checkout@v4

	- name: Checkout barraCuda (standalone math primal)
	uses: actions/checkout@v4
	with:
	repository: ${{ github.repository_owner }}/barraCuda
	path: ../barraCuda
	sparse-checkout: crates/barracuda

	- name: Install stable toolchain
	uses: dtolnay/rust-toolchain@stable

	- name: Cache cargo
	uses: actions/cache@v4
	with:
	path: \|
	~/.cargo/bin/
	~/.cargo/registry/index/
	~/.cargo/registry/cache/
	~/.cargo/git/db/
	target/
	key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.toml') }}

	- name: Install socat
	run: sudo apt-get update && sudo apt-get install -y socat

	- name: Build primal binary
	run: cargo build --bin neuralspring --features primal

	- name: IPC smoke test (health.liveness)
	run: \|
	SOCKET_DIR=$(mktemp -d)
	export BIOMEOS_SOCKET_DIR="${SOCKET_DIR}"
	export FAMILY_ID=smoke
	SOCKET_PATH="${SOCKET_DIR}/neural-spring-smoke.sock"

	# Start primal in background (socket: $BIOMEOS_SOCKET_DIR/$CARGO_PKG_NAME-$FAMILY_ID.sock)
	cargo run --bin neuralspring --features primal -- serve &
	PRIMAL_PID=$!

	# Wait for socket to appear (up to 10s)
	for i in $(seq 1 20); do
	if [ -S "${SOCKET_PATH}" ]; then
	echo "Socket ready after $((i * 500))ms"
	break
	fi
	sleep 0.5
	done

	if [ ! -S "${SOCKET_PATH}" ]; then
	echo "FAIL: Socket not created within 10s"
	kill $PRIMAL_PID 2>/dev/null \|\| true
	exit 1
	fi

	# Send JSON-RPC health.liveness probe
	RESPONSE=$(echo '{"jsonrpc":"2.0","method":"health.liveness","params":{},"id":1}' \| socat - UNIX-CONNECT:"${SOCKET_PATH}")
	echo "Response: ${RESPONSE}"

	# Verify response contains result (not error)
	if echo "${RESPONSE}" \| python3 -c "import sys,json; r=json.load(sys.stdin); assert 'result' in r, f'No result: {r}'; print('PASS: health.liveness')"; then
	echo "IPC smoke test passed"
	else
	echo "FAIL: Invalid response"
	kill $PRIMAL_PID 2>/dev/null \|\| true
	exit 1
	fi

	# Clean shutdown
	kill $PRIMAL_PID 2>/dev/null \|\| true
	wait $PRIMAL_PID 2>/dev/null \|\| true
	rm -rf "${SOCKET_DIR}"

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V123: typed errors, module decomposition, CI hardening, doc alignment #121

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V123: typed errors, module decomposition, CI hardening, doc alignment #121

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