OpenROAD Bug Fixer
The-OpenROAD-Project/OpenROAD
Fixes an OpenROAD bug from a GitHub issue or error code: finds the root cause, implements the fix, adds a regression test and prepares a signed-off commit.
Generates professional maintainer-grade responses for Stereopy GitHub issues.
Install Stereopy Issue Responder
$ npx skills add STOmics/Stereopy --skill stereopy-issue-responder -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install STOmics/Stereopy stereopy-issue-responder --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.cursor/skills/stereopy-issue-responder .claude/skills/stereopy-issue-responder && rm -rf skills-srcUse ~/.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/
Install the "stereopy-issue-responder" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-issue-responder into .claude/skills/stereopy-issue-responder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-issue-responder", 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 install https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-issue-responderType 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.
$ npx skills add STOmics/Stereopy --skill stereopy-issue-responder -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install STOmics/Stereopy stereopy-issue-responder --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.cursor/skills/stereopy-issue-responder .agents/skills/stereopy-issue-responder && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "stereopy-issue-responder" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-issue-responder into .agents/skills/stereopy-issue-responder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-issue-responder", 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.
$ npx skills add STOmics/Stereopy --skill stereopy-issue-responder -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install STOmics/Stereopy stereopy-issue-responder --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.cursor/skills/stereopy-issue-responder .cursor/skills/stereopy-issue-responder && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "stereopy-issue-responder" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-issue-responder into .cursor/skills/stereopy-issue-responder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-issue-responder", 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 https://github.com/STOmics/Stereopy.git --path .cursor/skills/stereopy-issue-responder--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add STOmics/Stereopy --skill stereopy-issue-responder -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install STOmics/Stereopy stereopy-issue-responder --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.cursor/skills/stereopy-issue-responder .gemini/skills/stereopy-issue-responder && rm -rf skills-srcUse ~/.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/
Install the "stereopy-issue-responder" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-issue-responder into .gemini/skills/stereopy-issue-responder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-issue-responder", 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.
$ gh skill install STOmics/Stereopy stereopy-issue-responderInstalls 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).
$ npx skills add STOmics/Stereopy --skill stereopy-issue-responder -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .github/skills && cp -r skills-src/.cursor/skills/stereopy-issue-responder .github/skills/stereopy-issue-responder && rm -rf skills-srcUse ~/.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/
Install the "stereopy-issue-responder" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-issue-responder into .github/skills/stereopy-issue-responder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-issue-responder", 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.
$ npx skills add STOmics/Stereopy --skill stereopy-issue-responder -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install STOmics/Stereopy stereopy-issue-responder --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/STOmics/Stereopy.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.cursor/skills/stereopy-issue-responder .opencode/skills/stereopy-issue-responder && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "stereopy-issue-responder" agent skill from https://github.com/STOmics/Stereopy/tree/main/.cursor/skills/stereopy-issue-responder into .opencode/skills/stereopy-issue-responder/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "stereopy-issue-responder", 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-issue-responder- GitHub stars
- 293
- Token cost
- ~1.3k tokens
- SKILL.md length
- 401 words
- Files
- 1
- Skills in repo
- 2
- Repo updated
- First seen
- Licence
- MIT
At a glance
Generates professional maintainer-grade responses for Stereopy GitHub issues.
- Works in 5 steps: classify issue type, → lead with a short answer, → explain findings grounded in code… → …
- The user asks to analyze an issue
- SKILL.md covers Purpose, Required Workflow, Response Template and Tone and Quality Bar, plus 2 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Stereopy Issue Responder is an agent skill from STOmics/Stereopy. Generates professional maintainer-grade responses for Stereopy GitHub issues. Use when the user asks to analyze an issue, draft a maintainer reply, classify bug vs usage question, explain root cause, propose fix plans, or provide clear next steps in English.
Its SKILL.md is about 1.3k 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 Root cause analysis. It works with GitHub. The repository describes itself as: A toolkit of spatial transcriptomic analysis. The licence is MIT.
When your agent uses it
- The user asks to analyze an issue
- Draft a maintainer reply
- Classify bug vs usage question
- Explain root cause
Example prompts
- “Use the stereopy-issue-responder skill to generate professional maintainer-grade responses for Stereopy GitHub issues”
- “/stereopy-issue-responder”
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- classify issue type,
- lead with a short answer,
- explain findings grounded in code behavior,
- propose actionable next steps with structured formatting,
- avoid speculation.
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
No scripts in the folder and no shell commands in SKILL.md (its code samples are markdown).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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 Issue Responder loads about 1.3k tokens when it runs. Until then it costs about 71 tokens; SKILL.md has 401 words of instructions outside code blocks.
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). 401 words, ~1,297 tokens.
Download SKILL.mdSave it as
.claude/skills/stereopy-issue-responder/SKILL.md (or your agent's skills folder).- name
- stereopy-issue-responder
- description
- Generates professional maintainer-grade responses for Stereopy GitHub issues. Use when the user asks to analyze an issue, draft a maintainer reply, classify bug vs usage question, explain root cause, propose fix plans, or provide clear next steps in English.
Stereopy Issue Responder
Purpose
Provide warm, professional, and maintainer-style issue responses in English for the Stereopy project.
The response should:
- classify issue type,
- lead with a short answer,
- explain findings grounded in code behavior,
- propose actionable next steps with structured formatting,
- avoid speculation.
Required Workflow
When asked about an issue:
Classify first
bugusage / questionfeature requestneeds more information
Ground in implementation
- Reference likely modules/functions in
stereo/:stereo/core/stereo_exp_data.pystereo/core/st_pipeline.pystereo/core/result.pystereo/io/reader.pystereo/io/writer.pystereo/io/h5ad.pystereo/tools/*stereo/algorithm/*
- Use concrete behavior (types, result key conventions, io branches), not generic guesses.
- Reference likely modules/functions in
Apply Stereopy-specific checks
exp_matrixmay benp.ndarrayorscipy.sparsedata.tl.result[key]may bedictorDataFrame- H5AD can be standard AnnData or Stereopy-extended
cell_binsoften impliesbin_size=1
Deliver response in maintainer format
- Use the Response Template below
- Adapt wording to each specific issue — never sound robotic or copy-paste
Response Template
Dear @{username},
Thank you for {reporting this issue / your interest in Stereopy / reaching out}!
**Short answer:** {One-sentence conclusion or direct answer to the user's question.}
---
## Assessment
- **Type:** {bug | usage/question | feature request | needs-info}
- **Severity:** {low | medium | high}
- **Affected module:** `{stereo/path/file.py}`
## What Is Happening
{1-2 paragraphs explaining the behavior from a code-level perspective.
Reference specific files and functions. Be precise but accessible.}
## Is This Expected?
{Yes/No + brief explanation of why.}
## Recommended Workflow
**Step 1:** {First action}
{Concrete instructions, code snippet, or command.}
**Step 2:** {Second action}
{Concrete instructions.}
**Step 3 (optional):** {Third action}
## Useful References
| Resource | Purpose |
|----------|---------|
| [Tutorial/Doc Name](link) | Brief description |
| [API Reference](link) | Brief description |
## Alternative Approaches
If {condition or preference}:
- **Option A:** {Description with brief rationale}
- **Option B:** {Description with brief rationale}
## Notes
- {Important caveat or tip 1}
- {Important caveat or tip 2}
- {Important caveat or tip 3}
## Maintainer Note
{If bug: likely fix location, root cause summary, minimal fix scope.}
{If not bug: doc improvement or example to add.}
Please let us know if you have further questions!
Best regards,
Stereopy MaintainerTemplate Usage Rules
- Always include: Dear + Short answer + Assessment + What Is Happening + Recommended Workflow + closing
- Include when applicable: Useful References, Alternative Approaches, Notes, Maintainer Note
- Omit sections that are not relevant — do not leave empty sections
- For
bugtype: always include Maintainer Note - For
usage/questiontype: always include Useful References and Alternative Approaches if they exist - For
needs-infotype: keep it short — Assessment + what is missing + closing
Show full SKILL.md (188 more words)Show less
Tone and Quality Bar
- Address the user by their GitHub username: "Dear @username,"
- Always lead with a Short Answer (1 sentence) before detailed analysis
- Use tables for tutorials, references, and comparisons
- Provide Alternative Approaches when applicable
- Warm, professional, like a senior colleague helping a junior researcher
- No blame, no overconfident claims without evidence
- Prefer "Based on current implementation..." when certainty is limited
- Keep it practical and reproducible
- End with "Please let us know if you have further questions!"
- Sign off with "Best regards, Stereopy Maintainer"
Rules for Classification
Mark as bug only if at least one is true:
- traceback points into Stereopy logic and behavior is unintended;
- code path clearly mishandles data types/keys/format branches;
- output contradicts documented semantics.
Mark as usage/question if:
- behavior follows implementation conventions;
- user asks about interpretation, tolerance, reliability, parameter choice.
Mark as needs-info if missing:
- traceback,
- minimal reproducible snippet,
- file format + key parameters,
- version/environment details.
Bug-Pattern Hints
Check these first:
- Result-key / DataFrame key mismatch (
result.py) - Sparse-vs-dense assumptions (
issparsemissing) - H5AD Group vs Dataset branch mismatch (
reader.py/h5ad.py) - MSData scope-key misuse (
ms_pipeline.py) - Statistical edge cases in marker tests (
find_markers.py,mannwhitneyu.py)
© STOmics, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in .cursor/skills/stereopy-issue-responder of STOmics/Stereopy.
Open the folder on GitHubat commit 2b21b00
Compare with similar skills
Stereopy Issue Responder 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Stereopy Issue Responder this skillSTOmics/Stereopy | 293 | — | ~1.3k | Automated safety check: Pass | MIT | |
| OpenROAD Bug FixerThe-OpenROAD-Project/OpenROAD | 3.2k | — | ~784 | Automated safety check: Pass | BSD-3-Clause | |
| Octocode Code Researchbgauryy/octocode | 949 | — | ~1.5k | Automated safety check: Pass | MIT | |
| Triagebot Action Bug Triagewithastro/astro | 63k | — | ~639 | Automated safety check: Pass | Custom licence | |
| CI TriageMentra-Community/MentraOS | 2.4k | — | ~582 | Automated safety check: Pass | Apache-2.0 | |
| Reviewing Pull RequestsShopify/shopify-app-js | 543 | — | ~1.9k | Automated safety check: Pass | MIT |
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- Official
Triagebot Action Bug Triage
withastro/astro
Takes a bug report for the triagebot-action GitHub Action through reproduction, root-cause diagnosis, an intended-behavior check and a fix attempt.
CI Triage
Mentra-Community/MentraOS
Triage failing GitHub PR checks: list failures with gh, fetch capped Actions logs, skip non-Actions checks, and summarize root cause.
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Reviewing Pull Requests
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Reviews pull requests for Shopify/shopify-app-js with comprehensive analysis including semver compliance (MAJOR/MINOR/PATCH classification), single responsibility validation, pattern consistency…
Issue Brief
VasiHemanth/tokentelemetry
Explain a GitHub issue, discussion, or feature request in plain language before deciding whether to build it.
More from STOmics/Stereopy
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Works with
Categories
Questions about Stereopy Issue Responder
What does Stereopy Issue Responder do?
Generates professional maintainer-grade responses for Stereopy GitHub issues. Stereopy Issue Responder is an agent skill from STOmics/Stereopy. Generates professional maintainer-grade responses for Stereopy GitHub issues.
When should I use Stereopy Issue Responder?
Stereopy Issue Responder fits situations like: the user asks to analyze an issue; draft a maintainer reply; classify bug vs usage question; explain root cause.
How do I install Stereopy Issue Responder in Claude Code?
Run `npx skills add STOmics/Stereopy --skill stereopy-issue-responder -a claude-code`. Or copy the skill folder (.cursor/skills/stereopy-issue-responder in STOmics/Stereopy) into .claude/skills/stereopy-issue-responder in your project. Claude Code loads it when a task matches its description.
How do I install Stereopy Issue Responder in Codex?
Run `npx skills add STOmics/Stereopy --skill stereopy-issue-responder -a codex`. Or copy the skill folder (.cursor/skills/stereopy-issue-responder in STOmics/Stereopy) into .agents/skills/stereopy-issue-responder in your project. Codex loads it when a task matches its description.
Can I use Stereopy Issue Responder 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-issue-responder -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-issue-responder, .gemini/skills/stereopy-issue-responder, .github/skills/stereopy-issue-responder and .opencode/skills/stereopy-issue-responder in your project.
What does Stereopy Issue Responder need to run?
SKILL.md names no scripts, command-line tools or credentials: Stereopy Issue Responder is instructions for the agent only.
Does Stereopy Issue Responder access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Stereopy Issue Responder 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 Issue Responder use?
Stereopy Issue Responder 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 Issue Responder use?
About 1.3k tokens (SKILL.md is roughly 5.2k 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 Issue Responder?
Skills that share tags, products or a category with Stereopy Issue Responder: OpenROAD Bug Fixer (The-OpenROAD-Project/OpenROAD, 3.2k stars), Octocode Code Research (bgauryy/octocode, 949 stars), Triagebot Action Bug Triage (withastro/astro, 63k stars) and CI Triage (Mentra-Community/MentraOS, 2.4k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Stereopy Issue Responder?
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.