CLI¶

Manage data with LaminDB instances.

Manage connections¶

connect¶

Configure default instance for connections.

Python/R sessions and CLI commands will then auto-connect to the configured instance.

Pass a slug (account/name) or URL (https://lamin.ai/account/name).

See also: Connect in a Python session via connect().

Usage:

lamin connect [OPTIONS] INSTANCE

Options:
  --use_proxy_db  Use proxy database connection.
  --help          Show this message and exit.

info¶

Show info about the environment, instance, branch, space, and user.

See also: Print the instance settings in a Python session via settings().

Usage:

lamin info [OPTIONS]

Options:
  --schema  View database schema.
  --help    Show this message and exit.

init¶

Init a LaminDB instance.

See also: Init in a Python session via init().

Usage:

lamin init [OPTIONS]

Options:
  --storage TEXT  A local or remote folder (`'s3://...'` or `'gs://...'`).
                  Defaults to current working directory.
  --name TEXT     Instance name. If not passed, it will equal the folder name
                  passed to `storage`.
  --db TEXT       Database connection URL. Defaults to `None`, which implies
                  an SQLite file in the storage location.
  --modules TEXT  Comma-separated string of schema modules.
  --help          Show this message and exit.

disconnect¶

Clear default instance configuration.

See also: Disconnect in a Python session via disconnect().

Usage:

lamin disconnect [OPTIONS]

Options:
  --help  Show this message and exit.

Load, save, create & delete data¶

load¶

Load a file or folder into the cache or working directory.

Pass a URL, artifact, or transform. For example:

lamin load https://lamin.ai/account/instance/artifact/e2G7k9EVul4JbfsE
lamin load artifact --key mydatasets/mytable.parquet
lamin load artifact --uid e2G7k9EVul4JbfsE
lamin load transform --key analysis.ipynb
lamin load transform --uid Vul4JbfsEYAy5
lamin load transform --uid Vul4JbfsEYAy5 --with-env

Usage:

lamin load [OPTIONS] ENTITY

Options:
  --uid TEXT  The uid for the entity.
  --key TEXT  The key for the entity.
  --with-env  Also return the environment for a tranform.
  --help      Show this message and exit.

save¶

Save a file or folder.

Example: Given a valid project name “my_project”,

lamin save my_table.csv --key my_tables/my_table.csv --project my_project

By passing a --project identifier, the artifact will be labeled with the corresponding project. If you pass a --space or --branch identifier, you save the artifact in the corresponding Space or on the corresponding Branch.

Note: Defaults to saving .py, .ipynb, .R, .Rmd, and .qmd as Transform and other file types and folders as Artifact. You can enforce saving a file as an Artifact by passing --registry artifact.

Usage:

lamin save [OPTIONS] PATH

Options:
  --key TEXT          The key of the artifact or transform.
  --description TEXT  A description of the artifact or transform.
  --stem-uid TEXT     The stem uid of the artifact or transform.
  --project TEXT      A valid project name or uid.
  --space TEXT        A valid space name or uid.
  --branch TEXT       A valid branch name or uid.
  --registry TEXT     Either 'artifact' or 'transform'. If not passed, chooses
                      based on path suffix.
  --help              Show this message and exit.

create¶

Create a record for an entity.

Currently only supports creating branches and projects.

lamin create branch --name my_branch
lamin create project --name my_project

Usage:

lamin create [OPTIONS] ENTITY

Options:
  --name TEXT  A name.
  --help       Show this message and exit.

delete¶

Delete an entity.

Currently supported: branch, artifact, transform, collection, and instance. For example:

lamin delete https://lamin.ai/account/instance/artifact/e2G7k9EVul4JbfsEYAy5
lamin delete branch --name my_branch
lamin delete instance --slug account/name

Usage:

lamin delete [OPTIONS] ENTITY

Options:
  --name TEXT
  --uid TEXT
  --slug TEXT
  --force      Do not ask for confirmation (only relevant for instance).
  --help       Show this message and exit.

Describe, annotate & list data¶

describe¶

Describe an artifact.

Examples:

lamin describe --key example_datasets/mini_immuno/dataset1.h5ad
lamin describe https://lamin.ai/laminlabs/lamin-site-assets/artifact/6sofuDVvTANB0f48

See also: Describe an artifact in a Python session via describe().

Usage:

lamin describe [OPTIONS] [ENTITY]

Options:
  --uid TEXT  The uid for the entity.
  --key TEXT  The key for the entity.
  --help      Show this message and exit.

annotate¶

Annotate an artifact or transform.

Entity is either ‘artifact’ or ‘transform’. If not passed, chooses based on key suffix.

You can annotate with projects and valid features & values. For example,

lamin annotate --key raw/sample.fastq --project "My Project"
lamin annotate --key raw/sample.fastq --features perturbation=IFNG,DMSO cell_line=HEK297
lamin annotate --key my-notebook.ipynb --project "My Project"

Usage:

lamin annotate [OPTIONS] [ENTITY]

Options:
  --key TEXT       The key of an artifact or transform.
  --uid TEXT       The uid of an artifact or transform.
  --project TEXT   A valid project name or uid.
  --features TEXT  Feature annotations. Supports: feature=value,
                   feature=val1,val2, or feature="val1","val2"
  --help           Show this message and exit.

list¶

List records for an entity.

lamin list branch
lamin list space

Usage:

lamin list [OPTIONS] ENTITY

Options:
  --name TEXT  A name.
  --help       Show this message and exit.

Configure¶

switch¶

Switch between branches or spaces.

lamin switch --branch my_branch
lamin switch --space our_space

Usage:

lamin switch [OPTIONS]

Options:
  --branch TEXT  A valid branch name or uid.
  --space TEXT   A valid branch name or uid.
  --help         Show this message and exit.

cache¶

Manage cache.

Usage:

lamin cache [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  clear  Clear the cache directory.
  get    Get the cache directory.
  set    Set the cache directory.

settings¶

Manage settings.

Call without subcommands and options to show settings:

lamin settings

Allows to get and set these settings:

work-dir → work_dir
private-django-api → private_django_api
branch → current branch (use lamin switch --branch to change)
space → current space (use lamin switch --space to change)

Examples for getting a setting:

lamin settings get work-dir
lamin settings get branch

Examples for setting the working directory:

lamin settings set work-dir .  # set work-dir to current directory
lamin settings set work-dir ~/my-project  # set work-dir to ~/my-project
lamin settings set work-dir none  # unset work-dir

Usage:

lamin settings [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  get  Get a setting.
  set  Set a setting.

migrate¶

Manage database schema migrations.

Usage:

lamin migrate [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  create  Create a new migration.
  deploy  Deploy migrations.
  squash  Squash migrations.

Auth¶

login¶

Log into LaminHub.

lamin login prompts for your API key unless you set it via environment variable LAMIN_API_KEY.

You can create your API key in your account settings on LaminHub (top right corner).

After authenticating once, you can re-authenticate and switch between accounts via lamin login myhandle.

See also: Login in a Python session via login().

Usage:

lamin login [OPTIONS] [USER]

Options:
  --help  Show this message and exit.

logout¶

Log out of LaminHub.

Usage:

lamin logout [OPTIONS]

Options:
  --help  Show this message and exit.

Other¶

lamin get¶

Query metadata about an entity.

Currently equivalent to lamin describe.

Usage: lamin get [OPTIONS] [ENTITY]

Options:
  --uid TEXT  The uid for the entity.
  --key TEXT  The key for the entity.
  --help      Show this message and exit.

lamin run¶

Run a compute job in the cloud.

This is an EXPERIMENTAL feature that enables to run a script on Modal.

Example: Given a valid project name “my_project”,

lamin run my_script.py --project my_project

Usage: lamin run [OPTIONS] FILEPATH

Options:
  --project TEXT    A valid project name or uid. When running on Modal,
                    creates an app with the same name.  [required]
  --image-url TEXT  A URL to the base docker image to use.
  --packages TEXT   A comma-separated list of additional packages to install.
  --cpu FLOAT       Configuration for the CPU.
  --gpu TEXT        The type of GPU to use (only compatible with cuda images).
  --help            Show this message and exit.