lamindb 0.32.0rc1__py2.py3-none-any.whl → 0.33.0__py2.py3-none-any.whl

lamindb/dev/db/_add.py

@@ -29,14 +29,25 @@ Guide: :doc:`/guide/add-delete`.
 
 Example:
 
->>> # add a record (by passing a record)
->>> ln.add(wetlab.Experiment(name="My test", biometa_id=test_id))
->>> # update an existing record
->>> experiment = ln.select(wetlab.Experiment, id=experiment_id).one()
->>> experiment.name = "New name"
+1) Add a record (by passing a record)
+>>> ln.add(lns.Pipeline(name="My pipeline", v="1"))
+Pipeline(id="0Cb86EZj", name="My pipeline", v="1", ...)
+
+2) Update an existing record
+>>> pipeline = ln.select(lns.Pipeline, id="0Cb86EZj").one()
+>>> pipeline.name = "New name"
 >>> ln.add(experiment)
->>> # add a record by fields if not yet exists
->>> ln.add(wetlab.Experiment, name="My test", biometa_id=test_id)
+Pipeline(id="0Cb86EZj", name="New name", v="1", ...)
+
+3) Add a record if not exist in the DB
+>>> # add a record if the metadata combination is not already exist in the DB
+>>> # if exists, returns the existing record from the DB
+>>> ln.add(lns.Pipeline, name="My pipeline", v="1")
+>>> # under the hood, this runs a query first based on passed fields
+>>> # equivalent to the following:
+>>> pipeline = ln.select(lns.Pipeline, name="My pipeline", v="1").one_or_none()
+>>> if pipeline is None:
+>>>     ln.add(pipeline)
 
 Args:
     record: One or multiple records as instances of `SQLModel`.
@@ -93,6 +104,10 @@ def add(  # type: ignore
     db_error = None
     for record in records:
         write_objectkey(record)
+        # the following ensures that queried objects (within __init__)
+        # behave like queried objects, only example right now: Run
+        if hasattr(record, "_ln_identity_key") and record._ln_identity_key is not None:
+            record._sa_instance_state.key = record._ln_identity_key
         session.add(record)
     try:
         session.commit()

lamindb/schema/__init__.py

@@ -12,13 +12,6 @@ Import this submodule as::
 Core entities
 =============
 
-Data objects ({class}`lamindb.DObject`) are transformed by runs:
-
-.. autosummary::
-   :toctree: .
-
-   Run
-
 Runs transform data using code:
 
 .. autosummary::
@@ -27,13 +20,6 @@ Runs transform data using code:
    Pipeline
    Notebook
 
-Grouping data objects by features:
-
-.. autosummary::
-   :toctree: .
-
-   Features
-
 Users, projects, storage locations, and usage:
 
 .. autosummary::
@@ -84,7 +70,7 @@ from lnschema_core import (
 from packaging import version as _v
 
 _check_v = {
-    "bionty": "0.8.0rc2",
+    "bionty": "0.8.0",
     "wetlab": "0.13.4",
 }
 

lamindb-0.33.0.dist-info/METADATA

@@ -0,0 +1,236 @@
+Metadata-Version: 2.1
+Name: lamindb
+Version: 0.33.0
+Summary: LaminDB: Manage R&D data & analyses.
+Author-email: Lamin Labs <laminlabs@gmail.com>
+Description-Content-Type: text/markdown
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Dist: lndb>=0.37.4
+Requires-Dist: lnschema_core==0.29.5
+Requires-Dist: lnschema_wetlab==0.13.4
+Requires-Dist: lnschema_bionty==0.8.0
+Requires-Dist: nbproject>=0.8.3
+Requires-Dist: readfcs>=1.1.0
+Requires-Dist: anndata>=0.8.0
+Requires-Dist: hjson
+Requires-Dist: sqlmodel>=0.0.8
+Requires-Dist: typeguard
+Requires-Dist: tabulate
+Requires-Dist: erdiagram
+Requires-Dist: zarr
+Requires-Dist: pre-commit ; extra == "dev"
+Requires-Dist: nox ; extra == "dev"
+Requires-Dist: laminci>=0.2.5 ; extra == "dev"
+Requires-Dist: pytest>=6.0 ; extra == "test"
+Requires-Dist: coverage ; extra == "test"
+Requires-Dist: pytest-cov ; extra == "test"
+Requires-Dist: scanpy ; extra == "test"
+Requires-Dist: scikit-learn>=1.1.1 ; extra == "test"
+Requires-Dist: nbproject_test>=0.3.0 ; extra == "test"
+Requires-Dist: psycopg2-binary ; extra == "test"
+Requires-Dist: matplotlib<3.7 ; extra == "test"
+Project-URL: Home, https://github.com/laminlabs/lamindb
+Provides-Extra: dev
+Provides-Extra: test
+
+[![Stars](https://img.shields.io/github/stars/laminlabs/lamindb?logo=GitHub&color=yellow)](https://github.com/laminlabs/lamindb)
+[![codecov](https://codecov.io/gh/laminlabs/lamindb/branch/main/graph/badge.svg?token=VKMRJ7OWR3)](https://codecov.io/gh/laminlabs/lamindb)
+[![pypi](https://img.shields.io/pypi/v/lamindb?color=blue&label=pypi%20package)](https://pypi.org/project/lamindb)
+
+# LaminDB: Manage R&D data & analyses
+
+_Curate, store, track, query, integrate, and learn from biological data._
+
+LaminDB is an open-source data lake for R&D in biology. It manages indexed **object storage** (local directories, S3, GCP) with a mapped **SQL database** (SQLite, Postgres, and soon, BigQuery).
+
+One cool thing is that you can readily create distributed _LaminDB instances_ at any scale. Get started on your laptop, deploy in the cloud, or work with a mesh of instances for different teams and purposes.
+
+```{warning}
+
+Public beta: Currently only recommended for collaborators as we still make breaking changes.
+
+```
+
+## Installation
+
+LaminDB is a python package available for Python versions 3.8+.
+
+```shell
+pip install lamindb
+```
+
+## Import
+
+In your python script, import LaminDB as:
+
+```python
+import lamindb as ln
+```
+
+## Quick setup
+
+Quick setup on the command line:
+
+- Sign up via `lamin signup <email>`
+- Log in via `lamin login <handle>`
+- Set up an instance via `lamin init --storage <storage> --schema <schema_modules>`
+
+:::{dropdown} Example code
+
+```shell
+lamin signup testuser1@lamin.ai
+lamin login testuser1
+lamin init --storage ./mydata --schema bionty,wetlab
+```
+
+:::
+
+See {doc}`/guide/setup` for more.
+
+## Track & query data
+
+### Track data sources, data, and metadata
+
+::::{tab-set}
+:::{tab-item} Within an interactive notebook
+
+```{code-block} python
+import lamindb as ln
+
+ln.Run() # data source (a run record) is created
+#> ℹ️ Instance: testuser2/mydata
+#> ℹ️ User: testuser2
+#> ℹ️ Loaded run:
+#> Run(id='L1oBMKW60ndt5YtjRqav', notebook_id='sePTpDsGJRq3', notebook_v='0', created_by='bKeW4T6E', created_at=datetime.datetime(2023, 3, 14, 21, 49, 36))
+
+df = pd.DataFrame({"a": [1, 2], "b": [3, 4]})
+
+# create a data object with SQL metadata record including hash
+# link run record
+dobject = ln.DObject(df, name="My dataframe")
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c')
+
+# upload serialized version to the configured storage
+# commit a DObject record to the SQL database
+ln.add(dobject)
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))
+```
+
+:::
+:::{tab-item} Within a regular pipeline
+
+```{code-block} python
+# create (or query) a pipeline record
+pipeline = lns.Pipeline(name="My pipeline")
+#> Pipeline(id='fhn5Zydf', v='1', name='My pipeline', created_by='bKeW4T6E')
+
+# create a run from the above pipeline as the data source
+run = ln.Run(pipeline=pipeline)
+#> Run(id='2aaKWH8dwBE6hnj3n9K9', pipeline_id='fhn5Zydf', pipeline_v='1', created_by='bKeW4T6E')
+
+# access pipeline from run via
+print(run.pipeline)
+#> Pipeline(id='fhn5Zydf', v='1', name='My pipeline', created_by='bKeW4T6E')
+
+df = pd.DataFrame({"a": [1, 2], "b": [3, 4]})
+
+# create a data object with SQL metadata record including hash and link run record
+dobject = ln.DObject(df, name="My dataframe", source=run)
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c')
+
+# Tip: If you work with a single thread, you can pass `global_context=True` to ln.Run(), allowing you to omit source=run
+
+# upload serialized version to the configured storage
+# commit a DObject record to the SQL database
+ln.add(dobject)
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))
+```
+
+:::
+::::
+
+### Query & load data
+
+```python
+dobject = ln.select(ln.DObject, name="My dataframe").one()
+#> [DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))]
+df = dobject.load()
+#>      a	b
+#>  0	1	3
+#>  1	2	4
+```
+
+Get the data ingested by the latest run:
+
+```python
+run = ln.select(ln.Run).order_by(ln.Run.created_at.desc()).first()
+#> Run(id='L1oBMKW60ndt5YtjRqav', notebook_id='sePTpDsGJRq3', notebook_v='0', created_by='bKeW4T6E', created_at=datetime.datetime(2023, 3, 14, 21, 49, 36))
+dobject = ln.select(ln.DObject).where(ln.DObject.source == run).all()
+#> [DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))]
+```
+
+<br>
+
+See {doc}`/guide/track` for more.
+
+## Track biological metadata
+
+### Track biological features
+
+```python
+import bionty as bt  # Lamin's manager for biological knowledge
+import lamindb as ln
+
+ln.Run()  # assume we're in a notebook and don't need to pass pipeline_name
+
+# a sample single cell RNA-seq dataset
+adata = ln.dev.datasets.anndata_mouse_sc_lymph_node()
+
+# Create a reference
+# - ensembl id as the standardized id
+# - mouse as the species
+reference = bt.Gene(species="mouse")
+
+# parse gene identifiers from data and map on reference
+features = ln.Features(adata, reference)
+#> 🔶 id column not found, using index as features.
+#> ✅ 0 terms (0.0%) are mapped.
+#> 🔶 10000 terms (100.0%) are not mapped.
+# The result is a hashed feature set record:
+print(features)
+#> Features(id='2Mv3JtH-ScBVYHilbLaQ', type='gene', created_by='bKeW4T6E')
+# genes records can be accessed via:
+print(features.genes[:3])
+#> [Gene(id='ENSMUSG00000020592', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000034931', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000071005', species_id='NCBI_10090')]
+
+# track data with features
+dobject = ln.DObject(adata, name="Mouse Lymph Node scRNA-seq", features=features)
+
+# access linked gene references
+print(dobject.features.genes[:3])
+#> [Gene(id='ENSMUSG00000020592', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000034931', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000071005', species_id='NCBI_10090')]
+
+# upload serialized data to configured storage
+# commit a DObject record to the SQL database
+# commit all linked features to the SQL database
+ln.add(dobject)
+```
+
+<br>
+
+See {doc}`/guide/features` for more.
+
+```{tip}
+- Each page in this guide is a Jupyter Notebook, which you can download [here](https://github.com/laminlabs/lamindb/tree/main/docs/guide).
+- You can run these notebooks in hosted versions of JupyterLab, e.g., [Saturn Cloud](https://github.com/laminlabs/run-lamin-on-saturn), Google Vertex AI, and others.
+- We recommend using [JupyterLab](https://jupyterlab.readthedocs.io/) for best notebook tracking experience.
+```
+
+📬 [Reach out](https://lamin.ai/contact) to report issues, learn about data modules that connect your assays, pipelines & workflows within our data platform enterprise plan.
+

{lamindb-0.32.0rc1.dist-info → lamindb-0.33.0.dist-info}/RECORD

@@ -1,11 +1,12 @@
-lamindb/__init__.py,sha256=0GzDN8eM_-IvXxV50fX2vSZJPVeRgjbQ1kZ_hFkykEs,4541
-lamindb/_check_versions.py,sha256=kixg_wyP9-GPWmyuLmsECcxTZANPlH60OoTQAVtAT84,1004
-lamindb/_delete.py,sha256=7hrMmpAsFoRhdXL32hbyGlCsFv7N0fOpsxxitMno6sc,4338
+lamindb/__init__.py,sha256=1qOrs9tEMQVexTUI2xUHCJFdE8feiWgT1IxKcWhvNwU,4583
+lamindb/_check_versions.py,sha256=3pOwEFLxMQLxnIg2408vDoAzvOEIJJB9zlOboOdiBiA,1003
+lamindb/_context.py,sha256=11eKvLvGpNzJT3I1JcTb06FkSJjot4T6Of9MMthcBlY,7334
+lamindb/_delete.py,sha256=h9rEwsfmyR2qKZBTMH6pR_v36_K4WCpE6nAoA8oXvGw,4662
 lamindb/_folder.py,sha256=JGK1saXTa_j4OdWmD2VmlaasdSpLYTq5tSgLsh2hPA8,5201
-lamindb/_load.py,sha256=m4WHbH_nPq8dMNsO4A9MysWnDdOpMj_Wy5OwzaSmL0I,1696
+lamindb/_load.py,sha256=bkxlQudPzxEyj3bG5PK3MiD00lL__0tragrwMQIU-U0,1337
 lamindb/_logger.py,sha256=d1jQdFL4gMKbzcc1dMOgKoEaUlWhyK-VsnxYLlG9caY,48
-lamindb/_nb.py,sha256=PYekGogvdWqQVw8s5DhzqFvuPGo173RTa7sOCJieZlU,6439
-lamindb/_record.py,sha256=XSmeaJq2lJtKgtaRUbWEvg1j962yZQ6UvNkw-wTWERE,10434
+lamindb/_nb.py,sha256=1Sgv-XC3Y2-yzS5CUh25wAtk8GJd-Y5GjEdwyueAJP4,3780
+lamindb/_record.py,sha256=krx8WmANrrG_W4AQqFyVR0UGr4NsVcQrSP5D6FKYD0k,11593
 lamindb/_settings.py,sha256=dX1A2Hx5aSRC4YjY5jF2J1Tv5K8w_UOuAPFCcxdpMHI,818
 lamindb/_subset.py,sha256=37DH5HxG0xdmc4kBBypanYWuMlMKumTKH6IM8mcG-ps,2430
 lamindb/_view.py,sha256=WsBT9VZGUJyT3sGcJfQYtZXM5T6G9O6NfUWeGFV0UQY,1364
@@ -15,7 +16,7 @@ lamindb/dev/_docs.py,sha256=0ha3cZqzvIQnAXVC_JlAiRrFi3VpEEVookP_oURhBr4,240
 lamindb/dev/datasets/__init__.py,sha256=BvV0ONUj0Iz5JIawb8ow2TpLOQIuEsvGW7_1zdbXrxU,613
 lamindb/dev/datasets/_core.py,sha256=h-I3fIEyhKaOryo9aCn2Wgmh_jN-Xa5Z0TJwEi1lbtw,7434
 lamindb/dev/db/__init__.py,sha256=Rp9LZ2QPQxEF6J_z2M8vUrUZztG0qQdf9j3Zi3dJhRQ,216
-lamindb/dev/db/_add.py,sha256=RxPfwpvFnuIS8-dOp7fzvYf8sNhMYIpf3I9NbEBMvg8,8940
+lamindb/dev/db/_add.py,sha256=30pm1XLBHWsn5Wi53mJArkFlE9f1Sy9CDQ2u89vsBcI,9660
 lamindb/dev/db/_core.py,sha256=6x9fj0LxxPtrPJ7t5Ee_-e1AJgh5H2KI33VnLjuVZXg,897
 lamindb/dev/db/_select.py,sha256=IE_Nwh_kFXRzIJpz4rsSIOaxFTt9jwkncvIK6KUO15Q,7424
 lamindb/dev/db/_session.py,sha256=Vwt2gItSnFoHTTtXVZ77ZxyCNjwca9b0MkViWnxemqc,1855
@@ -32,10 +33,7 @@ lamindb/dev/object/_anndata_sizes.py,sha256=OOM9mJmhvho5JacsuMsHTXoWfvF0vjxRvg_P
 lamindb/dev/object/_core.py,sha256=z42LBQb_zICJrY7vXI2GrBzpnDN3WhFmW32STfAgzis,900
 lamindb/dev/object/_lazy_field.py,sha256=KJG8YpA_Y0UWvEu4K-h-J69J29Q-tdnutEEutVijX0M,4116
 lamindb/dev/object/_subset_anndata.py,sha256=t8vIJfKLxl386pIURHm8yk49Vg1NPUK-Bxv06KRUZRU,3533
-lamindb/knowledge/__init__.py,sha256=XSeFHBfjUxCLnbC6SSW3QdWPdfGaKwf_LSbW9qgR44A,655
-lamindb/knowledge/_core.py,sha256=9C-8TTMsyAwgFYCJVjsi8LEVbOh2HZaCU4q3qm-RzUk,1639
-lamindb/knowledge/_lookup.py,sha256=RvUsYMS6d58zgCZy6WmCJJpCnQvSXua9FivgW2iVwjY,404
-lamindb/schema/__init__.py,sha256=w8odXPFGtkXC5HcyfaH3t8iC9_2eEseuIk5VLbEJEWo,2167
+lamindb/schema/__init__.py,sha256=cN4PH_UzNANQcPbsWkMmjsPt3JUQuKmU2D_RDn4oy5E,1975
 lamindb/schema/_core.py,sha256=knEAUQqkNZMYUotEEW_Yo6D1Ijw6gnUpcyh7iPjjFK4,2109
 lamindb/schema/_table.py,sha256=yEPakpgx3R7ytBe-n4NgmOwfOuiYoOLuE7uXT16TqGQ,1509
 lamindb/schema/dev/__init__.py,sha256=XvATVfSXU9DPLiNTsKqQMprMvdGEdojkvsBXmJdUe1E,128
@@ -44,8 +42,8 @@ lamindb/schema/dev/sqlmodel.py,sha256=qscffXVlPKE18OP2duCkRo8ZQQf6VNYUMDI4D65z-X
 lamindb/schema/dev/type.py,sha256=V1mrlmkdQQWOi20SwsZutccKf8n1b0jD0E60bRPxZI0,114
 lamindb/setup/__init__.py,sha256=jPc-SG6T_GQXfh81I86v_Yj2XFBS8FPuY5I0sGwIRJc,213
 lamindb/setup/dev.py,sha256=7wl6L-Gj3eV2mmsnxFeuqcaEkmGN1QyQm0bCEDyddFI,84
-lamindb-0.32.0rc1.dist-info/entry_points.txt,sha256=8ro7RnWnay39wF5Ojvnfnd8TvyI7WrPOCVQHNxZAA6w,44
-lamindb-0.32.0rc1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.32.0rc1.dist-info/WHEEL,sha256=96_DCfscDnVj9fVNwi1rfifiRwfpxLjwXWglVksjj_E,99
-lamindb-0.32.0rc1.dist-info/METADATA,sha256=5zQ_wQt_7S-PZYcUpuf0bGeaJuT4tIIMrYAQsbvhZmE,5328
-lamindb-0.32.0rc1.dist-info/RECORD,,
+lamindb-0.33.0.dist-info/entry_points.txt,sha256=8ro7RnWnay39wF5Ojvnfnd8TvyI7WrPOCVQHNxZAA6w,44
+lamindb-0.33.0.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.33.0.dist-info/WHEEL,sha256=kdeDBNPvBI0w3meLKPoGgAnEr54n1jzrZWUoaLmGzVY,99
+lamindb-0.33.0.dist-info/METADATA,sha256=DoyNt1jUs-X3cbz9gkDTk9nUL74sRFY8m9pLHFA8FUM,8736
+lamindb-0.33.0.dist-info/RECORD,,

{lamindb-0.32.0rc1.dist-info → lamindb-0.33.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: flit 3.7.1
+Generator: flit 3.8.0
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any

lamindb/knowledge/__init__.py

@@ -1,34 +0,0 @@
-"""Knowledge.
-
-Feature tables from bionty:
-
-.. autosummary::
-   :toctree: .
-
-   Species
-   Gene
-   Protein
-   CellMarker
-   Tissue
-   CellType
-   Disease
-
-Lookup knowledge table identifiers:
-
-.. autosummary::
-   :toctree: .
-
-   lookup
-"""
-
-
-from lamin_logger import logger
-
-from ._core import CellMarker, CellType, Disease, Gene, Protein, Species, Tissue
-from ._lookup import lookup
-
-# currently shows up also when initializing ln.DObject, so not emit it yet
-# logger.warning(
-#     "The lamindb.knowledge API is deprecated.\nPlease, use bionty directly.\nYou can"
-#     " replace all occurances of ln.knowledge with bionty without breaking changes!"
-# )

lamindb/knowledge/_core.py

@@ -1,71 +0,0 @@
-import bionty as bt
-
-
-class Species(bt.Species):
-    """Bionty Species.
-
-    See `bionty.Species <https://lamin.ai/docs/bionty/bionty.Species>`__.
-    """
-
-    def __init__(self, id="name") -> None:
-        super().__init__(id=id)
-
-
-class Gene(bt.Gene):
-    """Bionty Gene.
-
-    See `bionty.Gene <https://lamin.ai/docs/bionty/bionty.Gene>`__.
-    """
-
-    def __init__(self, species="human", id="ensembl_gene_id") -> None:
-        super().__init__(species=species, id=id)
-
-
-class Protein(bt.Protein):
-    """Bionty Protein.
-
-    See `bionty.Protein <https://lamin.ai/docs/bionty/bionty.Protein>`__.
-    """
-
-    def __init__(self, species="human", id="uniprotkb_id") -> None:
-        super().__init__(species=species, id=id)
-
-
-class CellMarker(bt.CellMarker):
-    """Bionty CellMarker.
-
-    See `bionty.CellMarker <https://lamin.ai/docs/bionty/bionty.CellMarker>`__.
-    """
-
-    def __init__(self, species="human", id="name") -> None:
-        super().__init__(species=species, id=id)
-
-
-class CellType(bt.CellType):
-    """Bionty CellType.
-
-    See `bionty.CellType <https://lamin.ai/docs/bionty/bionty.CellType>`__.
-    """
-
-    def __init__(self, id="ontology_id") -> None:
-        super().__init__(id=id)
-
-
-class Tissue(bt.Tissue):
-    """Bionty Tissue.
-
-    See `bionty.Tissue <https://lamin.ai/docs/bionty/bionty.Tissue>`__.
-    """
-
-    def __init__(self, id="ontology_id") -> None:
-        super().__init__(id=id)
-
-
-class Disease(bt.Disease):
-    """Bionty Disease.
-
-    See `bionty.Disease <https://lamin.ai/docs/bionty/bionty.Disease>`__.
-    """
-
-    def __init__(self, id="ontology_id") -> None:
-        super().__init__(id=id)

lamindb/knowledge/_lookup.py

@@ -1,18 +0,0 @@
-from bionty import lookup as bionty_lookup
-
-
-class lookup:
-    """Lookup identifiers of knowledge tables."""
-
-    pass
-
-
-def _get_all_methods(lookup):
-    return [i for i in dir(lookup) if not i.startswith("_")]
-
-
-for module in [bionty_lookup]:
-    methods = _get_all_methods(module)
-    for method in methods:
-        model = getattr(module, method)
-        setattr(lookup, method, staticmethod(model))

lamindb-0.32.0rc1.dist-info/METADATA

@@ -1,178 +0,0 @@
-Metadata-Version: 2.1
-Name: lamindb
-Version: 0.32.0rc1
-Summary: LaminDB: Manage R&D data & analyses.
-Author-email: Lamin Labs <laminlabs@gmail.com>
-Description-Content-Type: text/markdown
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Requires-Dist: lndb==0.37.1
-Requires-Dist: lnschema_core==0.29.1
-Requires-Dist: lnschema_wetlab==0.13.4
-Requires-Dist: lnschema_bionty==0.8.0rc2
-Requires-Dist: nbproject>=0.8.2
-Requires-Dist: readfcs>=1.1.0
-Requires-Dist: anndata>=0.8.0
-Requires-Dist: hjson
-Requires-Dist: sqlmodel>=0.0.8
-Requires-Dist: typeguard
-Requires-Dist: tabulate
-Requires-Dist: erdiagram
-Requires-Dist: zarr
-Requires-Dist: pre-commit ; extra == "dev"
-Requires-Dist: nox ; extra == "dev"
-Requires-Dist: laminci>=0.2.5 ; extra == "dev"
-Requires-Dist: pytest>=6.0 ; extra == "test"
-Requires-Dist: coverage ; extra == "test"
-Requires-Dist: pytest-cov ; extra == "test"
-Requires-Dist: scanpy ; extra == "test"
-Requires-Dist: scikit-learn>=1.1.1 ; extra == "test"
-Requires-Dist: nbproject_test>=0.3.0 ; extra == "test"
-Requires-Dist: psycopg2-binary ; extra == "test"
-Requires-Dist: matplotlib<3.7 ; extra == "test"
-Project-URL: Home, https://github.com/laminlabs/lamindb
-Provides-Extra: dev
-Provides-Extra: test
-
-[![Stars](https://img.shields.io/github/stars/laminlabs/lamindb?logo=GitHub&color=yellow)](https://github.com/laminlabs/lamindb)
-[![codecov](https://codecov.io/gh/laminlabs/lamindb/branch/main/graph/badge.svg?token=VKMRJ7OWR3)](https://codecov.io/gh/laminlabs/lamindb)
-[![pypi](https://img.shields.io/pypi/v/lamindb?color=blue&label=pypi%20package)](https://pypi.org/project/lamindb)
-
-# LaminDB: Manage R&D data & analyses
-
-_Curate, store, track, query, integrate, and learn from biological data._
-
-LaminDB is an open-source data lake for R&D in biology. It manages indexed **object storage** (local directories, S3, GCP) with a mapped **SQL database** (SQLite, Postgres, and soon, BigQuery).
-
-One cool thing is that you can readily create distributed _LaminDB instances_ at any scale. Get started on your laptop, deploy in the cloud, or work with a mesh of instances for different teams and purposes.
-
-```{warning}
-
-Public beta: Currently only recommended for collaborators as we still make breaking changes.
-
-```
-
-## Installation
-
-LaminDB is a python package available for Python versions 3.8+.
-
-```shell
-pip install lamindb
-```
-
-## Import
-
-In your python script, import LaminDB as:
-
-```python
-import lamindb as ln
-```
-
-## Quick setup
-
-Quick setup on the command line:
-
-- Sign up via `lamin signup <email>`
-- Log in via `lamin login <handle>`
-- Set up an instance via `lamin init --storage <storage> --schema <schema_modules>`
-
-:::{dropdown} Example code
-
-```shell
-lamin signup testuser1@lamin.ai
-lamin login testuser1
-lamin init --storage ./mydata --schema bionty,wetlab
-```
-
-:::
-
-See {doc}`/guide/setup` for more.
-
-## Track & query data
-
-### Track data source & data
-
-::::{tab-set}
-:::{tab-item} Within a notebook
-
-```{code-block} python
-ln.nb.header()  # data source is created and linked
-
-df = pd.DataFrame({"a": [1, 2], "b": [3, 4]})
-
-# create a data object with SQL metadata record
-dobject = ln.DObject(df, name="My dataframe")
-
-# upload the data file to the configured storage
-# and commit a DObject record to the SQL database
-ln.add(dobject)
-```
-
-:::
-:::{tab-item} Within a pipeline
-
-```{code-block} python
-# create a pipeline record
-pipeline = lns.Pipeline(name="my pipeline", version="1")
-
-# create a run from the above pipeline as the data source
-run = lns.Run(pipeline=pipeline, name="my run")
-
-df = pd.DataFrame({"a": [1, 2], "b": [3, 4]})
-
-# create a data object with SQL metadata record
-dobject = ln.DObject(df, name="My dataframe", source=run)
-
-# upload the data file to the configured storage
-# and commit a DObject record to the SQL database
-ln.add(dobject)
-```
-
-:::
-::::
-
-### Query & load data
-
-```python
-dobject = ln.select(ln.DObject, name="My dataframe").one()
-df = dobject.load()
-```
-
-<br>
-
-See {doc}`/guide/ingest` for more.
-
-## Track biological features
-
-```python
-import bionty as bt
-
-# An sample single cell RNA-seq dataset
-adata = ln.dev.datasets.anndata_mouse_sc_lymph_node()
-
-# Start to track genes mapped to a Bionty Entity
-# - ensembl id as the standardized id
-# - mouse as the species
-reference = bt.Gene(id=bt.gene_id.ensembl_gene_id, species=bt.Species().lookup.mouse)
-
-# Create a data object with features
-dobject = ln.DObject(adata, name="Mouse Lymph Node scRNA-seq", features_ref=reference)
-
-# upload the data file to the configured storage
-# and commit a DObject record to the sql database
-ln.add(dobject)
-```
-
-<br>
-
-See {doc}`/guide/link-features` for more.
-
-```{tip}
-- Each page in this guide is a Jupyter Notebook, which you can download [here](https://github.com/laminlabs/lamindb/tree/main/docs/guide).
-- You can run these notebooks in hosted versions of JupyterLab, e.g., [Saturn Cloud](https://github.com/laminlabs/run-lamin-on-saturn), Google Vertex AI, and others.
-- We recommend using [JupyterLab](https://jupyterlab.readthedocs.io/) for best notebook tracking experience.
-```
-
-📬 [Reach out](https://lamin.ai/contact) to report issues, learn about data modules that connect your assays, pipelines & workflows within our data platform enterprise plan.
-