lamindb-core 2.3a1__py3-none-any.whl

lamindb/__init__.py

@@ -0,0 +1,239 @@
+"""A data framework for biology.
+
+Installation::
+
+   pip install lamindb
+
+If you just want to *read* data from a LaminDB instance, use :class:`~lamindb.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 <https://lamin.ai>`__ and invite collaborators.
+If you prefer to work with a local database (no login required), 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, parameters, and environments of notebooks, scripts, and functions.
+
+.. autosummary::
+   :toctree: .
+
+   track
+   finish
+   flow
+   step
+
+Artifacts & storage locations
+=============================
+
+Files, folders & arrays and their storage locations.
+
+.. autosummary::
+   :toctree: .
+
+   Artifact
+   Storage
+
+Transforms & runs
+=================
+
+Data transformations and their executions.
+
+.. autosummary::
+   :toctree: .
+
+   Transform
+   Run
+
+Records, labels, features & schemas
+===================================
+
+Create labels and manage flexible records, e.g., for samples or donors.
+
+.. autosummary::
+   :toctree: .
+
+   Record
+   ULabel
+
+Define features & schemas to validate artifacts & records.
+
+.. autosummary::
+   :toctree: .
+
+   Feature
+   Schema
+
+Project management
+==================
+
+.. autosummary::
+   :toctree: .
+
+   Branch
+   Space
+   Project
+   User
+   Collection
+   Reference
+
+Basic utilities
+===============
+
+Connecting, viewing database content, accessing settings & run context.
+
+.. autosummary::
+   :toctree: .
+
+   DB
+   connect
+   view
+   save
+   UPath
+   settings
+   context
+
+Curators and integrations
+=========================
+
+.. autosummary::
+   :toctree: .
+
+   curators
+   integrations
+
+Examples, errors & setup
+========================
+
+.. autosummary::
+   :toctree: .
+
+   examples
+   errors
+   setup
+
+Developer API
+=============
+
+.. autosummary::
+   :toctree: .
+
+   base
+   core
+   models
+
+"""
+
+# ruff: noqa: I001
+# denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
+__version__ = "2.3a1"
+
+import warnings as _warnings
+
+# through SpatialData
+_warnings.filterwarnings(
+    "ignore", message="The legacy Dask DataFrame implementation is deprecated"
+)
+
+from lamindb_setup._check_setup import _check_instance_setup
+from lamindb_setup._connect_instance import connect
+from lamindb_setup.core.upath import UPath
+
+from . import base, errors, setup
+
+_check_instance_setup(from_module="lamindb")
+
+from .core._functions import flow, step, tracked
+from ._view import view
+from .core._context import context
+from .core._settings import settings
+from .models import (
+    Artifact,
+    Collection,
+    Feature,
+    Project,
+    Reference,
+    Run,
+    Schema,
+    Storage,
+    Transform,
+    ULabel,
+    User,
+    Space,
+    Branch,
+    Record,
+    DB,
+)
+from .models.save import save
+from . import core
+from . import integrations
+from . import curators
+from . import examples
+
+track = context._track
+finish = context._finish
+settings.__doc__ = """Global live settings (:class:`~lamindb.core.Settings`)."""
+context.__doc__ = """Global run context (:class:`~lamindb.core.Context`)."""
+
+from django.db.models import Q
+
+Param = Feature  # backward compat
+
+__all__ = [
+    # data lineage
+    "track",
+    "finish",
+    "step",
+    "flow",
+    # registries
+    "Artifact",
+    "Storage",
+    "Transform",
+    "Run",
+    "Feature",
+    "ULabel",
+    "Schema",
+    "Record",
+    "User",
+    "Collection",
+    "Project",
+    "Space",
+    "Branch",
+    "Reference",
+    # other
+    "connect",
+    "view",
+    "save",
+    "UPath",
+    "settings",
+    "context",
+    "DB",
+    # curators and integrations
+    "curators",
+    "integrations",
+    # examples, errors, setup
+    "examples",
+    "errors",
+    "setup",
+    # low-level functionality
+    "base",
+    "core",
+    "models",
+]