Tatopenn/dense-Evolution

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A high-performance quantum simulation toolkit Statevector/MPS engines with compilation, noise, VQE, QEC, chemistry, and agent-native tooling.

---

Table of Contents

• What It Is
• Install
• Quick Start
• Architecture
• Contributing

▍ What It Is

Dense Evolution is a high-performance statevector simulator engineered for deep NISQ circuits, VQE pipelines, and QML workloads. It eliminates Kronecker product overhead entirely via stride-sliced linear kernel fusion compiled through JAX XLA — keeping memory at the theoretical minimum of 2ⁿ × 16 bytes.

📖 Full documentation, API reference, and worked examples →

A Streamlit dashboard (app_dashboard.py) is a Quantum-Composer-style circuit editor — Graphical Builder, Circuit, Statevector, Probabilities, and Q-sphere tabs, every one backed by a real DenseSVSimulator run — launched locally with streamlit run app_dashboard.py. VQE, real molecular Hamiltonians, ZNE mitigation, QM/MM forces, MD trajectories, and vector healing live in the Composer web app's local kernel (local_site/app/server.py, see "Composer" below) and its MCP server (mcp_server/, see "MCP Server" below), not in the Streamlit dashboard. legacy/dash.py is the original Google Colab notebook this was ported from, kept for reference only (not installable — see the file header).

---

▍ Install

pip install dense-evolution  # JAX is a core dependency, installed by default

# full stack: GPU · dashboard · Qiskit/PennyLane interop
pip install dense-evolution[full]

# just the interop bridge
pip install dense-evolution[qiskit]
pip install dense-evolution[pennylane]

# Composer's local kernel (see "Composer" below)
pip install dense-evolution[composer]

# MCP server for the Composer kernel (see "MCP Server" below)
pip install dense-evolution[mcp]

# development
git clone https://github.com/tatopenn-cell/Dense-Evolution.git
cd Dense-Evolution && pip install -e .[full]

macOS note on dense-evolution[qiskit]: Qiskit's own QuantumCircuit.__init__ is known to segfault the whole process on macOS/arm64 (see v8.1.43 below for the full reproduction — an upstream Qiskit bug, not something Dense-Evolution can fix from its side). dense_evolution/interop.py now warns (RuntimeWarning, once per process) the first time you touch the Qiskit bridge on sys.platform == 'darwin', but it does not block — some Qiskit/macOS combinations may work fine. If you hit a crash, pip install dense-evolution[pennylane] gives the same circuit-interop functionality without constructing any Qiskit object.

Google Colab (3 lines):

!git clone https://github.com/tatopenn-cell/Dense-Evolution.git
%cd Dense-Evolution
!pip install -e .

---

▍ Quick Start

from dense_evolution import DenseSVSimulator, QASMParser

# parse any OpenQASM 2.0 / 3.0 string -- single-qubit rotations, a barrier
# (a real OpenQASM synchronization marker: parsed like hardware would, no
# effect on the simulated state), then an entangling layer
qasm = """
OPENQASM 2.0;
include "qelib1.inc";
qreg q[3];
rx(pi/3) q[0];
ry(pi/4) q[1];
h q[2];
barrier q;
cx q[0], q[1];
cx q[1], q[2];
rz(pi/6) q[2];
"""

parser = QASMParser()
circuit = parser.parse(qasm)

sim = DenseSVSimulator(n_qubits=3)
sim.run_circuit_jit(circuit.to_tuples())

probs = sim.get_probabilities()
sv    = sim.get_statevector()
# probs = [0.3201 0.3201 0.0549 0.0549 0.0183 0.0183 0.1067 0.1067]

Dashboard (local, Streamlit):

pip install "dense-evolution[dashboard]"  # JAX already included by default
streamlit run app_dashboard.py

Anti-OOM for large circuits:

from dense_evolution import Chunk

sim = Chunk(27)                                    # logical 27 qubits
circuit_ops = [['h', i] for i in range(27)]
sim.run_chunk(circuit_ops, chunk_size_gates=500)   # SafeMemoryGuard active

---

▍ Architecture

dense_evolution/
├── circuits/            [subpackage] gate-level primitives
│   ├── gates.py            GATES{} · PARAMETRIC_GATES{} · GATE_IDS{}
│   ├── registry.py         hardware detection · JAX/CuPy/NumPy flags · NoiseModel (Kraus channels)
│   ├── parser.py           QASMParser · QASMCircuit · OpenQASM 2.0 / 3.0
│   ├── compiler.py         QuantumTranspiler · _apply_gate_fast_step (jit) · gate decomposition
│   ├── topology.py         entangling_layer — linear/circular/full/star/brick patterns
│   ├── qft.py              Quantum Fourier Transform circuit builder
│   └── trotter.py          pauli_rotation_ops · trotter_evolve_ops — real-time Hamiltonian evolution as gates
├── backends/             [subpackage] statevector execution engines
│   ├── statevector.py      DenseSVSimulator · run_batch_jit · vmap batch VQE
│   └── mps.py              MPSSimulator — matrix-product-state backend, JAX-backed
├── physics/              [subpackage] quantum-information primitives
│   ├── entropy.py          partial_trace · von_neumann_entropy · mutual_information (multi-qubit, MSB-first)
│   ├── observables.py      Pauli-string expectation values, O(2ⁿ) direct from a statevector
│   ├── states.py           common state-preparation circuits (Bell, GHZ, W, ...) as gate tuples
│   ├── fermions.py         majorana_pauli_terms — Majorana-fermion → qubit (Jordan-Wigner) mapping
│   └── qec.py              pauli_commutes · compute_syndrome · erasure_aware_decode (code-agnostic stabilizer QEC)
├── mitigation/           [subpackage] error mitigation and density-matrix diagnostics
│   ├── zne.py               richardson_extrapolate · zero_noise_extrapolation · zne_density_matrix · jsd_predictive_zne_density_matrix · uhlmann_fidelity (+ jit variants)
│   ├── healing.py            predictive state engine · Phi_AB · vettore dinamico · MemoryReflectionEngine
│   ├── renyi.py              sandwiched_renyi_divergence — non-commuting-aware density-matrix divergence (fixed from a Colab bug, Dense-Evolution-Discovery Experiment 29)
│   └── magic_entropy.py      magic_entropy — single-qubit non-stabilizerness via the real Key Unitary construction (Dense-Evolution-Discovery Experiment 30)
├── solvers/              [subpackage] variational/chemistry solvers
│   ├── autodiff.py         circuit_to_energy_fn — the real, public VQE gradient engine
│   ├── harrison_tb.py      sp3 tight-binding Hamiltonians, Harrison universal parameter table
│   └── vhd_tb.py           sp3s* tight-binding, Vogl-Hjalmarson-Dow material-specific parameters
├── native_hf/            [subpackage] from-scratch Hartree-Fock (elements outside PennyLane's STO-3G table)
│   ├── scf.py               self-consistent-field loop
│   ├── bridge.py            hands off the converged result to PennyLane's fermionic_observable/jordan_wigner
│   └── boys.py, gaussians.py, overlap.py, kinetic.py, coulomb.py, assembly.py, cartesian.py, basis.py   Obara-Saika integral machinery
├── interop/              [subpackage]
│   └── qiskit_pennylane.py   run_qiskit_circuit / run_pennylane_circuit / from_qiskit / from_pennylane
├── utils/                [subpackage]
│   ├── drawing.py           plain-text circuit diagrams (ASCII, console-safe)
│   └── measurement.py       statevector → finite-shot counts, sampling helpers
├── chunk.py              SafeMemoryGuard · MemoryChunker · CircuitChunker · Chunk (Anti-OOM) — not moved into a subpackage
├── cli.py                `dense-evolution` console script — serve · offline-composer · mcp — not moved into a subpackage
└── random_circuit.py     random circuit generation for benchmarking/fuzz-testing — not moved into a subpackage

Every module has a backward-compatible shim at its old top-level path (e.g. dense_evolution/mitigation.py, dense_evolution/entropy.py, dense_evolution/healing.py, dense_evolution/mps.py, dense_evolution/simulator.py, dense_evolution/observables.py, dense_evolution/states.py, dense_evolution/qec.py, dense_evolution/fermions.py, dense_evolution/gates.py, dense_evolution/registry.py, dense_evolution/parser.py, dense_evolution/compiler.py, dense_evolution/topology.py, dense_evolution/qft.py, dense_evolution/trotter.py, dense_evolution/autodiff.py, dense_evolution/harrison_tb.py, dense_evolution/vhd_tb.py, dense_evolution/drawing.py, dense_evolution/measurement.py) — a ~10-line re-export, nothing else. from dense_evolution.mps import MPSSimulator keeps working unchanged, identically to before the split. renyi.py/magic_entropy.py are new (never had an old top-level path, so no shim needed); import them from dense_evolution.mitigation directly. Full history: the 7-subpackage split (tracking issue #76) shipped completely in v8.1.61; native_hf/ was added separately in v8.1.59.

tools/                              (apps built on the library, not part of it — see prog.txt Sezione 1)
├── ia_utils/
│   ├── vector_healing.py            median_healing · enhanced_dense_healing_hybrid (NaN/Inf-safe, lazy JAX import; trigger_mode='phi'|'adaptive')
│   └── adversarial_vector_attack.py  craft_adversarial_healing_perturbation — gradient-based red-teaming against the differentiable Phi-Trigger
├── dashboard_core/
│   ├── engine.py                     run_circuit_from_qasm — real DenseSVSimulator execution, shared by app_dashboard.py and local_site/app/server.py
│   ├── graphical_builder.py          drag-and-drop grid ops → native gate tuples (app_dashboard.py's Graphical Builder tab)
│   ├── circuit_builder_component.py  Streamlit component backing that grid
│   ├── circuit_diagram.py            plain matplotlib circuit diagrams (no Qiskit QuantumCircuit ever constructed)
│   ├── state_visuals.py              native statevector histogram / Bloch / Q-sphere rendering
│   ├── visuals.py                    circuit/histogram/qsphere/Bloch figure wrappers used by app_dashboard.py
│   ├── qasm_library.py               preset OpenQASM circuits (Bell, GHZ, ...)
│   ├── system_limits.py              RAM-based safe qubit ceiling
│   ├── hamiltonians.py                real molecular Hamiltonians (PennyLane Hartree-Fock) — served by local_site/app/server.py, not app_dashboard.py
│   ├── vqe.py                         VQE engine — served by local_site/app/server.py, not app_dashboard.py
│   ├── qmmm.py                        Hellmann-Feynman QM/MM forces + MD trajectories — served by local_site/app/server.py, not app_dashboard.py
│   ├── mitigation.py                  Zero-Noise Extrapolation (statevector + density-matrix) — served by local_site/app/server.py, not app_dashboard.py
│   ├── vector_healing.py              dense_evolution.healing / ia_utils.vector_healing bridge — served by the MCP server, not app_dashboard.py
│   └── wormhole.py                    binary sparse SYK model — traversable-wormhole-inspired teleportation (see "MCP Server" below)
├── app_dashboard.py                   Streamlit "Quantum Composer" clone — Graphical Builder/Circuit/Statevector/Probabilities/Q-sphere tabs only, `streamlit run tools/app_dashboard.py`
└── mcp_server/server.py               dense_evolution_mcp — MCP adapter over the Composer kernel (see "MCP Server" below)

research/                           (not installed as a module -- reference/experimentation only)
├── local_site/app/server.py       Composer's local FastAPI compute kernel — full feature set: VQE, molecular Hamiltonians, QM/MM, MD, mitigation, wormhole teleportation, vector healing (see "Composer" below)
├── experiments/                    exploratory scripts not promoted to the library (matrix-healing budget/ZNE variants, vector-healing outlier correction)
├── wormhole_syk.py                 the original wormhole research reproduction + its own verification suite, reference only (see research/wormhole_syk.md)
└── legacy/dash.py                  original Colab notebook, reference only

Data flow per run (app_dashboard.py):

▶ Esegui
└─ dc.run_circuit_from_qasm()        dense_evolution QASMParser → DenseSVSimulator (JIT) → shots
    ├─ dc.draw_circuit_figure()      Circuit tab
    ├─ dc.histogram_figure()         Probabilities tab
    └─ dc.qsphere_figure()           Q-sphere tab

---

▍ Core Features

Feature	Detail
Linear Kernel Fusion	Stride-sliced tensor ops via JAX XLA — zero Kronecker matrices
Parametric Batch JIT	run_batch_jit() evaluates full parameter grids in one jax.vmap + jax.jit call
Circuit Chunking	Fixed-size JIT blocks eliminate tracer overhead on 1000+ gate circuits
Kraus Noise Channels	depolarizing amplitude_damping phase_damping bitflip combined — stochastic, O(2ⁿ) cost
Real Device Noise	noise_model_from_qiskit_backend — Dense-Evolution noise spec built from a Qiskit BackendV2's own calibration data (live or fake/mock, e.g. FakeSherbrooke), deduplicated per unique gate/qubit target
Differentiable Circuits	circuit_to_energy_fn — pure JAX energy_fn(theta, h_matrix), jax.value_and_grad-composable, verified against finite differences to ~1e-11
Differentiable Noise	NoiseSpec — noise as a JAX PyTree accepted natively by circuit_to_energy_fn; the whole theta → noisy statevector → energy path stays inside one jax.jit/jax.grad/jax.vmap trace
Zero-Noise Extrapolation	mitigation.py — zne_density_matrix (Smolin-Gambetta-Smith physical projection), jsd_predictive_zne_density_matrix (adaptive, photon-loss-validated), uhlmann_fidelity
Density-Matrix Diagnostics	mitigation.py — sandwiched_renyi_divergence (non-commuting-aware, order-α), magic_entropy (single-qubit non-stabilizerness, zero for all six stabilizer states)
Shadow-Based Estimation	mitigation.py — sample_classical_shadow/magic_entropy_from_shadows (median-of-means classical-shadows estimator for magic_entropy, from randomized measurement snapshots instead of the exact state), approx_shadow_std/fit_shadow_sample_complexity (empirically-derived error guidance)
VQE + ADAM	Hellmann-Feynman gradient · positional parameter injection into any OpenQASM 2.0 circuit
Anti-OOM Engine	SafeMemoryGuard blocks execution before JAX raises RESOURCE_EXHAUSTED
Predictive Healing	healing.py — Φ_AB alignment, dynamic vector, Σ-sync, MemoryReflectionEngine
Vector Sequence Healing	ia_utils/ — median_healing, enhanced_dense_healing_hybrid — NaN/Inf-safe, lazy JAX import
Adversarial Robustness Testing	ia_utils.adversarial_vector_attack.craft_adversarial_healing_perturbation — PGD-style minimal perturbation, flips the healing Phi-Trigger either direction
STIM Bridge	to_stim — Clifford-only op-list → stim.Circuit, for cross-validation against STIM's stabilizer simulator/decoder tooling
Native Hartree-Fock	dense_evolution.native_hf — from-scratch JAX/Obara-Saika ab-initio HF engine for elements outside PennyLane's own STO-3G table (H–Ne), auto-used by the Hamiltonian Library for e.g. Si2
Erasure-Aware QEC Decoding	dense_evolution.qec — code-agnostic Pauli commutation/syndrome primitives plus a decoder that corrects up to d-1 known-location (erasure) errors on a distance-d stabilizer code, vs. floor((d-1)/2) for a standard syndrome-only decoder (Grassl, Beth & Pellizzari 1997); validated on the Steane [[7,1,3]] code against STIM's HERALDED_ERASE channel, 0 failures on >60,000 double-erasure shots
Backend Agnostic	NumPy CPU · JAX XLA CPU/TPU · CuPy CUDA — runtime selection, zero code changes
Live Dashboard	app_dashboard.py — Streamlit Quantum-Composer clone, 5 tabs (Graphical Builder/Circuit/Statevector/Probabilities/Q-sphere) per simulation run

---

▍ Scientific Validation & Applications

To demonstrate the numerical accuracy and stability of Dense Evolution, the simulator was stress-tested across 3,500 continuous spatial sampling points to compute a Silicon Dimer (Si2) Dissociation Curve via Variational Quantum Eigensolver (VQE), using a small active space/basis (raw script linked below).

• Numerical Precision: Calculations are locked at Double Precision (float64), proving the simulator's resilience against cumulative machine epsilon errors (~ 1.11 × 10⁻¹⁶) across thousands of sequential circuit executions.
• Honest caveat, corrected in v8.1.59: this scan's own minimum (~3.55 Å below, negative total energy) is an artifact of its small active-space/basis choice, not the real physical Si2 equilibrium — the real experimental/literature bond length is 2.184 Å (Balamurugan & Prasad, arXiv:cond-mat/0108426). This claim went unverified in earlier README revisions; it's stated correctly here and Si2 is now in the Hamiltonian Library below at its real geometry, computed by the new native Hartree-Fock engine since Si is outside PennyLane's own bundled STO-3G table.
• Run this molecular experiment instantly on Google Colab Free Tier: Open Notebook on Google Colab

---

============================================================
🔬 MOLECULAR VQE: EXACT POTENTIAL ENERGY CURVE (PEC)
============================================================
Distanza R: 1.200 Å | Energia Totale Molecola: +155.761158 eV
Distanza R: 1.671 Å | Energia Totale Molecola: +34.372692 eV
Distanza R: 2.142 Å | Energia Totale Molecola: +6.583098 eV
Distanza R: 2.614 Å | Energia Totale Molecola: +0.727422 eV
Distanza R: 3.085 Å | Energia Totale Molecola: -0.253226 eV
Distanza R: 3.557 Å | Energia Totale Molecola: -0.273498 eV
Distanza R: 4.028 Å | Energia Totale Molecola: -0.170948 eV
Distanza R: 4.500 Å | Energia Totale Molecola: -0.093048 eV

Variational Quantum Chemistry Plot

Below is the physical validation plot showing the Born-Oppenheimer potential energy curve:

👉 For the full suite of physical benchmarks, including the Transverse Field Ising Model (TFIM) and Phase Transition mappings, visit the main Dense-Evolution-Discovery repository. You can also view the raw script for this specific molecular run here.

---

▍ API Reference

DenseSVSimulator

sim = DenseSVSimulator(
    n_qubits   : int,
    use_gpu    : bool = False,
    use_float32: bool = False,
)

Method	Description
set_initial_state(state=None)	Reset to |0⟩ⁿ or inject custom statevector
run_circuit(circuit, transpile=True)	Plain (non-JIT) gate execution — takes the tuple format below
run_circuit_jit(circuit)	JIT-compiled gate execution — primary execution path (renamed from run_circuit_jit_beast_mode in 8.1.46; old name still works, deprecated)
run_circuit_with_chunking(circuit, chunk_size=500)	Chunked execution for long circuits
run_batch_jit(base_circuit, parameter_batch)	vmap over parameter grid — returns full batch of statevectors (renamed from run_parametric_batch_jit in 8.1.46; old name still works, deprecated)
get_probabilities() → np.ndarray	|ψ_i|² for all basis states
get_statevector() → np.ndarray	Full complex statevector
measure(qubit_idx) → int	Projective measurement with state collapse
memory_mb() → float	Current RAM usage in MB
apply_gate_1q(gate, qubit)	Apply arbitrary 2×2 unitary
apply_gate_2q(gate, q1, q2)	Apply arbitrary 4×4 unitary

QASMParser

parser  = QASMParser()
circuit = parser.parse(qasm_str)   # → QASMCircuit
valid, msg = parser.validate(circuit)

QASMCircuit fields: n_qubits, n_cbits, ops (list of gate dicts, e.g. {'name': 'h', 'qubits': [0], 'params': []}). Use circuit.to_tuples() to convert ops to the (name, qubit0[, qubit1, ...][, param0, ...]) tuple format that run_circuit / run_circuit_jit expect — don't build that format by hand.

NoiseModel

noise = NoiseModel()
noise.apply_to_sv(sv, n=4, model='depolarizing', p=0.01, rng=rng)
desc  = NoiseModel.kraus_description('amplitude_damping')

End-to-end: parse → run → apply noise

parser  = QASMParser()
circuit = parser.parse(qasm_str)                  # → QASMCircuit
sim     = DenseSVSimulator(n_qubits=circuit.n_qubits)
sim.run_circuit(circuit.to_tuples())               # dicts -> tuples, then execute

sv_noisy = NoiseModel().apply_to_sv(
    sim.get_statevector(), n=circuit.n_qubits, model='depolarizing', p=0.01,
    rng=np.random.default_rng(42),
)

Chunk (Anti-OOM)

sim = Chunk(
    n_qubits         : int,
    chunk_size_gates : int   = 500,
    memory_threshold : float = 0.15,   # block below 15% free RAM
    use_gpu          : bool  = False,
    use_float32      : bool  = False,
)
sim.run_chunk(circuit, chunk_size_gates=500)

Backward-compatibility aliases: chunk1 = MemoryChunker, chunk2 = Chunk, Chunk2Incrociato = Chunk.

ia_utils.vector_healing

from ia_utils.vector_healing import median_healing, enhanced_dense_healing_hybrid

healed, radius   = median_healing(vettori, radius_baseline=None)
healed, metadata = enhanced_dense_healing_hybrid(vettori, radius_baseline=None)

See IA Utils — Vector Sequence Healing above for details.

ia_utils.adversarial_vector_attack

A gradient-based (PGD-style) robustness test for enhanced_dense_healing_hybrid's Phi-Trigger decision. Full method and validation: docs/api/ia_utils_adversarial_vector_attack.md.

from ia_utils.adversarial_vector_attack import craft_adversarial_healing_perturbation

result = craft_adversarial_healing_perturbation(
    vettori, target_idx=10, epsilon=0.1, direction="flip_to_dynamic",  # or "flip_to_static"
)
result["success"], result["perturbed_vettori"], result["perturbation_norm"]

---

▍ Gate Library

Fixed gates (no parameters):

Gate	Symbol	Gate	Symbol
h	Hadamard	x	Pauli-X
y	Pauli-Y	z	Pauli-Z
s	S gate	sdg	S† gate
t	T gate	tdg	T† gate
sx	√X gate	id	Identity
cx	CNOT	cz	CZ
cy	CY	swap	SWAP
iswap	iSWAP	ecr	ECR
ccx	Toffoli

Parametric gates:

Gate	Parameters	Description
rx(θ)	θ	X-rotation
ry(θ)	θ	Y-rotation
rz(θ)	θ	Z-rotation
p(λ)	λ	Phase gate
u1(λ)	λ	U1 (≡ p)
u2(φ, λ)	φ, λ	U2 rotation
u3(θ, φ, λ)	θ, φ, λ	Generic single-qubit
cp(λ, ctrl, tgt)	λ	Controlled-Phase
crz(λ, ctrl, tgt)	λ	Controlled-RZ

---

▍ Interop — Qiskit / PennyLane

Run a circuit you already wrote in Qiskit or PennyLane on Dense-Evolution's simulator, no manual gate-by-gate rewrite. Both bridges go through OpenQASM 2.0 (qiskit.qasm2.dumps / qml.to_openqasm) and the existing QASMParser — not a bespoke translator, so gate coverage matches whatever the parser/simulator already support (see Gate Library above).

from qiskit import QuantumCircuit
from dense_evolution import run_qiskit_circuit

qc = QuantumCircuit(2)
qc.h(0)
qc.cx(0, 1)

sim, probs = run_qiskit_circuit(qc)   # probs already in Qiskit's own bit order

import pennylane as qml
from dense_evolution import run_pennylane_circuit

dev = qml.device("default.qubit", wires=2)

@qml.qnode(dev)
def circuit():
    qml.Hadamard(wires=0)
    qml.CNOT(wires=[0, 1])
    return qml.probs(wires=[0, 1])

sim, probs = run_pennylane_circuit(circuit)   # no reordering needed, see below

from_qiskit(circuit) / from_pennylane(circuit) return a QASMCircuit (structural conversion only) for anyone who wants to manage their own DenseSVSimulator/Chunk instead of the convenience runners above.

Also included: noise_model_from_qiskit_backend (real device calibration → Dense-Evolution noise spec) and to_stim (Clifford-only bridge to STIM's stabilizer tooling). Bit-order convention, known limits (classical control flow, composite gates, differentiability), and full detail on both bridges: docs/api/interop.md.

---

▍ Differentiable Circuits — circuit_to_energy_fn

The real VQE gradient engine (jax.value_and_grad through a jax.lax.scan-based circuit template, verified against finite differences to ~1e-11) used to live only inside dashboard_core.py, unreachable from outside the Streamlit app. It's now public, dependency-light (needs only the base dense-evolution install, no dashboard/pandas/streamlit), and composes directly with the interop bridge above:

import jax
from dense_evolution import QASMParser, circuit_to_energy_fn

circ = QASMParser().parse("OPENQASM 2.0; include \"qelib1.inc\"; qreg q[1]; rx(0.5) q[0];")
energy_fn, n_params = circuit_to_energy_fn(circ, circ.n_qubits)

h_matrix = ...  # your Hamiltonian, shape (2**n_qubits, 2**n_qubits)
theta = jax.numpy.zeros(n_params)

(energy, statevector), grad = jax.value_and_grad(energy_fn, argnums=0, has_aux=True)(theta, h_matrix)

energy_fn(theta, h_matrix, stato_zero=None) -> (energy, statevector) is a pure JAX function differentiable in theta; stato_zero defaults to |0...0⟩. circuit can come from QASMParser.parse, from_qiskit, or from_pennylane interchangeably — this is what closes the interop bridge's non-differentiability gap noted above.

---

▍ Noise Models

All channels applied as post-circuit stochastic Kraus operations on the full statevector.

Model	Kraus operators	Physical process
ideal	I	Noiseless
depolarizing	{√(1−p)I, √(p/3)X, √(p/3)Y, √(p/3)Z}	Isotropic Pauli error
amplitude_damping	{K₀=diag(1,√(1−γ)), K₁=[[0,√γ],[0,0]]}	T₁ energy relaxation
phase_damping	{K₀, K₁}	T₂ dephasing
bitflip	{√(1−p)I, √p·X}	Bit flip σₓ
combined	depolarizing(p/2) ∘ amplitude_damping(p/3)	Worst-case NISQ

Fidelity metrics computed on every noisy run: Bhattacharyya F = Σᵢ √(pᵢqᵢ) and TVD = ½Σᵢ|pᵢ−qᵢ|. Each channel draws one fire/no-fire decision per qubit per shot — the same convention STIM's DEPOLARIZE1(p) uses.

NoiseSpec composes noise natively into circuit_to_energy_fn (a JAX PyTree accepted as energy_fn's fourth argument — noise stays inside the same jax.jit/jax.grad/jax.vmap trace as theta, no external step):

import jax
from dense_evolution import QASMParser, circuit_to_energy_fn, NoiseSpec

energy_fn, n_params = circuit_to_energy_fn(circuit, n_qubits)
noise = NoiseSpec(model='depolarizing', p=0.05, jax_key=jax.random.PRNGKey(0))
energy, sv = energy_fn(theta, h_matrix, noise=noise)

Sampling history, apply_to_sv's rng/jax_key precedence rules, and full channel detail: docs/api/registry.md.

---

▍ Mitigation & Predictive Healing

Active error tracking and stabilization integrated natively into the simulation runtime via healing.py.

Model	Operators	Description
dephasing_tracking	Δ_pre_emp ∘ Σ	Predictive deviation vs ideal eigenstate
phi_ab_alignment	Φ_AB(state_A, state_B, ipg)	Semantic + coherence alignment between two quantum states
vettore_dinamico	V_din = K · log(E_B/E_A) · Φ_AB	Log-differential energetic evolution vector

All core functions compiled via @jax.jit. Event history managed by MemoryReflectionEngine with JAX Zero-Drift spectral aggregation.

Zero-Noise Extrapolation (dense_evolution.mitigation)

The primitives above are building blocks, not a runnable mitigation pipeline by themselves. mitigation.py is the orchestrator: it exposes ZNE under the names the field already uses (richardson_extrapolate, zero_noise_extrapolation, noise_factors) so it's discoverable without first learning the Δ_pre_emp/Φ_AB vocabulary above — the primitives themselves are not renamed, only composed.

Function	Signature	Description
richardson_extrapolate	(expectation_values, noise_factors)	Plain N-point Lagrange extrapolation to zero noise. Reduces exactly to the textbook (3, -3, 1) coefficients at noise_factors=(1,2,3)
zero_noise_extrapolation	(expectation_values, noise_factors, sigma_at_base_noise=None, target_sigma_ideal=10.0)	Standard entry point. Falls back to richardson_extrapolate when sigma_at_base_noise is omitted; otherwise perturbs the 3-point Richardson coefficients via calculate_delta_preemp — Dense-Evolution's "predictive healing" ZNE variant. Only defined for exactly 3 noise factors; raises NotImplementedError otherwise rather than guessing

import dense_evolution as de

e1, e2, e3 = 1.234, 0.876, 0.611          # values at 1x, 2x, 3x noise
plain = de.zero_noise_extrapolation([e1, e2, e3], [1.0, 2.0, 3.0])

# with a measured coherence signal at the base noise level, the
# extrapolation is nudged by how far it is from the ideal target:
healed = de.zero_noise_extrapolation([e1, e2, e3], [1.0, 2.0, 3.0],
                                      sigma_at_base_noise=9.3, target_sigma_ideal=10.0)

richardson_extrapolate/zero_noise_extrapolation accept array-valued expectation_values too (e.g. a full probability distribution per noise scale, extrapolated elementwise), not just scalars — this is what the Streamlit dashboard's Mitigation (ZNE) tab uses under the hood (dashboard_core.mitigation_runner.run_mitigation_sweep): run the active circuit at 1x/2x/3x the configured noise probability, extrapolate the whole probability vector (and fidelity) to zero noise, reusing these two functions exactly as-is.

---

▍ Erasure-Aware QEC Decoding — dense_evolution.qec

Code-agnostic stabilizer-code primitives plus a decoder that corrects known-location (erasure) errors past a standard decoder's reach. Full math, citations, and validation details: docs/api/qec.md.

from dense_evolution import compute_syndrome, erasure_aware_decode

stabilizers = ['IIIXXXX', 'IXXIIXX', 'XIXIXIX', 'IIIZZZZ', 'IZZIIZZ', 'ZIZIZIZ']  # Steane [[7,1,3]]
syndrome = compute_syndrome('IIIZIII', stabilizers)                              # Z error on qubit 3
corrected = erasure_aware_decode(syndrome, heralded_qubits=[3], n_qubits=7, stabilizers=stabilizers)

---

▍ IA Utils — Vector Sequence Healing

ia_utils/vector_healing.py — standalone module for cleaning sequences of vectors (e.g. hidden states / embeddings) that may contain NaN or Inf entries. Both functions preprocess the input (Inf → NaN → column-mean imputation) before healing, so corrupted values never propagate into the output.

Function	Approach	Returns
median_healing(vettori, radius_baseline=None)	scipy.ndimage.median_filter, dynamic radius min(20, max(3, n // 3))	(healed: np.ndarray, radius: int)
enhanced_dense_healing_hybrid(vettori, radius_baseline=None)	Blends the dense_evolution.healing Φ-trigger logic with a median fallback, decided per-step	(healed: np.ndarray, metadata: dict)

enhanced_dense_healing_hybrid metadata:

Key	Type	Description
fallback_triggered	bool	True only if the input contained genuine NaN/Inf corruption AND the median fallback fired to correct it -- does not reflect Phi-Trigger corrections on structurally noisy-but-valid data
adaptive_radius_used	int	Baseline radius actually applied
reconstruction_error	float	Mean norm of the correction applied vs. the sanitized input

import numpy as np
from ia_utils.vector_healing import median_healing, enhanced_dense_healing_hybrid

vettori = np.random.default_rng(0).normal(size=(50, 128))
vettori[10, 3] = np.nan          # simulate a corrupted hidden state
vettori[30, 7] = np.inf

healed, radius = median_healing(vettori)

healed_hybrid, meta = enhanced_dense_healing_hybrid(vettori)
print(meta)
# {'fallback_triggered': True, 'adaptive_radius_used': 16, 'reconstruction_error': 11.48}

jax is imported lazily inside enhanced_dense_healing_hybrid (a leftover from when JAX was optional) — harmless now that dense-evolution always installs JAX as a core dependency, but it does mean median_healing and the module import itself never actually needed it in the first place.

---

▍ Anti-OOM Chunk Engine

All operations parcellized dynamically using a 4-layer architectural shield.

Layer	Class	Role
1	SafeMemoryGuard	Pre-allocation RAM check — blocks before JAX raises RESOURCE_EXHAUSTED
2	MemoryChunker	Geometry calculator — computes num_chunks, chunk_dim, chunk_size_bits from available RAM without any JAX allocation
3	CircuitChunker	Per-slice execution — SafeMemoryGuard fires before every gate-slice dispatch
4	Chunk	Top-level wrapper — logical n_qubits decoupled from physical allocation at safe_qubits

Benchmark vs PennyLane — Windows CPU (8 GB RAM)

Dense Evolution maintains constant ~2 GB RAM at any qubit count via dynamic chunking. PennyLane allocates the full statevector — OOM beyond 26q.

Qubits	Hilbert Space	PennyLane	PennyLane RAM	Dense Evolution	Dense RAM	Chunk Geometry
24	16,777,216	✅	307 MB	✅	516 MB	1× (2²⁷)
26	67,108,864	✅	1,074 MB	✅	2,050 MB	1× (2²⁷)
28	268,435,456	❌ OOM	—	✅	2,050 MB	2× (2²⁷)
30	1,073,741,824	❌ OOM	—	✅	2,048 MB	8× (2²⁷)
32	4,294,967,296	❌ OOM	—	✅	2,048 MB	32× (2²⁷)

from dense_evolution import Chunk

sim = Chunk(27)
sim.run_chunk([['h', i] for i in range(27)], chunk_size_gates=500)

print(sim)
# Chunk(n_qubits=27, safe_qubits=27, num_chunks=1,
#       chunk_size_bits=27, mem_per_chunk=2048.0 MB, ram_free=42.3%, has_jax=True)

Distributed dispatch across a device mesh — run_chunk_distributed

run_chunk()'s multi-chunk path (num_chunks > 1) solves "RAM of one process" — every chunk lives in the same machine's memory, even though the kernel that moves them is JIT-fused. run_chunk_distributed() solves a different constraint: "more qubits than fit on one device," with one physical chunk pinned to its own JAX device (v1 scope: jax.device_count() must be >= num_chunks, exactly one chunk per device — a hybrid multi-chunk-per-device scheme is future work).

from dense_evolution import Chunk

sim = Chunk(30)  # num_chunks > 1 on most machines
sim.run_chunk_distributed([['h', i] for i in range(30)])

Cross-chunk gate mixing (a gate touching one of the top m = n_qubits - chunk_size_bits "chunk-select" qubits) becomes real point-to-point network communication — jax.lax.ppermute, the same pairwise-exchange pattern distributed statevector simulators use, exchanging edge data only with the fixed XOR-stride partner device, never gathering the full state onto any single device. A gate entirely within a chunk's local qubits, or a control-chunk/target-local gate (decidable from each device's own chunk index alone), needs no communication at all.

Requires jax.device_count() >= num_chunks; raises RuntimeError with the exact count needed otherwise. For local testing without real multi-GPU hardware, force extra simulated CPU devices via XLA_FLAGS=--xla_force_host_platform_device_count=N (set before the process starts — JAX's device count is fixed at first initialization, not changeable at runtime) — this validates the sharding/communication logic is correct, not real GPU-to-GPU network performance, which needs actual multi-GPU/multi-host hardware to measure honestly.

---

▍ Benchmarks

Measured on Google Colab Free Tier (CPU runtime)

Metric	Value
Numerical drift (30-layer Ansatz, 1360 gates)	Δ = 1.11 × 10⁻¹⁶
Memory footprint @ 20q	32 MB (float64) · 16 MB (float32)
JIT compile overhead (first run)	< 400 ms
Gate throughput after warm-up	> 10⁶ gates/s (CPU)
Maximum tested qubits (Colab Free)	24q stable · 33q high-RAM runtime
Anti-OOM latency reduction (static JIT cache)	−86.47%

---

▍ Composer — Interactive Web UI

A real circuit editor (graphical drag-and-drop or OpenQASM 2.0), running every circuit on the actual DenseSVSimulator — statevector, probabilities, Q-sphere, Bloch spheres, a native circuit diagram (plain matplotlib, no Qiskit QuantumCircuit ever constructed), plus real molecular Hamiltonians (PennyLane Hartree-Fock), VQE, ZNE mitigation, and a "Scan energia" panel computing a bond-length ground-state-energy curve (e.g. a dissociation curve) in one click instead of one point at a time. No mocked data anywhere: every number on the page comes from a real run. Every request has a client-side timeout (30s default, 10 minutes for VQE/MD-trajectory calls) with a clear error instead of hanging forever indistinguishable from normal progress.

The page is public, the compute is yours. tatopenn-cell.github.io/Dense-Evolution/composer is static — it talks to a local kernel that runs on your own machine, not a shared server. Get the kernel running with the installer for your OS (walks you through what it does before doing anything, no silent steps):

• Windows: installer/install-composer.bat
• macOS / Linux: installer/install-composer.sh
• Uninstall: installer/uninstall-composer.bat / installer/uninstall-composer.sh

The installer's only real job is pip install dense-evolution[composer] plus some optional shortcuts — the kernel itself is one plain console command, install it by hand instead if you'd rather skip the installer (works the same from PowerShell, cmd, bash, or zsh — it's a normal Python entry point, not a shell script):

pip install dense-evolution[composer]

dense-evolution serve                        # starts the kernel at http://127.0.0.1:8800
dense-evolution offline-composer [DEST]      # downloads the real Composer page for use with no internet
                                              # (DEST defaults to ./composer-offline)

serve is what the published page's banner is waiting for — reload the page once it's running and the banner turns from "kernel not found" to connected. offline-composer downloads the actual live page (not a separate hand-maintained copy) plus every asset it references, keeping the same relative layout so it opens correctly via file://.

---

▍ MCP Server — drive the Composer kernel from an agent

dense_evolution_mcp (mcp_server/) is an MCP (Model Context Protocol) server: 21 tools, one per Composer kernel endpoint plus a batch energy scan, a batch wormhole sweep, and a vector-healing pass, letting an MCP-aware agent (Claude Code, Claude Desktop, ...) run circuits, compute molecular ground-state energies, run VQE, get QM/MM forces, run MD trajectories, apply ZNE mitigation, run traversable-wormhole-inspired quantum teleportation, and heal a noisy vector sequence directly — without a browser. A thin adapter, not a reimplementation: every tool calls the same kernel serve starts above; local_site/app/server.py itself gained three new endpoints (/api/wormhole_select_instance, /api/wormhole_teleportation, /api/vector_healing) but no existing endpoint changed.

pip install dense-evolution[mcp]

dense-evolution serve   # start the kernel first, in one terminal (see Composer above)
dense-evolution mcp     # in another terminal, or registered with your MCP client's config

Register with Claude Code:

claude mcp add dense_evolution -- dense-evolution mcp

• Molecule-name tools accept a short id ("H2", "LiH", "HeH+") or the kernel's full descriptive catalog name — resolved from the live catalog, not hardcoded.
• dense_evolution_energy_scan computes the ground-state energy at several geometries in one call (the same capability the Composer page's "Scan energia" panel gives a human).
• dense_evolution_wormhole_select_instance / _wormhole_teleportation / _wormhole_scan run a real traversable-wormhole-inspired quantum teleportation protocol (Gao-Jafferis-Wall theory, arXiv:2604.10090) on a binary sparse SYK model — see dashboard_core/wormhole.py and research/wormhole_syk.md for the physics. Unlike _energy_scan, the wormhole sweep runs sequentially, not concurrently (each call is a real multi-second simulation; concurrent calls were found to crash the kernel via a BLAS/eigh thread-safety issue).
• dense_evolution_vector_healing reintegrates the predictive-healing engine (dense_evolution.healing's Phi-Trigger primitives, via ia_utils.vector_healing.enhanced_dense_healing_hybrid) that shipped with the pre-rebuild dashboard_core's Streamlit "AI healing shield" middleware, left behind (not removed) when dashboard_core was rebuilt around the Composer kernel — see dashboard_core/vector_healing.py. Cleans a noisy (n_steps, dim) sequence (VQE telemetry, MD trajectory, or any other vector sequence): per step, keeps genuine dynamics, replaces static noise with the local median, always sanitizes NaN/Inf.
• Large arrays are truncated to their most significant entries, and images are saved to disk (path returned) rather than inlined as base64, so a tool response stays usable in an agent's context.
• mcp_server/README.md has full setup details; a project-scoped Claude Code skill (.claude/skills/dense-evolution-mcp/) documents how to use the tools effectively — which tool for which task, known cost/qubit caps, why arrays are truncated.

---

▍ Dashboard Panels (app_dashboard.py)

Tab	Contents
Graphical Builder	Drag-and-drop gate grid (dashboard_core.mount_circuit_builder) — loads straight into the Circuit editor as OpenQASM
Circuit	Native matplotlib circuit diagram of the parsed OpenQASM (dashboard_core.draw_circuit_figure)
Statevector	Full complex amplitude table (real/imaginary/magnitude/phase) for every basis state above threshold
Probabilities	Shot histogram sampled from the computed statevector (dashboard_core.histogram_figure)
Q-sphere	Q-sphere rendering of the statevector (dashboard_core.qsphere_figure)

VQE Results, MD Results, and Performance-style telemetry panels (energy convergence, QM/MM trajectories, Pearson heatmaps) are not part of this Streamlit dashboard — that functionality lives in the Composer web app (see "Composer" below), driven by the same dashboard_core VQE/QM/MM/mitigation modules through local_site/app/server.py.

---

▍ VQE Engine

Built on circuit_to_energy_fn (see previous section) — no separate mechanism. Parameter injection:

1. Counting parametric gates (rx ry rz p u1 cp crz) → n_params
2. Initializing θ ∈ ℝⁿ uniform in [−π, π]
3. Injecting θ[i] sequentially by gate order, via a -1.0 sentinel in the compiled op template patched in with jnp.where inside a jax.lax.scan — never a Python float() call, which would sever the JAX trace and make the gradient below fake.

Compatible with any custom OpenQASM 2.0 string without pre-labelling.

Gradient & update rule:

$$\frac{\mathrm{\partial }E}{\mathrm{\partial }{\theta }_i}=⟨\psi (\theta )\mid \frac{\mathrm{\partial }H}{\mathrm{\partial }{\theta }_i}\mid \psi (\theta )⟩\theta \leftarrow \theta -\frac{\alpha {\widehat{m}}_t}{\sqrt{{\widehat{v}}_t}+\epsilon }\backslash frac\{\backslash partial\; E\}\{\backslash partial\; \backslash theta\_i\}\; =\; \backslash left\backslash langle\backslash psi(\backslash theta)\backslash left|\backslash frac\{\backslash partial\; H\}\{\backslash partial\; \backslash theta\_i\}\backslash right|\backslash psi(\backslash theta)\backslash right\backslash rangle\; \backslash qquad\; \backslash theta\; \backslash leftarrow\; \backslash theta\; -\; \backslash frac\{\backslash alpha\backslash ,\backslash hat\{m\}\_t\}\{\backslash sqrt\{\backslash hat\{v\}\_t\}+\backslash varepsilon\}$$

Telemetry columns (→ df_vqe_telemetry):

Column	Unit	Description
VQE_Energy	Ha	⟨ψ|H|ψ⟩
Entropy	bit	−Tr(ρ log₂ ρ)
Purity	—	Tr(ρ²) ∈ [1/d, 1]
Gradient	—	‖∇L‖ — barren plateau detection
Noise_Factor	—	Fidelity-derived noise proxy
Theta_Correction	rad	ADAM step norm

---

▍ Hamiltonian Library

Real Hartree-Fock + fermion-to-qubit mapping, exact dense diagonalization for the ground-state energy. _get_hamiltonian dispatches per molecule to PennyLane's own qchem pipeline (Jordan-Wigner or Bravyi-Kitaev — both represent the identical physical Hamiltonian, just a different qubit basis) when every element is in PennyLane's bundled STO-3G table, or to Dense-Evolution's own native_hf engine otherwise. dashboard_core.MOLECULE_CATALOG:

Molecule	Qubits	Bond length	E₀ (Ha, Jordan-Wigner)	Engine
H₂	4	0.7414 Å	−1.1373	PennyLane dhf
HeH⁺	4	0.7743 Å	−3.0157	PennyLane dhf
H₃⁺ (D3h triangle)	6	0.8738 Å	−1.2973	PennyLane dhf
LiH	12	1.5949 Å	−7.8824	PennyLane dhf
H₂O (104.5°, frozen-core O 1s)	12	0.9584 Å	−75.0127	PennyLane dhf
Si₂	8	2.184 Å (real equilibrium, active space too small to reproduce as its own minimum — see v8.1.59 changelog)	−570.6861	native_hf

Custom molecules: any atomic symbols + [[x, y, z], ...] geometry in Ångström, same Hartree-Fock pipeline (PennyLane or native_hf, dispatched automatically) — capped at 12 qubits (exact dense diagonalization's real limit here, rejected with a clear error before PennyLane runs rather than attempted and failing expensively). dense_evolution_energy_scan (MCP) / the Composer's "Scan energia" panel compute this at several geometries in one call, e.g. a dissociation curve.

---

▍ Circuit Library (20 presets)

All circuits stored as OpenQASM 2.0 strings in dashboard_core.QASM_LIBRARY.

States — Bell state (2q), GHZ (3q/4q/8q), W state (3q), Superposition (1q)

Entangling layers — linear/ring/full/star/brick topology, 5q each (dense_evolution.topology.entangling_layer)

Algorithms — Quantum Fourier Transform (3q), Grover search (3q, target |111⟩), Deutsch-Jozsa (2+1q, balanced oracle), Bernstein-Vazirani (3+1q, secret 101), Toffoli/CCX (3q, T-gate decomposition), Quantum Teleportation (3q, deferred-measurement principle — verified fidelity 1.0000000000 across 5 random states), Quantum Phase Estimation (3-qubit counting register on a T-gate — verified probability 1.0000 on the exact expected phase, not merely the most likely outcome)

Testing — Random circuit, fixed seed (3q and 5q variants)

---

▍ Changelog

v8.1.62

• New mitigation.sample_classical_shadow/magic_entropy_from_shadows/approx_shadow_std/fit_shadow_sample_complexity: a classical-shadows-based estimator for magic_entropy from randomized measurement snapshots. Distinct API shape from every other function in mitigation -- sampling (sample_classical_shadow) and estimation (magic_entropy_from_shadows) are separate steps, since shadow data can come from this simulator (oracle Born-rule sampling) or, in principle, real hardware measurement logs reconstructed the same way. Originated from a Colab proposal for a shadows.py module with a real bug (a missing transpose in its purity estimator's U-statistic contraction, silent whenever every snapshot happened to be real-valued) -- fixed, then extended to magic_entropy using the same multi-copy trick Huang, Kueng & Preskill (2020, arXiv:2002.08953) state "readily generalizes to higher order polynomials." Matured across three real gaps found and closed in Dense-Evolution-Discovery Experiment 31 before promotion: the purity-estimator bug itself, plain averaging replaced with real median-of-means robustness (verified: tolerates a 40%-corrupted contiguous measurement block, unlike a naive mean, which is dragged from 1.0 to -19.4 under the same corruption), and an empirically-fitted sample-complexity curve (std(n) ~ 11.75 / n^0.546 from 20 independent trials per snapshot count, exponent consistent with the ~0.5 theory predicts) exposed as approx_shadow_std (a rough built-in guide) and fit_shadow_sample_complexity (calibrate your own curve for a specific state). Not jax.jit-compatible, unlike the rest of this subpackage -- median-of-means uses numpy.median, which has no equivalent JAX primitive at this scale.
• New mitigation.sandwiched_renyi_divergence/sandwiched_renyi_divergence_jit and mitigation.magic_entropy/magic_entropy_jit: two full-density-matrix diagnostics. Both originated as Colab proposals with real bugs, fixed and validated in Dense-Evolution-Discovery before promotion. sandwiched_renyi_divergence (Muller-Lennert et al., arXiv:1306.3142) had a clamp bug that silently zeroed the divergence for the normal (non-commuting-state) case, and a deeper bug returning a finite wrong-signed number instead of +inf on a genuine support mismatch at alpha>1 -- both fixed (Experiment 29); its originally proposed use case (replacing the JSD-based truncation criterion in mps.py's bond-dimension search) was independently disproven (rho, sigma commute on that diagonal singular-value spectrum, so a non-commuting-aware divergence adds nothing there) -- promoted instead for the genuinely non-commuting full-density-matrix use case it was validated against, alongside uhlmann_fidelity. magic_entropy (Bu, Gu, Jaffe, arXiv:2306.09292) replaces a different Colab proposal -- a pairwise "Quantum Ruzsa Divergence" that turned out to have no valid definition for qubits at all (the source paper's own pairwise convolution needs s^2+t^2=1 mod d, unsolvable at d=2) -- with the paper's real qubit-valid construction: a 3-fold self-convolution "Key Unitary", verified basis-state by basis-state against the paper's own Lemma 9 identity, giving zero for all six single-qubit stabilizer states and 0.811 bits for the standard T/H magic states (Experiment 30). Both are differentiable through jax.grad; magic_entropy needs no _eigh_degenerate_safe-style treatment even at exactly degenerate points (e.g. the fully mixed state) since it only ever needs eigenvalues, never eigenvectors. A classical-shadows-based estimator for magic_entropy (Experiment 31) is now also promoted -- see the next entry.
• New trigger_mode='adaptive' option for ia_utils.vector_healing.enhanced_dense_healing_hybrid. Dense-Evolution-Discovery Experiment 27 found the default Phi-Trigger (dense_evolution.mitigation.healing.evaluate_phi_trigger, fixed |v_dinamic| > 0.01 threshold) classifies ~85-90% of ordinary noisy, uncorrupted rows as needing median-fallback replacement -- confirmed across 4 corruption types x 40 seeds. The new opt-in 'adaptive' mode (a NaN/Inf-aware, MAD-adaptive local-deviation trigger) cuts that false-positive rate to ~10-13% while matching or exceeding the Phi-Trigger's recall on every corruption type tested, including one (spike+NaN combined) where the original trigger itself only caught 28.7% of corrupted rows. Kept opt-in with 'phi' as the unchanged default: ia_utils.adversarial_vector_attack's gradient-based red-teaming specifically targets the differentiable Phi-Trigger mechanism, and the new trigger is not differentiable the same way.

v8.1.61

• Full architectural refactor of the dense_evolution/ package root -- what was a flat directory of ~30 modules is now organized into 7 thematic subpackages (utils/, interop/, physics/, circuits/, backends/, mitigation/, solvers/), an explicit __all__ on the top-level package (59 names, verified via AST parsing against the real from .X import Y statements rather than transcribed by hand), and a tests/ suite split into unit/ (24 files, one per library module) and integration/ (19 files, multi-module and tools/-app coverage). Every moved module keeps a backward-compatible re-export shim at its old top-level path (e.g. from dense_evolution.mps import MPSSimulator keeps working unchanged, identically to before this release) -- skipped only where the new subpackage name matches the old module's own basename (e.g. interop.py -> interop/), since Python resolves an import to a same-named package over a plain module file regardless, making a shim file there dead code. Each subpackage moved in its own CI-gated PR (7 for the split itself, plus dedicated PRs for the public API surface, internal-import cleanup, and the tests/ reorganization), verified end to end with a real python -m build --wheel + clean-venv install, not just editable-mode local testing. Two real bugs were found and fixed along the way, both while auditing the refactor's own PRs rather than assumed correct: a Hartree-Fock SCF non-convergence for Si2 caused by near-degenerate orbitals at the active-space boundary (fixed with linear density damping, Szabo & Ostlund ch. 3.4.9), and a test file's repo-root path computation that was off by one directory level after being moved one level deeper into tests/integration/.

v8.1.60

• New dense_evolution.qec: code-agnostic stabilizer-code utilities and an erasure-aware decoder. pauli_commutes/compute_syndrome are generic Pauli-string commutation/syndrome primitives (work against any list of stabilizer generators, not a hand-built code-specific table); erasure_aware_decode exploits known error locations (e.g. a heralded lost photon in a dual-rail photonic qubit) to correct up to d-1 erasures on a distance-d stabilizer code, versus only floor((d-1)/2) for a standard syndrome-only decoder blind to error locations (Grassl, Beth & Pellizzari, "Codes for the quantum erasure channel", Phys. Rev. A 56, 33, 1997). Returns None — never a guess — when the observed syndrome is unresolved or ambiguous given the heralded qubits. Promoted from Dense-Evolution-Discovery's Steane [[7,1,3]] code investigation (scripts/steane_code_block6_erasure_conversion.py), where a Steane-specific version was first built and validated against STIM's native HERALDED_ERASE noise channel: 0 decoding failures across every double-erasure shot tested (>60,000 shots total, 40,000 trials × 10 physical error rates), versus a real ~25% failure rate for the standard decoder. This generalized version is validated by exact reproduction of that original result (bit-for-bit identical, same seed) using only the new code-agnostic primitives — not just a separately-verified equivalent. All three functions also importable from the top-level package (from dense_evolution import pauli_commutes, compute_syndrome, erasure_aware_decode).

v8.1.59

• New dense_evolution.native_hf: a from-scratch, JAX-vectorized Hartree-Fock engine for elements outside PennyLane's own bundled STO-3G table (which stops at Ne, so Si and everything past it previously failed with No built-in STO-3G basis data for: ...). Implements the standard Obara-Saika recursion (Obara & Saika, J. Chem. Phys. 84, 3963, 1986) for overlap/kinetic/nuclear-attraction/electron-repulsion integrals over s/p shells (degree ≤ 1), each shell-pair/quartet's primitive sum and Cartesian-component slicing fused into one jax.jit-compiled call (looping that eagerly, one jnp.ndarray slice per primitive combination, cost as much per-call dispatch overhead as the very Python-loop-bound autograd tracing this was built to avoid — profiled directly: 482 of 483 total seconds in PennyLane's own dhf integral loop for Si2/STO-3G). Basis-set parameters come from the basis_set_exchange package, so any element it has STO-3G data for works, not just PennyLane's H–Ne table. Only the Hartree-Fock/integral stage is native — the converged result still goes to PennyLane's own fermionic_observable + jordan_wigner for the qubit mapping, since that stage is already fast (under 2 seconds) and well-tested. An element needing d-orbitals or higher (e.g. Fe) fails with a clear NotImplementedError naming the real limitation, not a silent wrong energy for an incomplete basis. Verified element-wise against an independent JAX Hartree-Fock implementation (lowdanie/hartree-fock-solver, "slaterform", Apache-2.0) to machine precision on individual integrals and to 10 significant figures on Si2/STO-3G's full SCF energy; the complete pipeline (native HF → qubit Hamiltonian → exact diagonalization) reproduces PennyLane's own dhf-based ground-state energy exactly at the same geometry/active space. Design and algorithm structure were informed by studying slaterform's JAX implementation of Obara-Saika and PennyLane's own white paper (Delgado et al., "Differentiable quantum computational chemistry with PennyLane", arXiv:2111.09967) — no source from either is copied.
• dashboard_core.hamiltonians gains Si2 in MOLECULE_CATALOG (real equilibrium R = 2.184 Å, Balamurugan & Prasad, "Effect of hydrogen on ground state structures of small silicon clusters", arXiv:cond-mat/0108426) — this corrects an earlier, unverified "~3.55 Å" dissociation-curve claim that had appeared in this same README with no script backing it; Si2 wasn't even representable in this project's own molecule catalog until this release. _get_hamiltonian now dispatches to PennyLane's own qchem pipeline when every requested symbol is in its bundled STO-3G table, or to native_hf otherwise, so existing molecules (H2/HeH+/H3+/LiH/H2O) are completely unaffected. Given only 4 active electrons/orbitals for Si2 (freezing all 20 core electrons across both atoms), this active space is honestly too small to reproduce 2.184 Å as its own energy minimum — a direct 10-point bond-length scan (1.9–4.0 Å) found its minimum at the 1.9 Å edge of the range, not an interior point — stated plainly in the catalog entry's own comment rather than silently picking a geometry that flatters the active-space choice.

v8.1.58

• New dense_evolution.interop.noise_model_from_qiskit_backend -- converts a Qiskit BackendV2's own calibration data (backend.target, real per-qubit/per-gate error rates -- works for live backends and fake/mock backends carrying a real historical snapshot, e.g. qiskit_ibm_runtime.fake_provider.FakeSherbrooke) into a Dense-Evolution-native noise specification (a list of {'gate', 'qubits', 'model': 'depolarizing', 'p'} dicts, each directly usable as NoiseModel.apply_to_sv's model/p/qubits arguments), so a simulation can run under a real device's measured error rates instead of an idealized channel. Promoted from Dense-Evolution-Discovery's Steane-code hardware bridge script (scripts/steane_code_block5_qiskit_bridge.py), validated there against FakeSherbrooke (real IBM Eagle-127 historical calibration, encoded-state fidelity 0.8828 under its real ECR/SX/RZ error rates). Preserves a real bug fix found while building the original script: calling Qiskit Aer's add_quantum_error once per gate occurrence in a circuit (instead of once per unique qubit/gate target) composes the same Kraus channel with itself repeatedly, blowing up to multi-GB memory from the resulting Kraus-term combinatorial explosion -- this function dedupes by (gate, qargs) before ever emitting a spec entry, so it can't reproduce that bug by construction. An optional circuit= argument restricts the result to just the targets a specific circuit uses (still one entry per unique target, matched order-independently on the qubit tuple since NoiseModel.apply_to_sv only ever applies independent single-qubit channels per target anyway). New tests/test_interop_calibration_noise.py: real calibration extraction off FakeSherbrooke, a regression test that 500 repeated occurrences of the same two targets still collapse to one spec entry each (would have caught the original bug), and a Bell-state sanity check (real calibrated error rates give a mean fidelity strictly between 0 and 1 over 300 trials, not a silent no-op).

v8.1.56

• New mitigation.jsd_predictive_zne_density_matrix -- density-matrix ZNE with a Jensen-Shannon-divergence-informed coefficient nudge, for noise whose scale-to-output-distribution relationship isn't perfectly smooth. Prototyped and validated first in Dense-Evolution-Discovery's photonic_predictive_zne.py for photon-loss noise (photon loss on a dual-rail-encoded qubit is this library's amplitude_damping channel), grounded in real literature: Mills & Mezher, "Mitigating photon loss in linear optical quantum circuits" (arXiv:2405.02278), find plain scalar ZNE does not beat postselection for discrete-variable photon loss -- reproduced directly (scalar ZNE went unphysical, fidelity > 1.0, at 14/16 swept points), while zne_density_matrix avoids that failure mode by construction. The new function's signal (Jensen-Shannon divergence between measurement-probability distributions at consecutive noise scales) needs no external calibration or oracle access to an ideal state -- a first design reusing calculate_delta_preemp for this purpose had a negligible effect by construction (its fixed nudge constants were tuned for an unrelated, differently-scaled use case). Rectified so the nudge only applies when a detected nonlinearity signal is positive, reducing EXACTLY to plain zne_density_matrix otherwise (zero risk in that regime, verified to ~1e-8). Validated on a real, seed-diverse sample (72 points: 12 photon-loss rates x 6 independent seeds, K=200 trajectories each) before promotion: among 46 points where the mechanism activates, 76.1% improve over plain zne_density_matrix, mean fidelity gain +0.0055, p=0.0003 (one-sample t-test), positive in 6/6 independent seeds -- the win rate and effect size were larger on the big sample than the small one that first suggested it, not smaller. Honest caveat, checked directly rather than assumed: a follow-up comparison in Dense-Evolution-Discovery against TRUE postselection (discarding shots where a photon-loss event was heralded, not an approximation -- see that repo's photonic_zne_multi_circuit_postselection.py) across 2 circuit families and 3 qubit counts (18 configurations) found postselection still wins in 14/18 cases; this function narrows the gap to postselection versus plain zne_density_matrix but does not close it. Worth using when postselection isn't viable (loss events not independently heralded, or discarding too large a fraction of shots) -- not a general replacement for postselection when postselection is available.

v8.1.55

• mitigation.uhlmann_fidelity/uhlmann_fidelity_jit are now safe to differentiate through even when rho_A has (near-)degenerate eigenvalues -- e.g. a near-pure state's noisy density matrix, or (the sharpest case) the fully mixed state, whose eigenvalues are all tied. JAX's own jnp.linalg.eigh gradient rule divides by lambda_i - lambda_j, which is exactly 0/0 at degenerate eigenvalues -- a well-documented category of AD failure (JAX issues #2311/#8732; general treatment in Kasim, "Derivatives of partial eigendecomposition of a real symmetric matrix for degenerate cases", arXiv:2011.04366). Fixed with a new internal _eigh_degenerate_safe (jax.custom_jvp): masks the singular term to 0 for near-degenerate eigenvalue pairs instead of letting it blow up, replacing the previous NaN with a well-defined (if not maximally sharp) subgradient. Forward-pass values are bit-identical to before (same underlying eigh call, only the backward rule differs) -- verified against an independent numpy reference on random density matrices (diff ~1e-14) and confirmed the fully-mixed-state gradient, previously all-NaN, is now finite (both checked directly, not assumed from the general theory).
• Real bug fixed: NoiseModel.apply_to_sv's amplitude_damping channel fired its decay branch with a flat probability gamma, independent of the qubit's actual population in |1⟩ -- the correct single-trajectory ("quantum jump") unraveling requires the Born-rule probability P(K1) = gamma * |v1|^2 (a qubit with no |1⟩ population must never decay). Verified analytically (exact branch-probability-weighted expectation, no Monte Carlo sampling noise) that the old formula diverged from the true amplitude-damping Kraus channel by up to 0.13 (max density-matrix-element error) for superposition states at gamma=0.5 -- only matched by coincidence for a pure |1⟩ state, where |v1|^2=1 makes the flat and state-dependent probabilities equal. Independently cross-checked against John Preskill's Ph219/CS219 Chapter 3 (Caltech lecture notes): its own derivation of this channel (system-environment isometry + partial trace) gives the same K0/K1 this code already used -- the missing piece was always the firing probability, not the Kraus operators. Fixed formula verified two ways: exact branch-probability expectation matches the textbook Kraus channel to 0.00000000 across 16 test cases (4 states x 4 gamma values including gamma=0/1), and a 300,000-trajectory Monte Carlo average converges to within expected statistical noise (0.001, matching the ~1/sqrt(K) prediction).
• New ia_utils.adversarial_vector_attack.craft_adversarial_healing_perturbation -- a gradient-based stress test for ia_utils.vector_healing.enhanced_dense_healing_hybrid's Phi-Trigger decision, adapted from IGME's chained-differentiable-attack idea (arXiv:2607.27465, "IGME: Efficient Chained Method Ensemble for Transferable Semantic Segmentation Attacks", He & Zhang), applied to vector sequences instead of image segmentation. evaluate_phi_trigger (dense_evolution.healing) thresholds |v_dinamic| with a hard step (not differentiable at the boundary), but v_dinamic itself is built entirely from JAX-differentiable ops -- this crafts a minimal perturbation (PGD-style, projected into an L2 epsilon-ball) that flips the trigger either direction: flip_to_dynamic (evade -- make static-looking corruption pass through unhealed) or flip_to_static (suppress -- make genuine dynamic signal get wrongly median-replaced). Verified end-to-end against the real enhanced_dense_healing_hybrid pipeline (not just the isolated trigger proxy) for both directions. Two real bugs found and fixed during verification, not assumed correct: (1) the default step_size used to scale with the epsilon budget, which made a larger budget converge to a worse result (verified directly: non-monotonic in epsilon) -- now a small fixed default independent of epsilon; (2) calculate_phi_ab's [0,1] clip can saturate for inputs whose semantic distance exceeds MAX_SEMANTIC_DISTANCE, giving an exact-zero gradient -- a real property of the underlying formula, now detected and reported (perturbation_norm == 0, success == False) rather than silently misreported as "no better point found".

v8.1.54

• Added CITATION.cff and a "Cite This" section (README + docs) for academic citations, following the standard Citation File Format (recognized by GitHub's own "Cite this repository" button). Archived on Zenodo -- concept DOI 10.5281/zenodo.21855643, version DOI 10.5281/zenodo.21855644 for this release.
• dashboard_core.hamiltonians.build_molecular_hamiltonian now validates its geometry input instead of letting bad input surface as a raw IndexError deep inside PennyLane's internals or silently produce a NaN Hamiltonian. New _validate_geometry checks: geometry has shape (n_atoms, 3), symbols/geometry lengths match, all coordinates are finite, and no two atoms are closer than a physically-realistic 0.3 Å floor (MIN_NUCLEAR_DISTANCE_ANGSTROM, matching the same floor dashboard_core.qmmm already uses for MD trajectories). Verified directly: a symbols/geometry length mismatch, non-finite coordinates, wrong geometry shape, and overlapping atoms each now raise a clear ValueError instead of the prior crash/silent-NaN behavior; valid geometries are unaffected.
• dashboard_core.qmmm.run_md_trajectory gains an fd_step_angstrom parameter (default 0.001, unchanged) and now actually forwards it to compute_hellmann_feynman_forces on every step -- previously the parameter existed one level down but run_md_trajectory never exposed or passed it through, so callers silently always got the default finite-difference step regardless of what they asked for. Verified: a coarser fd_step_angstrom now measurably changes the per-step numerical-derivative force estimate, confirming the value reaches the real per-step calculation.
• ia_utils.vector_healing.enhanced_dense_healing_hybrid's inner dense_evolution.healing/jax import is now guarded -- previously an unguarded import deep inside the function, so a real import failure (e.g. ia_utils used standalone, missing one of its own transitive dependencies) surfaced as a bare ModuleNotFoundError with no hint what the function actually needed. Now raises a clear ImportError naming both the requirement and the underlying cause. Verified against a real forced import failure, not a simulated downstream consequence.
• mcp_server/server.py's _save_png no longer lets DENSE_EVOLUTION_MCP_IMAGE_DIR grow without bound -- every include_visualizations=True tool call wrote a new timestamped PNG with no cleanup, so a long-running MCP session accumulated files indefinitely. New _prune_old_images keeps at most DENSE_EVOLUTION_MCP_IMAGE_MAX_FILES (env var, default 500) of the most recently written PNGs, deleting the oldest first; 0 or negative disables pruning.
• dashboard_core.wormhole.run_wormhole_protocol / run_wormhole_protocol_finite_beta / find_delta_beta_bands now share an LRU-memoized diagonalization (_cached_finite_beta_layout, maxsize=32) instead of each redoing the H/V eigendecomposition from scratch on every call -- real cost for a caller re-running the same (n_majorana, k_terms, J, seed) instance with different mu/t0/t1/beta, previously identical work repeated every time. Verified bit-identical output before/after, and that repeat calls at the same instance are real cache hits (not just equal-by-coincidence). run_wormhole_protocol_trotter is unaffected -- it evolves via a Trotterized gate circuit and never diagonalizes anything.
• ia_utils.vector_healing.enhanced_dense_healing_hybrid's baseline_mean no longer recomputes np.mean over the lookback window from scratch every iteration -- harmless with the default adaptive radius (capped at 20), but an explicit caller-supplied radius_baseline is unbounded, and a value >= n degenerates the window to a cumulative one from the start, making the whole loop genuinely O(n²). Now an incremental sliding-window sum (add the newest element, subtract the one that just fell out of the window), O(1) amortized per step regardless of radius_baseline. Verified bit-identical to the old per-iteration recomputation across every tested radius, including the pathological unbounded case; isolated benchmark (n=3000, hidden_dim=768, unbounded radius): the baseline_mean computation itself dropped from 1.52s to 0.016s (~97x) -- the end-to-end function's wall-clock gain is much smaller in practice, since the per-iteration JAX call overhead in this same loop (untouched by this fix) dominates total runtime regardless of radius_baseline.

v8.1.53

• New: dashboard_core.wormhole.run_wormhole_protocol_finite_beta -- the exact-backend wormhole-teleportation protocol (run_wormhole_protocol), but with the real finite-temperature thermofield double arXiv:2604.10090 actually uses (|TFD> = (1/sqrt(Z)) * exp(-beta*H_tot/4) |I>, Eq. S8, beta=3 per Section S2), instead of the beta=0 simplification (plain Bell pairs) every other backend in this module uses. On real hardware exp(-beta*H/4) is non-unitary and needs an approximate 96-parameter variational circuit (~92.7% fidelity, the paper's own Section S2); this classical statevector simulation applies the exact non-unitary filter directly via eigendecomposition -- no hardware constraint, no approximation. beta=0 reproduces the existing backends' result exactly (verified to ~1e-9 in tests/test_wormhole.py, not just assumed).
• New private helpers _finite_beta_layout_precomputed / _run_finite_beta_precomputed for callers scanning many (beta, mu) points at a fixed seed (e.g. a beta sweep): diagonalizing H_tot and the coupling V turned out to be ~58% of a single call's cost and is identical across every beta/mu value at fixed seed -- precomputing it once instead of on every call measured ~78x faster per point after the one-time setup cost, for a 3-point sweep.
• New: dashboard_core.wormhole.find_delta_beta_bands -- segments the sign-dependent teleportation signal delta(beta) into constant-sign bands over an inverse-temperature range, instead of reporting a single sign at one fixed beta. Motivated by a real finding while exploring run_wormhole_protocol_finite_beta above: the sign is not stable across beta for many instances (verified on 10 known 34/11-matched seeds -- 4 never flip over beta in [0, 6], the other 6 flip 1-3 times each), so a single per-instance sign can be misleading. Crossing points are linearly interpolated between grid points, not just snapped to the scan resolution. Reuses the same seed's eigendecomposition across the whole scan.
• dashboard_core.wormhole.commuting_pair_count rewritten from O(2n_qubits) dense-matrix commutators to O(n_qubits) Pauli-dict comparison** -- two Pauli strings commute iff they disagree (both non-identity, different operators) on an even number of qubits, a direct per-pair count instead of building a dense 2**n_qubits x 2**n_qubits matrix per term and computing a real matrix commutator per pair. Measured: 14.2s per call at n_qubits=10 (n_majorana=20) with the old implementation vs. <1ms with the new one (~14,000,000x). Verified to return bit-identical results to the old implementation across 200 real SYK instances at n_majorana=8 plus additional checks at n_majorana=12/16, and seed 61 still matches the paper's own reported 34 commuting / 11 anticommuting ratio. select_good_instance (which calls this once per candidate seed during instance selection) benefits directly -- this is what made screening thousands of candidates at larger n_majorana impractically slow before.
• Real bug fixed: DenseSVSimulator.measure()'s JAX-backend probability/collapse computation was reading and collapsing the WRONG qubit's marginal whenever qubit_idx != n-1-qubit_idx. Verified directly: applying X to qubit 0 of a 2-qubit register, then measure(0), returned 0 instead of 1. Root cause: the JAX branch reshapes the statevector to a [2]*n tensor and uses jax.numpy.moveaxis -- the same indexing scheme apply_gate_1q uses (moveaxis(sv_nd, qubit, -1), qubit axis == qubit index directly, extensively tested elsewhere in this suite) -- but measure() was instead moving axis phys = n-1-qubit_idx, which is only correct for the separate NumPy branch's flat/stride-based indexing, not this reshape-based one. Found while investigating an unrelated review claim about measure()'s RNG choice -- the test suite's own conftest.py had been silently shadowing the real (broken) implementation with a separately hand-maintained, already-fixed copy for an unknown amount of time, via a full-method monkeypatch applied at test-collection time; removed that shadow copy so the test suite now actually exercises the shipped code.
• Real bug fixed: u2 (a 1-qubit, 2-parameter gate) crashed with a TypeError in DenseSVSimulator.run_circuit (the eager path) -- its dispatch used to branch purely on total argument count, and u2's 3-element args tuple (qubit, phi, lam) collided with cp/crz's own 3-element shape (q1, q2, theta), so u2 was mis-dispatched as a 2-qubit gate and its 2-parameter lambda was called with only 1 argument. Now dispatched by gate name (gates._TWO_QUBIT_PARAMETRIC_GATES), not argument count.
• Silent-drop-instead-of-raise fixed in circuit_to_energy_fn's JIT template builder: any gate name without a GATE_IDS entry (e.g. u2/u3, whose 2-3 independent parameters this template's one-parameter-per-row shape can't represent) used to be silently skipped from the traced circuit, giving a silently WRONG energy/gradient with no error. Now raises a clear ValueError naming the unsupported gate.
• mps.MPSSimulator._svd_truncate's eager path now uses the already-existing, already-verified _vectorized_chi_search instead of a host-syncing Python while loop that re-computed the Jensen-Shannon divergence from scratch on every bond-dimension increment. The vectorized replacement was already written and used by the JIT path, and already verified (0 mismatches across 171 real _svd_truncate calls, 4 configurations including the budget-violation fallback) -- it just was never wired into the eager path itself until now.
• DenseSVSimulator.measure() gains an optional jax_key parameter for explicit, seedable randomness via jax.random.choice, matching registry.NoiseModel.apply_to_sv's own established jax_key convention -- independent of NumPy's global RNG state. Default (None) keeps the original np.random.choice behavior unchanged.
• _prepare_finite_beta_tfd_sv no longer constructs a second DenseSVSimulator just to apply one swap gate -- the message-injection SWAP is exactly an axis-swap on the statevector reshaped to [2]*n_full (the same MSB-first indexing apply_gate_1q/measure() use), verified bit-identical to the simulator-gate version directly. Real overhead removed from every point of a (beta, mu) sweep (find_delta_beta_bands calls this once per grid point).
• dashboard_core.vqe.run_vqe's two assert n_params == ... sanity checks replaced with raise ValueError -- assert is stripped entirely under python -O, so a UCCSD/hardware-efficient parameter-count desync with circuit_to_energy_fn would have silently propagated into a shape mismatch far downstream instead of failing here with a clear cause.
• dashboard_core.vector_healing's ia_utils.vector_healing import is no longer unconditional -- it ships in the same distribution as dashboard_core so this shouldn't normally fail, but ia_utils.vector_healing's own dependency chain (dense_evolution.healing, which needs JAX) could still fail transitively, previously taking down the entire dashboard_core package at import time for an unrelated gap. Deferred to run_vector_healing's call site with a clear ImportError instead.
• dashboard_core.engine._to_qiskit_bit_order's O(2n_qubits) index permutation is now cached per n_qubits** (@lru_cache, read-only array) instead of rebuilt from scratch on every call -- real cost for circuits re-run repeatedly at the same qubit count (a fixed molecule/preset re-run with different parameters, the common case).
• mcp_server/server.py's _request now reuses a single httpx.AsyncClient instead of opening a fresh one (TCP handshake) per tool call, real overhead for an MCP session calling many tools in a row. Cache key is (_TEST_TRANSPORT identity, KERNEL_URL), correctly invalidating across the test suite's transport/URL swaps -- verified by rerunning the full mcp_server test suite, not just assumed safe.
• run_wormhole_protocol / _finite_beta_layout_precomputed now check available RAM before building their dense 2**n_full x 2**n_full H/V matrices (the same dense_evolution.chunk.SafeMemoryGuard anti-OOM guard dashboard_core.engine already uses elsewhere) -- a large n_majorana used to be an unhandled OOM crash instead of a clear, actionable MemoryPressureError. Verified directly: n_majorana=8 unaffected (exact same result as before), n_majorana=24 now raises a clear error instead of trying to allocate ~1 TB.
• 35 new/updated tests across tests/test_wormhole.py, tests/test_simulator.py, tests/test_autodiff.py, tests/test_dashboard_engine.py, tests/test_dashboard_vector_healing.py (new file), and tests/test_mcp_server.py; full suite passes with zero regressions.

v8.1.52

• MCP Registry ownership verification marker added (<!-- mcp-name: io.github.tatopenn-cell/dense-evolution -->, hidden HTML comment right after the ASCII banner) -- required by the official MCP Registry to verify this PyPI package's ownership before dense_evolution_mcp can be published there. No functional change; this version exists solely so the marker is present in the README rendered as this release's PyPI description (PyPI descriptions are fixed per version, so the marker had to ship in a new release rather than editing an already-published one).

v8.1.51

• trotter_evolve_ops gains order=2 (Strang/symmetric product formula) alongside the existing default order=1 -- quadratically more accurate for the same n_steps (verified: infidelity drops ~16x per step doubling vs. order=1's ~4x, against scipy.linalg.expm), at 2x gates/step. Useful anywhere gate count directly limits circuit noise.
• dashboard_core.qmmm.run_md_trajectory now catches a diverging MD trajectory early: raises a clear RuntimeError if two atoms end up closer than a physically-motivated 0.3 Å floor after a step, instead of silently feeding a near-collided geometry into Hartree-Fock (which diverges rather than failing informatively) -- the real failure mode of a too-large dt_fs with light atoms. The check (_assert_no_nuclear_collision) lives at the real-simulation boundary in run_md_trajectory, not the bare md_step primitive.
• Real bug fixed: DenseSVSimulator.run_batch_jit's initial statevector was hardcoded to complex128 regardless of self.dtype/use_float32, silently ignoring the instance's own configured precision on every VQE-gradient-batch call -- a separate instance of the same bug class run_circuit_jit already had a documented fix for. Now derives from self.dtype, matching the rest of the JIT path.
• 124 tests pass across the three affected modules, all new behavior covered by new tests, no regressions.

v8.1.50

• New: reintegrated vector healing (dense_evolution.healing's Phi-Trigger predictive-healing primitives, via ia_utils.vector_healing.enhanced_dense_healing_hybrid) into the kernel and MCP server -- implemented and tested since before the dashboard_core rebuild, but unreachable from any user-facing path until now. dashboard_core/__init__.py's own docstring had flagged this as pending ("will be reintegrated selectively once this base is solid").
  • New dashboard_core.vector_healing: run_vector_healing (+ VectorHealingResult), a thin wrapper mirroring mitigation.py's shape -- per step of an (n_steps, dim) sequence, a Phi-Trigger decides whether the change from a local baseline looks like genuine dynamics (kept) or static noise (replaced by the local median); NaN/Inf entries are always sanitized first regardless.
  • New Composer kernel endpoint: POST /api/vector_healing.
  • New dense_evolution_mcp tool: dense_evolution_vector_healing. Bringing the tool count to 21.
  • Tests at both the kernel (TestClient) and MCP (ASGITransport) layers verify a genuine outlier vector gets replaced by the local median, and that malformed input (wrong shape) returns a 400 rather than a raw traceback.
  • docs/api/healing.md gained real prose (was a bare mkdocstrings directive before) explaining the primitives, the applied layer, and the reintegration path -- plus an honest note that mitigation.py's other healing-adapted branch (zero_noise_extrapolation's sigma_at_base_noise) is a separate, still-unwired follow-up, not silently conflated with this change: calculate_advanced_sigma (the usual source of a real sigma_at_base_noise value) needs kappa/H/Psi/Omega_sync/tau_K inputs whose provenance in a ZNE context isn't yet designed.

v8.1.49

• New: real traversable-wormhole-inspired quantum teleportation (Gao-Jafferis-Wall theory, arXiv:2604.10090), on a binary sparse Sachdev-Ye-Kitaev (SYK) model -- reproduced as an actual verified simulation, not decoration: an earlier, discarded dashboard_core circuit used the right vocabulary (SYK scrambling, a phase "kick") but ran on a single qubit register, which the no-signaling theorem forbids from ever showing the protocol's real sign-dependent signature, verified directly (identical results for either sign of the kick). The real recipe needs two coupled chaotic systems, a message injected via a separate reference-qubit pair, a real bilinear L-R coupling, and a mutual-information readout (not a single-qubit expectation value) -- see research/wormhole_syk.md for the full derivation and every verification step (Majorana anticommutation, SYK Hermiticity, Bell-pair/GHZ mutual information, the paper's own instance-selection criterion, Trotter-vs-exact convergence).
  • New dense_evolution modules: fermions.py (majorana_pauli_terms -- Majorana-fermion → qubit Jordan-Wigner mapping), entropy.py (partial_trace, von_neumann_entropy, mutual_information -- multi-qubit, MSB-first, distinct from dashboard_core/state_visuals.py's older single-qubit little-endian version), trotter.py (pauli_rotation_ops, trotter_evolve_ops -- real-time Hamiltonian evolution as an actual gate circuit, verified to fidelity 1.0 against scipy.linalg.expm and to converge smoothly to exact evolution as Trotter step count increases). Generic building blocks, not specific to the wormhole experiment -- promoted from the original research/wormhole_syk.py reproduction once verified, with real tests (tests/test_fermions.py, tests/test_entropy.py, tests/test_trotter.py) checked against known-exact cases (anticommutation relations, textbook Bell-pair/GHZ mutual information, exact expm), not just import smoke tests.
  • New dashboard_core.wormhole: the SYK/wormhole-specific logic (build_sparse_syk_terms, commuting_pair_count, select_good_instance, run_wormhole_protocol, run_wormhole_protocol_trotter) that stays genuinely specific to this experiment, built on the promoted dense_evolution utilities above -- mirrors how dashboard_core.hamiltonians/vqe are structured.
  • New Composer kernel endpoints: POST /api/wormhole_select_instance, POST /api/wormhole_teleportation (backend='exact'|'trotter') -- both real, tested end to end against a live kernel, reproducing the exact reference values from the original research reproduction (seed 61, t0=0.3, t1=0.60: I(mu=+12)=0.01326/0.01301 exact/Trotter, I(mu=-12)=0.01793/0.01821).
  • New dense_evolution_mcp tools: dense_evolution_wormhole_select_instance, _wormhole_teleportation, _wormhole_scan (batch t1 sweep, both mu signs, matching the _energy_scan pattern). Bringing the tool count to 20.
  • Real bug found and fixed: dense_evolution_wormhole_scan's first implementation ran every sweep point (and both mu signs within a point) concurrently via asyncio.gather, mirroring _energy_scan's pattern -- but this protocol's per-call cost is far higher (real exact diagonalization or a real Trotterized circuit over the full L+R+P+Q system, several seconds per call, not a cheap Hamiltonian lookup), and concurrent calls crashed the kernel process outright with a Windows access-violation inside concurrent numpy.linalg.eigh calls (a BLAS thread-safety issue under this protocol's heavier linear algebra). Found by actually running the batch tool's tests, not assumed safe by analogy to _energy_scan. Fixed by running sweep points sequentially; documented in the tool's own docstring so a sweep's real wall-clock cost (several minutes for 20 points) isn't a surprise.
  • 26 new dense_evolution unit tests, 14 new kernel/MCP end-to-end tests (all against the real, live kernel/simulator -- no mocked physics), pinned against the exact numeric reference values established during the original research reproduction.

v8.1.48

• New: dense_evolution_mcp, an MCP (Model Context Protocol) server for the Composer kernel (mcp_server/, dense-evolution[mcp] extra, dense-evolution mcp console subcommand) -- 17 tools, one per local_site/app/server.py endpoint plus dense_evolution_energy_scan, letting an MCP-aware agent (Claude Code, Claude Desktop, ...) drive circuit runs, molecular Hamiltonians, VQE, QM/MM forces, MD trajectories, and ZNE mitigation directly, without a browser. A thin adapter, not a reimplementation -- every tool calls the same kernel the published Composer page uses; local_site/app/server.py itself is untouched.
  • Molecule-name tools accept either a short id ("H2", "LiH", "HeH+") or the kernel's full descriptive catalog name, resolved from the live catalog rather than hardcoded -- found to matter after actually using the adapter for a real task (an H2 dissociation curve), where reproducing the full "H2 (Idrogeno) - R = 0.7414 A [equilibrio reale]"-style string across several tool calls was itself a source of friction.
  • New: dense_evolution_energy_scan -- ground-state energy at several geometries (e.g. a bond-length dissociation curve) in one call instead of one per point; points run concurrently, and a failing point (e.g. one needing too many qubits) is reported with its own error instead of aborting the rest of the scan.
  • Large arrays (statevector/probabilities) are truncated to their most significant entries, and circuit/histogram/Q-sphere/Bloch images are saved to disk and returned as file paths rather than inlined as base64, so a tool response stays usable in an agent's context instead of flooding it with a wall of numbers or an unreadable image blob.
  • Real bug found and fixed: mcp 2.0.0 (released days before this work, now what pip install mcp gets unpinned) renamed FastMCP to MCPServer and moved it from mcp.server.fastmcp to mcp.server.mcpserver -- passed every local test regardless because the dev environment had the older 1.28.1 cached, and only surfaced on CI's clean install (ModuleNotFoundError: No module named 'mcp.server.fastmcp'). Fixed by migrating the two affected import lines; confirmed directly against a real 2.0.0 install that the rest of the API (@mcp.tool(name=..., annotations={...}) with a plain dict, Pydantic model parameters, mcp.run(), decorated functions staying directly callable) is unchanged between the two majors.
  • 24 new tests (tests/test_mcp_server.py), 85.86% coverage on mcp_server/server.py (Codecov codecov/patch on this release: 100% of the diff) -- routed through httpx.ASGITransport straight into the real, in-process kernel app rather than a live subprocess, so every test still exercises the real DenseSVSimulator/PennyLane Hartree-Fock, no mocked physics, the same principle test_local_site_server.py already used for the kernel itself.
• Composer page: added request timeouts (api() had none at all -- a genuinely slow or stuck request left "...in corso" on screen forever, indistinguishable from normal progress; 30s default, 10 minutes for VQE/MD-trajectory calls, matching the "can take minutes" warning already shown for those) and a "Scan energia" panel computing a bond-length ground-state-energy curve in one click, reusing the existing geometry-generator helper instead of requiring "Compute ground state" to be clicked once per point by hand -- the same dissociation-curve gap fixed above for the MCP adapter, now fixed for human visitors too. Verified in a real headless-Chromium session (Playwright) against a live kernel: connects, computes a real 5-point curve with the correct minimum, button disables while running and re-enables after, validation errors display correctly, and a real VQE run still completes with no console errors.

v8.1.47

• run_circuit_jit / run_batch_jit renamed (from run_circuit_jit_beast_mode / run_parametric_batch_jit) is now on PyPI -- this was already on main/GitHub since right after v8.1.46 but held back from release; batched in here. The old names still work, emitting a DeprecationWarning.
• New: dense_evolution.harrison_tb -- dependency-free (numpy only) sp3 tight-binding Hamiltonian builder using Harrison's universal parameter table (one fixed set of 4 eta coefficients for every element pair, atomic term values from Harrison's Solid State Table). Builds single-bond dimers (sp3_dimer_hamiltonian) and full periodic zinc-blende crystals via Bloch sums (zincblende_hamiltonian) -- no PySCF/OpenFermion/SCF anywhere. Zero per-material setup cost, at the price of accuracy (real-material validation: Dense-Evolution-Discovery).
• New: dense_evolution.vhd_tb -- sp3s* tight-binding using Vogl-Hjalmarson-Dow (1983) material-specific fitted parameters (16 zinc-blende/diamond semiconductors), far more accurate than harrison_tb's universal table at the cost of a fitted parameter row per material. band_extrema_along_path scans a k-space line to find the true valence-band max / conduction-band min for indirect-gap materials (Si, Ge), where the minimum sits off-Gamma and reading only Gamma gives the wrong number. Found and fixed a Hermiticity bug in the reference implementation ported from while building this (Hac.conjugate() without transposing).

v8.1.46

• Composer ships: the interactive web UI (feature/composer) merged into main and is now published at tatopenn-cell.github.io/Dense-Evolution/composer -- a graphical/OpenQASM circuit editor running every circuit on the real DenseSVSimulator, plus real molecular Hamiltonians, VQE, and ZNE mitigation. The page is static; it talks to a local compute kernel (local_site/app/server.py) the visitor runs on their own machine via pip install dense-evolution[composer] -- never a shared server, nothing sent anywhere else.
• Every dashboard_core visualization is now Qiskit-free, not just optional-without-it: the circuit diagram, histogram, Q-sphere, and Bloch spheres are all native matplotlib/numpy (dashboard_core.circuit_diagram, dashboard_core.state_visuals). This closes three real macOS segfault sites v8.1.44's fix didn't cover (the Circuit-diagram panel still built a QuantumCircuit there) and removes qiskit/streamlit as hard dependencies of the Composer kernel entirely -- both were previously imported at module level in dashboard_core, so the kernel failed to even start without them installed, discovered by actually running the installer on a clean machine. Q-sphere/Bloch spheres are computed directly from the statevector's own reduced density matrices (partial trace), verified against known physics (a Bell pair's each qubit comes back exactly maximally mixed) and performance-tested up to 24 qubits (worst case ~7s, vs. qiskit.visualization.plot_bloch_multivector's ~252s at just 12 qubits -- the reason that panel needed a qubit-count skip in the first place, now removed).
• Two new real memory-safety gaps closed: dashboard_core.mitigation's two ZNE panels and dashboard_core.hamiltonians.build_molecular_hamiltonian's dense diagonalization never checked SafeMemoryGuard before allocating (unlike engine.py, which always did) -- the density-matrix ZNE variant and the Hamiltonian's eigvalsh are both quadratically worse than a plain statevector at the same qubit count, and the Composer's own geometry generators let a visitor build an arbitrarily long atom chain with no smaller natural ceiling. Both now guard, sized for what they actually allocate.
• dense-evolution console script + [composer] extra: dense-evolution serve starts the local kernel; dense-evolution offline-composer [DEST] downloads the real published Composer page (not a hand-maintained copy) for use with no internet, preserving its real relative asset layout. Full installers for Windows/macOS/Linux (installer/) install the kernel, optionally download the offline copy, and optionally add Desktop/Start Menu-or-app-menu/autostart shortcuts for both the online and offline entry points -- reversible via matching uninstallers. All of it verified by actually running the installer end-to-end on a real machine (not just reading the code): found and fixed a real bug in the offline downloader (it tried to fetch navigation <link> tags pointing at other pages, not real assets) this way.

v8.1.45

• dashboard_core.vqe.run_vqe now optimizes both ansatz families entirely on dense_evolution's own engine -- dense_evolution.autodiff.circuit_to_energy_fn (JAX-differentiable) plus a hand-rolled Adam loop, no PennyLane device/QNode/optimizer involved in the optimization itself anywhere in this module. Hardware-efficient was a direct fit (its RY/CX ansatz is plain OpenQASM). UCCSD was not: PennyLane's own decomposition of qml.UCCSD reuses each of the molecule's few real weights across several RX/RZ gates per excitation (the Trotter exponentiation of that excitation's Pauli-string terms), while circuit_to_energy_fn treats every parametric gate occurrence as an independent free parameter. Solved with an affine parameter expansion (full_gate_values = baseline + expansion_matrix @ real_weights) derived by directly probing PennyLane's own decomposition at zero and at each basis weight vector -- verified to reproduce PennyLane's own reported energy to floating-point noise (2.5e-14) for arbitrary weight vectors, and composed with circuit_to_energy_fn this stays JAX-differentiable in the small real weight vector by ordinary chain rule, so the same Adam loop optimizes it. PennyLane's only remaining role anywhere in this module is the real Hartree-Fock + Jordan-Wigner mapping itself (dashboard_core.hamiltonians), not something worth reimplementing. Re-verified end-to-end against H2: hardware-efficient converges to -1.13726 Hartree (exact -1.13727), UCCSD to 6e-6 Hartree from exact.

v8.1.44

• Added: pauli_hamiltonian_to_matrix(terms, n_qubits) -- builds the real dense Hermitian Hamiltonian matrix for a weighted sum of Pauli strings (sum_i coeff_i * P_i, each P_i a Kronecker product of per-qubit Pauli matrices), the explicit-matrix counterpart to pauli_sum_expectation (which deliberately never builds it). Verified against qml.matrix() for H2/HeH+/H3+/LiH (identical matrix and ground-state energy, not just close) and against an independent brute-force numpy.kron reference across 50 random multi-term Hamiltonians.
• Reintegrated dashboard_core onto main (previously moved off for a ground-up rebuild) with real molecular quantum chemistry built on top of it: real molecular Hamiltonians (PennyLane Hartree-Fock, Jordan-Wigner/Bravyi-Kitaev mapping -- verified spectrum-identical, as it must be -- catalog of H2/HeH+/H3+/LiH/H2O, H2O using a real frozen-core active space to stay at 12 qubits), real VQE (hardware-efficient and UCCSD ansätze, Adam + adjoint differentiation on lightning.qubit; UCCSD's decomposed circuit verified to reproduce PennyLane's own reported energy to 1e-14 when executed independently on dense_evolution), real Hamiltonian mixing (weighted sum of two same-qubit-count molecules), and real Zero-Noise Extrapolation (both scalar Pauli-expectation and density-matrix variants, each an ensemble average over many stochastic noise-channel draws, not a single trajectory).
  • Real bug found: dashboard_core.engine.run_circuit_from_qasm and both functions in dashboard_core.mitigation called QuantumCircuit.from_qasm_str -- a second, independent instance of the macOS QuantumCircuit segfault documented in v8.1.43, this time in a genuine production code path (the Composer's Circuit-diagram panel and its two ZNE panels), not just a test. Fixed two different ways depending on whether a real Qiskit circuit object was actually needed downstream: engine.py still needs one (for the diagram), so it now parses with dense_evolution's own QASMParser and builds the QuantumCircuit from the parsed gate tuples via plain method calls, never touching qasm2; mitigation.py never needed a Qiskit object at all, so it now runs straight off QASMParser + DenseSVSimulator.run_circuit, removing the risk entirely rather than working around it.
  • Real gap found: CI never installed pylatexenc, required by circuit.draw(output='mpl') -- failed identically on every OS (Ubuntu included), unrelated to the macOS issue above.
  • 41 new tests (test_dashboard_hamiltonians.py, test_dashboard_vqe.py, test_dashboard_mitigation.py, test_dashboard_system_limits.py) closing the coverage gap Codecov flagged right after reintegration (vqe.py 7.6%, hamiltonians.py 22.0%, mitigation.py 35.4%, system_limits.py 42.9%) -- real molecular ground-state energies checked against known values, real VQE convergence for both ansatz families, real noise-channel decay and fidelity-correction behavior, not mocks.
  • The Composer web app itself (local_site/, FastAPI + vanilla JS, the interactive frontend built on this dashboard_core) stays off main on feature/composer -- not yet ready to ship alongside the package release.

v8.1.43

• Added: seven standard-convenience functions Qiskit/PennyLane ship as everyday API that this package didn't: entangling_layer(n, pattern='linear'|'circular'|'full'|'star'|'brick'), pauli_expectation/pauli_sum_expectation (Pauli-string expectation values via O(dim) bit manipulation, never building the 2^n_qubits Hamiltonian matrix), ghz_state(n), sample_counts(sv, n_shots) (Qiskit-style get_counts()), statevector_fidelity(a, b) (the pure-state counterpart to uhlmann_fidelity, which only handles density matrices), qft(n, inverse=False, do_swaps=True), random_circuit(n_qubits, n_gates, ...), and draw_circuit(circuit, n_qubits) (plain-text diagrams). The first five were confirmed as real gaps, not speculative additions: the same patterns were found hand-duplicated with no shared, tested implementation across 20+ VQE/observable scripts and every test/experiment that preps a GHZ or Bell state, in this repo and the sibling Dense-Evolution-Discovery. qft/random_circuit/draw_circuit round out the pass for completeness (no internal duplication motivated them the same way).
  • Real bug found and fixed while verifying pauli_expectation: the first implementation assumed qubit q is bit q of the basis-state index. DenseSVSimulator actually stores qubit 0 as the most significant bit (confirmed empirically and matches conftest.py's own patched measure(): phys_q = self.n - 1 - qubit_idx). Fixed and re-verified — 500 random 4-qubit states cross-checked against brute-force dense Pauli matrices (numpy.kron), exact match (max error 0.00e+00). qft was verified the same way: max error 1.4e-15 against the analytic DFT matrix across 1-4 qubits, plus an exact QFT-then-inverse-QFT round trip.
  • Real bug caught before commit: draw_circuit's first version used Unicode box-drawing characters (─│●), which crashed print() on a default Windows console (cp1252 can't encode them). Switched to plain ASCII (-|*) — a diagram meant for a terminal or log file has to survive whatever console encoding the caller has.
  • 72 new tests across test_topology.py/test_observables.py/test_states.py/test_measurement.py/test_qft.py/test_random_circuit.py/test_drawing.py.
• Added: macos-latest to the CI test matrix (previously ubuntu-latest only), prompted by a direct question about macOS support that had never actually been verified. This surfaced two real, unrelated macOS-only process crashes, both fixed:
  • Qiskit itself segfaults on macOS CI runners. qiskit.circuit.QuantumCircuit.__init__ — the simplest possible call, QuantumCircuit(3) — reproducibly crashed the whole process (SIGSEGV) on Python 3.10/3.11/3.12, macos-latest (arm64), deterministically at the same line every time. Not a Dense-Evolution bug: every Dense-Evolution-only test passed cleanly on macOS before hitting this file. First fix attempt (skipif on the test class) didn't actually solve it — qiskit = pytest.importorskip('qiskit') is a class-body statement, and pytest runs class bodies at collection time regardless of a skip marker on the class, so qiskit was still being imported into the process either way, and the crash just moved to a non-deterministic segfault during interpreter shutdown instead. Real fix: guard the class definition itself behind if sys.platform == 'darwin', so the class body never executes there at all; a pytest.mark.skip-decorated empty stub stands in for visibility. TestPennyLaneInterop, same file, unaffected either way.
  • A second, unrelated shutdown-time segfault, independent of Qiskit. Confirmed by the above fix: with Qiskit fully removed from the macOS process, the exact same class of crash (SIGSEGV, exit 139) still happened on Python 3.10/macos-latest — every one of 523 tests passing, coverage.xml already written, pytest's own summary already printed, then a crash a few seconds later during Python interpreter finalization. Points to native-extension teardown (most likely JAX/XLA's runtime shutdown on macOS ARM, a known category of issue unrelated to this package's own code). Fixed with a trylast pytest_sessionfinish hook in conftest.py that calls os._exit(exitstatus) on macOS right after pytest's own work — and pytest-cov's coverage.xml write — are done, bypassing the interpreter-finalization phase that was crashing. No-op on Windows/Linux.
  • CI now runs 6 jobs (2 OSes x 3 Python versions) instead of 3; all green.

v8.1.42

• Added: a full documentation site, tatopenn-cell.github.io/Dense-Evolution — MkDocs + Material, auto-deployed to GitHub Pages on every push to docs/**/mkdocs.yml/dense_evolution/** via .github/workflows/docs.yml. The full API reference (api/*.md, 11 module pages) is generated directly from this codebase's own docstrings via mkdocstrings (docstring_style: google), not hand-duplicated; the Changelog and License pages are single-sourced from this README and license.md via mkdocs-include-markdown-plugin so they can't drift out of sync. Two real bugs surfaced only by the strict-mode CI build, both fixed before the first deploy: a docstring bracket sequence in QASMCircuit.to_tuples misparsed as a broken markdown link by mkdocs-autorefs, and a Linux/Windows filesystem case-sensitivity mismatch (docs/LICENSE.md including ../LICENSE.md, but the tracked file is lowercase license.md) that only failed on the Linux CI runner, not locally.
  • First honest self-review pass (rereading the live site page by page rather than assuming it was finished) found and fixed 6 real gaps: the Getting Started Zero-Noise-Extrapolation example referenced undefined variables and couldn't actually be run as published; the dashboard command didn't mention app_dashboard.py only exists in a cloned checkout, not the pip package; there was no examples/tutorial page beyond the short Quick Start (added docs/examples.md — density-matrix ZNE healing, MPS for low-entanglement circuits, differentiable VQE, each adapted from already-tested code — experiments/matrix_healing_zne.py, test_mps.py, test_autodiff.py — not written fresh); related API pages had no cross-links (mitigation.md ↔ healing.md/registry.md, mps.md ↔ chunk.md/simulator.md); there was no favicon/logo (hand-authored docs/assets/favicon.svg, a qubit-orbit glyph in the site's own cyan accent); and there was no architecture diagram (added a Mermaid module-dependency graph to docs/index.md, traced from the real import statements in every dense_evolution/*.py file, not an idealized layering).
  • Second review pass found 3 more: API reference function signatures rendered as cramped single-line text because mkdocstrings needs Black or Ruff installed to format them (added ruff to the docs extras — confirmed via a before/after strict rebuild that signatures now render properly indented); this README's own ## ▍ Benchmarks section (real throughput/PennyLane-comparison numbers) had no path onto the site at all (added docs/benchmarks.md, single-sourced from this file); and CONTRIBUTING.md existed in the repo but wasn't linked from the site nav (added docs/contributing.md — also fixed two of its relative links, to license.md/SECURITY.md, to absolute GitHub URLs so they resolve correctly both on GitHub and once included into the docs site, the same class of case-sensitivity fragility as the earlier LICENSE.md bug).
  • Added: test_docs_examples.py, run in CI (ci.yml) on every push — locates each Python code block actually published in getting-started.md/examples.md by its section heading and executes it directly (not a hand-maintained copy), asserting on real output (ZNE fidelity improves, GHZ probabilities are exactly 0.5/0.5, VQE converges well below the Hamiltonian's mid-spectrum). A future signature change anywhere these examples touch now fails CI immediately instead of silently going stale until someone rereads the site by hand. Also brought CONTRIBUTING.md's own "Running tests" command back in sync with what CI actually runs — it had already drifted, missing four test files, before this release.
  • This README now links the docs site prominently (a docs badge alongside the existing CI/PyPI badges, plus a callout line right under "What It Is").

v8.1.41

• Added: test coverage tracking via pytest-cov ([tool.coverage.run]/[tool.coverage.report] in pyproject.toml, a dev extras group, a coverage step in CI uploading coverage.xml as an artifact -- codecov badge/upload would need a CODECOV_TOKEN the user sets up themselves, not done here). Real measured project-wide coverage, honestly characterized before writing anything: an initial pass found 84.1%, driven up to 94.4% (449/450 tests passing, one isolated failure confirmed to be the same RAM-pressure artifact already documented for TestChunkMultiPiece, not a regression) by closing genuinely untested code paths across dashboard_core/md_telemetry.py (39.8%→100%), dashboard_core/qasm_library.py (61.1%→100%), dashboard_core/simulation_runner.py (64.4%→87.6%), dense_evolution/chunk.py (63.6%→95.9%), dense_evolution/registry.py (84.9%→99.5%), and dense_evolution/parser.py (87.6%→97.4%). dense_evolution/simulator.py (72.5%→78.6%) is limited by a confirmed coverage-tooling artifact, not a real gap: DenseSVSimulator.measure() is already thoroughly tested (TestMeasurement, 5 pre-existing tests) but coverage/pytest-cov fails to trace it correctly inside this specific large test suite -- confirmed directly with an isolated coverage.Coverage() script (bypassing pytest entirely) that the method traces correctly on its own, so no duplicate tests were added for it. dashboard_core/interactive_panel.py (82.0%) was deliberately left as-is, out of scope -- it overlaps with the separate, larger, not-yet-started "rebuild launch_interactive_panel with full Streamlit parity" task.
  • Real bug found and fixed along the way: dashboard_core.simulation_runner.estrai_valore_puro silently returned 0 for any numeric string input (e.g. estrai_valore_puro("3.5") returned 0, not 3.5) -- every Python str has a .index() method, so hasattr(elemento, 'index') was true for any string, routing it into the "object with an .index attribute" branch before ever reaching the isinstance(str) numeric-parsing block below it; calling .index() with no arguments always raised TypeError, silently caught and falling through to 0. If the QASM parser ever handed this function a string-typed qubit index or parameter, it was silently read as 0 instead of the real value. Fixed by moving the isinstance(str) check to run first.
  • chunk.py's biggest apparent gap (~200 lines, the distributed multi-device kernel) turned out to be a measurement gap, not a test gap: it's already covered by TestChunkDistributed, which only runs under XLA_FLAGS=--xla_force_host_platform_device_count=8 in a separate pytest invocation (same as CI already does) -- combining both invocations' coverage data gave the real 95.9% number.
  • 61 new tests total across test_dense_evolution.py and test_dashboard_core.py.

v8.1.40

• Added: full jax.jit-compatible coverage for every function in dense_evolution.mitigation -- richardson_extrapolate_jit, zero_noise_extrapolation_jit (the predictive-healing branch), polynomial_extrapolate_jit, uhlmann_fidelity_jit, zne_density_matrix_jit. Each is a jit-safe _core (no np.iscomplexobj/np.asarray/float() calls on possibly-traced values -- those break jax.jit tracing) plus an unchanged eager wrapper, the same split already used by dense_evolution.mps's _jsd_vectors_jax/_jsd_vectors. Verified: each _jit variant matches its eager counterpart exactly; all compose correctly together inside a single outer jax.jit (the realistic use case -- several of these called in sequence inside a step function passed to jax.lax.scan, not each jitted in isolation). Real measured speedup on the full zne_density_matrix pipeline (not a single function): 4.5x-150x across 2x2-32x32 matrices, positive in every case tested.
  • Checked and rejected a suggestion (from the same external-AI source as v8.1.39's rewrite) to mark target_sigma_ideal static via functools.partial(static_argnames=...): calculate_delta_preemp already uses jnp.where internally, not a Python if, so it's trace-safe as a dynamic value -- marking it static would force a fresh XLA recompilation every time a caller varies it, with no benefit. Confirmed directly by testing both ways before deciding, not by assumption.
  • This closes out the density-matrix ZNE healing work for now. A further step -- wiring these functions into MPSSimulator so error mitigation can run on tensor-network-simulated circuits -- was scoped and intentionally deferred: it requires noise-channel support for MPS (doesn't exist yet, a large feature on its own -- MPO-based or trajectory-based), reduced (not global) density-matrix extraction via partial trace (also doesn't exist yet), and handling the multiple-noise-scale requirement ZNE needs, none of which reduce to "just call the existing functions." A global density matrix is the wrong target for large-qubit MPS use in the first place -- materializing a full 2^n x 2^n matrix defeats MPS's own reason for existing. Tracked separately, not started here.

v8.1.39

• Changed: project_to_physical/uhlmann_fidelity rewritten as fully vectorized, jax.jit-compatible JAX (no Python while/for loop over eigenvalues) -- the previous versions had a dynamic Python loop that isn't traceable, forcing a host round-trip on every call. project_to_physical now uses Euclidean projection onto the probability simplex (Held, Wolfe & Crowder 1974; also Duchi et al. 2008) applied to the eigenvalues -- a different, fully array-vectorized algorithm for the exact same convex projection problem Smolin-Gambetta-Smith's paper solves (unique global minimum, so any correct algorithm must agree). uhlmann_fidelity now computes Tr(sqrt(inner)) as the sum of inner's eigenvalues' square roots instead of reconstructing the full matrix square root. Both verified numerically identical to the previous versions (~1e-15 max difference on the SGS paper's own worked example and 30 random test matrices) and confirmed to actually compile and run under jax.jit. No behavior change for any existing caller -- same inputs, same outputs, just usable inside a jitted pipeline (e.g. jax.lax.scan) going forward.
  • Originated as a suggestion from an external AI (Gemini), independently verified numerically before adopting -- same source also proposed reintroducing the predictive-healing coefficient perturbation (calculate_delta_preemp) for the density-matrix case as "the real improvement." That specific claim was rejected: it directly contradicts the already-measured result that the perturbation's effect is negligible (~0.14% coefficient shift even at a large observed coherence deviation, confirmed with a live numeric trace, not assumed) -- an external source getting a plausible-sounding architecture story right doesn't make an unverified empirical claim inside it right; each part was checked on its own.

v8.1.38

• Documented: zne_density_matrix's docstring extended with a broader honest finding beyond v8.1.37's original single-configuration result. experiments/matrix_healing_zne_sweep.py (new) sweeps GHZ states from 2 to 5 qubits across all 5 NoiseModel channels (depolarizing, bitflip, phaseflip, amplitude_damping, combined). First pass (3 seeds, K=150 trajectories, 60 runs) looked mixed -- 54/60 positive, mean delta +0.09, but apparently unreliable for phaseflip/amplitude_damping (small or net-negative deltas at some qubit counts). Investigated further before trusting it: richardson_extrapolate's 3-point Lagrange coefficients (3, -3, 1) amplify statistical noise in their inputs (sum of squares 19x a single raw measurement's variance), so an undersampled density-matrix estimate makes the corrected result noisy even when the correction itself is sound -- confirmed directly by re-running the same "failing" configurations at higher K (300-1200 trajectories, more seeds), which turned them consistently and strongly positive. Re-ran the full sweep properly (K=400, 5 seeds, 100 runs total): 96/100 positive, mean delta +0.12, every single (qubit count, noise channel) combination net positive on average, growing to +0.20-0.25 at 5 qubits for depolarizing/bitflip. The 4 remaining negative runs are small (worst -0.02), consistent with residual Monte Carlo noise, not a systematic failure. No code behavior changed -- this is a documentation update, but the earlier "unreliable for phaseflip/amplitude_damping" wording in an intermediate draft of this entry was itself wrong and has been corrected here before ever reaching PyPI.
  • zne_density_matrix's docstring carries the corrected numbers plus a practical caveat for callers: correction quality depends on rho_at_scales being a low-noise (large-enough-K) estimate to begin with -- an inherent property of Richardson-style extrapolation's noise amplification, not a bug in this function.
  • Also tested: whether more noise-scale points (4, 5, or denser spacing) improve exact interpolation further. They don't -- more points make Lagrange coefficients larger (worse with denser spacing, a Runge's-phenomenon-like effect), amplifying noise further: mean delta drops from +0.148 (3 points, the original choice) to +0.081 (5 points, same spacing) to -0.220 (5 points, denser spacing -- actively worse than not correcting at all on some channels).
• Added: dense_evolution.mitigation.polynomial_extrapolate -- least-squares polynomial extrapolation to zero noise, generalizing richardson_extrapolate. At exactly degree + 1 points it's mathematically identical to exact interpolation (verified to 1e-12); with MORE points it becomes an overdetermined fit that trades a little bias for real variance reduction instead of the exact interpolation instability above. zne_density_matrix now uses this (degree=2 default) instead of richardson_extrapolate -- at the standard 3-point setup this changes nothing (mathematically identical, all prior tests pass unchanged), but makes "pass more noise-scale points" safe instead of a trap.
  • Real, measured gain, fixed total measurement budget (experiments/matrix_healing_fixed_budget.py, the fair comparison -- splitting the same total number of Monte Carlo trajectories differently, not spending more): 3 points x K=400 (1200 total, classic 3-point ZNE) vs. 5 points x K=240 (1200 total, degree=2 fit) vs. 7 points x K=171 (~1200 total). 5 points matches or slightly beats the 3-point mean improvement (+0.150 vs +0.148) with 19% lower variance (std 0.050 vs 0.062) -- a free reliability gain at equal experimental cost. 7 points trades a little mean (+0.132) for 30% lower variance (std 0.043), a genuine tradeoff point.
  • Tested and rejected, for honesty: (1) applying zero_noise_extrapolation's existing predictive-healing coefficient perturbation (calculate_delta_preemp, originally designed for scalar coherence signals around target_sigma_ideal=10) to density matrices, using either matrix purity or Jensen-Shannon divergence (dense_evolution.mps._jsd_vectors) as the coherence signal -- no measurable effect even amplified 100x over its default strength. (2) Selecting the polynomial degree per-run via leave-one-out cross-validation on the noisy points themselves -- worse than a fixed degree (mean +0.113 vs +0.150, higher variance), because LOOCV on few noisy points is biased toward under-fitting. (3) Selecting degree via the same JSD coherence signal -- no exploitable correlation found between JSD and which degree actually performs best (degree 2 and 3 win about equally often across the whole measured JSD range). None of these are shipped; degree=2 fixed remains the best-tested default.

v8.1.37

• Added: dense_evolution.mitigation.zne_density_matrix/project_to_physical/uhlmann_fidelity -- Zero-Noise Extrapolation extended from scalars/vectors to full density matrices, for noisy simulations tracked as ρ rather than a single statevector. project_to_physical implements Smolin, Gambetta & Smith's "Maximum Likelihood, Minimum Effort" (2012, arXiv:1106.5458) eigenvalue-projection algorithm (transcribed and checked against the paper's own worked numeric example before use) to correct the raw richardson_extrapolate output on a matrix stack -- polynomial extrapolation across noise-scaled density matrices is not itself guaranteed to be a valid (positive-semidefinite) density matrix, even when every input was. uhlmann_fidelity is a validation-only utility (F(ρ_A,ρ_B) = (Tr√(√ρ_A ρ_B √ρ_A))², reduces to |⟨ψ_A|ψ_B⟩|² for pure states, verified directly) -- deliberately not accepted as an input anywhere in the correction path, keeping "the ideal state is a grading criterion, not something the algorithm gets to see" structural rather than a convention callers have to remember on their own (the general principle: an error-mitigation technique that needs to know the answer already isn't one).
  • Honest, measured result (experiments/matrix_healing_zne.py, reproducible): 2-qubit Bell state, NoiseModel depolarizing noise at base_p=0.05, scales 1x/2x/3x, a 200-trajectory Monte Carlo density-matrix estimate per scale, averaged over 4 independent random seeds -- raw noisy fidelity ~0.865, corrected (extrapolated + projected) fidelity ~0.947, a real improvement of ~+0.08, positive individually on every seed tested (range +0.060 to +0.106). This is one measured data point in one noise regime, not a general guarantee -- other noise models, circuits, or noise strengths are untested and may behave differently; the docstrings say exactly this, not more.
  • This formalizes an experiment built directly on top of v8.1.36's richardson_extrapolate complex-dtype fix -- the same experiment run before that fix gave an invalid, misleadingly negative result (corrected fidelity worse than raw) purely because the bug was silently discarding the density matrices' imaginary parts, not because the technique doesn't work.

v8.1.36

• Fixed: dense_evolution.mitigation.richardson_extrapolate (and zero_noise_extrapolation's healing-adapted branch) hardcoded dtype=jnp.float64 for expectation_values, silently discarding the imaginary part of complex input with only a low-signal ComplexWarning, no explicit error. Real inputs (the only case exercised by any existing caller) were unaffected, but any complex-valued caller -- e.g. extrapolating density-matrix entries, which are complex off-diagonal in general -- got a silently wrong, purely-real result. Found while building a density-matrix-healing experiment on top of this function; verified directly pre-fix (richardson_extrapolate([1+2j, 3+4j], ...) returned a purely real value, dropping real information). Fixed by picking values's dtype from the input itself (jnp.complex128 if np.iscomplexobj(expectation_values), else jnp.float64 -- identical behavior to before for every existing real-valued call site, verified: all prior tests pass unchanged).

v8.1.35

• Added: MPSSimulator.run_circuit_jit(ops) -- a jax.lax.scan-fused, @jax.jit-compiled whole-circuit execution path for MPSSimulator, which previously had zero @jax.jit anywhere in the file: every gate ran as an eager JAX call, and the adaptive bond-dimension search inside _svd_truncate was a Python while loop forcing a host-device sync on every 2-qubit gate. Measured directly on a 60-qubit/428-gate stress circuit (the same one used to originally diagnose this): 88.9s (eager) -> 0.74s (fused, steady-state post-compile), ~120x faster, now within range of Qiskit Aer's MPS backend (0.64s) on the same circuit -- same physics exactly (chi_used=16, budget_violations=0, avg_JSD=0.0000, matching the eager run's own summary).
  • The two root causes, quantified before fixing: (1) zero JIT fusion -- confirmed via direct grep, not assumed; (2) non-adjacent 2-qubit gates expand into a SWAP chain at runtime, multiplying the real SVD-bearing gate count 2.4x on the stress circuit (187 logical 2-qubit gates -> 451 real apply_gate_2q calls, counted directly).
  • New technique (no precedent for this specific problem in chunk.py's own earlier JIT fusion, issue #5, whose geometry never changes gate-to-gate): the bond-dimension search is now a single vectorized pass (JSD computed for every candidate truncation size at once via jax.vmap, replacing the incrementing while loop) over gamma/lambda tensors padded to a fixed max_bond size always, with the real bond dimension tracked as a traced scalar and everything beyond it zero-masked rather than dynamically sliced (jax.lax.scan's carry requires constant shape/dtype every step). Non-adjacent gates are expanded into their SWAP-chain-equivalent adjacent-only op sequence at Python pre-compile time instead of via runtime dispatch, mirroring chunk.py::_compile_multi_chunk_ops's "all gate-identity branching happens before tracing starts" principle.
  • apply_gate_1q/apply_gate_2q/_apply_nonlocal_2q (the eager path) are unchanged and still available -- run_circuit_jit is a new, additional entry point, not a replacement. Explicit, intentional trade-off: the fused path pads every gamma/lambda to max_bond for the rest of the instance's lifetime after the call, trading this module's adaptive-memory benefit (its whole point for very large, low-entanglement circuits) for speed -- use the eager methods directly when memory, not speed, matters more.
  • Verified in 5 separately-checked stages, each against real data before moving to the next: (1) the vectorized bond-dimension search matches the eager while loop's (chi_new, jsd_val) exactly across 171 real cases from real circuits, including the budget-violation fallback; (2) the SWAP-chain pre-expansion matches the real runtime dispatch's exact call sequence across all 330 (q1, q2) pairs for 3 qubit counts, plus an end-to-end final-state replay check; (3) the fused kernel matches DenseSVSimulator on real entangling circuits (TVD < 1e-6) and matches the eager path bit-for-bit (fidelity 1.0 to machine precision) even under a genuine budget_violations truncation scenario, both dtypes; (4) entanglement_entropy/_bond_history/jsd_per_bond/truncation_errors/budget_violations end up populated identically to the eager path (machine-precision match), sourced from jax.lax.scan's stacked per-step diagnostics instead of Python list appends; (5) the real speed number above.
  • contract_to_statevector generalized (.squeeze(axis=0)/.squeeze(axis=-1) -> [0]-indexing) to work correctly on both the original unpadded boundary tensors (identical behavior, verified against the full existing test suite) and the new padded ones.

v8.1.34

• Fixed: QASMParser._eval_param silently returned 0.0 for any gate-parameter expression it couldn't evaluate -- a malformed expression like rx(pi * / 2) q[0]; parsed successfully and silently produced rx(0.0), a different, valid circuit, with no signal a typo had happened. Found via an independent code-review report, reproduced directly (ast.parse('pi * / 2', mode='eval') itself correctly raises SyntaxError -- the bug was a blanket except Exception: return 0.0 around it, added when the previous raw-eval() code-execution vulnerability was fixed, that swallowed genuine syntax errors along with rejected/malicious expressions). Now raises ValueError instead, for both cases -- malformed expressions and disallowed/malicious ones alike (still structurally blocked by the same AST node-type whitelist either way, just explicit about it instead of silent). Same class of silent-wrong-behavior issue already fixed for unknown gate names and mismatched parameter batches (v8.1.27, issues #4/#6). 2 existing security tests (test_eval_param_blocks_sandbox_escapes, the full-parse exploit test) updated to expect the raised exception instead of a silent 0.0; 2 new regression tests added for the originally-reported malformed-expression case.

v8.1.33

• Fixed: MPSSimulator._apply_nonlocal_2q silently swapped which qubit acted as gate-argument-1 vs gate-argument-2 whenever a non-adjacent 2-qubit gate (abs(q1-q2) != 1) was called with q1 > q2 -- e.g. apply_cx(ctrl=3, tgt=1) -- because the SWAP chain always ends up applying the gate at (min(q1,q2), min(q1,q2)+1) regardless of the caller's original argument order. For an asymmetric gate like CNOT this silently applied the wrong gate (control/target inverted) with no error or warning. Found via an independent code-review report, reproduced directly before trusting it: building a 4-qubit GHZ state via H(0), CX(0,3), CX(3,1), CX(1,2) gave fidelity 0.25 against the exact GHZ state ((|0000⟩+|1001⟩)/√2 instead of (|0000⟩+|1111⟩)/√2). Fixed with the same q1>q2 normalization apply_gate_2q's adjacent-qubit branch already used (transpose the gate's tensor axes, swap q1/q2) applied before the SWAP chain runs -- same fidelity check now reads 0.9999999657714559. Affects apply_cx/apply_cz/apply_swap/apply_ccx for any non-adjacent qubit pair called in decreasing order, reachable from dashboard_core's engine='mps' option on any QASM circuit with such a gate. 6 new regression tests in test_mps.py (direct repro, cross-check against DenseSVSimulator, non-adjacent unordered-control Toffoli, both float32/float64).
• Checked, not changed: the same external report also flagged MPSSimulator.get_top_k_probable_states's amplitude summation as a potential bug -- independently re-verified against the exact contraction (matches to machine precision) and against the module's own documented history of already fixing exactly this class of bug. No live issue found. Its performance observation (the while loop in _svd_truncate isn't jax.jit-compiled) is real but is a speed question, not correctness, and is deliberately out of scope here.
• Added: dashboard_core.run_md_telemetry now computes real molecular-dynamics-style telemetry (exact phase evolution under the selected diagonal Hamiltonian, plus dense_evolution's own NoiseModel driving a physically-grounded thermal-noise channel) whenever a compatible Hamiltonian and the circuit's current statevector are supplied, instead of always returning the synthetic placeholder data (run_md_simulation_dummy, documented as a placeholder since it was first written) that shipped every prior version. Falls back to the same labeled mock when no compatible Hamiltonian is active -- the result now carries df.attrs['is_real']/df.attrs['note'] so callers (and the UI) can show honestly whether a given MD panel is real or a demonstration, rather than presenting synthetic numbers as if they were physics. Energy/entropy/purity are all genuinely computed (purity via an ensemble-averaged density matrix, exact given the ensemble -- every LIBRERIA_HAMILTONIANE entry is ≤6 qubits, so this stays cheap). Wired into both ui_pages/quantum_simulator.py (Streamlit) and the new interactive panel below with a visible "DATI REALI" / "MOCK" badge on the MD tab.
• Added: dashboard_core.launch_interactive_panel -- a full ipywidgets-based interactive dashboard for Colab/Jupyter, built directly on dashboard_core's existing functions (not a port of the old legacy/dash.py notebook export). Same panels as the Streamlit page (Overview, Fisica Stato, Mosaico, VQE Results, MD Results, Performance, 3D Helix, Hamiltonian, Mitigation (ZNE)) and the same sidebar controls (circuit source, engine, noise, ZNE/predictive healing, VQE, custom Hamiltonian, MD), driven by ipywidgets instead of Streamlit's rerun model -- stays inside a single notebook cell's output, no external tunnel/link. Requires the dashboard extra's ipywidgets>=8.0.0 (now included in that extra).

v8.1.32

• Added: dashboard_core.mitigation_runner.run_mitigation_sweep/dashboard_core.mitigation_panel.build_panel_mitigation -- Zero-Noise Extrapolation and predictive healing, wired into the Streamlit dashboard as a real feature for the first time (dense_evolution.mitigation/dense_evolution.healing existed in the core package but had zero references anywhere in the dashboard before this). Runs the active circuit at 3 noise scales (1x/2x/3x the sidebar's noise probability) and extrapolates to zero noise via zero_noise_extrapolation, reused exactly as-is -- no reimplementation of the Richardson/healing math in the dashboard layer. New sidebar section ("🩹 Error Mitigation (ZNE)") and a new "Mitigation (ZNE)" tab showing fidelity-vs-noise-scale and ideal/raw/ZNE-corrected probability overlays; the healing-adapted path's coherence signal (sigma_at_base_noise) reuses the shot-noise binomial sigma already computed and shown elsewhere in the dashboard (build_panel_overview's NISQ Shot Histogram) as a pragmatic proxy, documented as such rather than presented as a first-principles derivation.
• Fixed: dense_evolution.mitigation.richardson_extrapolate raised ValueError: Incompatible shapes for broadcasting whenever expectation_values[i] was itself array-valued (e.g. a full probability distribution per noise scale, not a bare scalar) -- found building the panel above, where each noise scale's "expectation value" is naturally a whole probability vector. Root cause: stacking expectation_values via jnp.asarray and multiplying by the (n,)-shaped Lagrange coefficients relied on JAX's default trailing-axis broadcast alignment, which pairs the coefficients against the last axis of the stacked array instead of the leading "one row per noise scale" axis. Fixed by reshaping the coefficients to broadcast against the leading axis explicitly and summing over axis=0 -- a no-op reshape for the pre-existing scalar case (verified: all prior scalar-input tests pass unchanged), now also correct for vector/array-valued inputs.
• Fixed: dashboard_core.run_simulation's seed parameter only ever reached np.random.seed() (shot sampling) -- for a JAX statevector (the normal case), the actual noise channel applied via NoiseModel.apply_to_sv was never given rng=/jax_key=, so it silently fell back to OS-entropy randomness regardless of seed. Two calls with the identical seed produced different noisy results. Found as a flaky test (run_mitigation_sweep's 3-noise-scale sweep, same seed passed to each scale, expected -- and needed, for a meaningful extrapolation -- the same underlying noise realization scaled by p, got a fresh random one each time). Fixed by passing rng=np.random.default_rng(seed) explicitly to apply_to_sv.
• Refactor: dashboard_core.py (1900-line single file) split into a package (dashboard_core/: qasm_library, hamiltonians, simulation_runner, vqe_engine, md_telemetry, plot_theme, metrics, panels, helix_3d, mitigation_runner, mitigation_panel, provenance) behind a backward-compatible __init__.py façade re-exporting the same public surface -- import dashboard_core as dc and every dc.xxx call site unchanged, verified via the existing test suite passing identically with zero test-file edits. _series_plot/_series_enhanced/_energy_enhanced (three near-duplicate time-series plotting functions, _energy_enhanced duplicating _series_enhanced's logic inline instead of calling it) unified into one parameterized _series_plot. Hardcoded color literals in build_panel_fisica/vqe_results/md_results/performance that exactly matched an existing plot_theme.C value now reference it instead of repeating the literal -- zero visual change, by construction; near-miss shades (close but not identical to a C[...] value) deliberately left alone rather than forced onto the "closest" key, which would have been a small but real, unauthorized color drift.
• Also fixed: .github/workflows/ci.yml never ran test_mitigation.py or test_mps.py.
• Refactor (ui_pages/, repo-only, not part of the pip package): the gradient header banner, the "run → session_state → guard → render" early-return pattern, and the neutral AI-shield metadata dict were each copy-pasted across 2-3 of quantum_simulator.py/vector_healing.py/quantum_scars.py/ai_middleware.py instead of shared. New ui_pages/components.py helpers (render_page_banner, render_run_guard, render_matplotlib_figure) and AI_SHIELD_NEUTRAL_META replace them -- same visuals, one place to change instead of three. Fixes, as a side effect, three independently-drifted hardcoded version numbers in the page banners (v8.1.9/v8.1.7/v8.1.22) plus a fourth in app_dashboard.py's own st.set_page_config/docstring -- all four now read dense_evolution.__version__ instead of a stale literal. Verified: existing test_ai_middleware.py/test_quantum_scars.py pass unchanged (22/22); all ui_pages modules import cleanly; the actual Streamlit server started and served all 3 page routes with no server-side exceptions in the log (no automated UI test exists for this layer, per the pre-existing documented gap -- this is the closest verification available without a browser screenshot tool in this environment).

v8.1.31

• Changed: dashboard_core (the compute/panel layer behind the Streamlit dashboard) is now part of the installable package (pyproject.toml's packages), not repo-only -- pip install dense-evolution[dashboard,jax] alone now gives import dashboard_core as dc with the full 53-circuit QASM library and every panel builder, no git clone required. Superseded within the same release by v8.1.32's package split (dashboard_core.py → dashboard_core/) -- the packaging mechanism changed from a single py-modules entry to a real package directory, but the end result (pip install alone is sufficient) is unchanged.

v8.1.30

• Added: Chunk.run_chunk_distributed -- dispatches the multi-chunk kernel across a real JAX device mesh (jax.shard_map + jax.lax.ppermute) instead of one process's RAM, one physical chunk per device (issue #1, v1 scope: jax.device_count() >= num_chunks). Cross-chunk gate mixing becomes point-to-point communication via ppermute, keyed on the fixed XOR-stride pairing between chunk indices -- the same pairwise-exchange pattern real distributed statevector simulators use; gates entirely local to a chunk, or with a chunk-select control and a local target (decidable from a device's own chunk index alone), need no communication at all. Verified for correctness against DenseSVSimulator on simulated multi-device CPU (XLA_FLAGS=--xla_force_host_platform_device_count=N) across all 6 gate/qubit-location cases individually, randomized mixed circuits at num_chunks in {4, 8}, and both dtypes -- CI now runs these in a dedicated step with 8 simulated devices (they skip cleanly on a single-device run). Real GPU-cluster network performance is not and cannot be measured in a single-device CI environment -- honest scope: this validates the sharding/communication logic is correct, not real multi-GPU throughput.
• Fixed while building it: the ppermute permutation for each chunk-select qubit was built inside a Python list comprehension with the loop variable referenced directly in the lambda body -- classic late-binding closure bug, every branch silently used the last qubit's stride regardless of which was actually selected at runtime (only the branch for the last-iterated qubit happened to come out correct, which is exactly the failure pattern that surfaced it: q0/q1 wrong, q2 right, on a 3-chunk-select-qubit circuit). Fixed by binding the fully-precomputed static perm list as a default argument, evaluated eagerly at lambda-creation time instead of looked up by reference at call time.
• Also fixed: .github/workflows/ci.yml never ran test_mitigation.py or test_mps.py -- both existed and passed locally but had never actually executed in CI. Added to the main test run.

v8.1.29

• Added: dense_evolution.NoiseSpec -- a JAX PyTree (model/qubits static, p/jax_key as leaves, registered via jax.tree_util.register_pytree_node) that circuit_to_energy_fn's energy_fn now accepts as a fourth noise= argument, applying NoiseModel.apply_to_sv natively inside the same traced computation as theta (issue #8, scoped up from #7's narrower fix). Removes the need for an external, Python-side noise-application step and manual PRNG key bookkeeping around a training loop -- jax_key is a pytree leaf, so it flows through jax.jit/jax.grad/jax.vmap/jax.lax.scan the same way any other JAX array does, with no OS-entropy fallback (reproducibility is structural, not opt-in). Verified: reproducible from the same key, energy differs from the ideal circuit under nonzero p, gradient w.r.t. theta flows correctly through the noisy pipeline, jax.vmap over a batch of independent keys works with no external Python loop, jax.jit-wrapped result matches eager evaluation exactly.
• Fixed: found while wiring the above -- NoiseModel.apply_to_sv's if model == 'ideal' or p <= 0.0: return sv early-exit raised TracerBoolConversionError as soon as p became a traced value (e.g. a NoiseSpec leaf under jax.jit) -- exactly the case #8 asked to enable. Fixed with a targeted try/except around only the p <= 0.0 optimization: every channel's math already reduces to a no-op at p=0 (fire = r < p is always False), so skipping the shortcut and falling through is still correct, it just loses the eager-mode fast path when p can't be checked concretely.
• Note: noise.p is technically a differentiable pytree leaf, but the gradient through it is ~0 almost everywhere in practice -- the existing channels sample via a hard threshold (fire = r < p), not usefully differentiable without a smooth relaxation (e.g. Gumbel-softmax). Not addressed here, out of scope for what #8 asked (removing the state/key workaround, not making noise strength itself gradient-optimizable).

v8.1.28

• Note: v8.1.27 was published to PyPI from a stale local checkout that predated the mitigation.py module and the #4/#6/#7 fixes below -- the installable v8.1.27 package on PyPI does not contain them, despite this changelog. PyPI doesn't allow re-uploading files under an already-published version, so this release exists specifically to ship the real content. If you're on 8.1.27, upgrade to 8.1.28 -- don't rely on 8.1.27's changelog matching what you actually have installed (same situation as v8.1.15, see that entry below).

v8.1.27

• Added: dense_evolution.mitigation -- a Zero-Noise Extrapolation orchestrator (richardson_extrapolate, zero_noise_extrapolation, both exported from package root) using the field's standard ZNE vocabulary, composed on top of healing.py's existing primitives rather than duplicating or renaming them. Motivated by the ZNE+predictive-healing combination previously existing only as hand-written logic (_static_richardson/_adaptive_healing_richardson) inside a downstream repo's test file, calling calculate_delta_preemp as one ingredient with no reusable, standard-named entry point in the package itself -- undiscoverable by name for anyone (human or AI) reading dense_evolution looking for "ZNE". richardson_extrapolate generalizes to N arbitrary noise factors (verified: reduces exactly to the textbook (3, -3, 1) 3-point coefficients at noise_factors=(1,2,3), and is exact on synthetic linear data); the healing-adapted path is scoped to exactly 3 noise factors -- the only case it has been derived and verified against (cross-checked numerically against the original 3-point formula) -- and raises NotImplementedError rather than silently generalizing an unverified formula for other point counts.
• Breaking: run_circuit/run_circuit_jit_beast_mode/run_parametric_batch_jit now raise ValueError on an unrecognized gate name instead of silently dropping the gate (issue #4). Verified pre-fix: run_circuit_jit_beast_mode([('h', 0), ('ch', 0, 1), ('x', 2)]) executed only h/x, ch vanished with no error or warning -- a typo in a gate name ('crx' instead of 'crz') used to silently run a different circuit than the one written. Anyone relying on the old silent-skip behavior will now get an explicit error instead -- there is no legitimate use case for a gate name silently doing nothing.
• Breaking: run_parametric_batch_jit now validates parameter_batch.shape[1] against the actual number of parametric gates (rx/ry/rz/p/u1/phase/cp/crz/cphase) in base_circuit, raising ValueError on a mismatch instead of letting JAX's default out-of-bounds indexing clip silently (issue #6). This is the same positional-slot contract responsible for two independently-discovered corrupted-results bugs in a downstream repo (Dense-Evolution-Discovery v2.1.0): a literal-float rotation gate still consumes a column, it is never exempt, and a grid built assuming otherwise used to produce a plausible-looking but wrong statevector with no signal that anything was off.
• Fixed: NoiseModel.apply_to_sv used to silently ignore rng whenever sv was a JAX array, drawing from OS entropy instead -- a caller seeding rng = np.random.default_rng(42) for reproducibility got a different, non-reproducible result on every call, silently (issue #7). Verified pre-fix directly: two consecutive calls with the identical seeded rng and identical input diverged. Found while reviewing an end-to-end QML+noise+ZNE test script combining circuit_to_energy_fn, NoiseModel, and the new zero_noise_extrapolation under one jax.value_and_grad -- gradients did flow correctly through the whole pipeline (that part worked as intended), but the epoch-to-epoch loss instability in that script traced back to this, not to the optimizer or to mitigation.py. Fixed: when sv is a JAX array and jax_key isn't given explicitly, rng (if given) now derives the JAX key (rng.integers(...) seeds jax.random.PRNGKey) instead of being ignored -- a fresh, identically-seeded rng now reproduces the exact same sequence of keys across separate runs, matching the guarantee the NumPy path already gave. jax_key, when given explicitly, still takes precedence over a derived one. Making apply_to_sv itself composable inside a single jax.jit block (no internal Python-level branching or OS-entropy side effects) is a larger, separate redesign -- not done here, see issue #7 for the remaining scope.

v8.1.26

• Verified, no bug found: two areas flagged as untested in a prior RAM-constrained environment -- Chunk's genuine multi-chunk dispatch (num_chunks > 1) on a 2-qubit gate spanning the very first (chunk-select) and very last (local) qubit of the register, and QASMParser's handling of for-loops with an unresolvable bound (an undeclared bound variable, so _resolve_int_expr returns None) -- both confirmed correct. Closed the real test-coverage gap: 4 new tests in TestChunkMultiPiece (the long-range 2-qubit gate case, plus MemoryPressureError actually firing on simulated low RAM for both the num_chunks==1 and num_chunks>1 code paths -- previously only ever exercised indirectly, never asserted on directly) and 6 new tests in TestQASMForLoop (unresolvable for bound stripped cleanly with following code preserved -- verified via probability comparison, not just the op list -- while blocks, multiple unresolvable constructs in sequence, and a resolvable for-unroll immediately followed by an unresolvable if-strip).

v8.1.25

• Fixed: MPSSimulator._svd_truncate used to silently violate jsd_budget whenever max_bond was too small for the circuit's real entanglement -- the while jsd_val > self.jsd_budget and chi_new < max_possible loop exits with no signal once chi_new hits max_bond, even if jsd_val is still far above budget. summary()'s avg_JSD only reports the mean of the per-step local errors, not the accumulated global error, so it can read deceptively low while the final contracted state is badly wrong -- verified directly on an 8-qubit/15-layer entangling circuit with max_bond=2: TVD ~0.97 against DenseSVSimulator (a near-total mismatch) while avg_JSD read a reassuring-looking 0.0534. Added a budget_violations counter (incremented every time this happens, exposed in summary()) and a UserWarning on the first violation ("bond dimension capped at max_bond=..., jsd_budget=... not honored ... results may be unreliable") -- not an exception, so existing code that tolerates the tradeoff keeps working, but now with an explicit, checkable signal instead of a silently-optimistic average.

v8.1.24

• Fixed: dense_evolution.healing.calculate_phi_ab raised ValueError: Clip received a complex value when called with complex statevectors (e.g. sim.get_statevector()) -- jnp.dot(semantic_change, ipg_vector) is the bilinear (non-conjugated) product on complex arrays and stays complex, which then hit jnp.clip at the end of the function. Fixed by using jnp.real(jnp.vdot(...)) -- the correct Hermitian-inner-product real part, identical to jnp.dot for the real-valued inputs every existing caller already uses (ia_utils.vector_healing.enhanced_dense_healing_hybrid), and now also correct for genuinely complex input. Verified against a manual NumPy Re(vdot(...)) calculation on a case with nonzero imaginary amplitudes (H+S gates), not just the crash repro (H+CX alone never produces a nonzero imaginary part, so it only proved "doesn't crash," not "computes the right number").
• Fixed: ia_utils.vector_healing.median_healing/enhanced_dense_healing_hybrid emitted RuntimeWarning: Mean of empty slice whenever an input column was entirely NaN -- np.nanmean on an all-NaN slice returns NaN with a warning (silently caught and zeroed by the very next line, so the output was already correct, only the warning was noise). Fixed by pre-replacing whole all-NaN columns with 0.0 before calling nanmean, so it never sees an empty slice -- verified byte-identical output, zero warnings, in both functions (the preprocessing block was duplicated verbatim in each).
• Fixed: enhanced_dense_healing_hybrid's fallback_triggered metadata flag used to reflect only the internal Phi-Trigger heuristic classifying a step as "static", regardless of whether the input actually contained any NaN/Inf -- verified directly that a clean, uncorrupted random Gaussian array (no corruption at all) still came back fallback_triggered=True. Root cause: the heuristic is tuned for trajectories with real underlying dynamics (verified separately against a real noisy VQE run, where it correctly stayed quiet at low noise and fired at high noise) and mistakes pure structureless IID noise -- which has no coherent trend to recognize as "genuine change" -- for anomalous static behavior on nearly every step. fallback_triggered is now gated on the original input actually containing NaN/Inf (checked before sanitization) in addition to the fallback having fired -- the dashboard's "Fallback scattato" indicator will now only light up for genuine NaN/Inf corruption, not general noise-driven Phi-Trigger corrections (those corrections still happen internally, they're just no longer mislabeled as a NaN/Inf fallback).
• Docs: removed two README rows (kappa_stabilization, richardson_integration) describing functions that never existed in dense_evolution/healing.py (confirmed against the full 140-line file -- 7 functions plus MemoryReflectionEngine, neither name present anywhere), and corrected two code examples that still showed a median_fallback_threshold parameter on enhanced_dense_healing_hybrid that was removed from the actual function signature back when its corresponding UI slider was dropped (commit 69fc8a4) without updating the docs to match.

v8.1.23

• Added: MPSSimulator (dense_evolution/mps.py, re-exported from the package root) -- a JAX-backed Matrix Product State simulator with adaptive SVD-truncated bond dimension. Verified exact against DenseSVSimulator on entangling circuits (TVD=0). Selectable as a dashboard engine (Quantum Simulator page) for circuits up to 24 qubits; for larger low-entanglement circuits, get_probabilities_sampled/get_top_k_probable_states scale to hundreds of qubits without ever materializing a (2**n,) statevector.
• Fixed: large-qubit circuits submitted through the dashboard used to crash the whole Streamlit process (uncatchable OS-level OOM) instead of failing cleanly. They now route automatically through the existing Chunk anti-OOM wrapper, which raises a catchable, informative MemoryPressureError instead.
• Changed (breaking): JAX is now a required core dependency (dependencies, not optional-dependencies) -- pip install dense-evolution installs it by default, no [jax] extra needed anymore. Every simulator backend in this package already required JAX in practice; the previous try/except ImportError numpy-fallback path was never a real, maintained alternative and is no longer reachable (the numpy code itself is left in place for reference, just dead). If you were pinning an environment without JAX and relying on degraded-numpy behavior, this release will break that -- install dense-evolution<8.1.23 to keep the old behavior.

v8.1.22

• Added: ui_pages/quantum_scars.py — a new "Quantum Scars" dashboard page (app_dashboard.py's st.navigation), an interactive live demo of the PXP quantum many-body scar model (Rydberg blockade): builds H_PXP via sparse Pauli operators, exact-diagonalizes it (scipy.linalg.eigh, cached via st.cache_resource keyed on qubit count — the first use of that decorator in this codebase, since diagonalizing a dense 2**n_qubits matrix is genuinely expensive and depends only on that one slider), propagates a Néel initial state under real-time Hamiltonian evolution, injects real noise via NoiseModel.apply_to_sv, and lets you compare fidelity revival with no protection, a cheap constraint-subspace projection (no extra diagonalization needed — a combinatorial mask of which computational-basis bitstrings have no two adjacent 1-bits), or an idealized exact-eigenstate "tower" projection. Distills the investigation already published at quantum_scar_investigation — which found no genuine scar in Dense Evolution's own frustrated Ising grids (wrong observable + gauge equivalence), then validated the same verification pipeline against PXP, where scars are real and well documented — into something runnable instead of only readable. Verified via streamlit.testing.v1.AppTest (real button-click simulation, zero exceptions) and a new test_quantum_scars.py (17 tests, all passing) unit-testing the numerical core directly: validity-mask combinatorics, H_PXP Hermiticity and Hilbert dimension, fidelity=1/norm-preservation under propagation, and both projections staying normalized with zero weight outside their target subspace.

v8.1.21

• Added: QASMCircuit.__iter__ — duck-types a parsed circuit as an iterable of the same tuples .to_tuples() returns, so it works anywhere a plain circuit list is expected (Chunk.run_chunk, QuantumTranspiler.transpile, ...) without remembering to call .to_tuples() first. Found via a user's own Colab testing: Chunk.run_chunk(QASMParser().parse(qasm)) — a very natural thing to try — raised TypeError: 'QASMCircuit' object is not iterable.
• Fixed / Performance: Chunk's multi-chunk dispatch (num_chunks > 1) used to apply every gate through a Python loop calling non-JIT apply_gate_1q/apply_gate_2q — measured 6x slower than run_circuit_jit_beast_mode on an identical workload. Replaced with a single jax.lax.scan over the whole circuit operating directly on the stacked (num_chunks, chunk_dim) representation — never materializing a (2**n_qubits,) array, preserving the anti-OOM property Chunk exists for. The 6 gate/qubit-location cases were ported formula-for-formula from the old Python-loop implementation and verified case-by-case against it (all 18 pre-existing TestChunkMultiPiece tests, which cross-check against DenseSVSimulator, pass unchanged against the new kernel) before the old code was removed. Gate coverage is now built via GATE_IDS instead of the old GATES/PARAMETRIC_GATES lookup, aligning it with beast-mode's own coverage. Measured speedup on the exact benchmark that surfaced the problem (10 qubits/200 gates/4 forced chunks): 2.2s → 0.42s, now close to beast-mode's 0.37s on the same non-chunked workload.
• Note: a Colab report of "17s vs milliseconds" that prompted this investigation turned out, on reproduction, to be num_chunks==1 (not the multi-chunk path at all) — 0.49s locally on the identical circuit, most likely first-time JIT compilation overhead on Colab's specific hardware rather than a code defect. The 6x slowdown that was real and is fixed here was found and confirmed with a separate synthetic benchmark (num_chunks forced via monkeypatch), not the original report.

v8.1.20

• Fixed: from_pennylane/run_pennylane_circuit silently renumbered qubits whenever wires weren't touched in ascending order — both PennyLane's qml.to_openqasm and the older tape.to_openqasm() number exported QASM qubits by first-touch order, not by actual wire index (e.g. PauliX(wires=2) then CNOT(wires=[2,1]) exported as x q[0]; cx q[0],q[1];, silently mapping wire 2→q[0] and wire 1→q[1]). Found via independent fuzz testing (20 random circuits touching 4 wires in random order: 9/20 matched PennyLane's own results before the fix, 20/20 after). Fixed by passing an explicit wires= argument — the device's declared wire order for a QNode, the tape's own wires sorted ascending for a bare tape — forcing the true wire order into the export instead of relying on touch order.
• Fixed: NoiseModel.apply_to_sv's depolarizing channel (and the combined channel's depolarizing sub-channel) picked which Pauli error (X/Y/Z) to apply using thresholds p/3 and 2p/3 compared against a draw uniform on the full [0,1) range — but that draw should only ever decide which Pauli fires, independent of the overall fire-rate p, so the thresholds needed to be the fixed values 1/3 and 2/3 instead. The bug skewed every depolarizing/combined-noise circuit heavily toward Z regardless of p (verified: at p=0.3, P(X|fire)=P(Y|fire)=10%, P(Z|fire)=80% instead of the documented 33.3% each — confirmed both via an isolated 100k-sample trace of the raw branch logic and via full statevector simulation, both matching the bug's predicted skew to within statistical noise). Found via independent statistical fuzz testing comparing measured frequencies against the analytic prediction — a test that only checks "the channel runs without crashing" would never have caught this. bitflip, phaseflip, and amplitude_damping were verified unaffected (correct by construction, don't use this three-way branch).
• Docs: opened a tracking issue for a related robustness gap found during the same fuzzing pass — unrecognized gate names (a typo like 'crx' instead of 'crz', or any gate not in GATE_IDS) are silently dropped everywhere in the simulator instead of raising, same pattern already documented for the Qiskit interop bridge's unsupported custom gates. Not fixed here — would be a breaking-change decision for run_circuit/run_circuit_jit_beast_mode/run_parametric_batch_jit's public behavior, tracked separately.

v8.1.19 — Security fix

• Fixed (security): QASMParser's gate-parameter evaluator (_eval_param, used for expressions like rx(...), p(...)) called eval() with {'__builtins__': {}} as its only protection. That blocks direct builtin names (open, len, __import__, ...) but does not block attribute/dunder traversal of the live Python object graph (().__class__.__bases__[0].__subclasses__()...), which needs no builtin name at all — from there, any class loaded in the process is reachable, including ones whose __globals__ reference os/subprocess. Verified directly: a crafted gate-parameter expression, passed through the public QASMParser.parse() entry point (the primary entry point of the whole library — used by the dashboard, the Qiskit/PennyLane interop bridge, and any direct usage), executed successfully. Anyone parsing untrusted QASM text was affected, in every previously published version. Fixed by replacing eval() with an AST node-type whitelist evaluator (_eval_ast_node) — only literals, +-*/%** arithmetic, and calls/lookups restricted to the documented math environment (pi, sin, sqrt, ...) are ever evaluated; an ast.Attribute node (produced by any . in the expression) is never one of the handled cases, so attribute-based escapes are structurally impossible rather than blocklisted. _resolve_int_expr (QASM3 for-loop bounds) used the same eval() pattern but was already protected by a pre-filter regex rejecting any non-arithmetic character — verified safe before this fix — now shares the same AST evaluator for consistency, so no raw eval()/exec() remains anywhere in the codebase (confirmed via full-repo search). No public API or behavior change for legitimate expressions — every previously-supported parameter syntax (pi, pi/2, sqrt(2), cos(0.3), etc.) evaluates identically.

If you parse QASM text from any source you don't fully trust, upgrade immediately.

v8.1.18

• Fixed: removed a global warnings.filterwarnings('ignore') from registry.py, run unconditionally on import dense_evolution. It silenced every Python warning process-wide for the importing user's whole session — not just this package's, but their own code's and every other library's too. Inherited unchanged from the original Colab notebook (added in v8.0.6, never reconsidered once this became a real pip package). Concretely masked real signal: the JAX float64→float32 truncation UserWarnings visible throughout this project's own test output (precision silently lost under use_float32=True) would have been invisible to anyone using the package normally.

v8.1.17

• Added: donate_argnums=(0,) on run_circuit_jit_beast_mode's statevector buffer — the only one of _compile_and_run_circuit_jit's four call sites where it's safe (self.sv is always rebound immediately after, verified across chunked/repeated calls and separate simulator instances). run_parametric_batch_jit (its init_sv is a vmap-broadcast closure shared across the whole batch) and circuit_to_energy_fn's VQE loop (same stato_zero reused every epoch) are deliberately left un-donated — donating there would make JAX raise on the second use instead of helping. Verified with a real measurement, not just a claim: RSS growth on a 22-qubit/300-gate circuit drops from +89.4MB to +4.5MB.

v8.1.16

• Note: v8.1.15's published PyPI package does not contain the from_pennylane Python 3.10 fix described below, despite the changelog entry — the fix landed in the repo before the PyPI upload, but the actual pip install-able wheel/sdist for 8.1.15 was built and uploaded from an earlier commit. PyPI doesn't allow re-uploading files under an already-published version, so this release exists specifically to ship that fix as an installable package. If you're on 8.1.15, upgrade to 8.1.16 — don't rely on 8.1.15's changelog matching what you actually have installed.

v8.1.15

• Added: dense_evolution.autodiff.circuit_to_energy_fn(circuit, n_qubits) — the real VQE gradient engine (jax.value_and_grad through a jax.lax.scan circuit template, verified against finite differences to ~1e-11) is now public API, independent of dashboard_core.py/Streamlit. Takes a QASMCircuit — the same type from_qiskit/from_pennylane return — so it closes the non-differentiability gap documented in v8.1.14: circuit_to_energy_fn(from_pennylane(qnode, ...), n_qubits) now gives a real, non-zero jax.grad, verified directly, where run_pennylane_circuit alone silently returned 0.0.
• Changed: dashboard_core.py's _build_vqe_template/_vqe_energy_fn removed — _run_vqe_telemetry_body now calls the same public circuit_to_energy_fn, one engine instead of two copies of the same math that could silently drift apart. Verified behaviorally identical: all existing dashboard VQE tests pass unchanged, same tolerances.
• Fixed: found while testing the newly-public API — calling the engine on a circuit with zero parametric gates crashed on empty-array indexing during JAX tracing. Previously unreachable because dashboard_core.py always special-cased n_params == 0 before calling in; a real gap once this became public API someone could call directly. Fixed with a static (non-traced) branch.
• Docs: the README's VQE Engine section had drifted stale, still describing the deleted risolvi_qasm() mechanism from before the real-gradient rewrite — corrected, and a new "Differentiable Circuits" section documents circuit_to_energy_fn with a verified end-to-end example.
• Fixed: from_pennylane broke on Python 3.10 — CI caught it (3.10 job red, 3.11/3.12 green). Newer PennyLane releases dropped Python 3.10 support, so pip resolves an older PennyLane (0.42.3) there instead of the version this bridge was built against (0.45.1); qml.to_openqasm(tape) behaves incompatibly between the two for a bare tape/QuantumScript input (crashes with AttributeError: 'QuantumTape' object has no attribute 'func' on the older one). Verified against both versions directly (installed 0.42.3 in an isolated venv to reproduce). from_pennylane now picks whichever serialization path the installed PennyLane version actually supports instead of assuming the newer one unconditionally.

v8.1.14

• Added: interop bridge for Qiskit and PennyLane — from_qiskit/from_pennylane convert an existing circuit to a QASMCircuit by reusing the existing QASMParser (via qiskit.qasm2.dumps / qml.to_openqasm) instead of a bespoke gate-by-gate translator; run_qiskit_circuit/run_pennylane_circuit execute it directly on DenseSVSimulator. Handles the bit-order mismatch explicitly instead of leaving it as a silent trap: Qiskit indexes arrays little-endian (qubit 0 = LSB), Dense-Evolution is MSB-first everywhere else in the codebase, so run_qiskit_circuit reorders its output to match Qiskit's own convention (verified against Statevector(...).probabilities() on an asymmetric circuit); PennyLane's own wire order already matches Dense-Evolution's natively (verified the same way), so run_pennylane_circuit does not reorder — kept as two separate code paths on purpose. New optional extras dense-evolution[qiskit] / dense-evolution[pennylane].
• Fixed: found while building the Qiskit bridge — qiskit.qasm2.dumps exports composite gates (e.g. mcx) as a gate NAME params { ... } definition on a single line, the same brace-delimited block corruption already fixed for QASM3 for/if/while/def in v8.1.13, just not covered because gate wasn't in that fix's keyword set (verified: before the fix, a 4-qubit circuit using mcx silently inflated to n_qubits=5 with a ghost op). Extended the same brace-matching preprocessor to also strip gate definitions cleanly.

v8.1.13

• Fixed: QASMParser declared OpenQASM 3.0 support but for/if/while/def blocks — brace-delimited, not ;-terminated — were mishandled by the naive split(';') statement splitter: a for-loop's body was never extracted, and its closing } merged into whatever real statement followed on the same line, corrupting it too (verified: for int i in [0:2] { h q[i]; } cx q[0],q[1]; produced a single ghost op named '}', with the loop body lost and the real cx silently dropped — executed circuit stayed |000⟩ at 100% probability, no error). Needed for writing VQE ansätze with a loop over qubits instead of one line per qubit. Added _process_block_constructs, run before the ;-split: for-loops with resolvable integer bounds (literals, or int/const int variables declared earlier in the source — QASM3's inclusive-end range semantics) are now genuinely unrolled by substituting the loop variable into the body per iteration; if/while/def blocks and for-loops with unresolvable bounds are cleanly stripped instead of corrupting the source that follows them.

v8.1.12

• Fixed: run_circuit_jit_beast_mode / run_parametric_batch_jit silently dropped cy, cp, crz, u1, p, sx — they weren't in GATE_IDS, so if name not in GATE_IDS: continue skipped them with no error (verified: h(0);h(1);crz(0,1,1.2) produced the exact same output as h(0);h(1) alone). dashboard_core.py already treats these as first-class gates, so any circuit using them — dashboard-built or hand-written QASM — silently ran the wrong physics through the fast path nearly everything uses. Added the missing GATE_IDS entries and the missing kernel implementations for cy/crz/sx in _apply_gate_fast_step — crz specifically needed its own kernel, not reuse of cp's (CP phases |11⟩ only; CRZ phases the target conditioned on its own bit, a different gate).
• Fixed: run_circuit_jit_beast_mode used the raw qubit index as bit position (LSB-first) instead of the documented MSB-first convention (phys = n_qubits - 1 - qubit) used by run_circuit()/apply_gate_1q()/apply_gate_2q()/measure() elsewhere in the simulator. Pre-existing, not introduced by the fix above — found while verifying it, masked until now because every beast-mode circuit tested to date happened to be symmetric under qubit reversal (Bell states, GHZ states, uniform superpositions), so the wrong labeling never showed up in the probabilities. Verified with X on qubit 0 in a 3-qubit register: gave index 1 (LSB) instead of index 4 (MSB, correct). do_1q/do_2q now compute physical bit positions consistently with the rest of the simulator; Chunk's num_chunks==1 (via beast mode) and num_chunks>1 (via apply_gate_1q/apply_gate_2q) paths are now finally consistent with each other too.
• Fixed: the VQE gradient (run_vqe_telemetry) was never a real derivative — grad_vqe_params[i] = 0.5*(energy-target)*sin(theta[i]) + gaussian_noise, no jax.grad, no parameter-shift rule, no backprop on θ anywhere in the codebase (the only real jax.value_and_grad usage, in QMMMForceEngine, differentiates classical QM/MM forces w.r.t. atomic positions, not circuit parameters). risolvi_qasm (the old circuit-building path) converted θ to a Python float before use, severing the JAX trace, so backprop couldn't pass through it. Replaced with a real jax.grad pipeline reusing run_parametric_batch_jit's own sentinel-injection pattern (θ substituted via jnp.where inside a jax.lax.scan, never a float() call) — verified against a finite-difference gradient (~1.5e-10 agreement) on a real circuit from QASM_LIBRARY, and confirmed genuine Adam-optimizer convergence (monotonic energy descent to a minimum) over 40 epochs, unlike the old noisy formula. Public signature and DataFrame columns of run_vqe_telemetry unchanged.

v8.1.11

• Fixed: dash.py (the original Colab notebook) was declared as an installable module (py-modules = ["dash"]) with the same name as the real Plotly dash package, itself listed as an optional dependency in the very same pyproject.toml — a genuine packaging collision, not just a local dev annoyance. It also had unconditional module-level from google.colab import files / import ipywidgets, so import dash crashed immediately outside Colab. Nothing in the maintained codebase (dashboard_core.py/app_dashboard.py, the real Streamlit port) imports it anymore. Moved to legacy/dash.py (reference only, not packaged), removed from py-modules. The dashboard extra now installs what the real dashboard actually needs (streamlit, pandas, seaborn, plotly) instead of the unused dash package.
• Docs: README's Quick Start (the very first example in the file) passed circuit.ops — raw dicts — to run_circuit_jit_beast_mode, which expects the tuple format from circuit.to_tuples(); crashed with KeyError: 0. Fixed, and the "Dashboard" quick-start snippet now points at streamlit run app_dashboard.py instead of the retired Colab-only import dash pattern.

v8.1.10

• Fixed: run_circuit_jit_beast_mode / run_parametric_batch_jit — a gate referencing a qubit index out of range silently corrupted the entire statevector to zero instead of raising (verified: get_probabilities().sum() went from 1.0 to 0.0, no exception). apply_gate_1q/apply_gate_2q already validated qubit indices, but these two JIT fast paths build their own compiled ops and never called them. Both now validate before dispatch, matching the existing behavior of the non-JIT path.
• Fixed: Chunk — for n_qubits beyond the RAM-safe budget (chunk_size_bits), it silently ran the circuit on a smaller inner simulator (min(n_qubits, chunk_size_bits)) instead of genuinely chunking: num_chunks/chunk_dim were computed but never used to combine multiple pieces. Found testing Chunk(n_qubits=28): get_probabilities() returned 2**27 elements, not 2**28. Now implements real multi-chunk simulation (RAM-only, no disk paging — covers moderate overflow beyond the safe budget, not arbitrarily large qubit counts): num_chunks independent chunk-sized simulators held in memory, with gate dispatch across chunk boundaries for all six local/chunk-select combinations. Verified against a plain DenseSVSimulator running the identical circuit (exact match, not just "looks right"). A sized RAM check now raises MemoryPressureError up front if the chunks wouldn't fit, instead of attempting and OOMing.

v8.1.9

• Fixed: ia_utils/vector_healing.py — enhanced_dense_healing_hybrid had an unreachable third branch (a dense/blend fallback): the underlying trigger signal from evaluate_phi_trigger is strictly binary (0.0/1.0), so the branch could never execute. Collapsed to the genuine 2-state logic (pass-through vs. median fallback); runtime output is unchanged since the branch never ran.
• Fixed: dashboard_core.py — run_simulation / run_vqe_telemetry mutated the process-wide JAX jax_enable_x64 flag without ever restoring it, so running one float32 simulation silently downgraded numerical precision for unrelated code later in the same process (e.g. the Vector Healing page, which sets no precision of its own). Both now save/restore the flag around their own execution.
• Docs: README's NoiseModel example called a nonexistent .apply() method with a wrong parameter name (n_qubits instead of n) — corrected to apply_to_sv(sv, n=..., ...). Documented QASMCircuit.to_tuples() and DenseSVSimulator.run_circuit, which already existed and work correctly but were never mentioned in the README.

v8.1.8

• Fixed: parser.py — controlled two-qubit gates (cx/cy/cz/cp/crz) parsed from QASM in the dashboard layer had control and target swapped relative to compiler.py's documented (gate, control, target) contract, breaking entanglement for circuits run through the dashboard. The core QASMCircuit.to_tuples() path was already correct.
• Fixed: parser.py — range syntax (q[0:3]) on single-qubit gates only applied to the first qubit in the range, silently dropping the rest. Now expands into one gate application per qubit, matching the parser's own documented contract.
• Fixed: from dense_evolution import Chunk raised ImportError — Chunk is now re-exported from the package root. Added get_probabilities()/get_statevector() to Chunk for parity with DenseSVSimulator.
• Removed: dense_evolution/test2.py and stress_test.py — byte-identical, assertion-free debug scripts that shipped inside every install with 0% test coverage. Their one real check (Kraus noise is genuinely stochastic across independent runs) is now a real regression test.

v8.1.7

• ia_utils/ — new package: median_healing, enhanced_dense_healing_hybrid for vector sequence healing (NaN/Inf-safe)
• jax import in ia_utils.vector_healing made lazy — importable without the [jax] extra
• Fixed reconstruction_error telemetry returning NaN when input contained NaN/Inf
• Added scipy to core dependencies (was used but undeclared)

v8.1.6

• Modular package structure (dense_evolution/ directory)
• Split registry.py, gates.py, healing.py, chunk.py into dedicated modules

v8.1.5

• chunk.py — SafeMemoryGuard: hard block at configurable free-RAM threshold (default 15%), soft warning at 2× threshold, gc.collect() before every check
• chunk.py — Chunk no longer subclasses DenseSVSimulator; inner simulator allocated at safe_qubits only — eliminates RESOURCE_EXHAUSTED on 28q–34q circuits
• chunk.py — CircuitChunker.split_circuit RAM-checks every gate-slice before dispatch
• chunk.py — MemoryChunker attributes (num_chunks, chunk_size_bits, dtype) forwarded as @property on Chunk for benchmark compatibility

v8.1.0

• healing.py — Predictive State Engine: calculate_phi_ab, calculate_vettore_dinamico, calculate_delta_preemp, evaluate_phi_trigger, calculate_jax_reflection — all @jax.jit
• MemoryReflectionEngine — event logging + JAX Zero-Drift spectral aggregation

v8.0.x

• run_parametric_batch_jit() — jax.vmap over full parameter grids in single XLA call
• run_circuit_jit_beast_mode() — static JIT compilation with QuantumTranspiler
• OpenQASM 2.0/3.0 dual-mode parser with paren-depth-aware expression splitting
• NoiseModel Kraus channels in registry.py

---

▍ License

Business Source License 1.1 — converts automatically to Apache 2.0 on 1 June 2029.

• Non-commercial use: unrestricted
• Commercial use: ≤ 24 allocated qubits · ≤ 1,000 circuits/day · ≤ 10,000 shots/circuit
• Attribution required: © 2026 Salvatore Pennacchio <[email protected]> — Dense Evolution

Full text: LICENSE.md

---

▍ Cite This

If Dense-Evolution is useful in academic work, please cite it via the metadata in CITATION.cff (recognized by GitHub's own "Cite this repository" button, and by reference managers that support the Citation File Format).

Archived on Zenodo:

• Concept DOI (always resolves to the latest version): 10.5281/zenodo.21855643
• This release (v8.1.61): 10.5281/zenodo.22009005

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_{© 2026 Salvatore Pennacchio — Dense Evolution}