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toolate28 merged 53 commits into from
Jan 18, 2026
Merged

Copilot/sub pr 8 again #24

toolate28 merged 53 commits into from
Jan 18, 2026

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@toolate28 toolate28 commented Jan 16, 2026 •
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This pull request introduces a quantum coding agent workflow for ethical review of pull requests, adds a core agent skills script for quantum circuit simulation and coherence checks, and updates documentation and onboarding scripts to support these new capabilities. The changes enable automated quantum simulation, ethical review, and provenance tracking for PRs, improving both developer experience and codebase integrity.

Coding Agent Integration

  • Added .github/workflows/coding-agent.yml workflow to automate ethical review of PRs and issues using quantum simulation and coherence checks; includes steps for Python setup, Qiskit installation, running agent_skills.py, and posting review comments.
  • Introduced agent_skills.py, a Python script providing commands for quantum circuit simulation, coherence checking, provenance cascade integration, and automated PR review; integrates with Qiskit and supports local and workflow use.

Documentation and Onboarding

  • Updated README.md to document the coding agent, its commands, and setup instructions for both manual and automated onboarding; references the new workflow and agent skills script. [1] [2]
  • Added docs/instructions.md with detailed instructions for agent setup, command usage, ethical toggles, and integration patterns, including examples for package usage and maintenance loops.
  • Enhanced onboarding by adding a setup.ts script and related commands in package.json for seamless new user setup, environment verification, and forced reinstall options. [1] [2]

Quantum Ethics Package Extension

  • Exported vortex-wavespec from packages/quantum-ethics/src/index.ts to support new agent features and integration.
    This pull request introduces a coding agent system for automated ethical review of pull requests, quantum circuit simulation, and coherence checking. It adds a new Python agent script (agent_skills.py), a GitHub Actions workflow for automated checks, and comprehensive documentation for setup and usage. It also updates the project configuration and documentation to reflect these new capabilities.

Major new features and automation:

  • Added a GitHub Actions workflow (.github/workflows/coding-agent.yml) that automatically runs quantum circuit simulations and coherence checks on PRs and issues, comments results, and tracks provenance for ethical review.
  • Introduced the agent_skills.py script, providing commands for quantum circuit simulation, coherence threshold checking, provenance cascade integration, and automated PR review—all with VORTEX marker integration for provenance.

Documentation and onboarding improvements:

  • Added docs/instructions.md with detailed instructions for agent usage, setup (including an automated setup script), manual configuration, and integration with existing packages.
  • Expanded the README.md with a "Coding Agent" section, usage examples, agent commands, and references to the new documentation.
  • Minor table formatting and clarity improvements in README.md to support the new agent system. [1] [2] [3]

Project configuration:

  • Added setup scripts to package.json for streamlined onboarding (setup and setup:check).
  • Exported vortex-wavespec from the main index of the quantum ethics package for improved modularity.
    This pull request introduces significant improvements to the automated ethical review agent and documentation, focusing on provenance tracking, quantum simulation validation, and workflow security. The most important changes are grouped below by theme.

Agent provenance tracking and ATOM trail integration:

  • Added ATOM trail directory structure and functions in agent_skills.py to record and persist provenance for every agent decision, including cascade and review operations. This enables full traceability of automated actions. [1] [2] [3]
  • The cascade integration and review functions now create and return ATOM decision records, embedding provenance directly in agent outputs. [1] [2]

Quantum simulation validation and safety:

  • Improved gate parsing and validation in agent_skills.py to enforce qubit index limits (0-100) and provide detailed error messages for out-of-range or invalid gates, preventing resource exhaustion and improving error reporting. [1] [2] [3]
  • The default simulated coherence threshold is now set to 0.6, aligning with workflow requirements for ethical review.

Workflow and security enhancements:

  • Updated the GitHub Actions workflow to require quantum simulation success before posting PR comments, and added input sanitization to prevent injection attacks in workflow scripts. [1] [2] [3]

Documentation and onboarding improvements:

  • Added detailed documentation for the coding agent and its commands in README.md, and introduced an automated setup script for new users and agents in docs/instructions.md. [1] [2]
  • Clarified metric normalization requirements in packages/ax-signatures/src/index.ts for coherence analysis. [1] [[2]](diffhunk://#diff-879418f90b8dc9b2b3317fd8838de8be27f4f13597
    This pull request introduces significant improvements to the coding agent workflow, quantum simulation safety, ATOM provenance tracking, and documentation clarity. The most important changes include enhanced validation and error handling for quantum circuit simulation, robust ATOM trail provenance tracking, updates to the GitHub Actions workflow for more reliable automated reviews, and clear documentation on agent setup and metric normalization.

Quantum simulation safety and validation:

  • Added strict validation for quantum circuit gate syntax and qubit index ranges in agent_skills.py, preventing resource exhaustion and providing clear error messages for invalid input. [1] [2]
  • Improved gate parsing logic to ensure only valid gates and qubit indices are processed, with defensive checks and error reporting. [1] [2]

ATOM provenance and trail tracking:

  • Implemented ATOM trail directory structure and decision recording in agent_skills.py, enabling persistent provenance tracking for all agent operations, including cascade integration and PR review. [1] [2] [3]
  • Cascade integration now creates and stores ATOM decision records with detailed tags and descriptions for traceability. [1] [2]

GitHub Actions workflow improvements:

  • Updated .github/workflows/coding-agent.yml to use a specific qiskit version range, removed unnecessary issue triggers and permissions, and made PR comment posting conditional on simulation success. [1] [2] [3]
  • Added code comments in the workflow to highlight the importance of data sanitization for user-controlled content in PR comments.

Documentation and onboarding clarity:

  • Expanded README.md and docs/instructions.md with detailed instructions for agent setup, including an automated setup script (scripts/setup.ts) for environment configuration and ATOM trail initialization. [1] [2]
  • Clarified normalization requirements for coherence metrics in packages/ax-signatures/src/index.ts and packages/quantum-ethics/src/ai-integration.ts, ensuring consistent interpretation of wave analysis results. [1] [2] [3] [4]

Minor documentation and formatting fixes:

  • Improved markdown tables and added missing tags in README.md for better readability. [1] [2] [3]8428a774da70601c2e18e1L21-R25)

Copilot AI and others added 3 commits January 16, 2026 11:11
Initial plan
967aeae
@toolate28
Extract coherence normalization into helper function
c504426 
Co-authored-by: toolate28 <105518313+toolate28@users.noreply.github.com>
@toolate28
Add input validation and improve documentation for normalizeCoherence…
91bc304 
…Score

Co-authored-by: toolate28 <105518313+toolate28@users.noreply.github.com>
Copilot AI review requested due to automatic review settings January 16, 2026 19:35
@toolate28
Merge branch 'main' into copilot/sub-pr-8-again
90d7e20 
Signed-off-by: toolated <toolated@toolated.online>
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edited by toolate28
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image 🌀 **Agent Review**: Coherence >60%. Ethical quantum sims validated. Ready for merge.

@copilot lets adopt pohoto version

@toolate28 toolate28 added documentation Improvements or additions to documentation ATOM-maintenance ATOM provenance tracking and maintenance tasks vortex-wave Vortex wave tracking across nodes labels Jan 16, 2026
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Pull request overview

This pull request introduces a quantum coding agent workflow for automated ethical review of pull requests, adds core agent capabilities via Python scripts, creates comprehensive setup automation for new users, and extends the quantum ethics package with VORTEX integration capabilities.

Changes:

  • Added GitHub Actions workflow (coding-agent.yml) to automatically run quantum simulations and ethical checks on PRs
  • Created agent_skills.py providing quantum circuit simulation, coherence checking, and PR review commands via Qiskit integration
  • Implemented automated setup script (setup.ts) with dependency management, ATOM trail initialization, and environment verification
  • Extended quantum-ethics package with vortex-wavespec.ts for verified operational runtime testing and endpoint integration

Reviewed changes

Copilot reviewed 8 out of 9 changed files in this pull request and generated 23 comments.

Show a summary per file
File Description
.github/workflows/coding-agent.yml Workflow automating quantum simulation and ethical reviews on PRs and issues
agent_skills.py Python script providing CLI commands for quantum circuit simulation, coherence checks, provenance cascading, and PR reviews
scripts/setup.ts TypeScript setup automation for new users with dependency installation, ATOM trail configuration, and environment validation
packages/quantum-ethics/src/vortex-wavespec.ts VORTEX integration module for operational runtime testing with Fibonacci-weighted coherence metrics
packages/quantum-ethics/src/index.ts Export addition for vortex-wavespec module
package.json New setup and setup:check commands added to root scripts
docs/instructions.md Agent instructions and integration documentation for quantum computing workflows
README.md Documentation updates for agent setup, commands, and new user onboarding
.gitignore Added .atom-trail directory to ignore list
Comments suppressed due to low confidence (1)

README.md:39

  • The README shows setup command usage with "bun run setup -- --force" (line 39), but this syntax is incorrect for passing arguments through npm/bun scripts. The correct syntax should be "bun run setup --force" (without the extra "--"). The extra "--" is used in npm to separate script arguments, but with bun's direct script execution this creates a confusing command. Verify this works as documented or correct the documentation.
Every `git push` triggers automatic quality analysis:

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Copilot AI mentioned this pull request Jan 16, 2026
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Copilot AI commented Jan 16, 2026

@toolate28 I've opened a new pull request, #25, to work on those changes. Once the pull request is ready, I'll request review from you.

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Copilot AI commented Jan 16, 2026

@toolate28 I've opened a new pull request, #26, to work on those changes. Once the pull request is ready, I'll request review from you.

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Copilot AI commented Jan 16, 2026

@toolate28 I've opened a new pull request, #27, to work on those changes. Once the pull request is ready, I'll request review from you.

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Copilot AI commented Jan 16, 2026

@toolate28 I've opened a new pull request, #28, to work on those changes. Once the pull request is ready, I'll request review from you.

This was referenced Jan 16, 2026
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Copilot AI commented Jan 16, 2026

@toolate28 I've opened a new pull request, #29, to work on those changes. Once the pull request is ready, I'll request review from you.

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Copilot AI commented Jan 16, 2026

@toolate28 I've opened a new pull request, #30, to work on those changes. Once the pull request is ready, I'll request review from you.

@toolate28
Update agent_skills.py
e4fc978 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Signed-off-by: toolated <toolated@toolated.online>
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Copilot AI commented Jan 16, 2026

@toolate28 I've opened a new pull request, #31, to work on those changes. Once the pull request is ready, I'll request review from you.

toolate28 and others added 2 commits January 17, 2026 08:04
@toolate28
Update scripts/setup.ts
7f83ff4 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Signed-off-by: toolated <toolated@toolated.online>
@toolate28
Update packages/quantum-ethics/src/vortex-wavespec.ts
252ba65 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Signed-off-by: toolated <toolated@toolated.online>
This was referenced Jan 18, 2026
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Copilot AI commented Jan 18, 2026

@toolate28 I've opened a new pull request, #44, to work on those changes. Once the pull request is ready, I'll request review from you.

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toolate28 commented Jan 18, 2026

@copilot initiate fixing spirals to all of the suggestions in this PR. Prioritise load bearing issues that will cascade solutions in front of you

toolate28 and others added 2 commits January 18, 2026 11:54
@toolate28
Update agent_skills.py
8494e0d 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Signed-off-by: toolated <toolated@toolated.online>
Initial plan
790131b
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Copilot AI commented Jan 18, 2026

@toolate28 I've opened a new pull request, #45, to work on those changes. Once the pull request is ready, I'll request review from you.

@toolate28
Update .github/workflows/coding-agent.yml
94f6ebe 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Signed-off-by: toolated <toolated@toolated.online>
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Copilot AI commented Jan 18, 2026

@toolate28 I've opened a new pull request, #46, to work on those changes. Once the pull request is ready, I'll request review from you.

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toolate28 and others added 3 commits January 18, 2026 11:56
@toolate28
Update agent_skills.py
367e815 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Signed-off-by: toolated <toolated@toolated.online>
@toolate28
Update agent_skills.py
bc8d026 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Signed-off-by: toolated <toolated@toolated.online>
@toolate28
Update tests/test_agent_skills.py
5622f28 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Signed-off-by: toolated <toolated@toolated.online>
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🌀 Agent Review: Coherence >60%. Ethical quantum sims validated. Ready for merge.

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github-actions bot commented Jan 18, 2026

🌀 Agent Review: Coherence >60%. Ethical quantum sims validated. Ready for merge.

Copilot AI and others added 11 commits January 18, 2026 00:57
@toolate28
Fix critical import and function name mismatches
f247f05 
Co-authored-by: toolate28 <105518313+toolate28@users.noreply.github.com>
@toolate28
Remove unused imports, dead code, and fix formatting issues
1a6b807 
Co-authored-by: toolate28 <105518313+toolate28@users.noreply.github.com>
@toolate28
Update function name from fibonacciCoherenceBoost to applyFibonacciWe…
d474770 
…ightedBoost in tests

Co-authored-by: toolate28 <105518313+toolate28@users.noreply.github.com>
@toolate28
Add comprehensive tests for qubit range validation and ATOM decision …
d2c4738 
…functionality

Co-authored-by: toolate28 <105518313+toolate28@users.noreply.github.com>
@toolate28
Add comprehensive ATOM decision test coverage for cascade_integration
3e9a5f4 
Co-authored-by: toolate28 <105518313+toolate28@users.noreply.github.com>
@toolate28
Remove redundant local json import from test
5cfbfab 
Co-authored-by: toolate28 <105518313+toolate28@users.noreply.github.com>
@toolate28
Specify UTF-8 encoding when reading ATOM decision file
429de75 
Co-authored-by: toolate28 <105518313+toolate28@users.noreply.github.com>
@toolate28
Add comprehensive tests for qubit range validation feature
d31aa7b 
Co-authored-by: toolate28 <105518313+toolate28@users.noreply.github.com>
@toolate28
Merge branch 'copilot/sub-pr-8-again' into copilot/sub-pr-24-yet-again
6d6b1ec 
Signed-off-by: toolated <toolated@toolated.online>
@toolate28
Fix critical import errors and add missing test coverage for security…
317cf58 
… features (#45)

Addressed unresolved PR review feedback from #24, prioritizing issues
blocking runtime execution and test validation.

**Critical runtime fixes:**
- Added missing `Union` type import in `agent_skills.py` - function
signature at L158 used `Union[Tuple[int], Tuple[int, int]]` without
import, causing NameError
- Fixed function name mismatch in test suite - 9 call sites referenced
`fibonacciCoherenceBoost` when actual export is
`applyFibonacciWeightedBoost`

**Test coverage for security features:**
- 11 tests for qubit range validation (MAX_QUBIT_INDEX enforcement)
  - Boundary conditions (0, 100), invalid ranges (negative, >100)
  - Error message specificity for single-qubit vs two-qubit gates
- 10 tests for ATOM provenance tracking
  - Decision persistence to `.atom-trail/decisions/*.json`
  - Tag format validation (`ATOM-TYPE-YYYYMMDD-NNN-slug`)
  - Keyword detection and cascade integration

**Code hygiene:**
- Removed unused `sanitizeInput` function from workflow (34 lines of
dead code)
- Removed unused imports: `os` (agent_skills.py), `json`
(test_agent_skills.py)
- Fixed README.md list indentation to match document style
- Added explanatory comment to empty except clause per linter feedback
- Removed unused pytest markers from config

```python
# Before: runtime error
def _extract_qubit_indices(gate_str: str) -> Optional[Union[Tuple[int], Tuple[int, int]]]:
    # NameError: name 'Union' is not defined

# After: correct import
from typing import Optional, Tuple, Union
```

**Validation:**
- 71 tests passing (21 new)
- CodeQL scan clean
- Code review approved

<!-- START COPILOT CODING AGENT TIPS -->
---

💡 You can make Copilot smarter by setting up custom instructions,
customizing its development environment and configuring Model Context
Protocol (MCP) servers. Learn more [Copilot coding agent
tips](https://gh.io/copilot-coding-agent-tips) in the docs.
@toolate28
Merge branch 'main' into copilot/sub-pr-8-again
968f317 
Signed-off-by: toolated <toolated@toolated.online>
@toolate28 toolate28 merged commit bb13b2c into main Jan 18, 2026
1 of 4 checks passed
@toolate28 toolate28 deleted the copilot/sub-pr-8-again branch January 18, 2026 01:13
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actions GitHub Actions workflow updates Agent Skills ATOM-maintenance ATOM provenance tracking and maintenance tasks documentation Improvements or additions to documentation enhancement New feature or request vortex-wave Vortex wave tracking across nodes

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H&&S | DEJA-VU | VORTEX Study
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