v0.9.6 — Security + repo hygiene + docs refresh

Patch release with three security fixes, eight Dependabot dev-tool bumps,
input-validation hardening of analysis/koopman.py, repository-hygiene
changes, and a sweep of stale counts across the documentation tree.

Security

• Pytest CVE-2025-71176 — bumped via PR #37 to pytest 9.0.3
  (fixes the /tmp/pytest-of-{user} directory pattern that allows
  local users to cause a denial of service or possibly gain
  privileges on UNIX).
• rand RUSTSEC-2026-0097 — bumped to 0.9.4 in
  scpn_quantum_engine/Cargo.lock (the previous 0.9.2 was unsound
  when a custom log logger calls rand::rng() from inside the
  logger, producing aliased &mut BlockRng).
• scripts/retrieve_ibm_job.py — no longer prints the first 50
  characters of the IBM Cloud CRN read from the vault. Resolves
  CodeQL alert #79 (py/clear-text-logging-sensitive-data).

Added

• analysis/koopman.py input validation — build_koopman_generator
  and koopman_analysis reject malformed input (non-square K,
  length-mismatched omega/theta_ref, NaN/Inf entries) and cap
  n_oscillators at MAX_OSCILLATORS_DEFAULT = 32 to prevent an
  unbounded n²×n² allocation followed by a multi-minute eigvals
  call. 13 new tests cover every guard branch.
• docs/pipeline_performance.md §21 publishes measured
  Python↔Rust speedups (4.7× – 19.5× across five paired benchmarks)
  and an explicit decision rule for when a new acceleration backend
  enters the build matrix.

Changed

• CI dev-tool matrix synced to current upstreams (PRs #36–#42):
  pytest 9.0.3, mypy 1.20.1, ruff 0.15.10, hypothesis 6.151.13,
  build 1.4.3, actions/upload-artifact 7.0.1,
  pypa/gh-action-pypi-publish 1.14.0.
• Public-facing docs scrubbed of self-applied quality labels (elite,
  STRONG tests, SUPERIOR documentation) in CHANGELOG.md,
  docs/changelog.md, docs/test_infrastructure.md,
  docs/symmetry_decay_guess.md, docs/dynq_qubit_mapping.md and 27
  test docstrings. Domain-technical uses (STRONG correlation
  verdict in stats tables, STRONG coupling in biochemical
  notebooks) are kept — they are field terminology.
• Stale counts refreshed across README.md, docs/architecture.md,
  docs/index.md, docs/pipeline_performance.md and
  docs/test_infrastructure.md: subpackages 19 → 20 (with the
  April-2026 psi_field/ and fep/ rows added), test suite 4 771 /
  4 828 → 4 841, pipeline-wiring 113 → 155, Rust path 51 → 68 tests
  over 37 functions, __all__ 77 → 104 symbols, three duplicate
  phantom rows removed from the docs/index.md package map.

Repository hygiene

• .coordination/sessions/ and .coordination/handovers/ are now
  local-only — 16 historical files untracked via git rm --cached.
• New .gitignore patterns for paper-extraction working files,
  .agent_metadata.json, and root-level misplaced handover_*.md.

Notes

• v0.9.4 and v0.9.5 were tagged but never released as GitHub
  releases. v0.9.6 captures all post-v0.9.3 work and is the first
  GitHub release since v0.9.3.
• See CHANGELOG.md for the full entry, including the v0.9.5 body of
  work (MS-QEC, FEP, Ψ-field, Phase 1 IBM Heron r2 hardware campaign,
  GUESS, DynQ, ICI / hypergeometric pulse shaping).

🤖 Generated with Claude Code

v0.9.3 — IBM Hardware Campaign Complete

Highlights

IBM Quantum Hardware (ibm_fez, Heron r2, 156 qubits)

• 20/20 experiments completed — 22 jobs, 176,000+ shots
• CHSH Bell inequality violation: S = 2.165 (>8σ above classical limit)
• QKD bit error rate: 5.5% (below BB84 threshold of 11%)
• 16-qubit Kuramoto dynamics with visible coupling structure
• ZNE stable across fold levels 1–9

Rust Acceleration Engine (15 functions)

• Hamiltonian construction: 5,401× faster than Qiskit (n=4)
• OTOC computation: 264× faster than scipy (n=4)
• Lanczos operator Lanczos: 27× faster than numpy (n=3)
• 8 modules on Rust fast path via knm_to_dense_matrix

Scientific Findings (16 figures)

• Critical coupling K_c(∞) ≈ 2.2 (BKT finite-size scaling)
• DTC survives heterogeneous frequencies (first measurement)
• Non-ergodic regime: Poisson level spacing + sub-thermal eigenstate entanglement
• OTOC scrambling 4× faster at strong coupling

Publications (GitHub Pages)

• Preprint: Quantum Kuramoto-XY on 156-qubit processor
• Synchronisation Witness Operators (no prior art)
• DLA Parity Theorem (exact formula)

Infrastructure

• JAX GPU backend for vectorised coupling scans
• PyPI Rust wheel CI for 5 platforms
• Kaggle notebook for GPU validation

Full changelog: v0.9.2...v0.9.3

v0.9.0

v0.9.0 — Production/Stable

508 tests · 99.6% coverage · mypy clean · security scanning in CI

Added

• 100% line coverage: 13 new tests closing 19 uncovered lines across 9 files
• Security scanning CI job (bandit + pip-audit)
• .github/CODEOWNERS
• Input validation: QuantumPetriNet (shape checks), QLiF (dt/n_shots), QAOA_MPC (p_layers)
• WEIGHT_SPARSITY_EPS constant; Shor & Preskill citation on QBER_SECURITY_THRESHOLD
• ZNE experiments now return R_std_per_scale (shot-noise error bars per noise scale)
• _run_vqe() returns energy_std (convergence stability metric)
• Runner timeout_s parameter + job metadata logged to jobs.json + retrieve_job() recovery
• examples/07_crypto_bell_test.py — CHSH violation demo
• examples/08_dynamical_decoupling.py — XY4 DD vs raw fidelity comparison
• notebooks/05_crypto_and_entanglement.ipynb — Bell test, correlator matrix, QKD, key rate
• Shared test fixtures: knm_4q, knm_8q, rng
• Dataclass field docs on LockSignatureArtifact and LayerStateArtifact

Fixed

• q_disruption.py: magic 16 replaced with 2**self.n_data_qubits
• Bare 1e-15 replaced with WEIGHT_SPARSITY_EPS across 3 source files
• Weak test assertions tightened

Changed

• Development Status :: 5 - Production/Stable
• TYPE_CHECKING blocks excluded from coverage
• Test count: 483 → 508

Full changelog: v0.8.0...v0.9.0

v0.6.4

What changed

Docs/metadata hardening round.

• Fix stale test counts in docs (411/424 → 442)
• Update figures/generate_header.py version string
• Complete README architecture tree (3 missing files)
• Add scpn-phase-orchestrator to Related Repositories
• Update SECURITY.md supported versions (0.6.x)
• Add pip ecosystem to dependabot monitoring
• Add v0.6.1–v0.6.4 entries to changelogs
• Version bump 0.6.2 → 0.6.4 across all metadata files

v0.6.2

What's Changed

Fixed

• Notebook 01/03/04: classical_kuramoto_ode → classical_kuramoto_reference import
• Notebook 03: ZNE scales [1,2,3,4,5] → [1,3,5,7,9] (odd required by gate_fold_circuit)
• Notebook 04: rewrite to 8-qubit Trotter + 16-layer classical reference (16-qubit statevector intractable on laptop)
• Remove misplaced docs/SESSION_LOG and docs/HANDOVER (duplicates of .coordination/)

Added

• figures/generate_knm_heatmap.py + figures/knm_heatmap.png — 16×16 K_nm coupling matrix with annotated calibration anchors
• Knm heatmap figure in README
• All 4 notebooks executed with embedded outputs
• ROADMAP: post-2030 timeline qualifier on fault-tolerant bullet

Stats

• 442 tests passing
• ruff check clean

v0.6.1 — Quantum-Native SCPN Phase Dynamics and Control

v0.6.1 — 2026-03-01

Patch release: mypy fixes, Zenodo metadata, CI dependency updates.

Changes

• Fix mypy errors in bridge module (FloatArray type alias, Path(None))
• Enriched .zenodo.json and CITATION.cff for DOI minting
• Bump actions/checkout 4→6, actions/setup-python 5→6, codecov/codecov-action 4→5

v0.6.0 Highlights

• 0.05% VQE ground-state error on 4-qubit XY Hamiltonian (ibm_fez, Heron r2)
• Trotterized 16-layer UPDE solver with quantum phase evolution
• QAOA-MPC binary controller, quantum Petri nets, quantum SNNs
• ZNE/DD error mitigation + toric-code QEC with MWPM decoder
• Phase-orchestrator bridge: Knm→Hamiltonian compilation for any domain

Stats

• 442 tests, 99% line coverage, Python 3.9–3.12
• Docs: https://anulum.github.io/scpn-quantum-control

pip install scpn-quantum-control==0.6.1

v0.5.1 — Fix PyPI version mismatch

Fixed

• __version__ now reports "0.5.1" (v0.5.0 on PyPI shipped with "0.4.0" due to tag/commit ordering)
• pyproject.toml, CITATION.cff, test_public_api.py all synced to 0.5.1

Upgrade

pip install --upgrade scpn-quantum-control

No code changes from v0.5.0 — this is a metadata-only patch.

v0.5.0 — Crypto Hardware Experiments

What's New

3 Crypto Hardware Experiments

• bell_test_4q: CHSH Bell inequality test — certifies K_nm entanglement on hardware via ZZ/ZX/XZ/XX correlators
• correlator_4q: 4×4 connected ZZ correlation matrix — validates coupling topology in hardware measurements
• qkd_qber_4q: Quantum bit error rate from Z-basis and X-basis measurements — checks BB84 security threshold (QBER < 0.11)

All three reuse the existing VQE ground-state preparation (prepare_key_state) and follow the standard experiment signature. Awaiting March QPU budget for ibm_fez execution.

Documentation Sweep

• Toned down over-claiming language ("first quantum simulation" → "hardware attempt at full 16-layer UPDE snapshot")
• Fixed stale counts everywhere: 411 tests across 46 files, 20 experiments in registry
• Rewrote ROADMAP.md (was listing v0.2.0 as future)
• Added crypto module documentation to README, quickstart, index, experiment roadmap
• Added Claim 6 (crypto) to paper claims document
• Marked 3 crypto hardware experiments as implemented in research branch docs

Numbers

• Tests: 411 passing (408 → 411)
• Experiments: 20 in ALL_EXPERIMENTS (17 → 20)
• Modules: 8 (qsnn, phase, control, bridge, crypto, qec, mitigation, hardware)

Full Changelog

https://github.com/anulum/scpn-quantum-control/blob/main/CHANGELOG.md

v0.3.0 — Transparency & Discoverability Overhaul

What's New

This release transforms scpn-quantum-control from an opaque prototype into a self-contained research asset. The technical substance (199 tests, 0.05% VQE on IBM Heron r2, 98% line coverage) was already solid — now it's visible.

Added

• README rewrite: motivating abstract explaining SCPN→XY isomorphism, "Background" section with Kuramoto-to-Hamiltonian derivation, all 4 figures embedded with captions, expanded example table with descriptions, "Related Repositories" section
• Paper 27 citation: formal working paper reference in README and docs/equations.md
• docs/equations.md: SCPN overview and UPDE definition added; equations document is now self-contained
• examples/README.md: guided walkthrough of all 6 examples with physics context
• HARDWARE_RESULTS.md: layer naming convention section explaining L1-L16 mapping
• Docstrings: 27 public functions and 3 classes documented across 15 source files
• GitHub discoverability: 10 repository topics, description, issue templates, PR template

Changed

• CI mypy scope: expanded from bridge/ only to full mypy (27 source files, zero errors)
• VALIDATION.md: test count 88→199, classical references now point to in-repo functions instead of external packages
• Badges: test count 88→199, added version badge

Install

pip install scpn-quantum-control==0.3.0

Stats

• 199 tests, 98% line coverage
• 27 source files pass mypy strict
• 0.05% VQE ground-state error on IBM Heron r2 (156 qubits)
• 4 figures embedded in README with captions

Full changelog: https://github.com/anulum/scpn-quantum-control/blob/main/CHANGELOG.md