Agent skill

Stereopy Maintainer

Stereopy project maintenance guide for code review, bug fixing, and feature development.

MITAuto-check passedDevelopment

Install Stereopy Maintainer

skills CLI

$ npx skills add STOmics/Stereopy --skill stereopy-maintainer -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install STOmics/Stereopy stereopy-maintainer --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.cursor/skills/stereopy-maintainer .claude/skills/stereopy-maintainer && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "stereopy-maintainer" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-maintainer into .claude/skills/stereopy-maintainer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-maintainer", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-maintainer

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add STOmics/Stereopy --skill stereopy-maintainer -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install STOmics/Stereopy stereopy-maintainer --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.cursor/skills/stereopy-maintainer .agents/skills/stereopy-maintainer && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "stereopy-maintainer" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-maintainer into .agents/skills/stereopy-maintainer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-maintainer", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add STOmics/Stereopy --skill stereopy-maintainer -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install STOmics/Stereopy stereopy-maintainer --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.cursor/skills/stereopy-maintainer .cursor/skills/stereopy-maintainer && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "stereopy-maintainer" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-maintainer into .cursor/skills/stereopy-maintainer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-maintainer", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/STOmics/Stereopy.git --path .cursor/skills/stereopy-maintainer

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add STOmics/Stereopy --skill stereopy-maintainer -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install STOmics/Stereopy stereopy-maintainer --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.cursor/skills/stereopy-maintainer .gemini/skills/stereopy-maintainer && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "stereopy-maintainer" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-maintainer into .gemini/skills/stereopy-maintainer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-maintainer", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install STOmics/Stereopy stereopy-maintainer

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add STOmics/Stereopy --skill stereopy-maintainer -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .github/skills && cp -r skills-src/.cursor/skills/stereopy-maintainer .github/skills/stereopy-maintainer && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "stereopy-maintainer" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-maintainer into .github/skills/stereopy-maintainer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-maintainer", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add STOmics/Stereopy --skill stereopy-maintainer -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install STOmics/Stereopy stereopy-maintainer --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.cursor/skills/stereopy-maintainer .opencode/skills/stereopy-maintainer && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "stereopy-maintainer" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-maintainer into .opencode/skills/stereopy-maintainer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-maintainer", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: stereopy-maintainer
GitHub stars: 293
Token cost: ~1.7k tokens
SKILL.md length: 583 words
Files: 1
Skills in repo: 2
Repo updated: Jul 17, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Stereopy project maintenance guide for code review, bug fixing, and feature development.

Works in 6 steps: KeyError in result.py — key not… → sparse/dense mismatch — code assumes… → H5AD format confusion — Stereopy adds… → …
Working on stereo/ source code
SKILL.md covers Architecture at a Glance, Critical Type Guards, Module Map and Known Bug Patterns, plus 5 more sections
Calls python, pip and pytest

What it does

Stereopy Maintainer is an agent skill from STOmics/Stereopy. Stereopy project maintenance guide for code review, bug fixing, and feature development. Use when working on stereo/ source code, fixing GitHub issues, reviewing PRs, adding tools or algorithms, modifying I/O formats, or debugging data pipeline errors.

Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Development, covering Debugging and Data pipelines and ETL. It works with GitHub. The repository describes itself as: A toolkit of spatial transcriptomic analysis. The licence is MIT.

When your agent uses it

Working on stereo/ source code
Fixing GitHub issues
Modifying I/O formats
Debugging data pipeline errors

Example prompts

“/stereopy-maintainer”

Requirements

Python 3

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

KeyError in result.py — key not registered, or DataFrame column renamed
sparse/dense mismatch — code assumes ndarray but gets csr_matrix
H5AD format confusion — Stereopy adds custom groups (exp_matrix@raw, sn, layers)
MSData scope_key — generate_scope_key(scope) not generate_scope_key(_names)
mannwhitneyu overflow — NaN/inf or all-zero columns in input
DataFrame column mismatch — df['gene_name'] vs df['genes'] vs var.index

What it can do on your machine

Read from SKILL.md and the folder at commit 2b21b00. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
- python
- pip
- pytest
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Stereopy Maintainer loads about 1.7k tokens when it runs. Until then it costs about 68 tokens; SKILL.md has 583 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~68
When it runs · the whole SKILL.md, loaded when a task matches: ~1.7k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from STOmics/Stereopy at commit 2b21b00, republished under its MIT licence (© STOmics). 583 words, ~1,654 tokens.

Download SKILL.mdSave it as .claude/skills/stereopy-maintainer/SKILL.md (or your agent's skills folder).

name: stereopy-maintainer
description: Stereopy project maintenance guide for code review, bug fixing, and feature development. Use when working on stereo/ source code, fixing GitHub issues, reviewing PRs, adding tools or algorithms, modifying I/O formats, or debugging data pipeline errors.

Stereopy Maintainer Skill

Architecture at a Glance

StereoExpData (stereo/core/stereo_exp_data.py)
│  Core container: exp_matrix, cells, genes, position
│  exp_matrix: np.ndarray | scipy.sparse.spmatrix
│  bin_type: 'bins' | 'cell_bins'
│
├── .tl → StPipeline (stereo/core/st_pipeline.py)
│   │  Runs tools, stores results
│   └── .result → Result (stereo/core/result.py)
│       Dict-like, keys categorized by type:
│       CLUSTER: leiden, louvain, phenograph, annotation
│       REDUCE: umap, pca, tsne
│       CONNECTIVITY: neighbors
│       HVG: highly_variable_genes → renamed 'hvg'
│       MARKER_GENES: marker_genes → renamed 'rank_genes_groups'
│       SCT: sctransform
│
├── AnnBasedStereoExpData (AnnData-backed variant)
│   └── .tl.result → AnnBasedResult
│
└── MSData (stereo/core/ms_data.py)
    │  Multi-sample container, holds multiple StereoExpData
    └── .tl → MSDataPipeLine (stereo/core/ms_pipeline.py)

Critical Type Guards

Always check these before operating — runtime types vary:

Variable	Possible Types	Guard
`exp_matrix`	`np.ndarray`, `scipy.sparse.*`	`issparse(m)`
`data.tl.result[key]`	`dict`, `pd.DataFrame`	`isinstance(v, dict)`
`Cell/Gene .to_df()` columns	`str`, `object`	`.astype(str)`
H5AD format	standard AnnData, Stereopy-extended	check for `@` keys

Module Map

Module	Path	Responsibility
Data model	`stereo/core/stereo_exp_data.py`	`StereoExpData`, `AnnBasedStereoExpData`
Cell/Gene	`stereo/core/cell.py`, `gene.py`	Cell and Gene metadata containers
Pipeline	`stereo/core/st_pipeline.py`	Tool execution, `@logit` decorator
Multi-sample	`stereo/core/ms_data.py`, `ms_pipeline.py`	`MSData`, scope management
Results	`stereo/core/result.py`	`Result`, `AnnBasedResult`, key routing
Reader	`stereo/io/reader.py`	Multi-format input (h5ad, gef, gem, loom, h5ms)
Writer	`stereo/io/writer.py`	Multi-format output
H5AD helpers	`stereo/io/h5ad.py`	Low-level HDF5 read/write
Tools	`stereo/tools/*.py`	High-level analysis (clustering, markers, dim_reduce)
Algorithms	`stereo/algorithm/*.py`	Low-level compute (mannwhitneyu, sctransform)
Plots	`stereo/plots/*.py`	Visualization
Config	`stereo/stereo_config.py`	Global settings
Logging	`stereo/log_manager.py`	`logger` instance

Known Bug Patterns

When diagnosing issues, check these patterns first:

KeyError in result.py — key not registered, or DataFrame column renamed
- Check RENAME_DICT, CLUSTER_NAMES, MARKER_GENES_NAMES
- Result value can be dict or DataFrame — caller must handle both
sparse/dense mismatch — code assumes ndarray but gets csr_matrix
- Always use issparse() before .toarray(), indexing, or arithmetic
- exp_matrix type depends on file format and preprocessing history
H5AD format confusion — Stereopy adds custom groups (exp_matrix@raw, sn, layers)
- Standard AnnData readers won't find these
- reader.py handles both formats, check isinstance(f[k], h5py.Group) vs Dataset
MSData scope_key — generate_scope_key(scope) not generate_scope_key(_names)
- scope is the correct parameter, not the internal _names attribute
mannwhitneyu overflow — NaN/inf or all-zero columns in input
- Pre-filter with x_mask for valid indices
DataFrame column mismatch — df['gene_name'] vs df['genes'] vs var.index
- Use .loc[df['genes'], 'real_gene_name'] pattern for safe access

Code Style

4-space indentation, no tabs
Google-style docstrings with Parameters / Returns sections
Import order: stdlib → third-party (numpy, pandas, scipy, anndata) → local (stereo.*)
Logging: from stereo.log_manager import logger
Type hints optional but encouraged
Tools registered via StPipeline methods with @logit decorator

Development Workflow

Fixing a Bug

Read the traceback — extract file path, line number, error type
Locate the code — read the full function containing the bug
Understand context — trace data flow through the pipeline
Check type guards — is it a sparse/dense or dict/DataFrame issue?
Minimal fix — only change what's broken
Verify syntax — python -c "import ast; ast.parse(open('file.py').read())"
Verify import — PYTHONPATH=. python -c "from stereo.module import Class"
Commit — fix #N: brief description

Show full SKILL.md (206 more words)Show less

Adding a New Tool

Create stereo/tools/your_tool.py
Add method to StPipeline in stereo/core/st_pipeline.py
Register result key in Result categories if needed
Add corresponding test in tests/test_your_tool.py
Add plotting if applicable in stereo/plots/

Adding a New Algorithm

Create stereo/algorithm/your_algo.py or subpackage
Wire it from a tool in stereo/tools/
Handle sparse/dense input explicitly
Add to __init__.py exports if public

Modifying I/O

Reader changes go in stereo/io/reader.py
Writer changes go in stereo/io/writer.py
Low-level HDF5 operations use stereo/io/h5ad.py
Always handle both h5py.Group and h5py.Dataset for H5AD keys
Test with both standard AnnData and Stereopy-extended H5AD files

Testing

Test files: tests/test_*.py, pytest style
Stereopy has heavy dependencies — avoid pip install stereopy in CI
Use PYTHONPATH=. for import-based testing
For quick validation: AST parse + import check
Full test suite run via pytest tests/ -x --tb=short

File Format Reference

Format	Ext	Reader Function	Notes
H5AD	`.h5ad`	`read_stereo_h5ad`	Stereopy extended with `@` groups
H5MS	`.h5ms`	`read_h5ms`	Multi-sample, Stereopy-specific
GEF	`.gef`	`read_gef`	BGI spatial format
GEM	`.gem`	`read_gem`	Tab-separated text
Loom	`.loom`	`read_loom`	HDF5-based

Constraints

Only modify stereo/ and tests/
Never change pyproject.toml, .github/, or version numbers
requires-python: >=3.8, <3.9 — be careful with newer syntax
Dependencies managed in requirements.txt, not inline
MIT License

Files

Just SKILL.md in .cursor/skills/stereopy-maintainer of STOmics/Stereopy.

Open the folder on GitHubat commit 2b21b00

Compare with similar skills

Stereopy Maintainer next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Stereopy Maintainer compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Stereopy Maintainer this skillSTOmics/Stereopy	293	—	~1.7k	Automated safety check: Pass	MIT	2 mo ago
Debugging Dagsastronomer/agents	451	—	~1.9k	Automated safety check: Pass	Apache-2.0	yesterday
Exposed Bug Fix WorkflowJetBrains/Exposed	9.3k	—	~3.8k	Automated safety check: Pass	Apache-2.0	today
OpenCLI Adapter Autofixjackwener/OpenCLI	30k	1 repos	~3.2k	Automated safety check: Pass	Apache-2.0	14 days ago
Issue Fixmono/SkiaSharp	5.6k	—	~5.1k	Automated safety check: Pass	MIT	today
React Router Bug Fix Workflowremix-run/react-router	57k	—	~1.3k	Automated safety check: Pass	MIT	today

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Questions about Stereopy Maintainer

What does Stereopy Maintainer do?

Stereopy project maintenance guide for code review, bug fixing, and feature development. Stereopy Maintainer is an agent skill from STOmics/Stereopy. Stereopy project maintenance guide for code review, bug fixing, and feature development.

When should I use Stereopy Maintainer?

Stereopy Maintainer fits situations like: working on stereo/ source code; fixing GitHub issues; modifying I/O formats; debugging data pipeline errors.

How do I install Stereopy Maintainer in Claude Code?

Run `npx skills add STOmics/Stereopy --skill stereopy-maintainer -a claude-code`. Or copy the skill folder (.cursor/skills/stereopy-maintainer in STOmics/Stereopy) into .claude/skills/stereopy-maintainer in your project. Claude Code loads it when a task matches its description.

How do I install Stereopy Maintainer in Codex?

Run `npx skills add STOmics/Stereopy --skill stereopy-maintainer -a codex`. Or copy the skill folder (.cursor/skills/stereopy-maintainer in STOmics/Stereopy) into .agents/skills/stereopy-maintainer in your project. Codex loads it when a task matches its description.

Can I use Stereopy Maintainer in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add STOmics/Stereopy --skill stereopy-maintainer -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/stereopy-maintainer, .gemini/skills/stereopy-maintainer, .github/skills/stereopy-maintainer and .opencode/skills/stereopy-maintainer in your project.

What does Stereopy Maintainer need to run?

Going by SKILL.md and its folder, Stereopy Maintainer needs the command-line tools its instructions call (python, pip and pytest). Our summary lists: Python 3.

Does Stereopy Maintainer access the network?

SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Stereopy Maintainer safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Stereopy Maintainer use?

Stereopy Maintainer is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Stereopy Maintainer use?

About 1.7k tokens (SKILL.md is roughly 6.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Stereopy Maintainer?

Skills that share tags, products or a category with Stereopy Maintainer: Debugging Dags (astronomer/agents, 451 stars), Exposed Bug Fix Workflow (JetBrains/Exposed, 9.3k stars), OpenCLI Adapter Autofix (jackwener/OpenCLI, 30k stars) and Issue Fix (mono/SkiaSharp, 5.6k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Stereopy Maintainer?

STOmics (a GitHub organization) maintains it in STOmics/Stereopy, which has 293 GitHub stars. The repository holds 2 skills in this directory. The repository was last updated on July 17, 2026.

Source: STOmics/Stereopy on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Stereopy Maintainer

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Stereopy Maintainer Skill

Architecture at a Glance

Critical Type Guards

Module Map

Known Bug Patterns

Code Style

Development Workflow

Fixing a Bug

Adding a New Tool

Adding a New Algorithm

Modifying I/O

Testing

File Format Reference

Constraints

Files

Compare with similar skills

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Questions about Stereopy Maintainer