Python: `lamindb`¶

A data framework for biology.

Installation:

pip install lamindb

If you just want to read data from a LaminDB instance, use DB:

import lamindb as ln

db = ln.DB("laminlabs/cellxgene")

To write data, connect to a writable instance:

lamin login
lamin connect account/name

You can create an instance at lamin.ai and invite collaborators. If you prefer to work with a local SQLite instance, run:

lamin init --storage ./quickstart-data --modules bionty

LaminDB will then auto-connect upon import and you can then create & save objects like this:

import lamindb as ln
# → connected lamindb: account/instance

ln.Artifact("my_dataset.parquet", key="datasets/my_dataset.parquet").save()

Lineage¶

Track inputs, outputs & environment of a notebook or script run.

`track`([transform, project, space, branch, ...])	Track a run of your notebook or script.
`finish`([ignore_non_consecutive])	Finish the run and write a run report.

Decorate a function with @tracked() to track inputs, outputs & environment of function executions.

Track function runs.

Files, folders & arrays and their storage locations.

`Artifact`()	Datasets & models stored as files, folders, or arrays.
`Storage`()	Storage locations of artifacts such as local directories or S3 buckets.

Data transformations and their executions.

`Transform`()	Data transformations such as scripts, notebooks, functions, or pipelines.
`Run`()	Runs of transforms such as the execution of a script.

Create labels and manage flexible records, e.g., for samples or donors.

`Record`()	Flexible metadata records.
`ULabel`()	Universal labels.

Define features & schemas to validate artifacts & records.

`Feature`()	Dimensions of measurement such as dataframe columns or dictionary keys.
`Schema`()	Schemas of datasets such as column sets of dataframes.

`User`()	Users.
`Collection`()	Versioned collections of artifacts.
`Project`()	Projects to label artifacts, transforms, records, and runs.
`Space`()	Workspaces with managed access for specific users or teams.
`Branch`()	Branches for change management with archive and trash states.
`Reference`()	References such as internal studies, papers, documents, or URLs.

Connecting, viewing database content, accessing settings & run context.

`DB`(instance)	Query any registry of any instance.
`connect`([instance])	Connect the global default instance.
`view`(*[, limit, modules, registries, df])	View metadata.
`save`(records[, ignore_conflicts, batch_size])	Bulk save records.
`UPath`(*args[, protocol])	Paths: low-level key-value access to files.
`settings`	Global live settings (`Settings`).
`context`	Global run context (`Context`).

`curators`	Curators.
`integrations`	Integrations.