| name | pipeline-drift-check |
| description | 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", "sync check", or "doc sync". Also trigger after the user edits any pipeline argparse, README, SLURM .sh runner, or the perturbNMF-runner skill references — and any time they ask whether parameter names in .py, .sh, README, and the skill files agree.
|
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---.
- Skipped directories:
JupterNote_Version, tests/, .git, __pycache__.
How to invoke
python3 /oak/stanford/groups/engreitz/Users/ymo/Tools/PerturbNMF/.claude/skills/pipeline-drift-check/scripts/check-pipeline-drift.py
Exit code is always 0. Output is the drift report (or a "no drift detected" line).
When you find drift
For each stale arg:
- Show the user the exact file and line(s) where the stale flag appears.
- Propose the fix (remove the stale flag, rename it, or add it to the .py if it should exist).
- Ask before editing — never silently rewrite README / .sh / skill files.
- After approved edits, re-run the script to confirm the report is clean.
Skip Jupyter notebooks and tests/ content unless the user explicitly asks.
Related
- There is a global SessionStart hook at
/home/users/ymo/.claude/scripts/check-pipeline-drift.py that runs the same logic automatically at the start of every session. This skill is for on-demand invocation mid-session (e.g., right after editing argparse, README, or skill references).
- Last verification snapshot:
.claude/skills/perturbNMF-runner-workspace/iteration-1/summary.md.
