tamarind-cli 0.1.0

Command-line interface for the Tamarind Bio platform — submit, monitor, and download protein/molecule jobs from your terminal or an AI agent.

Tamarind CLI

Command-line interface for the Tamarind Bio platform. Discover tools, submit and monitor protein / nucleic-acid / small-molecule jobs, and download results — from your terminal, a script, CI, or an AI coding agent (Claude Code, Codex, …).

The CLI is a thin client over the same API the Tamarind MCP server uses, so the two stay in lockstep. See docs/architecture.md for how drift is prevented.

Install

Once published to PyPI:

curl -fsSL https://install.tamarind.bio/cli/install.sh | sh
# or:
uv tool install tamarind-cli      # or: pipx install tamarind-cli

Before then (or to track the repo directly), install from git:

uv tool install "git+https://github.com/Tamarind-Bio/tamarind-cli"
# or: pipx install "git+https://github.com/Tamarind-Bio/tamarind-cli"

Releasing: tag a GitHub Release and the publish.yml workflow builds and uploads to PyPI via Trusted Publishing (configure the trusted publisher for tamarind-cli on PyPI first).

Authenticate

Get an API key from the Tamarind web app (Settings → API), then either:

export TAMARIND_API_KEY="sk_..."      # best for agents / CI
# or
tamarind auth login                    # stores it in ~/.tamarind/config.json
tamarind auth status

Quickstart

# 1. Find a tool
tamarind tools --function structure-prediction --modality protein
tamarind tools --search boltz

# 2. Inspect its parameters and grab a runnable example
tamarind schema boltz
tamarind schema boltz --example > job.yaml

# 3. Validate, then submit
tamarind validate boltz --input job.yaml
tamarind submit   boltz --input job.yaml --name my-run --wait --download ./out

# 4. Monitor / fetch
tamarind jobs
tamarind status my-run
tamarind results my-run --download ./out

Set individual fields inline instead of a file:

tamarind submit boltz \
  --set inputFormat=sequence \
  --set sequence=MKTVRQERLKSIVRIL... \
  --name quick-fold

Output for agents

Every command emits JSON when stdout is not a TTY, or with --json. Exit codes are stable: 0 ok, 3 auth, 4 not-found, 5 validation, 6 rate-limit.

tamarind jobs --json | jq '.jobs[] | select(.JobStatus=="Running")'

Commands

Group	Commands
Discover	tools, modalities, functions, schema
Submit	validate, submit, batch
Monitor	jobs, status, wait, results, logs
Files	files list, files upload, files delete, files folders
Lifecycle	cancel, delete
Auth	auth login, auth status, auth logout

Run tamarind <command> --help for full options.

Configuration

Setting	Flag	Env var	Default
API key	--api-key	TAMARIND_API_KEY	—
Job API base	--api-base	TAMARIND_API_BASE	https://app.tamarind.bio/api/
Catalog base	--catalog-base	TAMARIND_CATALOG_BASE	https://mcp.tamarind.bio
Profile	--profile	TAMARIND_PROFILE	default

Profiles (key + endpoints) are stored in ~/.tamarind/config.json. Use a profile to point at staging:

tamarind --profile staging --api-base https://staging.tamarind.bio/api/ auth login
TAMARIND_PROFILE=staging tamarind tools