Agent skill

Inputs V2 New Module

by saezlab in saezlab/pypath

Create a new pypath inputsv2 module for an external database.

GPL-3.0Auto-check passedWriting & Content

Install Inputs V2 New Module

skills CLI
$ npx skills add saezlab/pypath --skill inputs-v2-new-module -a claude-code

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

GitHub CLI
$ gh skill install saezlab/pypath inputs-v2-new-module --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/saezlab/pypath.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.agents/skills/inputs-v2-new-module .claude/skills/inputs-v2-new-module && 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/

Facts

Skill name
inputs-v2-new-module
GitHub stars
164
Token cost
~728 tokens
SKILL.md length
274 words
Files
1
Skills in repo
2
Repo updated
First seen
Licence
GPL-3.0

At a glance

Create a new pypath inputsv2 module for an external database.

  • Works in 5 steps: Research the source → Design the semantic mapping → Design raw parser output → …
  • Structured research
  • SKILL.md covers Rules, Workflow and What to report at the end
  • Calls uv and python

What it does

Inputs V2 New Module is an agent skill from saezlab/pypath. Create a new pypath inputsv2 module for an external database. Use for structured research, semantic mapping, CV review, implementation, and poetry-based smoke testing.

Its SKILL.md is about 730 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 uv and the inputsv2 framework.

It sits in Writing & Content, covering Creative writing and fiction. 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

  • Structured research
  • Semantic mapping
  • Poetry-based smoke testing

Example prompts

  • “/inputs-v2-new-module”

Requirements

  • Python 3
  • Compatibility (from SKILL.md): Requires the pypath repository with uv and the inputs_v2 framework.

Workflow steps

5 steps, taken from the step headings in SKILL.md.

  1. Research the source
  2. Design the semantic mapping
  3. Design raw parser output
  4. Implement
  5. Validate

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:

    • uv
    • python

    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 uv and the inputs_v2 framework.

    From compatibility in the SKILL.md frontmatter.

Context cost

Inputs V2 New Module loads about 728 tokens when it runs. Until then it costs about 47 tokens; SKILL.md has 274 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~47
When it runs · the whole SKILL.md, loaded when a task matches
~728

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). 274 words, ~728 tokens.

Download SKILL.mdSave it as .claude/skills/inputs-v2-new-module/SKILL.md (or your agent's skills folder).
name
inputs-v2-new-module
description
Create a new pypath inputs_v2 module for an external database. Use for structured research, semantic mapping, CV review, implementation, and poetry-based smoke testing.
compatibility
Requires the pypath repository with uv and the inputs_v2 framework.

inputs-v2-new-module

Create a new pypath.inputs_v2 module in a small number of explicit steps.

Rules

  • Research first; do not start coding immediately.
  • Prefer the upstream format with the best semantics and identifiers.
  • Design for the silver schema; avoid unsupported deep nesting.
  • Add new CV terms only when existing ones are not semantically correct.
  • Validate with uv run python -c ... before finishing.

Workflow

1. Research the source

Read:

  • pypath/inputs_v2/README.md
  • related modules in pypath/inputs_v2/
  • relevant entries in pypath/resources/urls.py, pypath/resources/descriptions.py, and pypath/resources/data/resources.json

Then inspect current upstream data.

Decide:

  • what formats exist
  • which format is best
  • what entity types / identifiers / species / license are available

Checkpoint: state the chosen source format and why.

2. Design the semantic mapping

Read:

  • pypath/inputs_v2/base.py
  • pypath/internals/tabular_builder.py
  • pypath/internals/silver_schema.py
  • one similar module, e.g. pypath/inputs_v2/signor.py

Decide:

  • dataset names
  • top-level entity type per dataset
  • identifiers, annotations, and membership
  • whether new CV terms are needed

Keep the plan simple and explicit.

Checkpoint: state the dataset plan and CV changes before coding.

3. Design raw parser output

If base parsers are enough, use them. Otherwise create pypath/inputs_v2/parsers/<resource>.py.

Raw records should be:

  • flat
  • stable
  • easy to map with FieldConfig / EntityBuilder

Prefer helpers for:

  • URL resolution
  • archive iteration
  • xref extraction
  • entity type inference

Checkpoint: inspect and print at least one raw record.

4. Implement

Create or update:

  • CV files if needed
  • pypath/inputs_v2/parsers/<resource>.py
  • pypath/inputs_v2/<resource>.py

Use:

  • ResourceConfig
  • Download
  • Dataset
  • EntityBuilder

Start with the highest-value dataset(s). Do not overbuild v1.

5. Validate

Run, when possible:

bash
python -m py_compile pypath/inputs_v2/<resource>.py pypath/inputs_v2/parsers/<resource>.py
bash
uv run python -c "from pypath.inputs_v2.<resource> import resource; print(next(resource.<dataset>.raw()))"
bash
uv run python -c "from pypath.inputs_v2.<resource> import resource; print(next(resource.<dataset>()))"

Repeat for each dataset.

What to report at the end

  1. Research summary
  2. Semantic design
  3. Files changed
  4. Validation commands run
  5. Open questions / next steps

Always include the exact uv run python -c ... commands for the new 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-new-module of saezlab/pypath.

Open the folder on GitHubat commit a9553ac

Compare with similar skills

Inputs V2 New Module 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.

Inputs V2 New Module compared with similar skills
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Python Manager Discoverymicrosoft/vscode-python-environments141—~2.7kAutomated safety check: PassMIT
Script Comparative Review Against HitsSupreme-Ultimate/novel-to-script-team175—~1.8kAutomated safety check: PassMIT
Story Multi-Perspective Reviewzenstory-ai/oh-story-claudecode7.4k3 repos~3kAutomated safety check: PassMIT
Story Toolbox Routerzenstory-ai/oh-story-claudecode7.4k1 repos~1.7kAutomated safety check: PassMIT

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Works with

Questions about Inputs V2 New Module

What does Inputs V2 New Module do?

Create a new pypath inputsv2 module for an external database. Inputs V2 New Module is an agent skill from saezlab/pypath. Create a new pypath inputsv2 module for an external database.

When should I use Inputs V2 New Module?

Inputs V2 New Module fits situations like: structured research; semantic mapping; poetry-based smoke testing.

How do I install Inputs V2 New Module in Claude Code?

Run `npx skills add saezlab/pypath --skill inputs-v2-new-module -a claude-code`. Or copy the skill folder (.agents/skills/inputs-v2-new-module in saezlab/pypath) into .claude/skills/inputs-v2-new-module in your project. Claude Code loads it when a task matches its description.

How do I install Inputs V2 New Module in Codex?

Run `npx skills add saezlab/pypath --skill inputs-v2-new-module -a codex`. Or copy the skill folder (.agents/skills/inputs-v2-new-module in saezlab/pypath) into .agents/skills/inputs-v2-new-module in your project. Codex loads it when a task matches its description.

Can I use Inputs V2 New Module 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-new-module -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-new-module, .gemini/skills/inputs-v2-new-module, .github/skills/inputs-v2-new-module and .opencode/skills/inputs-v2-new-module in your project.

What does Inputs V2 New Module need to run?

Going by SKILL.md and its folder, Inputs V2 New Module 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 uv and the inputs_v2 framework..

Does Inputs V2 New Module 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 New Module 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 New Module use?

Inputs V2 New Module 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 New Module use?

About 728 tokens (SKILL.md is roughly 2.9k 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 New Module?

Skills that share tags, products or a category with Inputs V2 New Module: Novel Writer (ZJU-REAL/Easel, 3.2k stars), Python Manager Discovery (microsoft/vscode-python-environments, 141 stars), Script Comparative Review Against Hits (Supreme-Ultimate/novel-to-script-team, 175 stars) and Story Multi-Perspective Review (zenstory-ai/oh-story-claudecode, 7.4k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Inputs V2 New Module?

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 7, 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.