repro-check 0.10.2

A runnability scaffold for reproducing computational papers (Python & R): makes old code run again, and hands back exactly where it stopped when it can't.

repro-check

What is this?

Old research code often stops working. You download the analysis from a paper, try to run it, and it crashes — a file path that no longer exists, a package that changed, a dependency nobody installed.

repro-check is a mechanic for that code. Point it at a repository and it finds the script (Python, R, or a Jupyter notebook), tries to run it, and applies known fixes when it breaks — repeating until one of two things is true:

• ✅ it runs — and you get a list of exactly what was changed, or
• ✋ it stops and hands off — telling you precisely where it got stuck and what a human needs to do next.

The one thing it will never do is pretend. A green result means the code runs — not that the results are scientifically correct. That harder question is left to you, on purpose. (More on this below under "Scope & honesty".)

pip install repro-check
repro-check github.com/owner/repo

---

A runnability scaffold for reproducing computational papers: it makes old code run again, and when it can't, hands back exactly where it stopped and what to do next. An agent loads it; it is not a standalone app and not a pass/fail judge.

Most published analysis code does not re-run. In an earlier study bundled with this repo (RUNNABILITY_STUDY.json), of 45 ReScience-C Python repositories cloned (43 evaluable, 2 dead links) only 28% ran to completion as-cloned under a 2026 environment; verified mechanical repair raised that to 37% (a further 9% rescued); the remaining 63% needed case-by-case reasoning. Dependency rot, removed APIs, environment quirks, and entry-point problems dominate — and fixing them is tedious, unrewarding, and only recently automatable, because it takes reasoning, not a fixed script.

Reproducible benchmark. That original study did not record its corpus URLs, so benchmark/rescience_manifest.json ships a fresh, re-runnable corpus of 22 Python replication repos taken from the ReScience journal bibliography. A full isolated run on a build-capable machine (benchmark/run_benchmark.py --clone --isolate, each repo in its own venv so installs can't leak between repos) measured 9/22 (41%) as-cloned → 12/22 (55%) after repro-check, with every remaining repo given a diagnosed hand-off. repro-check genuinely rescued three broken repos (henriques:2017, rostami:2017, viejo:2016 via the Py2 xrange fix). Of the ten hand-offs, most are a to-do list rather than dead ends: several are missing dependencies (install-resolvable on a machine with build tools) and a couple are removed-API drift; only one was a genuine code-logic bug correctly left to a human. Always pass --isolate for numbers you intend to quote — without it, one repo's installs leak into the next repo's as-cloned baseline and inflate the count. Regenerate the table yourself — see benchmark/README.md.

Try it in 30 seconds

pip install repro-check

Point it at a repo — a local checkout, or a git URL to clone and run in one step:

repro-check github.com/owner/repo        # clones, then runs
repro-check path/to/checkout             # or a local path

The bundled fixture is a deliberately-broken analysis (a hardcoded absolute data path + a removed np.float API) — exactly the kind of rot that stops old code:

Before — run the script the way the paper intended, and it dies:

$ python analysis.py
FileNotFoundError: [Errno 2] No such file or directory:
    '/home/researcher/project/data/measurements.csv'

After — point repro-check at the same repo:

$ repro-check fixtures/example_paper
✓ RUNS (RAN)  entry: analysis.py
  fix: repoint data path -> measurements.csv
  fix: np.float -> np.float64

It found the entry point, repaired both breakages, and proved it runs — exit code 0. When a failure instead needs your judgment, it stops honestly and tells you exactly what to do:

$ repro-check path/to/some_repo
# repro-check hand-off — needs agent
**Stopped at rung:** 0 (does not start)
**Entry point:** `run.py`

## Why it stopped
ran, but exited requiring command-line arguments (argparse)

## Suggested next action (CLI_ARGS)
Script needs run-time arguments. Read the repo README/usage for the required
flags, then re-run with them supplied.

## Run-time arguments this script needs
- required `--input` — path to the input CSV

Exit code 2 means needs a human/agent step (not a crash); 1 means a hard failure. That hand-off — not a guess — is the point. A terminal cast replaying this run (synthesized from the tool's real captured output) is in demo/quickstart.cast (play with asciinema: asciinema play demo/quickstart.cast).

Use it in CI (GitHub Action)

Guard your repo's runnability on every push. Add .github/workflows/repro-check.yml:

name: repro-check
on: [push, pull_request]
jobs:
  runnability:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: nelsonjordanme/repro-check@v0.10.2
        with:
          path: '.'
          fail-on-handoff: 'false'   # report-only; flip to 'true' to gate CI

The action installs repro-check, runs it, writes a summary panel to the job (status, entry point, fixes applied, the rung it certifies), and exposes steps.<id>.outputs.status. Exit mapping: runs → pass, hand-off → warning (fails the job only if fail-on-handoff: 'true'), hard failure → fail. Copyable examples are in examples/.

Live badge (optional). Add the badge-publish workflow from examples/badge-publish.yml — it writes a shields.io endpoint JSON to a badges branch — then embed:

![repro-check](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/OWNER/REPO/badges/badge.json)

The badge is honest by construction: it reads runs as-cloned / runs (after fixes) / needs a human step — never "reproducible", which repro-check deliberately never claims.

The model: scaffold clears the runway, agent flies the plane

repro-check owns the mechanical part and stops honestly at the judgment part:

• entry-point discovery + sane environment — finds what to run, sets PYTHONPATH, headless matplotlib, and the OpenMP duplicate-runtime workaround;
• a small set of verified mechanical fixes — removed numpy/yaml APIs, hardcoded paths, missing PyPI packages, Python-2 syntax, relative-import → run-as-module. Deliberately not an ever-growing auto-fix library;
• R projects too (v0.6) — a repo with no Python but .R/.Rmd files routes to an R engine that runs it under Rscript, installs missing CRAN/Bioconductor packages, and hands off honestly on missing data, interactive calls, or install failures;
• an honest hand-off at the seam — when a failure needs judgment, it returns a structured note: the stopping rung, what it already changed (a working migration diff), the exact traceback, and a specific keyed next action (CLI_ARGS, MISSING_DATA, DEP_INTERNAL, …). Acting on that note is the point.

It never emits a public "reproducible ✓/✗" badge. It stops at it runs and lets the human judge whether the science is sound.

Why this shape (what the study taught us)

We started intending an accumulating failure-pattern library as the core asset. The data corrected us: mechanical patterns are a small, quickly-exhausted set, and the moment one fix lands the next blocker is disproportionately a genuine human/agent step — missing data, a required run-time argument, an in-code error. So the durable value is the scaffold + honest hand-off, not the library. The pattern set is kept small and verified on purpose.

Layout

repro-check/
├── SKILL.md              # agent-facing model + usage contract
├── kernel.py             # engine: discover_entrypoint, attempt_executability,
│                         #   classify_failure, apply_patch, build_handoff, reproduce
│                         #   + R engine: attempt_r_executability, classify_r_failure
├── test_repro.py         # self-test against the bundled broken fixture
├── RUNNABILITY_STUDY.json# the 43-repo ReScience-C measurement behind the numbers
├── DEMO_end_to_end.json  # worked trace: scaffold → hand-off → agent → runs
└── fixtures/
    └── example_paper/    # a deliberately broken analysis with known ground truth
        ├── analysis.py       #   seeded bugs: hardcoded path, np.float, no seed
        ├── claims.json       #   the published numbers to check against
        └── data/measurements.csv

Quickstart

python test_repro.py
# PASS — 2 reproduced, 1 near, 0 need review
# repairs: ['PATH_HARDCODED', 'DEP_API_CHANGE']

Inside an agent session, load the skill and attempt any repo checkout:

result = attempt_executability("path/to/paper_checkout")
if result["status"] in ("RAN", "RAN_AS_IS"):
    print("runs —", result["patches"])          # what it took
else:
    print(render_handoff_md(result))             # where it stopped + next action

Then act on the hand-off: do the one judgment step suggested_next_action names (supply a CLI arg, locate a data file, pin a dependency) and re-run. See DEMO_end_to_end.json for a real worked example.

Scope & honesty

Rung 1 (runnability) is the default job; rung 2 (numeric reproduction) is opt-in and needs a human-supplied claims.json. It does not judge whether the method is correct (rung 3) or robust (rung 4). Reproducible ≠ correct: a running repo means it executes, not that the science is sound.

Status

v0.9.3 — trustworthy benchmark. The harness ran every repo in one shared environment, so a dependency installed for one repo leaked into later repos' as-cloned baseline and inflated the count (a real run drifted 8→11 as-cloned from leaked packages alone). New --isolate flag evaluates each repo in its own throwaway venv; the first isolated run measured a clean 9/22 as-cloned → 12/22 after repro-check. This is now the required setting for quotable numbers.

v0.9.2 — coverage wins from the real-repo benchmark. Running the reproducible ReScience corpus surfaced two gaps, now fixed: Python-2 builtins used at run time (xrange, unicode, basestring, raw_input, unichr, long) are rewritten to their Py3 equivalents via a token-level pass (PY2_NAME); and packaging scripts (setup.py etc.) are no longer mistaken for entry points — a repo whose only .py is packaging routes to its notebook / R content instead.

v0.9.1 — crash fix. A script that exits nonzero but prints nothing to stderr no longer crashes the engine; it hands off cleanly. Found during real-repo benchmark validation.

v0.9 — coverage + trust. Installs the repo's DECLARED environment (requirements.txt) before guessing deps one import at a time; a stale exact pin is relaxed to a floor as a flagged fix (PIN_RELAXED, "may change results"). Every green result now states its reproduction rung — certifies rung 1 (it runs), does NOT verify scientific correctness (rung 2+). And benchmark/run_benchmark.py regenerates the runnability table across a corpus so the quoted percentages are auditable and re-runnable.

v0.8 — reach. On PyPI: pip install repro-check. Runs straight from a repo URL (repro-check github.com/owner/repo shallow-clones then runs). And when the failing import is the repo's own package, an editable install (pip install -e . --no-deps) is applied automatically — closing the common "it's a package nobody installed" failure.

v0.7 — first-run experience + robustness. A "Try it in 30 seconds" before/after now leads the README, with a terminal cast in demo/. Three robustness fixes across languages: R build failures caused by a missing OS library name the exact system packages to install (R_SYSTEM_DEP); a genuine Bioconductor version-lockstep wall is surfaced honestly (R_BIOC_VERSION) rather than looping; dependency installs are gated by an available-memory check and a hard timeout, so a starved machine gets an honest "skipped" instead of an OOM-killed half-written package; and a notebook last run out of order is flagged with a caveat that a top-to-bottom run may not match the saved outputs.

v0.6 — R support. A repo with no Python entry point but .R/.Rmd files (or a DESCRIPTION) now routes automatically to an R engine: it discovers the entry script, runs it under Rscript (headless, writable user library), installs a missing CRAN or Bioconductor package, and re-runs — the same run→classify→fix→re-run→hand-off loop as Python. Grounded in an 11-repo biomedical-R feasibility pilot (R_PILOT_STUDY.json): most R failures are missing data or environment, not source-code rot, so the R fix set is install-focused (CRAN/Bioconductor) and hands off on missing data, interactive calls (file.choose/choose.dir), and install failures. If R is not installed, the engine returns an honest R_NOT_AVAILABLE note. Mixed Python+R repos still route to Python.

v0.5 — notebook support (largest .ipynb converted and run) and scope-aware NO_ENTRYPOINT reasons.

v0.3 — deepened the two hand-off / repair paths that matter most on real repos:

• Concrete run-time-argument hand-off. When a repo runs but exits demanding command-line arguments (the single most common wall past the first crash), the hand-off no longer just says "read the README" — it parses argparse output, the entry point's add_argument calls, and README examples to emit a ready-to-run suggested command, the required flags with their help text, and the data files in the repo that can fill path arguments.
• Dependency-free Python-2 print converter. Replaced the old lib2to3 fixer (removed in Python 3.13, which this project's own CI runs) with a self-contained converter that rewrites Py2 print statements and refuses to write syntactically broken source.

v0.2 — reframed from a pattern-library to a scaffold + hand-off after a 45-repo ReScience-C study (28% run as-cloned → 37% with verified repair). Engine validated on a synthetic fixture and demonstrated end-to-end on a real repo. The verified fix set is kept small on purpose; new traceback→repair patterns are welcome but only after verification on a real case.

License

MIT (suggested).