tvbo skills

Render TVBO’s AI-assistant skills (Claude Code, Cursor, Copilot, AGENTS.md, or a raw-API system prompt) and install them onto your machine. After installation, an AI assistant in your editor automatically loads the relevant TVBO context — what TVBO is, how to write a Dynamics, how to pick a backend, how to use the platform — without you pasting a system prompt every session.

Tip

For a narrative walkthrough (with screenshots and example conversations), see the Agentic Coding section. This page is the verb reference with every flag.

Synopsis

tvbo skills install   [OPTIONS]
tvbo skills uninstall [OPTIONS]
tvbo skills sync      [OPTIONS]   # maintainer-only

Quick start

pip install tvbo
tvbo skills install --target claude-code     # default: Claude Code, user scope

That writes four files under ~/.claude/skills/tvbo-*/SKILL.md:

Skill	What it teaches the AI
`tvbo-overview`	The three pillars (LinkML datamodel, ontology, Python package)
`tvbo-writing-models`	How to specify a `Dynamics` in YAML or Python
`tvbo-running-simulations`	How to run an experiment, choose a backend
`tvbo-platform`	How to use tvbo.charite.de

Skills load on demand — they cost nothing when you’re not working with TVBO.

`tvbo skills install`

tvbo skills install
    --target {claude-code,copilot,cursor,agents-md,prompt,all}   # default: claude-code
    --audience {user,maintainer,all}                              # default: user
    --scope {user,project}                                        # default: user
    --skill <name>        # filter; repeatable
    --out <path>          # override install dir / output file
    --force               # overwrite files not marked managed-by: tvbo
    --dry-run             # show what would happen, write nothing
    --strict              # exit non-zero if any skill is refused

Targets

Target	Produces	Default location
`claude-code`	`<dest>/tvbo-<name>/SKILL.md`	`~/.claude/skills/` (user) or `./.claude/skills/` (project)
`cursor`	`<dest>/tvbo-<name>.mdc`	`~/.cursor/rules/` or `./.cursor/rules/`
`copilot`	`<dest>/<name>.instructions.md`	`.github/instructions/` (repo-only; maintainer)
`agents-md`	Updates the skills-index region of `AGENTS.md`	`./AGENTS.md`
`prompt`	Concatenated markdown system prompt	stdout (or `--out path`)
`all`	Every applicable target	as above

Audiences

By default only the four user-audience skills are installed (the ones in the table above). The maintainer skills (git, writing-code, linkml-schema, codegen-templates, tests-and-backends, grill-me) are relevant only when working inside a clone of the tvbo repository. Opt in explicitly:

tvbo skills install --audience maintainer
tvbo skills install --audience all

Scope

tvbo skills install --scope user      # ~/.claude/skills/...     (default)
tvbo skills install --scope project   # ./.claude/skills/...     (committed alongside a notebook repo)

Use project when you want a tutorial repo to “ship” with the skills so a co-author sees the same AI behaviour after cloning.

Filtering

tvbo skills install --skill overview --skill writing-models

Names match either the canonical name (writing-models) or the installed name (tvbo-writing-models).

Raw-API / local-model usage

Need a single system prompt for Anthropic / OpenAI / Mistral SDK calls or for a local Ollama / vLLM / llama.cpp setup?

tvbo skills install --target prompt > tvbo-system-prompt.md
tvbo skills install --target prompt --skill overview --skill writing-models

Then feed tvbo-system-prompt.md as the system prompt in your script.

Upgrade / overwrite policy

TVBO stamps managed-by: tvbo into every file it writes. On subsequent installs:

File doesn’t exist → install it.
File exists, managed-by: tvbo → overwrite (it’s ours).
File exists, no marker → refused. You customised it, or another tool wrote it. Pass --force, or move it out of the way first.

tvbo skills install --dry-run    # see what would happen
tvbo skills install --force      # overwrite anyway
tvbo skills install --strict     # exit 1 if anything was refused (for CI)

Reporting

Every install prints:

skills install: installed=4 updated=0 refused=0 skipped=0

Counter	Meaning
`installed`	New file written
`updated`	Existing managed file overwritten
`refused`	Existing file, not managed-by tvbo, no `--force`
`skipped`	Skill filtered out by `--audience` / `--skill`

`tvbo skills uninstall`

tvbo skills uninstall --target claude-code        # ~/.claude/skills/tvbo-*
tvbo skills uninstall --target cursor             # ~/.cursor/rules/tvbo-*.mdc
tvbo skills uninstall --target all                # both
tvbo skills uninstall --dry-run                   # show, don't delete

Only files carrying the managed-by: tvbo marker are removed. Other skills in the same directory — including ones you wrote yourself — are untouched.

`tvbo skills sync` (maintainer)

Regenerates the adapter files inside this repository (.claude/skills/, .github/instructions/, the skills-index region of AGENTS.md) from the canonical sources in skills/. CI runs tvbo skills sync --check to prevent canonical-vs-adapter drift.

tvbo skills sync                       # regenerate
tvbo skills sync --check               # exit non-zero if anything would change
tvbo skills sync --repo-root /path/to/clone

End-users of the published tvbo wheel never need this command.