<!-- Source: https://docs.biosimulant.com/references/cli/command-reference -->

# CLI Commands

Generated from the canonical Python CLI 0.0.22. The same command parser, JSON schema, and exit codes run in Desktop, Cloud Studio, local terminals, CI, and servers.

Global options may appear before or after subcommands:

- `--data-dir`
- `--json`
- `--json-stream`
- `--legacy-json`
- `--no-open`
- `--profile`

## Utilities

### `biosimulant doctor`

Check the headless CLI and local runtime installation

```text
usage: biosimulant doctor [-h]

options:
  -h, --help  show this help message and exit
```

### `biosimulant commands list`

List the canonical machine-readable command catalog

```text
usage: biosimulant commands list [-h]

options:
  -h, --help  show this help message and exit
```

## Authentication

### `biosimulant auth login`

Store credentials for one registry

```text
usage: biosimulant auth login [-h] [--token-stdin] [registry]

positional arguments:
  registry

options:
  -h, --help     show this help message and exit
  --token-stdin
```

### `biosimulant auth status`

Inspect credentials for one registry

```text
usage: biosimulant auth status [-h] [registry]

positional arguments:
  registry

options:
  -h, --help  show this help message and exit
```

### `biosimulant auth logout`

Remove credentials for one registry

```text
usage: biosimulant auth logout [-h] [registry]

positional arguments:
  registry

options:
  -h, --help  show this help message and exit
```

## Labs and registry

### `biosimulant labs init`

Create a local runnable lab

```text
usage: biosimulant labs init [-h] --name NAME [--description DESCRIPTION]
                             [--force] [--empty] [--json]
                             [path]

positional arguments:
  path

options:
  -h, --help            show this help message and exit
  --name NAME
  --description DESCRIPTION
  --force
  --empty               Create only lab.yaml without a starter model
  --json
```

### `biosimulant labs create`

Create a managed local lab

```text
usage: biosimulant labs create [-h] --name NAME [--description DESCRIPTION]
                               [--force] [--empty] [--json]
                               [path]

positional arguments:
  path

options:
  -h, --help            show this help message and exit
  --name NAME
  --description DESCRIPTION
  --force
  --empty
  --json
```

### `biosimulant labs list`

List local labs

```text
usage: biosimulant labs list [-h] [--json] [root]

positional arguments:
  root

options:
  -h, --help  show this help message and exit
  --json
```

### `biosimulant labs get`

Inspect a local lab

```text
usage: biosimulant labs get [-h] [--root ROOT] [--json] [lab]

positional arguments:
  lab

options:
  -h, --help   show this help message and exit
  --root ROOT
  --json
```

### `biosimulant labs save`

Save a local lab

```text
usage: biosimulant labs save [-h] [--root ROOT]
                             [--manifest-file MANIFEST_FILE]
                             [--wiring-layout-file WIRING_LAYOUT_FILE]
                             [--clear-wiring-layout] [--json]
                             [lab]

positional arguments:
  lab

options:
  -h, --help            show this help message and exit
  --root ROOT
  --manifest-file MANIFEST_FILE
  --wiring-layout-file WIRING_LAYOUT_FILE
  --clear-wiring-layout
  --json
```

### `biosimulant labs rename`

Rename a local lab

```text
usage: biosimulant labs rename [-h] [--root ROOT] [--json]
                               target_or_name [name]

positional arguments:
  target_or_name
  name

options:
  -h, --help      show this help message and exit
  --root ROOT
  --json
```

### `biosimulant labs delete`

Delete a local lab

```text
usage: biosimulant labs delete [-h] [--root ROOT] [--yes] [--json] [lab]

positional arguments:
  lab

options:
  -h, --help   show this help message and exit
  --root ROOT
  --yes
  --json
```

### `biosimulant labs add-model`

Add a model to a lab

```text
usage: biosimulant labs add-model [-h] [--lab LAB] [--root ROOT]
                                  [--alias ALIAS] [--json]
                                  model

positional arguments:
  model

options:
  -h, --help     show this help message and exit
  --lab LAB
  --root ROOT
  --alias ALIAS
  --json
```

### `biosimulant labs change-model`

Change a lab model

```text
usage: biosimulant labs change-model [-h] [--lab LAB] [--root ROOT] [--json]
                                     alias model

positional arguments:
  alias
  model

options:
  -h, --help   show this help message and exit
  --lab LAB
  --root ROOT
  --json
```

### `biosimulant labs vendor-model`

Vendor a model into a lab

```text
usage: biosimulant labs vendor-model [-h] [--lab LAB] [--root ROOT]
                                     [--alias ALIAS] [--replace] [--json]
                                     model

positional arguments:
  model

options:
  -h, --help     show this help message and exit
  --lab LAB
  --root ROOT
  --alias ALIAS
  --replace
  --json
```

### `biosimulant labs inspect-owned`

Inspect lab-owned model sources

```text
usage: biosimulant labs inspect-owned [-h] [--root ROOT] [--json] [lab]

positional arguments:
  lab

options:
  -h, --help   show this help message and exit
  --root ROOT
  --json
```

### `biosimulant labs validate`

Validate a lab

```text
usage: biosimulant labs validate [-h] [--json] [lab]

positional arguments:
  lab

options:
  -h, --help  show this help message and exit
  --json
```

### `biosimulant labs run`

Run a lab

```text
usage: biosimulant labs run [-h] [--target TARGET] [--force]
                            [--registry-url REGISTRY_URL] [--no-install-deps]
                            [--dependency-root DEPENDENCY_ROOT]
                            [--results-file RESULTS_FILE]
                            [--report-file REPORT_FILE]
                            [--run-input-file RUN_INPUT_FILE] [--json]
                            [lab]

positional arguments:
  lab

options:
  -h, --help            show this help message and exit
  --target TARGET       Destination for auto-pulled registry refs
  --force               Replace an existing auto-pull target
  --registry-url REGISTRY_URL
  --no-install-deps
  --dependency-root DEPENDENCY_ROOT
                        Writable Lab-local dependency state directory for a
                        .bsilab archive
  --results-file RESULTS_FILE
  --report-file REPORT_FILE
                        Write a standalone HTML run report
  --run-input-file RUN_INPUT_FILE
                        JSON object containing parameters and
                        simulation_config overlays
  --json
```

### `biosimulant labs serve`

Serve a lab locally

```text
usage: biosimulant labs serve [-h] [--target TARGET] [--force]
                              [--registry-url REGISTRY_URL] [--host HOST]
                              [--port PORT] [--open] [--no-open]
                              [--no-install-deps] [--json]
                              [lab]

positional arguments:
  lab

options:
  -h, --help            show this help message and exit
  --target TARGET       Destination for auto-pulled registry refs
  --force               Replace an existing auto-pull target
  --registry-url REGISTRY_URL
  --host HOST
  --port PORT
  --open                Open browser automatically (default)
  --no-open             Do not open a browser automatically
  --no-install-deps
  --json
```

### `biosimulant labs package`

Build a lab package

```text
usage: biosimulant labs package [-h] [--out OUT] [--package PACKAGE_NAME]
                                [--version VERSION]
                                [--visibility {private,public}]
                                [--vendor-dependencies]
                                [--registry-url REGISTRY_URL] [--json]
                                [lab]

positional arguments:
  lab

options:
  -h, --help            show this help message and exit
  --out OUT
  --package PACKAGE_NAME
  --version VERSION
  --visibility {private,public}
  --vendor-dependencies
  --registry-url REGISTRY_URL
  --json
```

### `biosimulant labs search`

Search a Biosimulant registry

```text
usage: biosimulant labs search [-h] [--page PAGE] [--page-size PAGE_SIZE]
                               [--tags TAGS] [--registry-url REGISTRY_URL]
                               [--json]
                               [query]

positional arguments:
  query

options:
  -h, --help            show this help message and exit
  --page PAGE
  --page-size PAGE_SIZE
  --tags TAGS
  --registry-url REGISTRY_URL
  --json
```

### `biosimulant labs info`

Inspect registry lab metadata

```text
usage: biosimulant labs info [-h] [--registry-url REGISTRY_URL] [--json]
                             reference

positional arguments:
  reference

options:
  -h, --help            show this help message and exit
  --registry-url REGISTRY_URL
  --json
```

### `biosimulant labs versions`

List immutable registry versions

```text
usage: biosimulant labs versions [-h] [--page PAGE] [--page-size PAGE_SIZE]
                                 [--registry-url REGISTRY_URL] [--json]
                                 reference

positional arguments:
  reference

options:
  -h, --help            show this help message and exit
  --page PAGE
  --page-size PAGE_SIZE
  --registry-url REGISTRY_URL
  --json
```

### `biosimulant labs pull`

Pull a registry lab

```text
usage: biosimulant labs pull [-h] [--target TARGET] [--force] [--no-deps]
                             [--registry-url REGISTRY_URL] [--json]
                             reference

positional arguments:
  reference

options:
  -h, --help            show this help message and exit
  --target TARGET
  --force
  --no-deps
  --registry-url REGISTRY_URL
  --json
```

### `biosimulant labs publish`

Publish an immutable lab version

```text
usage: biosimulant labs publish [-h] [--visibility {private,public}]
                                [--registry-url REGISTRY_URL]
                                lab [reference]

positional arguments:
  lab
  reference

options:
  -h, --help            show this help message and exit
  --visibility {private,public}
  --registry-url REGISTRY_URL
```

### `biosimulant labs sync-status`

Compare a local lab with its registry version

```text
usage: biosimulant labs sync-status [-h] [--registry-url REGISTRY_URL] [lab]

positional arguments:
  lab

options:
  -h, --help            show this help message and exit
  --registry-url REGISTRY_URL
```

### `biosimulant labs release validate`

Validate a release manifest

```text
usage: biosimulant labs release validate [-h] [--json] manifest

positional arguments:
  manifest

options:
  -h, --help  show this help message and exit
  --json
```

### `biosimulant labs release build`

Build a release manifest

```text
usage: biosimulant labs release build [-h] [--out OUT] [--json] manifest

positional arguments:
  manifest

options:
  -h, --help  show this help message and exit
  --out OUT
  --json
```

### `biosimulant labs release publish`

Build and publish a release manifest

```text
usage: biosimulant labs release publish [-h] [--out OUT]
                                        [--registry-url REGISTRY_URL]
                                        [--dry-run]
                                        manifest

positional arguments:
  manifest

options:
  -h, --help            show this help message and exit
  --out OUT
  --registry-url REGISTRY_URL
  --dry-run
```

### `biosimulant labs release ci`

Validate, build, and publish a release manifest

```text
usage: biosimulant labs release ci [-h] [--out OUT]
                                   [--registry-url REGISTRY_URL] [--dry-run]
                                   manifest

positional arguments:
  manifest

options:
  -h, --help            show this help message and exit
  --out OUT
  --registry-url REGISTRY_URL
  --dry-run
```

## Runtime

### `biosimulant runtime status`

Inspect the managed runtime

```text
usage: biosimulant runtime status [-h]

options:
  -h, --help  show this help message and exit
```

### `biosimulant runtime detect-python`

Report the current Python runtime

```text
usage: biosimulant runtime detect-python [-h]

options:
  -h, --help  show this help message and exit
```

### `biosimulant runtime prepare`

Prepare an isolated execution runtime

```text
usage: biosimulant runtime prepare [-h] [--python PYTHON]

options:
  -h, --help       show this help message and exit
  --python PYTHON
```

## Runs

### `biosimulant runs list`

List managed runs

```text
usage: biosimulant runs list [-h] [--limit LIMIT] [--cursor CURSOR]

options:
  -h, --help       show this help message and exit
  --limit LIMIT
  --cursor CURSOR
```

### `biosimulant runs get`

Inspect a managed run

```text
usage: biosimulant runs get [-h] run_id

positional arguments:
  run_id

options:
  -h, --help  show this help message and exit
```

### `biosimulant runs create`

Create a managed run

```text
usage: biosimulant runs create [-h] [--inputs INPUTS]
                               [--compute-profile COMPUTE_PROFILE]
                               [--idempotency-key IDEMPOTENCY_KEY]
                               ref

positional arguments:
  ref

options:
  -h, --help            show this help message and exit
  --inputs INPUTS
  --compute-profile COMPUTE_PROFILE
  --idempotency-key IDEMPOTENCY_KEY
```

### `biosimulant runs start`

Start a created managed run

```text
usage: biosimulant runs start [-h] run_id

positional arguments:
  run_id

options:
  -h, --help  show this help message and exit
```

### `biosimulant runs cancel`

Cancel a managed run

```text
usage: biosimulant runs cancel [-h] run_id

positional arguments:
  run_id

options:
  -h, --help  show this help message and exit
```

### `biosimulant runs results`

Get managed run results

```text
usage: biosimulant runs results [-h] run_id

positional arguments:
  run_id

options:
  -h, --help  show this help message and exit
```

### `biosimulant runs logs`

Get managed run events or logs

```text
usage: biosimulant runs logs [-h] [--after AFTER] [--limit LIMIT] run_id

positional arguments:
  run_id

options:
  -h, --help     show this help message and exit
  --after AFTER
  --limit LIMIT
```

### `biosimulant runs upload`

Upload a managed run artifact

```text
usage: biosimulant runs upload [-h] run_id file

positional arguments:
  run_id
  file

options:
  -h, --help  show this help message and exit
```

### `biosimulant runs remote catalog`

List remote compute profiles

```text
usage: biosimulant runs remote catalog [-h]

options:
  -h, --help  show this help message and exit
```

### `biosimulant runs remote create`

Create a remote managed run

```text
usage: biosimulant runs remote create [-h] [--inputs INPUTS]
                                      [--compute-profile COMPUTE_PROFILE]
                                      ref

positional arguments:
  ref

options:
  -h, --help            show this help message and exit
  --inputs INPUTS
  --compute-profile COMPUTE_PROFILE
```

### `biosimulant runs remote get`

Inspect a remote managed run

```text
usage: biosimulant runs remote get [-h] run_id

positional arguments:
  run_id

options:
  -h, --help  show this help message and exit
```

### `biosimulant runs remote results`

Get remote run results

```text
usage: biosimulant runs remote results [-h] run_id

positional arguments:
  run_id

options:
  -h, --help  show this help message and exit
```

## Jobs

### `biosimulant jobs list`

List hosted jobs

```text
usage: biosimulant jobs list [-h] [--limit LIMIT]

options:
  -h, --help     show this help message and exit
  --limit LIMIT
```

### `biosimulant jobs get`

Inspect a hosted job

```text
usage: biosimulant jobs get [-h] job_id

positional arguments:
  job_id

options:
  -h, --help  show this help message and exit
```

## Stable aliases

### `biosimulant validate`

Alias for labs validate

```text
usage: biosimulant labs validate [-h] [--json] [lab]

positional arguments:
  lab

options:
  -h, --help  show this help message and exit
  --json
```

### `biosimulant run`

Alias for labs run

```text
usage: biosimulant labs run [-h] [--target TARGET] [--force]
                            [--registry-url REGISTRY_URL] [--no-install-deps]
                            [--dependency-root DEPENDENCY_ROOT]
                            [--results-file RESULTS_FILE]
                            [--report-file REPORT_FILE]
                            [--run-input-file RUN_INPUT_FILE] [--json]
                            [lab]

positional arguments:
  lab

options:
  -h, --help            show this help message and exit
  --target TARGET       Destination for auto-pulled registry refs
  --force               Replace an existing auto-pull target
  --registry-url REGISTRY_URL
  --no-install-deps
  --dependency-root DEPENDENCY_ROOT
                        Writable Lab-local dependency state directory for a
                        .bsilab archive
  --results-file RESULTS_FILE
  --report-file REPORT_FILE
                        Write a standalone HTML run report
  --run-input-file RUN_INPUT_FILE
                        JSON object containing parameters and
                        simulation_config overlays
  --json
```

## Related

- [Install and upgrade](/references/cli/installing) — pipx, uv, and pinned pip installation.
- [Registry references and authentication](/references/cli/registry-auth) — Hub and custom registries.
- [Machine-readable output](/references/cli/machine-output) — JSON, JSONL, and exit codes.
- [Native CLI migration](/references/cli/migration) — removed commands and compatibility shims.