pipeline-drift-check SKILL.md skillA
pipeline-drift-check from engreitzlab/perturbnmf is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add engreitzlab/perturbnmf/pipeline-drift-check@git:20260929.add0212Pins git:20260929.add0212 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- engreitzlab/perturbnmf
- Path
.claude/skills/pipeline-drift-check/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260929.add0212, committed Sep 29, 2026
- First version recorded
- Jun 9, 2026
- Size
- 3,022 bytes
- Repository stars
- 10
- License
- MIT
Detect parameter drift across the PerturbNMF pipeline. Cross-checks every `--flag` defined in `src/**/*.py` (argparse) and `src/**/*.R` (optparse) against what is mentioned in sibling README.md files, sibling .sh runners, and the perturbNMF-runner skill markdown (SKILL.md + references/*.md). Use this skill whenever the user says "check drift", "drift check", "check parameter drift", "run drift check", "are the docs in sync", "did I update everything", "check if README/sh/skill match the .py…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Pipeline Drift Check Skill
Detect param drift between source-of-truth argparse definitions and documentation/runner consumers in the PerturbNMF pipeline.
## What it checks
Source of truth: `add_argument("--flag", ...)` in every `src/**/*.py` and `make_option("--flag", ...)` in every `src/**/*.R`.
Consumers checked:
- **Sibling README.md** of each pipeline script — `--flag` mentions and `## Parameters` table rows must exist in that script's argparse.
- **Sibling .sh runner** — flags inside the `python3 <pipeline.py>` (or `Rscript`) block must exist in that script.
- **Skill markdown** (`.claude/skills/**/*.md`) — every `--flag` mentioned must be defined in *some* pipeline .py/.R, OR in a skill helper script under `.claude/skills/**/scripts/*.py`, OR in a test `conftest.py` `addoption()`.
## Suppressions (intentional, not bugs)
- Lines containing rename notes (`→`, `->`, "renamed", "formerly", "is now") — old names are documentation.
- Lines mentioning external CLI tools (`sacct`, `sbatch`, `jupyter`, `pytest`, etc.) — their flags belong to those tools.
- Wildcard prose placeholders like `--foo_*`.
- Skill convention placeholders: `--flag`, `--flag_name`, `---COMMENTED---`.
…Read the whole file at its exact version.
How to install
mdr add engreitzlab/perturbnmf/pipeline-drift-check@sha256:cfe4ff29de30a8afThe line at the top of this page pins the label git:20260929.add0212, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_qzsu6zvztxwowdbx)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between Jun 9, 2026 and Sep 29, 2026, about one every 112 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.add0212 latest | 2026-09-29 | add0212 | 3,022 B | A | view · diff |
| git:20260609.6e55238 | 2026-06-09 | 6e55238 | 3,210 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (3022 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
engreitzlab/perturbnmf · 10 stars · license MIT · pushed 2026-10-20 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_qzsu6zvztxwowdbx GET https://markdownregistry.com/api/v1/resolve?ref=engreitzlab/perturbnmf/pipeline-drift-check GET https://markdownregistry.com/api/v1/blob/cfe4ff29de30a8af8fd96e950aa8a41a9c30a8354ca68d58c4d11fbdb4b4df37
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.