MCP Server Builder
anthropics/skills
Guides the design and implementation of Model Context Protocol servers in TypeScript or Python, from tool naming and error messages to evaluation.
Convert an existing legacy pypath input module from pypath.inputs into a modern inputsv2 module.
GPL-3.0Auto-check passed
Install Inputs V2 Convert Legacy
$ npx skills add saezlab/pypath --skill inputs-v2-convert-legacy -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install saezlab/pypath inputs-v2-convert-legacy --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/saezlab/pypath.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.agents/skills/inputs-v2-convert-legacy .claude/skills/inputs-v2-convert-legacy && 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 "inputs-v2-convert-legacy" agent skill from https://github.com/saezlab/pypath/tree/master/.agents/skills/inputs-v2-convert-legacy into .claude/skills/inputs-v2-convert-legacy/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inputs-v2-convert-legacy", 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/saezlab/pypath/tree/master/.agents/skills/inputs-v2-convert-legacyType 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 saezlab/pypath --skill inputs-v2-convert-legacy -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install saezlab/pypath inputs-v2-convert-legacy --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/saezlab/pypath.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.agents/skills/inputs-v2-convert-legacy .agents/skills/inputs-v2-convert-legacy && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "inputs-v2-convert-legacy" agent skill from https://github.com/saezlab/pypath/tree/master/.agents/skills/inputs-v2-convert-legacy into .agents/skills/inputs-v2-convert-legacy/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inputs-v2-convert-legacy", 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 saezlab/pypath --skill inputs-v2-convert-legacy -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install saezlab/pypath inputs-v2-convert-legacy --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/saezlab/pypath.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.agents/skills/inputs-v2-convert-legacy .cursor/skills/inputs-v2-convert-legacy && 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 "inputs-v2-convert-legacy" agent skill from https://github.com/saezlab/pypath/tree/master/.agents/skills/inputs-v2-convert-legacy into .cursor/skills/inputs-v2-convert-legacy/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inputs-v2-convert-legacy", 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/saezlab/pypath.git --path .agents/skills/inputs-v2-convert-legacy--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 saezlab/pypath --skill inputs-v2-convert-legacy -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install saezlab/pypath inputs-v2-convert-legacy --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/saezlab/pypath.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.agents/skills/inputs-v2-convert-legacy .gemini/skills/inputs-v2-convert-legacy && 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 "inputs-v2-convert-legacy" agent skill from https://github.com/saezlab/pypath/tree/master/.agents/skills/inputs-v2-convert-legacy into .gemini/skills/inputs-v2-convert-legacy/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inputs-v2-convert-legacy", 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 saezlab/pypath inputs-v2-convert-legacyInstalls 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 saezlab/pypath --skill inputs-v2-convert-legacy -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/saezlab/pypath.git skills-src && mkdir -p .github/skills && cp -r skills-src/.agents/skills/inputs-v2-convert-legacy .github/skills/inputs-v2-convert-legacy && 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 "inputs-v2-convert-legacy" agent skill from https://github.com/saezlab/pypath/tree/master/.agents/skills/inputs-v2-convert-legacy into .github/skills/inputs-v2-convert-legacy/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inputs-v2-convert-legacy", 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 saezlab/pypath --skill inputs-v2-convert-legacy -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install saezlab/pypath inputs-v2-convert-legacy --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/saezlab/pypath.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.agents/skills/inputs-v2-convert-legacy .opencode/skills/inputs-v2-convert-legacy && 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 "inputs-v2-convert-legacy" agent skill from https://github.com/saezlab/pypath/tree/master/.agents/skills/inputs-v2-convert-legacy into .opencode/skills/inputs-v2-convert-legacy/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inputs-v2-convert-legacy", 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
inputs-v2-convert-legacy- GitHub stars
- 164
- Token cost
- ~867 tokens
- SKILL.md length
- 323 words
- Files
- 1
- Skills in repo
- 2
- Repo updated
- First seen
- Licence
- GPL-3.0
At a glance
Convert an existing legacy pypath input module from pypath.inputs into a modern inputsv2 module.
- Works in 5 steps: Audit the legacy module → Re-check current upstream data → Redesign for inputs_v2 → …
- Upstream re-checking
- SKILL.md covers Rules, Workflow and What to report at the end
- Calls uv and python
What it does
Inputs V2 Convert Legacy is an agent skill from saezlab/pypath. Convert an existing legacy pypath input module from pypath.inputs into a modern inputsv2 module. Use for legacy audit, upstream re-checking, semantic redesign, implementation, and parity-oriented smoke testing.
Its SKILL.md is about 870 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts. Compatibility notes: Requires the pypath repository with both legacy inputs and inputsv2 code available.
It works with Python. The repository describes itself as: Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles. The licence is GPL-3.0.
When your agent uses it
- Upstream re-checking
- Semantic redesign
- Parity-oriented smoke testing
Example prompts
- “/inputs-v2-convert-legacy”
Requirements
- Python 3
- Compatibility (from SKILL.md): Requires the pypath repository with both legacy inputs and inputs_v2 code available.
Workflow steps
5 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit a9553ac. 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:
uvpython
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use uv, 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.
Compatibility
Requires the pypath repository with both legacy inputs and inputs_v2 code available.
From compatibility in the SKILL.md frontmatter.
Context cost
Inputs V2 Convert Legacy loads about 867 tokens when it runs. Until then it costs about 59 tokens; SKILL.md has 323 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 saezlab/pypath at commit a9553ac, republished under its GPL-3.0 licence (© saezlab). 323 words, ~867 tokens.
Download SKILL.mdSave it as
.claude/skills/inputs-v2-convert-legacy/SKILL.md (or your agent's skills folder).- name
- inputs-v2-convert-legacy
- description
- Convert an existing legacy pypath input module from pypath.inputs into a modern inputs_v2 module. Use for legacy audit, upstream re-checking, semantic redesign, implementation, and parity-oriented smoke testing.
- compatibility
- Requires the pypath repository with both legacy inputs and inputs_v2 code available.
inputs-v2-convert-legacy
Convert a legacy pypath.inputs.* module to pypath.inputs_v2.* in a deliberate way.
Rules
- Do not blindly port old code.
- Treat the legacy module as a reference, not the specification.
- Re-check current upstream data before choosing the source.
- Preserve useful behavior intentionally; document deliberate differences.
- Validate both old and new behavior with small smoke tests.
Workflow
1. Audit the legacy module
Read the old module fully.
Identify:
- public functions
- upstream source(s)
- return type(s)
- identifier mapping, filtering, flattening, and lossy behavior
- helper modules it depends on
If practical, run a small sample from the old module.
Also check resource metadata in:
pypath/resources/urls.pypypath/resources/descriptions.pypypath/resources/data/resources.json- optionally
.agent/omnipath-resources.csvif useful
Checkpoint: state whether v1 should aim for parity, partial parity, or a cleaner redesign.
2. Re-check current upstream data
Inspect the current upstream source, not just the legacy URLs.
Decide:
- whether to keep the old source format
- or switch to a better current source
- what the current license, release pattern, and identifier richness are
Checkpoint: state the chosen source and why.
3. Redesign for inputs_v2
Read:
pypath/inputs_v2/README.mdpypath/inputs_v2/base.pypypath/internals/tabular_builder.pypypath/internals/silver_schema.py- one or more similar modern modules such as
reactome.py,signor.py,intact.py,hmdb.py
Decide:
- dataset names
- top-level entity type per dataset
- identifiers, annotations, membership
- what legacy behavior stays
- what intentionally changes
- whether new CV terms are needed
Checkpoint: state the dataset plan, semantic differences, and CV changes before coding.
4. Implement
Create or update:
- CV files if needed
pypath/inputs_v2/parsers/<resource>.pypypath/inputs_v2/<resource>.py
Keep raw records flat and mapping-friendly. Prefer a focused v1 over a full legacy clone.
5. Validate and compare
Run, when possible:
python -m py_compile pypath/inputs_v2/<resource>.py pypath/inputs_v2/parsers/<resource>.pyuv run python -c "from pypath.inputs import <legacy_module>; x = <legacy_call>; print(type(x)); print(next(iter(x)) if hasattr(x, '__iter__') else x)"uv run python -c "from pypath.inputs_v2.<resource> import resource; print(next(resource.<dataset>.raw()))"uv run python -c "from pypath.inputs_v2.<resource> import resource; print(next(resource.<dataset>()))"Compare:
- coverage
- identifier richness
- semantics preserved or improved
- intentional differences
If exact parity is not possible or not desirable, say so clearly.
What to report at the end
- Legacy audit
- Current upstream research
- Semantic redesign
- Files changed
- Validation commands run
- Parity / intentional differences
- Next steps
Always include the exact uv run python -c ... commands for the new inputs_v2 module.
© saezlab, GPL-3.0. 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 .agents/skills/inputs-v2-convert-legacy of saezlab/pypath.
Open the folder on GitHubat commit a9553ac
Compare with similar skills
Inputs V2 Convert Legacy 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 |
|---|---|---|---|---|---|---|
| Inputs V2 Convert Legacy this skillsaezlab/pypath | 164 | — | ~867 | Automated safety check: Pass | GPL-3.0 | |
| MCP Server Builderanthropics/skills | 180k | 63 repos | ~2.3k | Automated safety check: Pass | Apache-2.0 | |
| PDF Processinganthropics/skills | 180k | 48 repos | ~2k | Automated safety check: Pass | Proprietary | |
| NotebookLM Research AssistantPleasePrompto/notebooklm-skill | 7.8k | 14 repos | ~2.4k | Automated safety check: Notes | MIT | |
| Manim Video Productionbrowser-use/video-use | 28k | 6 repos | ~3k | Automated safety check: Pass | MIT | |
| Code Review ChecklistshareAI-lab/learn-claude-code | 78k | 5 repos | ~1.1k | Automated safety check: Pass | MIT |
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Questions about Inputs V2 Convert Legacy
What does Inputs V2 Convert Legacy do?
Convert an existing legacy pypath input module from pypath.inputs into a modern inputsv2 module. Inputs V2 Convert Legacy is an agent skill from saezlab/pypath.inputs into a modern inputsv2 module.
When should I use Inputs V2 Convert Legacy?
Inputs V2 Convert Legacy fits situations like: upstream re-checking; semantic redesign; parity-oriented smoke testing.
How do I install Inputs V2 Convert Legacy in Claude Code?
Run `npx skills add saezlab/pypath --skill inputs-v2-convert-legacy -a claude-code`. Or copy the skill folder (.agents/skills/inputs-v2-convert-legacy in saezlab/pypath) into .claude/skills/inputs-v2-convert-legacy in your project. Claude Code loads it when a task matches its description.
How do I install Inputs V2 Convert Legacy in Codex?
Run `npx skills add saezlab/pypath --skill inputs-v2-convert-legacy -a codex`. Or copy the skill folder (.agents/skills/inputs-v2-convert-legacy in saezlab/pypath) into .agents/skills/inputs-v2-convert-legacy in your project. Codex loads it when a task matches its description.
Can I use Inputs V2 Convert Legacy 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 saezlab/pypath --skill inputs-v2-convert-legacy -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/inputs-v2-convert-legacy, .gemini/skills/inputs-v2-convert-legacy, .github/skills/inputs-v2-convert-legacy and .opencode/skills/inputs-v2-convert-legacy in your project.
What does Inputs V2 Convert Legacy need to run?
Going by SKILL.md and its folder, Inputs V2 Convert Legacy needs the command-line tools its instructions call (uv and python). Our summary lists: Python 3. Compatibility (from SKILL.md): Requires the pypath repository with both legacy inputs and inputs_v2 code available..
Does Inputs V2 Convert Legacy access the network?
SKILL.md contains no URLs. Its commands use uv, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Inputs V2 Convert Legacy 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 Inputs V2 Convert Legacy use?
Inputs V2 Convert Legacy is published under the GPL-3.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Inputs V2 Convert Legacy use?
About 867 tokens (SKILL.md is roughly 3.5k 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 Inputs V2 Convert Legacy?
Skills that share tags, products or a category with Inputs V2 Convert Legacy: MCP Server Builder (anthropics/skills, 180k stars), PDF Processing (anthropics/skills, 180k stars), NotebookLM Research Assistant (PleasePrompto/notebooklm-skill, 7.8k stars) and Manim Video Production (browser-use/video-use, 28k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Inputs V2 Convert Legacy?
saezlab (a GitHub organization) maintains it in saezlab/pypath, which has 164 GitHub stars. The repository holds 2 skills in this directory. The repository was last updated on October 9, 2026.
Source: saezlab/pypath on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.