@pikaa-ai/pikaa 0.3.23 → 0.3.24

package/skills/peer-review/SKILL.md

@@ -1,288 +0,0 @@
----
-name: peer-review
-description: Prepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for authorized review of scientific manuscripts, protocols, preprints, or research proposals; reporting-guideline selection; claim–evidence checks; methods, statistics, reproducibility, ethics, figure/table, and citation critique; or revision-response planning.
-license: MIT
-compatibility: Python 3.11+ standard library. Bundled CLIs are deterministic and local-only; they accept bounded JSON, CSV, or Markdown and make no network, model, image, or external-service calls.
-metadata:
-  version: "2.1"
-  skill-author: K-Dense Inc.
----
-
-# Peer Review
-
-Support an accountable human reviewer with a rigorous, fair, actionable assessment. Treat every unpublished submission and review as confidential.
-
-## Mandatory safety boundary
-
-Before reading or analyzing unpublished content:
-
-1. Confirm the user is authorized by the publisher, editor, author, or other material owner.
-2. Check the target venue’s review, confidentiality, co-review, retention, and AI/tool policies.
-3. Record conflicts, competence limits, requested scope, and specialist-review needs.
-4. Default to local-only processing.
-
-If authorization is unclear, do not inspect or quote the manuscript. Ask for confirmation or use only the bundled local CLIs, whose reports do not echo manuscript text.
-
-Never:
-
-- Send unpublished manuscript, supplement, review, or editorial text to an external service without specific publisher/author authorization and venue permission
-- Upload confidential content to a public model, search engine, citation service, grammar tool, plagiarism checker, or image service
-- Reuse content for training, benchmarking, product improvement, or unrelated research
-- Read broad environment state, `.env` files, API keys, or credentials
-- Call a network, LLM, or image API from bundled tools
-- Invoke another skill or a PDF/image pipeline automatically
-- Impersonate an assigned reviewer, editor, journal, funder, or author
-- Fabricate manuscript details, review findings, citations, analyses, experiments, reproduction, or an editorial outcome
-- Announce a decision that belongs to an editor or panel
-
-Delete local copies and derivatives when policy requires; otherwise retain only what the controlling policy authorizes. Record deletion or retention without copying confidential content into the record.
-
-Read `references/ethical_review_practice.md` before handling confidential material.
-
-## Human accountability
-
-Label generated text as a working draft. The accountable human must:
-
-- Read the complete authorized submission and relevant supplements
-- Verify every factual statement, calculation, citation, and manuscript location
-- Resolve conflicts and disclose assistance as required
-- Rewrite comments in their own expert judgment
-- Submit through the authorized channel
-
-Automated coverage, consistency, or lint results are not peer review and do not establish manuscript merit.
-
-## Intake gate
-
-Copy and complete `assets/review_intake_template.json`, then run:
-
-```bash
-python3 scripts/validate_review_intake.py completed-intake.json
-```
-
-Proceed only when status is `READY_FOR_LOCAL_REVIEW`.
-
-The validator blocks:
-
-- Undocumented authorization
-- Missing human accountability
-- Unassessed or unresolved conflicts
-- Unknown review model or unchecked venue policy
-- Unauthorized AI assistance
-- External service use
-- Data reuse
-- Missing deletion/retention planning
-
-It validates declarations, not their truth.
-
-## Review workflow
-
-### 1. Establish scope and available evidence
-
-Record:
-
-- Submission type and stage
-- Review question and requested focus
-- Target venue and review model
-- Materials actually available: manuscript, supplements, protocol, registration, analysis plan, data/code statement, prior decision, or response letter
-- Competence areas and limits
-- Missing material that prevents assessment
-
-Do not infer absent content. Use “not reported” or “not available for review.”
-
-### 2. Orient without deciding
-
-Create a short neutral map:
-
-- Research question
-- Population or system
-- Design and unit
-- Intervention, exposure, test, or model
-- Comparator/reference
-- Outcomes and timing
-- Principal claims
-
-Do not write an acceptance/rejection recommendation. Identify what evidence would be needed to evaluate each claim.
-
-### 3. Select reporting guidance
-
-Copy `assets/study_profile_template.json` and run:
-
-```bash
-python3 scripts/select_reporting_guidelines.py local-profile.json
-```
-
-For checklist coverage:
-
-```bash
-python3 scripts/select_reporting_guidelines.py \
-  local-profile.json \
-  --coverage local-coverage.csv
-```
-
-Use the current base guideline, explanation/elaboration, applicable extensions, and target venue policy. See `references/reporting_standards.md`.
-
-**Critical distinction:** reporting completeness is not design quality, risk of bias, validity, or merit. Never convert missing items into an automatic score or publication judgment.
-
-### 4. Map claims to evidence
-
-Prioritize central, causal, mechanistic, safety, diagnostic, prediction, and generalization claims.
-
-For each claim, record:
-
-- Location and claim ID
-- Supporting result, figure, table, analysis, or citation IDs
-- Direction, magnitude, population, outcome, timepoint, and uncertainty alignment
-- Limitation or alternative explanation
-- Bounded requested action
-
-Run:
-
-```bash
-python3 scripts/validate_claim_evidence.py local-claim-matrix.csv
-```
-
-Start from `assets/claim_evidence_matrix_template.csv`. The report emits IDs and counts, not claim text.
-
-### 5. Review methods and statistics
-
-Assess in this order:
-
-1. Question and target quantity
-2. Design and unit of inference
-3. Sampling, allocation, controls, masking, and timing
-4. Sample-size or precision rationale
-5. Inclusion, exclusion, attrition, and missingness
-6. Analysis–design alignment and assumptions
-7. Multiplicity and prespecification
-8. Effect estimates, uncertainty, denominators, and harms
-9. Interpretation, causality, and generalizability
-
-Use `references/common_issues.md` and `references/statistical_reproducibility.md`.
-
-For a structured local audit:
-
-```bash
-python3 scripts/audit_statistics_reproducibility.py \
-  local-statistics-reproducibility.json
-```
-
-Start from `assets/statistical_reproducibility_template.json`. Request specialist review when a central method exceeds competence; do not hide uncertainty behind a generic critique.
-
-### 6. Review reproducibility and transparency
-
-Check, as applicable:
-
-- Protocol, registration, amendments, and analysis-plan consistency
-- Data provenance, exclusions, transformations, and accession IDs
-- Software, package, model, and parameter versions
-- Code, environment, seeds, run instructions, and tests
-- Data, code, materials, and model availability or justified restrictions
-- Domain metadata standards
-
-Do not claim reproduction unless authorized inputs were actually run with documented commands, environment, and outputs.
-
-### 7. Review ethics and integrity
-
-Check applicable approvals, consent, welfare, privacy, community governance, funding, sponsor role, conflicts, authorship/contribution, registration, biosafety, and dual-use concerns.
-
-Describe observable evidence and uncertainty. Do not accuse authors or investigate them. Route credible concerns through the confidential editor channel under venue policy.
-
-### 8. Review figures, tables, and citations
-
-For figures and tables, assess:
-
-- Consistency with text and supplements
-- Denominators, units, axes, scales, uncertainty, and legends
-- Accessible encoding and sufficient context
-- Image acquisition/processing disclosure and source-data policy
-
-This skill has no image-generation or PDF-conversion workflow. Use only user-authorized local artifacts and tools.
-
-For Pandoc-style citations such as `[@ref-id]`:
-
-```bash
-python3 scripts/audit_citations.py local-manuscript.md local-references.csv
-```
-
-Start from `assets/citation_references_template.csv`. This checks key consistency and identifier format only; it does not verify that a source exists or supports a claim.
-
-### 9. Draft actionable comments
-
-Generate a private scaffold only after intake passes:
-
-```bash
-python3 scripts/generate_review_scaffold.py \
-  completed-intake.json \
-  -o private-review.md
-```
-
-Every major/minor comment should include:
-
-- **Location**
-- **Observation**
-- **Evidence or criterion**
-- **Why it matters**
-- **Requested action**
-
-Prioritize:
-
-- Claim–evidence alignment
-- Methods and statistical validity
-- Reproducibility and transparency
-- Ethics and participant/animal protection
-- Reporting needed for appraisal
-- Figures, tables, limitations, and citations
-
-Requests for new work must be necessary to support a central claim and proportionate to scope. Offer narrowing, clarification, sensitivity analysis, correction, or limitation language when that is sufficient.
-
-### 10. Keep channels separate
-
-**Comments to authors** contain the scientific review, strengths, major/minor comments, and limitations.
-
-**Confidential comments to editor** contain only policy-appropriate conflicts, competence limits, assistance disclosure, specialist requests, or substantiated integrity/process concerns that require a separate route.
-
-Do not place ordinary criticism only in confidential notes. Do not reveal reviewer identity under an anonymized process.
-
-### 11. Lint and finalize
-
-```bash
-python3 scripts/lint_review.py private-review.md
-```
-
-The linter checks channel separation, unresolved placeholders, a narrow abusive-language lexicon, role/decision phrases, and required actionability fields. It emits line numbers and rule IDs, not review text. Human tone and scientific review remain mandatory.
-
-Before handoff:
-
-- Verify all locations and evidence.
-- Remove unsupported or speculative criticism.
-- Confirm professional, non-abusive language.
-- State review limits and specialist needs.
-- Disclose permitted assistance.
-- Remove all placeholders.
-- Ensure no invented citation, experiment, reanalysis, or outcome.
-- Follow the documented deletion/retention rule.
-
-## Local tool index
-
-- `scripts/validate_review_intake.py` — scope, authorization, conflicts, policy, handling
-- `scripts/select_reporting_guidelines.py` — dated selector and non-scoring coverage audit
-- `scripts/validate_claim_evidence.py` — claim/evidence alignment matrix
-- `scripts/audit_statistics_reproducibility.py` — methods/statistics/reproducibility checklist
-- `scripts/audit_citations.py` — local citation/reference consistency
-- `scripts/generate_review_scaffold.py` — separated private Markdown scaffold
-- `scripts/lint_review.py` — tone, channel, and actionability lint
-
-Full schemas and exit codes: `references/tool_reference.md`.
-
-## References and assets
-
-- `references/ethical_review_practice.md` — COPE/ICMJE duties, confidentiality, AI, channels
-- `references/reporting_standards.md` — current major guidelines and verified domain standards
-- `references/statistical_reproducibility.md` — methods, statistics, and reproducibility review
-- `references/common_issues.md` — contextual issue patterns and constructive responses
-- `references/security_validation.md` — baseline remediation and local scan results
-- `assets/source_ledger.csv` — authoritative sources verified 2026-07-23
-- `assets/reporting_guidelines.json` — local selector catalog
-- `assets/review_scaffold_template.md` — private structured draft
-
-The source ledger is dated. Recheck live primary sources and the target venue policy for a later review, without exposing confidential manuscript text in search queries.

package/skills/penetration-testing/SKILL.md

@@ -1,31 +0,0 @@
----
-name: penetration-testing
-description: "Defensive Penetration Testing & API Vulnerability Assessment - Threat modeling, endpoint security probing, authentication boundary verification, and defense-in-depth posture validation."
-risk: low
-source: built-in
----
-
-# Defensive Penetration Testing & API Security
-
-This skill guides defensive assessment of web applications, REST/GraphQL APIs, and distributed microservices.
-
-## Assessment Checklist
-
-### 1. Authentication & Session Security
-- [ ] JWT tokens have valid signature verification and explicit algorithm enforcement (reject `none` algorithm).
-- [ ] Refresh tokens are rotated and revoked upon logout.
-- [ ] Sensitive cookies use `HttpOnly`, `Secure`, and `SameSite=Strict/Lax` flags.
-- [ ] Rate limiting and brute-force protection are enforced on login, registration, and password reset endpoints.
-
-### 2. Authorization & Multi-Tenancy (BOLA / IDOR)
-- [ ] Users can only access resources belonging to their organization/account (`WHERE user_id = :current_user`).
-- [ ] Administrative routes require explicit privilege checks beyond just being logged in.
-- [ ] Object IDs cannot be sequentially enumerated or tampered with to access foreign records.
-
-### 3. Input Validation & Sanitization
-- [ ] All incoming payloads pass strict schema validation (e.g., Zod, Pydantic, Joi).
-- [ ] File uploads validate MIME type, file extension, and enforce size limits.
-- [ ] File paths from user inputs are sanitized against directory traversal (`../` or null bytes).
-
-### 4. Egress & SSRF Protection
-- [ ] Outbound webhooks and URL fetchers validate IP addresses and block private/loopback ranges (`127.0.0.1`, `10.0.0.0/8`, `169.254.169.254`).

package/skills/pennylane/SKILL.md

@@ -1,240 +0,0 @@
----
-name: pennylane
-description: Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch or JAX. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.
-license: Apache-2.0 license
-allowed-tools: Read Bash Python
-metadata:
-  version: "1.1"
-  skill-author: K-Dense Inc.
----
-
-# PennyLane
-
-## Overview
-
-PennyLane is a quantum computing library that enables training quantum computers like neural networks. It provides automatic differentiation of quantum circuits, device-independent programming, and seamless integration with classical machine learning frameworks.
-
-## Installation
-
-PennyLane 0.45.0 requires Python 3.11 or newer. Install using uv with pinned versions for reproducible environments:
-
-```bash
-uv pip install "pennylane==0.45.0"
-```
-
-For quantum hardware access, install the plugin matching the target provider. Start from a clean environment when adding or upgrading Qiskit because its dependency graph is strict.
-
-```bash
-# IBM Quantum
-uv pip install "pennylane-qiskit==0.45.0"
-
-# Amazon Braket
-uv pip install "amazon-braket-pennylane-plugin==1.34.1"
-
-# Google Cirq
-uv pip install "pennylane-cirq==0.44.0"
-
-# Rigetti Forest
-uv pip install "pennylane-rigetti==0.40.0"
-
-# IonQ
-uv pip install "pennylane-ionq==0.45.0"
-
-# High-performance local simulators
-uv pip install "pennylane-lightning==0.45.0"
-
-# Catalyst JIT compilation
-uv pip install "pennylane-catalyst==0.15.0"
-```
-
-## Quick Start
-
-Build a quantum circuit and optimize its parameters:
-
-```python
-import pennylane as qml
-from pennylane import numpy as np
-
-# Create device
-dev = qml.device('default.qubit', wires=2)
-
-# Define quantum circuit
-@qml.qnode(dev)
-def circuit(params):
-    qml.RX(params[0], wires=0)
-    qml.RY(params[1], wires=1)
-    qml.CNOT(wires=[0, 1])
-    return qml.expval(qml.PauliZ(0))
-
-# Optimize parameters
-opt = qml.GradientDescentOptimizer(stepsize=0.1)
-params = np.array([0.1, 0.2], requires_grad=True)
-
-for i in range(100):
-    params = opt.step(circuit, params)
-```
-
-## Core Capabilities
-
-### 1. Quantum Circuit Construction
-
-Build circuits with gates, measurements, and state preparation. See `references/quantum_circuits.md` for:
-- Single and multi-qubit gates
-- Controlled operations and conditional logic
-- Mid-circuit measurements and adaptive circuits
-- Various measurement types (expectation, probability, samples)
-- Circuit inspection and debugging
-
-### 2. Quantum Machine Learning
-
-Create hybrid quantum-classical models. See `references/quantum_ml.md` for:
-- Integration with PyTorch and JAX
-- Quantum neural networks and variational classifiers
-- Data encoding strategies (angle, amplitude, basis, IQP)
-- Training hybrid models with backpropagation
-- Transfer learning with quantum circuits
-
-### 3. Quantum Chemistry
-
-Simulate molecules and compute ground state energies. See `references/quantum_chemistry.md` for:
-- Molecular Hamiltonian generation
-- Variational Quantum Eigensolver (VQE)
-- UCCSD ansatz for chemistry
-- Geometry optimization and dissociation curves
-- Molecular property calculations
-
-### 4. Device Management
-
-Execute on simulators or quantum hardware. See `references/devices_backends.md` for:
-- Built-in simulators (default.qubit, lightning.qubit, default.mixed)
-- Hardware plugins (IBM, Amazon Braket, Google, Rigetti, IonQ)
-- Device selection and configuration
-- Performance optimization and caching
-- GPU acceleration and JIT compilation
-
-### 5. Optimization
-
-Train quantum circuits with various optimizers. See `references/optimization.md` for:
-- Built-in optimizers (Adam, gradient descent, momentum, RMSProp)
-- Gradient computation methods (backprop, parameter-shift, adjoint)
-- Variational algorithms (VQE, QAOA)
-- Training strategies (learning rate schedules, mini-batches)
-- Handling barren plateaus and local minima
-
-### 6. Advanced Features
-
-Leverage templates, transforms, and compilation. See `references/advanced_features.md` for:
-- Circuit templates and layers
-- Transforms and circuit optimization
-- Pulse-level programming
-- Catalyst JIT compilation
-- Noise models and error mitigation
-- Resource estimation
-
-## Common Workflows
-
-### Train a Variational Classifier
-
-```python
-# 1. Define ansatz
-@qml.qnode(dev)
-def classifier(x, weights):
-    # Encode data
-    qml.AngleEmbedding(x, wires=range(4))
-
-    # Variational layers
-    qml.StronglyEntanglingLayers(weights, wires=range(4))
-
-    return qml.expval(qml.PauliZ(0))
-
-# 2. Train
-opt = qml.AdamOptimizer(stepsize=0.01)
-weights = np.random.random((3, 4, 3))  # 3 layers, 4 wires
-
-for epoch in range(100):
-    for x, y in zip(X_train, y_train):
-        weights = opt.step(lambda w: (classifier(x, w) - y)**2, weights)
-```
-
-### Run VQE for Molecular Ground State
-
-```python
-from pennylane import qchem
-
-# 1. Build Hamiltonian
-symbols = ['H', 'H']
-geometry = np.array([[0.0, 0.0, -0.66140414], [0.0, 0.0, 0.66140414]])
-molecule = qchem.Molecule(symbols, geometry)
-H, n_qubits = qchem.molecular_hamiltonian(molecule)
-hf_state = qchem.hf_state(electrons=2, orbitals=n_qubits)
-singles, doubles = qchem.excitations(electrons=2, orbitals=n_qubits)
-s_wires, d_wires = qchem.excitations_to_wires(singles, doubles)
-
-# 2. Define ansatz
-@qml.qnode(dev)
-def vqe_circuit(params):
-    qml.BasisState(hf_state, wires=range(n_qubits))
-    qml.UCCSD(params, wires=range(n_qubits), s_wires=s_wires, d_wires=d_wires)
-    return qml.expval(H)
-
-# 3. Optimize
-opt = qml.AdamOptimizer(stepsize=0.1)
-params = np.zeros(len(singles) + len(doubles), requires_grad=True)
-
-for i in range(100):
-    params, energy = opt.step_and_cost(vqe_circuit, params)
-    print(f"Step {i}: Energy = {energy:.6f} Ha")
-```
-
-### Switch Between Devices
-
-```python
-# Same circuit, different backends
-circuit_def = lambda dev: qml.qnode(dev)(circuit_function)
-
-# Test on simulator
-dev_sim = qml.device('default.qubit', wires=4)
-result_sim = circuit_def(dev_sim)(params)
-
-# Run on quantum hardware
-from qiskit_ibm_runtime import QiskitRuntimeService
-
-service = QiskitRuntimeService()
-backend = service.least_busy(operational=True, simulator=False, min_num_qubits=4)
-dev_hw = qml.device('qiskit.remote', wires=backend.num_qubits, backend=backend)
-result_hw = circuit_def(dev_hw)(params)
-```
-
-## Detailed Documentation
-
-For comprehensive coverage of specific topics, consult the reference files:
-
-- **Getting started**: `references/getting_started.md` - Installation, basic concepts, first steps
-- **Quantum circuits**: `references/quantum_circuits.md` - Gates, measurements, circuit patterns
-- **Quantum ML**: `references/quantum_ml.md` - Hybrid models, framework integration, QNNs
-- **Quantum chemistry**: `references/quantum_chemistry.md` - VQE, molecular Hamiltonians, chemistry workflows
-- **Devices**: `references/devices_backends.md` - Simulators, hardware plugins, device configuration
-- **Optimization**: `references/optimization.md` - Optimizers, gradients, variational algorithms
-- **Advanced**: `references/advanced_features.md` - Templates, transforms, JIT compilation, noise
-
-## Best Practices
-
-1. **Start with simulators** - Test on `default.qubit` before deploying to hardware
-2. **Use parameter-shift for hardware** - Backpropagation only works on simulators
-3. **Choose appropriate encodings** - Match data encoding to problem structure
-4. **Initialize carefully** - Use small random values to avoid barren plateaus
-5. **Monitor gradients** - Check for vanishing gradients in deep circuits
-6. **Cache devices** - Reuse device objects to reduce initialization overhead
-7. **Profile circuits** - Use `qml.specs()` to analyze circuit complexity
-8. **Test locally** - Validate on simulators before submitting to hardware
-9. **Use templates** - Leverage built-in templates for common circuit patterns
-10. **Compile when possible** - Use Catalyst JIT for performance-critical code
-
-## Resources
-
-- Official documentation: https://docs.pennylane.ai
-- Codebook (tutorials): https://pennylane.ai/codebook
-- QML demonstrations: https://pennylane.ai/qml/demonstrations
-- Community forum: https://discuss.pennylane.ai
-- GitHub: https://github.com/PennyLaneAI/pennylane
-