Add research reproducibility intelligence suite

[kkudumu]

Summary

• add a self-contained research reproducibility intelligence suite for the issue AI-Powered Research Assistant Suite #16 assistant workflow
• implement auto peer-review reports, reproducibility checks, and research-gap discovery with deterministic scoring
• include sample project data, requirement mapping, tests, CLI demo, and a short demo GIF

Demo

• Demo video: https://raw.githubusercontent.com/kkudumu/SCIBASE.AI/kkudumu/research-repro-intelligence-16/research-reproducibility-intelligence/docs/demo.mp4
• Demo GIF: research-reproducibility-intelligence/docs/demo.gif
• CLI demo: npm run demo

Verification

• cd research-reproducibility-intelligence && npm run check
• cd research-reproducibility-intelligence && npm test
• cd research-reproducibility-intelligence && npm run demo
• git diff --check

@algora-pbc /claim #16

Closes #16

[kkudumu]

Follow-up pushed to strengthen the reproducibility-check scope from issue #16:

• added linked prior reproducibility attempts to the deterministic report
• sort attempt history by current artifact fingerprint match and recency
• expanded sample data, demo output, README, and tests around the linked-attempt path

Verification after the update:

• cd research-reproducibility-intelligence && npm run check
• cd research-reproducibility-intelligence && npm test
• cd research-reproducibility-intelligence && npm run demo
• git diff --check

[kkudumu]

Follow-up pushed in fb2585f to make the workflow automation requirement more explicit.

What changed:

• Added buildWorkflowOrchestration() to turn peer-review findings, reproducibility checks, and research-gap opportunities into staged actions.
• Each workflow action now carries owner assignment, status/blocker state, dependency ids, priority, recommendation text, and an evidence hash.
• Assistant packets now include workflow.blocked, workflow.riskScore, workflow.readyForInternalReview, workflow.stages, workflow.actions, and workflow.orchestrationHash.
• Demo fixture now includes workflow preferences so reviewers can see owner routing and deadline handling.
• Tests cover the orchestration stages, blocking review actions, ready reproducibility runbook action, gap dependencies, and assistant packet workflow output.

Verification rerun:

• npm run check
• npm test
• npm run demo
• git diff --check

[kkudumu]

Added a short demo video artifact for Algora/reviewer convenience:

• Demo video: https://raw.githubusercontent.com/kkudumu/SCIBASE.AI/kkudumu/research-repro-intelligence-16/research-reproducibility-intelligence/docs/demo.mp4
• Existing GIF remains at research-reproducibility-intelligence/docs/demo.gif
• CLI demo remains npm run demo

This is the same deterministic demo flow already covered by the local tests and README, now available as an MP4 video artifact.

[kkudumu]

Follow-up for the issue #16 reproducibility-checker scope.

Added commit 37a3a24 to make the reproducibility checker more concrete around sandbox execution evidence rather than only static file readiness. The update adds:

• disabled-network sandbox execution plan generation for runnable notebooks/scripts
• resource limits and read-only project / writable output mount contracts
• executable target commands for notebooks, Python, R, Rmd, Julia, and shell artifacts
• execution-evidence validation for exit code, output hashes, log URL, generated artifacts, reported artifacts, and missing runs
• reproducibility checks for sandbox plan readiness, clean sandbox evidence, and reported-output consistency
• sample fixture, tests, CLI demo output, README, and issue requirement-map updates

Verified locally:

• npm run check -> passed
• npm test -> passed
• npm run demo -> passed and now prints sandboxTarget plus sandboxSummary
• git diff --check -> passed

This keeps the contribution self-contained and credential-free while mapping more directly to the requested reproducibility checker and sandbox validation workflow.

[kkudumu]

Updated the existing demo video with narrated voiceover explaining every major change in this PR: peer-review diagnostics, reproducibility checks, research-gap scoring, workflow orchestration, prior attempts, sandbox execution plans, and sandbox evidence validation. The PR's existing demo-video link now points to the narrated MP4.