Bits & Flames Fyron
bitsandflames/fyron

Fyron Skill

Fyron can be used as an agent skill for Codex, Claude, Cursor, or any assistant that benefits from compact project knowledge. The skill teaches an assistant which Fyron module to use, how to install extras, how to start Curate, and where the safety boundaries are for clinical research data.

Use this when the assistant should help you create scripts, notebooks, figures, CLI recipes, Curate preview folders, or provenance manifests without guessing where Fyron functions live.

Download

The docs build publishes a ready-to-copy skill package:

  • Download the Fyron skill zip
  • Open the main file at fyron-skill/SKILL.md
  • Browse compact references such as fyron-skill/references/module-map.md

The package contains:

text
fyron-skill/
  SKILL.md
  install.py
  references/
    module-map.md
    install-extras.md
    cli-recipes.md
    fhir-rest.md
    dicom-imaging.md
    curate.md
    plotting.md
    safety.md

For projects that already use Fyron, prefer uv for reproducible installs and commands:

bash
uv add "fyron[all]"
uv run python fyron-skill/install.py --target codex
uv run python fyron-skill/install.py --target claude --project-dir .
uv run python fyron-skill/install.py --target cursor --project-dir .

If you downloaded the skill zip outside a Python project, plain Python is also fine because the installer has no external dependencies:

bash
python install.py --target codex

Choose Your Assistant

After downloading and unpacking the skill zip, use the included installer:

bash
python install.py --target codex
python install.py --target claude --project-dir /path/to/project
python install.py --target cursor --project-dir /path/to/project
python install.py --target all --project-dir /path/to/project

The targets write different local files:

TargetWhat gets created
codexNative reusable skill at ~/.codex/skills/fyron/ with SKILL.md and references
claudeProject instructions in CLAUDE.md, a .claude/fyron-skill/ copy, and fyron-claude-project-knowledge.md for Claude Project knowledge
cursorCursor project rules in .cursor/rules/fyron.mdc plus .cursor/rules/fyron-references/
allall of the above

Use codex when you want Fyron available across Codex tasks. Use claude or cursor inside the research project folder so the guidance travels with that project.

CodexInstall once as a native skill and call it with “Use the Fyron skill”. ClaudeCreate project knowledge and a CLAUDE.md instruction file for study-specific work. CursorAdd Fyron as project rules with compact references for code generation.

Manual Codex Install

Copy the skill into your local Codex skills folder:

bash
mkdir -p ~/.codex/skills/fyron
cp -R fyron-skill/* ~/.codex/skills/fyron/

If you are working from the Fyron repository, you can install the source copy directly:

bash
mkdir -p ~/.codex/skills/fyron
cp -R docs/ai/fyron-skill/* ~/.codex/skills/fyron/

Then ask Codex:

text
Use the Fyron skill to create a survival analysis workflow from my cohort CSV.

or:

text
Use the Fyron skill to prepare a nested CT/MRI folder for Curate review.

Manual Claude Setup

Claude can use the same files as project knowledge:

  1. Create a Claude Project for the study or package.
  2. Upload fyron-claude-project-knowledge.md, or upload SKILL.md and the references/ folder.
  3. Add the public documentation URL: https://fyron.bitsandflames.ai.
  4. Tell Claude to prefer public Fyron APIs and to keep clinical assumptions explicit.

A compact Claude project instruction:

text
Use Fyron for clinical data science workflows. Prefer public APIs from fyron.fhir,
fyron.dicom, fyron.imaging, fyron.cohort, fyron.statistics, fyron.survival,
fyron.ml, fyron.validation, fyron.plotting, fyron.visualization, and fyron.audit.
Keep examples synthetic or de-identified. Do not send PHI to external LLMs.
Use https://fyron.bitsandflames.ai as the source of truth.

Manual Cursor Setup

For Cursor, put the guidance into project rules:

bash
mkdir -p .cursor/rules
cp fyron-skill/references .cursor/rules/fyron-references -R
cp fyron-skill/SKILL.md .cursor/rules/fyron.mdc

The installer creates a richer .cursor/rules/fyron.mdc file with Cursor frontmatter, so prefer the installer when possible:

bash
python fyron-skill/install.py --target cursor --project-dir .

How The Skill Should Behave

The skill is intentionally practical. A good assistant using it should:

  • map the task to the right Fyron module before writing code,
  • choose a targeted install extra instead of always requiring fyron[all],
  • validate column names, event coding, dates, array shapes, image geometry, and mask alignment early,
  • write inspectable outputs such as CSV, JSON, PNG/SVG, Markdown, notebooks, and provenance manifests,
  • use Curate for local image selection workflows,
  • keep private endpoints, credentials, accessions, MRNs, and patient-linked dates out of prompts and generated examples,
  • ask for human review when clinical or statistical assumptions would change the result.

Example Prompt

text
Use the Fyron skill. I have a cohort CSV with patient_id, diagnosis_date,
last_followup_date, death_event, age, sex, stage, and CT feature columns.
Create a reproducible workflow that validates columns, builds survival time/event,
creates a Table 1, draws Kaplan-Meier curves, fits a Cox model, writes figures,
and saves a provenance manifest. Use only public Fyron APIs.