openproblems-submission

openproblems-submission is a cursor rule for Cursor from Rebell-Leader/SpatialAI_MCP. It costs 49 tokens per session (668 once invoked), scanned A, original, Apache-2.0.

A checklist for preparing a spatial transcriptomics method for an OpenProblems benchmark, a shared test suite for biological data-analysis methods. It covers the files, data formats, tests, and metadata needed for a contribution.

In plain words
What is it for?
Use it when adding a method to an OpenProblems task repository, checking whether a submission is ready, or preparing a Viash component for testing.
Why use it?
It helps catch interface, data, build, and reproducibility problems before you open a pull request.

Cursor rule for Cursor

Written for Cursor: installed under .cursor/. Also seen: mentions AGENTS.md.

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add rules/rebell-leader/spatialai_mcp/openproblems-submission
Clone the repo
git clone --depth 1 https://github.com/Rebell-Leader/SpatialAI_MCP

Made for: Cursor.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for openproblems-submission

README.md
[![agentmods](https://agentmods.dev/badge/rules/rebell-leader/spatialai_mcp/openproblems-submission.svg)](https://agentmods.dev/rules/rebell-leader/spatialai_mcp/openproblems-submission)
Your own site
<a href="https://agentmods.dev/rules/rebell-leader/spatialai_mcp/openproblems-submission"><img src="https://agentmods.dev/badge/rules/rebell-leader/spatialai_mcp/openproblems-submission.svg" alt="Measured on agentmods" height="20"></a>
Per session 49 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 668 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00049 $0.00668
Opus 5 $0.00024 $0.00334
Sonnet 5 $0.00010 $0.00134
Haiku 4.5 $0.00005 $0.00067

Measured 5d ago against content hash dec752437ea2, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-06, from the pricing page.

Security

Grade A, and why

openproblems-submission scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 5d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.cursor/rules/openproblems-submission.mdc · 54 lines

How it starts

The opening of the file, as written. The whole thing — 54 lines — stays where its author put it; the contents beside it link to each section on GitHub.

OpenProblems submission

Goal: a Viash component that conforms to a task's API, builds cleanly, passes the test profile, and is reproducible — ready for a PR.

Checklist

  1. Repo setup. Clone the target task_* repo and initialize the common/ git submodule (git submodule update --init --recursive). Read the repo's CONTRIBUTING / README for current conventions.

  2. Conform to the component API. Your config.vsh.yaml must __merge__ the correct comp_<stage>.yaml interface and match its inputs/outputs and info/metadata fields. Run analyze_workflow_configuration on the config.

  3. Data contract. Inputs/outputs are SpatialData (zarr) / AnnData as the stage requires. Validate test data with validate_spatial_data and confirm the elements the stage needs are present (check_spatial_data_compatibility for multi-file). State raw-vs-normalized expectations explicitly.

  4. Reproducibility. Build on the shared base images (openproblems/base_python:1 / base_r:1) with __merge__-ed setup partials rather than raw python:*/r-base images. Pin base-image tags and package versions — no unpinned latest. Provide the standard metadata (label, summary, description, links, references/doi) and document every parameter with a default and biological rationale.

  5. Build & test locally (server doesn't run these — use the terminal):

    • viash ns build
    • viash run config.vsh.yaml -- --input <test>.zarr --output tmp/out.zarr
    • viash test config.vsh.yaml — a unit test (test_resources) is expected for every component
    • nextflow run main.nf -profile test,docker
  6. Dependency sanity. Run analyze_workflow_dependencies across the workflow files to catch missing/conflicting containers or libraries.

  7. PR hygiene. Include test data + expected output, document parameter choices, and confirm CI (GitHub Actions) builds and runs the component.

Read the full file on GitHub · 54 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 5d ago First seen · 54 lines · 49 tokens per session scan A dec752437ea2

Subscribe to this mod's changes

openproblems-submission is a cursor rule published in the GitHub repository Rebell-Leader/SpatialAI_MCP (4 stars, last pushed 2mo ago), licensed Apache-2.0. It adds 49 tokens to every session and 668 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.