run-tests SKILL.md skillA
run-tests 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/run-tests@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/run-tests/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260929.add0212, committed Sep 29, 2026
- First version recorded
- Apr 24, 2026
- Size
- 10,091 bytes
- Repository stars
- 10
- License
- MIT
Run the cNMF benchmarking pipeline test suite end-to-end: clean previous outputs, run sk-cNMF (CPU) and torch-cNMF (GPU via SLURM) inference tests, evaluation tests, and summarize pass/fail results. Use this skill whenever the user says "run tests", "run the tests", "test the pipeline", "rerun tests", "run sk-cNMF tests", "run torch tests", "run inference tests", "run evaluation tests", or any variation asking to execute, rerun, or check the cNMF test suite. Also trigger when the user asks to…
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
# Run Tests Skill Run the cNMF benchmarking pipeline test suite. This cleans previous output, runs tests, and summarizes results. ## Environment - **Pipeline root**: `$PIPELINE_ROOT` — your PerturbNMF checkout (the SLURM test scripts require `export PIPELINE_ROOT=/path/to/PerturbNMF`) - **Inference tests**: `tests/Script/Stage1_Inference/` - **Evaluation tests**: `tests/Script/Stage2_Evaluation/` - **Output directory**: `tests/output/` - **Mini test dataset**: `tests/data/mini_ccperturb.h5ad` - **Inference conftest**: `tests/Script/Stage1_Inference/conftest.py` (fixtures, shared params) - **Evaluation conftest**: `tests/Script/Stage2_Evaluation/conftest.py` (h5mu loading, --inference-path) ## Test Suite ### Inference Tests | Test File | Backend | Runs on | Tests | Command | |-----------|---------|---------|-------|---------| | `tests/Script/Stage1_Inference/test_inference_sklearn.py` | sk-cNMF | CPU (direct or SLURM) | 9 (end-to-end + output assertion) | `python -m pytest tests/Script/Stage1_Inference/test_inference_sklearn.py -v --tb=short` | …
Read the whole file at its exact version.
How to install
mdr add engreitzlab/perturbnmf/run-tests@sha256:6a30e6827a9643a7The 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_q2gobk6mrcxojes7)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between Apr 24, 2026 and Sep 29, 2026, about one every 39 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.add0212 latest | 2026-09-29 | add0212 | 10,091 B | A | view · diff |
| git:20260605.fc130a2 | 2026-06-05 | fc130a2 | 10,087 B | A | view · diff |
| git:20260511.64275e1 | 2026-05-11 | 64275e1 | 10,202 B | A | view · diff |
| git:20260501.4bf662a | 2026-05-01 | 4bf662a | 9,673 B | A | view · diff |
| git:20260424.4c73572 | 2026-04-24 | 4c73572 | 9,249 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 (10091 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_q2gobk6mrcxojes7 GET https://markdownregistry.com/api/v1/resolve?ref=engreitzlab/perturbnmf/run-tests GET https://markdownregistry.com/api/v1/blob/6a30e6827a9643a7894e416690b90dca6720852d8fbf3fd6d7365e8d4c575fe7
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.
More from engreitzlab/perturbnmf
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