validate-reproducibility-paths

Metadata

Status	done
Assigned	`agent-685`
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-05-05T05:10:37.853059459+00:00
Started	2026-05-05T05:25:57.774712284+00:00
Completed	2026-05-05T05:40:18.700051077+00:00
Tags	`paper-prep,validation`, `eval-scheduled`
Eval score	0.84
└ blocking impact	0.85
└ completeness	0.85
└ constraint fidelity	0.85
└ coordination overhead	0.88
└ correctness	0.85
└ downstream usability	0.82
└ efficiency	0.80
└ intent fidelity	0.89
└ style adherence	0.82

Description

Reproducibility audit. Implement directly — do not decompose further.

Validation

Every script path cited in surveys (/moosefs/guarracino/HPRCv2/scripts/...) either copied into scripts/ of this repo OR listed explicitly in paper_prep/synthesis/SCRIPT_INVENTORY.md
Tool versions pinned (wfmash, pggb, odgi, impg, igraph/Leiden, R packages) → paper_prep/synthesis/VERSIONS.md
Every figure-source path in paper_prep/synthesis/MANUSCRIPT_SKELETON.md re-verified to exist on disk; missing files added to WORK_DECOMPOSITION.md ## Gaps
rpe1_subtelo.communities.tsv vs rpe1.communities.tsv filename inconsistency resolved (SURVEY_09 §5 #1)
Output: paper_prep/synthesis/SCRIPT_INVENTORY.md, VERSIONS.md

Inputs

paper_prep/synthesis/MANUSCRIPT_SKELETON.md, WORK_DECOMPOSITION.md
All 13 paper_prep/surveys/SURVEY_*.md

## Description
Reproducibility audit. Implement directly — do not decompose further.

## Validation
- [ ] Every script path cited in surveys (`/moosefs/guarracino/HPRCv2/scripts/...`) either copied into `scripts/` of this repo OR listed explicitly in `paper_prep/synthesis/SCRIPT_INVENTORY.md`
- [ ] Tool versions pinned (wfmash, pggb, odgi, impg, igraph/Leiden, R packages) → `paper_prep/synthesis/VERSIONS.md`
- [ ] Every figure-source path in `paper_prep/synthesis/MANUSCRIPT_SKELETON.md` re-verified to exist on disk; missing files added to WORK_DECOMPOSITION.md ## Gaps
- [ ] `rpe1_subtelo.communities.tsv` vs `rpe1.communities.tsv` filename inconsistency resolved (`SURVEY_09 §5 #1`)
- [ ] Output: `paper_prep/synthesis/SCRIPT_INVENTORY.md`, `VERSIONS.md`

## Inputs
- `paper_prep/synthesis/MANUSCRIPT_SKELETON.md`, `WORK_DECOMPOSITION.md`
- All 13 `paper_prep/surveys/SURVEY_*.md`

Depends on

Required by

Log

2026-05-05T05:25:54.952083546+00:00 Lightweight assignment: agent=Default Evaluator (31847164), exec_mode=full, context_scope=task, reason=Evaluator role with 0.90 score (449 completed tasks) is optimal for systematic reproducibility audit requiring path validation and documentation.
2026-05-05T05:25:57.774716292+00:00 Spawned by coordinator --executor claude --model opus
2026-05-05T05:26:13.952564731+00:00 Starting reproducibility audit. Reading inputs to extract script paths, tool versions, figure source paths.
2026-05-05T05:31:16.688472255+00:00 Inventory complete. Writing SCRIPT_INVENTORY.md, VERSIONS.md, and Gaps update.
2026-05-05T05:36:39.282654397+00:00 Validated: SCRIPT_INVENTORY.md (301 lines, all script paths cited in 13 surveys with absolute paths verified via ls). VERSIONS.md (96 lines, tool versions + 4 explicit Methods TODOs + assembly provenance). WORK_DECOMPOSITION.md ## Gaps appended with 12 audit-discovered items (gaps 11-22). rpe1 filename inconsistency RESOLVED (rpe1.* prefix is canonical, 37 communities, 2026-03-24).
2026-05-05T05:40:13.078928433+00:00 Committed: 617f401 — pushed to origin/wg/agent-685/validate-reproducibility-paths
2026-05-05T05:40:18.700055485+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-05T05:54:18.651836290+00:00 PendingEval → Done (evaluator passed; downstream unblocks)