rrdoctor 0.2.8

Get your research artifact reviewer-ready before you submit: reproducibility audits, dynamic verify, auto-fix, an agent-ready fix plan, and an ACM/NeurIPS Artifact Appendix generator.

Research Repo Doctor

Get your research artifact ready for Artifact Evaluation before the deadline: scan the repo, scaffold the easy fixes, verify the run path, and generate the appendix.

rrdoctor is a local CLI and GitHub Action for research artifact preparation. It audits whether a repo is reviewable, citable, and close to runnable; scaffolds safe mechanical fixes; maps findings to an AE-style readiness level; and turns the rest into a checklist any coding agent or human can finish.

AE deadline loop

uvx rrdoctor scan . --profile acm
uvx rrdoctor fix . --write
uvx rrdoctor appendix . --profile acm --output ARTIFACT_APPENDIX.md
uvx rrdoctor verify . --profile acm

For trusted repositories, rrdoctor verify --run can go beyond static checks and actually resolve dependencies and execute the declared entrypoint under a timeout.

What it catches

• "Your --seed flag does nothing." RRD052 spots code that declares a seed option but never calls random.seed, np.random.seed, torch.manual_seed, tf.random.set_seed, or random_state=seed.
• "This worked on my laptop." Local-only data paths, missing data provenance, and undocumented retrieval steps.
• "The environment silently changed." Unpinned dependencies, missing runtime versions, undeclared imports, and absent dependency manifests.
• "The notebook lies." Stale outputs, out-of-order execution, checkpoint artifacts, and secret-like notebook output.
• "Reviewers cannot tell how to cite or rerun this." Missing license, citation, CI, tests, changelog, results provenance, or experiment entrypoint.

Install

Run once, without installing:

uvx rrdoctor scan .

Alternatives:

pipx run rrdoctor scan .
pip install rrdoctor
rrdoctor scan .

Developer install from source:

git clone https://github.com/Tom409114/research-repo-doctor.git
cd research-repo-doctor
python -m pip install -e ".[dev]"
rrdoctor scan .

Fix the easy gaps

Let rrdoctor create the safe scaffolding for you. It is deterministic, idempotent, and never overwrites existing files.

rrdoctor fix . --write

It can scaffold missing governance docs, citation metadata, data/results provenance notes, a reproducible-seed helper, changelog entries, and common research .gitignore entries. The hard parts become a reviewable plan:

rrdoctor plan . --output plan.md

Use with your coding agent

Paste this into Claude Code, Cursor, GitHub Copilot, or any other coding agent:

Use rrdoctor as the deterministic, offline, no-API-key grader for this research repo.

Run:
rrdoctor scan . --format json --output baseline.json
rrdoctor plan . --output plan.md

Work through plan.md without weakening rrdoctor checks.

Definition of done:
rrdoctor scan . --baseline baseline.json --fail-on-new error

The final command is the objective gate: it verifies the agent's work against the starting baseline and fails only on newly introduced errors.

Keywords: research software, reproducibility, artifact evaluation, repository audit, auto-fix, coding agents, AGENTS.md, GitHub Action, notebooks, data availability, citation metadata.

Why this matters

Research code often lands on GitHub under deadline pressure. A reviewer or future lab member finds a promising repository and then loses hours because the environment is underspecified, data paths are local, notebooks contain stale outputs, dependencies are unpinned, or the citation is unclear.

Research Repo Doctor turns those recurring release blockers into deterministic checks with concrete remediation - and, where it is safe to do so, fixes them for you. It is built to sit in the ordinary maintenance path: run locally while preparing a release, then run automatically on pull requests through GitHub Actions.

The audit runs without an AI API key, network access, or hosted service. That same determinism makes it an honest grader: it can verify fixes made by a person or a coding agent.

audit -> fix -> plan -> (your coding agent / you) -> verify -> PR
  |       |       |                                  |
  |       |       rrdoctor plan                      rrdoctor scan --baseline
  |       rrdoctor fix --write                       --fail-on-new error
  rrdoctor scan

What's new in 0.2.8

• Better README run-path recognition: README-documented python -m package.train ... commands now count as experiment entrypoints when they map to local repository modules.
• Stronger dynamic verification for ML launchers: rrdoctor verify now recognizes module-runner commands such as python -m torch.distributed.run train.py ... when they include a local Python entrypoint.

What's new in 0.2.7

• Better citation scaffolds: rrdoctor fix --write now reads structured PEP 621 and Poetry metadata, preserves multiple authors, normalizes SSH git remotes, and handles git worktree origin URLs when generating CITATION.cff.
• Lower-noise dependency checks: RRD034 now understands PEP 621 environment markers and Poetry dependency groups, reducing undeclared-import false positives.

What's new in 0.2.6

• Lower-noise secret checks: Rcpp Generator token markers and public pkgdown docsearch.api_key search configuration no longer trigger RRD090, while generic credential-like API keys still do.
• More reliable corpus scans: the evaluation runner now falls back to GitHub archive downloads when git clone transport is flaky, without installing or executing target repositories.
• More manual calibration evidence: the public corpus snapshot now covers 60/60 successful static scans, 17 focused manual reviews, and 0 expected-absent regressions.

What's new in 0.2.5

• Model-release entrypoints: README-documented python scripts/*.py / python tools/*.py commands and pyproject-declared CLI commands now count as experiment entrypoints, reducing first-run false positives on repositories such as Segment Anything and Whisper.
• ML tools entrypoints: common tools/train.py, tools/test.py, and related ML framework commands now count for RRD050.
• Seed helper scaffolding: rrdoctor fix --write can scaffold a reproducible set_global_seed(seed) helper for RRD052 without overwriting project code.
• Corpus regression gates: entrypoint fixes are backed by focused review notes and expected_absent checks in the public evaluation corpus.

What's new in 0.2.4

• First-run trust improvements: root-level train.py/main.py/run.py, Snakemake/Nextflow workflows, and README run commands count as experiment entrypoints.
• Lower-noise security checks: notebook and repository secret detection now requires high-confidence credential-like values before raising blocking errors.
• More realistic README checks: concrete training, evaluation, benchmark, workflow, or reproduction commands count as evidence for reproducing results.
• Corpus-backed rule calibration: the public evaluation corpus tracks false-positive and false-negative review notes, expected-absent regression gates, and aggregate rule frequencies.
• Release hygiene: citation guidance detection recognizes README Citing sections, BibTeX, DOI links, and "please cite" text; local git tags count as deterministic version evidence.
• Release polish: the demo GIF is generated, issue access is open, and the committed self-scan report is 100/100.

What's new in 0.2.0

• rrdoctor fix provides deterministic, idempotent auto-fix for common gaps (governance docs, citation metadata, data/results provenance, seed helper scaffolding, changelog, ignore entries). Never overwrites.
• rrdoctor plan emits a tool-agnostic fix plan you can hand to any coding agent; every task names the deterministic check that verifies it.
• Baseline gating: rrdoctor scan --baseline report.json --fail-on-new error fails only on newly introduced findings, so large repos can adopt the audit incrementally.
• rrdoctor badge emits a Shields.io endpoint or SVG artifact-readiness badge.
• Artifact readiness labels map findings to an AE-style level: Available, Functional, or Reproduced-ready. The numeric score remains as a secondary triage signal.
• First-class PR automation: the Action posts a sticky PR comment, writes a job summary, and can attach the fix plan, using only the built-in GITHUB_TOKEN.
• New rules include unpinned dependencies, committed notebook checkpoints, pre-commit config, and an AGENTS.md task guide for agent and human contributors.

Quickstart

rrdoctor scan .                   # deterministic audit (Markdown report)
rrdoctor fix . --write            # apply safe scaffolding for easy gaps
rrdoctor plan . --output plan.md  # tool-agnostic work order for the rest
rrdoctor scan . --format json --output baseline.json --fail-on none
rrdoctor scan . --baseline baseline.json --fail-on-new error  # gate regressions

Stricter gate and report file:

rrdoctor scan . --profile strict --fail-on warning --output rrdoctor-report.md

Machine-readable and agent output:

rrdoctor scan . --format sarif --output rrdoctor.sarif --fail-on none
rrdoctor scan . --format agent --output fix-plan.md

Before a submission deadline:

rrdoctor appendix . --profile acm --output ARTIFACT_APPENDIX.md   # appendix + checklist mapping
rrdoctor verify . --profile neurips                               # L1/L2/L3 ladder (static)
rrdoctor verify . --run --timeout 600                             # actually build + run (trusted repos)

Submission profiles: acm, neurips, icml, ml-paper, fair4rs, joss (alongside the general minimal/standard/strict/ml tiers). Dependency and runtime checks also understand R (DESCRIPTION, renv.lock) and Julia (Project.toml), not just Python and JavaScript.

The audit -> fix -> verify loop

A deterministic checker is reproducible and trustworthy but cannot write prose or judge intent. A coding agent edits well but needs a precise specification and an objective definition of done. Research Repo Doctor gives you both:

1. Audit: rrdoctor scan produces deterministic findings.
2. Fix the easy ones: rrdoctor fix --write scaffolds governance docs, citation metadata, provenance notes, a seed helper, a changelog, and ignore entries (idempotent, never overwriting).
3. Plan the rest: rrdoctor plan emits a tool-agnostic work order. Paste it into the coding agent of your choice, attach it to an issue, or work it by hand.
4. Verify: re-run the audit against a baseline. Because verification is deterministic and key-free, it works as an honest grader for changes from any source.

See docs/agent-workflows.md and docs/autofix.md.

GitHub Action

Add one workflow to many repositories and get consistent reproducibility reports on pull requests and pushes. The Action requires no API key.

name: Reproducibility audit

on:
  pull_request:

permissions:
  contents: read
  pull-requests: write

jobs:
  rrdoctor:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: Tom409114/research-repo-doctor@v0.2.8
        with:
          profile: standard
          fail-on: none
          comment-pr: "true"     # sticky PR comment with the report
          step-summary: "true"   # report in the job summary
          plan: "true"           # attach an agent-ready fix plan
          appendix: "true"       # attach an Artifact Evaluation appendix
          verify: "true"         # attach the L1/L2/L3 verification ladder

For new-finding gating and a committed baseline, see docs/pull-request-automation.md.

Example output

Research Repo Doctor Summary
Profile: standard
Readiness: Functional
Score: 64/100
Errors: 0
Warnings: 5
Rules evaluated: 32

How to fix first:
- RRD030 No dependency manifest found: Add pyproject.toml, requirements.txt, or another manifest.
- RRD040 Data availability documentation missing: Add DATA.md, docs/data.md, or a README section.

Worked examples live in examples/reports/, including a fix plan and a self-scan report.

Commands

Command	Purpose
rrdoctor scan	Run the deterministic audit; supports --baseline and --fail-on-new.
rrdoctor fix	Apply safe, idempotent scaffolding for common gaps (--write to apply).
rrdoctor plan	Emit a tool-agnostic fix plan (Markdown or JSON).
rrdoctor verify	Reproducibility ladder L1/L2/L3; --run actually builds and executes.
rrdoctor appendix	Generate an ACM Artifact Appendix + ACM/NeurIPS checklist mapping.
rrdoctor badge	Emit an artifact-readiness badge (Shields.io endpoint or SVG).
rrdoctor mcp	Run the MCP server (scan/verify/appendix as agent tools).
rrdoctor init	Write a documented .rrdoctor.yml.
rrdoctor list-rules	List all registered rules.
rrdoctor explain RRD0xx	Explain a rule and how to remediate it.
rrdoctor doctor	Self-diagnostics.

Rule categories

Documentation, environment, data, experiments, notebooks, citation, governance, testing, CI, security, release, and metadata. The full table is in docs/checks.md; auto-fixable rules are marked there.

Reproducibility stance

Research Repo Doctor does not claim to prove a paper is reproducible. It checks release hygiene that makes reproduction possible to attempt. Reports are heuristic and should be reviewed by maintainers. Generated fixes are starting points and contain placeholders to complete before release.

Philosophy

Deterministic first. The scanner is understandable, testable, and useful with no network access. The core scanner will not add network calls, require a hosted-service API key, or fabricate adoption metrics. AI is something you bring to act on the output - never a dependency of the audit itself, and never tied to a single tool.

Configuration

version: 1
profile: standard
paths:
  exclude: [".git", ".venv", "node_modules", "__pycache__"]
thresholds:
  large_file_mb: 50
  large_notebook_output_kb: 1024
rules:
  RRD032:
    enabled: false
  RRD042:
    severity: warning
fail_on: error

See docs/configuration.md.

Contributing

Contributions are welcome. Start with CONTRIBUTING.md and AGENTS.md, open a rule request or false-positive report, and include a minimal fixture when possible.

Security

Do not report suspected credential exposure in a public issue. See SECURITY.md.

Citation

Use the included CITATION.cff or cite the archived release DOI: 10.5281/zenodo.21045373.

@software{research_repo_doctor_2026,
  title = {Research Repo Doctor},
  author = {{Research Repo Doctor Maintainers}},
  version = {0.2.8},
  year = {2026},
  doi = {10.5281/zenodo.21045373},
  url = {https://github.com/Tom409114/research-repo-doctor}
}

License

MIT. See LICENSE.