Biosimulant CLI

There is one headless biosimulant CLI. The same Python package, command parser, JSON schema, and exit codes run in Biosimulant Desktop, Cloud Studio, local terminals, CI, servers, and containers.

Desktop and Studio provide interfaces and managed environments around the CLI; neither defines a separate command platform.

Install

For an isolated command-line installation, pipx is recommended:

pipx install biosimulant
biosimulant --version

uv is a fast alternative:

uv tool install biosimulant

For a reproducible project environment, pin the package:

python -m pip install "biosimulant==0.0.22"

See Install and upgrade for platform setup, upgrades, and shell completion.

Cloud Studio workspaces already contain the CLI version tested with that workspace image. Desktop installs the exact checksum-verified package version associated with the app release.

Verify

biosimulant --version
biosimulant doctor
biosimulant runtime status --json

Authenticate

Biosimulant Hub is the default registry:

biosimulant auth login
biosimulant auth status

Authenticate to another Registry API v1 service by origin:

printf '%s\n' "$TOKEN" | \
  biosimulant auth login registry.example.com --token-stdin

Credentials are isolated per registry. Public pulls do not require authentication. See Registry references and authentication.

Registry implementers should use the Registry API v1 protocol reference, including discovery, token exchange, immutable publishing, and checksum verification.

Pull, validate, run, and publish

biosimulant labs pull acme/cell-study@1.0.0
biosimulant labs validate ./cell-study
biosimulant labs run ./cell-study --json
biosimulant labs publish ./cell-study

Custom registry references qualify the registry:

biosimulant labs pull registry.example.com/acme/cell-study@1.0.0

Versions are immutable. Pull may omit the version to resolve the registry default; publishing requires explicit package and version metadata.

biosimulant validate and biosimulant run are stable aliases for the corresponding labs commands.

Automation

Use --json for one schema-v1 result or --json-stream for ordered JSONL progress followed by one terminal result:

biosimulant --json labs validate ./cell-study
biosimulant labs run ./cell-study --json-stream

Global flags may appear before or after subcommands. See Machine-readable output for the envelope, progress contract, and exit-code table.

Command catalog

biosimulant commands list --json

The Command Reference is generated from that Python-owned catalog.

Labs Serve UI Install and upgrade