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Using PhytKit with an AI coding agent

Coding agents (Claude Code, Codex, Gemini CLI, Cursor and others) know little or nothing about PhytKit from their training. The phytkit package ships the guidance they need, an agent skill, and keeps it matched to the installed version.

Give a project the guidance

From the project folder, after pip install phytkit:

pk agent-files

This writes two files:

  • AGENTS.md: the installed version, where its skill is, and the skill's guidance: which tool fits which measurement, the checks to make on every fit, and the pitfalls. Codex, Cursor and most other agents read this file.
  • CLAUDE.md: the single line @AGENTS.md, so Claude Code reads the same file.

Run it again after upgrading phytkit. The output lists each file as written, unchanged or user-owned; --dry-run reports without writing, and --stdout prints the AGENTS.md text. In Python, use phytkit.agent_files(".").

Your own edits are safe. A file is rewritten only while its first line is the <!-- phytkit-managed-file ... --> marker. Delete that line and the file is yours: pk agent-files never touches it again. If you keep your own CLAUDE.md, add the line @AGENTS.md to it, and pk agent-files stops reminding you.

Turning it off. Set PHYTKIT_AGENT_FILES=0 (or off, false, no) and the command writes nothing. This is useful in a harness that runs it unconditionally.

Helios and Phytograph use the same marker line and the same kind of switch (HELIOS_GENERATE_AGENT_FILES, PHYTOGRAPH_AGENT_FILES), so one rule covers all three.

For Gemini CLI, which reads GEMINI.md by default, add AGENTS.md to context.fileName in its settings.

Install the skill itself

Harnesses that load skills from a folder can take the skill directly:

pk skills install                      # into .claude/skills/phytkit
pk skills install --to path/to/skills  # another harness's folder
pk skills path                         # where the installed package keeps it

A copy made by pk skills install is marked, and running the command again replaces it. A folder it didn't make is refused unless you pass --force. From Python, phytkit.skills_dir() returns the folder.

Claude Code plugin

The repository is also a Claude Code plugin marketplace. From a terminal:

claude plugin marketplace add PlantSimulationLab/PhytKit
claude plugin install phytkit@plantsimulationlab-phytkit

The plugin's skill is a short pointer: it finds the installed phytkit package and reads that version's skill. It therefore always matches what you have installed.

Without the Python package

These commands come with the Python package, because the skill they install is part of it. A pk built from source with cargo build reports not_applicable for them; use pip install phytkit instead.