lamindb 0.68.0__py3-none-any.whl → 0.68.2__py3-none-any.whl

lamindb/setup/__init__.py

@@ -1,8 +1,14 @@
 import lamindb_setup as _lamindb_setup
 from lamindb_setup import *  # noqa: F403
-from lamindb_setup import settings
+from lamindb_setup import (
+    connect,
+    delete,
+    init,
+    settings,
+)
 
-from . import dev
+from . import core
 
+del connect  # we have this at the root level, hence, we don't want it here
 __doc__ = _lamindb_setup.__doc__.replace("lamindb_setup", "lamindb.setup")
 settings.__doc__ = settings.__doc__.replace("lamindb_setup", "lamindb.setup")

lamindb/setup/{dev → core}/__init__.py

@@ -1,6 +1,4 @@
-"""Setup developer API.
-
-Settings:
+"""Core setup library.
 
 .. autosummary::
    :toctree:
@@ -10,7 +8,7 @@ Settings:
    StorageSettings
 
 """
-from lamindb_setup.dev import (  # pragma: no cover
+from lamindb_setup.core import (  # pragma: no cover
     InstanceSettings,
     StorageSettings,
     UserSettings,

{lamindb-0.68.0.dist-info → lamindb-0.68.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.68.0
+Version: 0.68.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,10 +9,10 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.62.0
-Requires-Dist: lamindb_setup==0.65.3
+Requires-Dist: lnschema_core==0.63.0
+Requires-Dist: lamindb_setup==0.66.1
 Requires-Dist: lamin_utils==0.13.0
-Requires-Dist: lamin_cli==0.8.1
+Requires-Dist: lamin_cli==0.9.3
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -24,8 +24,9 @@ Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: aiobotocore[boto3]>=2.5.4,<3.0.0 ; extra == "aws"
+Requires-Dist: s3fs==2023.12.2 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.12.2 ; extra == "aws"
-Requires-Dist: bionty==0.41.0 ; extra == "bionty"
+Requires-Dist: bionty==0.42.0 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
@@ -59,14 +60,11 @@ Provides-Extra: zarr
 
 # LaminDB - A data framework for biology
 
-LaminDB is an open-source Python framework to manage biological data & analyses:
-
-- Access data & metadata across storage & databases.
+- Access storage & databases with one Python API & CLI.
 - Track data lineage across notebooks & pipelines.
 - Manage registries for experimental metadata & in-house ontologies.
-- Validate, standardize & annotate data.
-- Organize and share data across a mesh of LaminDB instances.
-- Manage data access, leverage an auditable system of record.
+- Validate, standardize & annotate.
+- Collaborate across a mesh of distributed LaminDB instances.
 
 ## Documentation
 

lamindb-0.68.2.dist-info/RECORD

@@ -0,0 +1,49 @@
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lamindb/core/hashing.py

@@ -1,62 +0,0 @@
-"""Hashing.
-
-.. autosummary::
-   :toctree: .
-
-   hash_set
-   hash_file
-
-"""
-
-import base64
-import hashlib
-from typing import List, Set, Tuple
-
-
-def to_b64_str(bstr: bytes):
-    b64 = base64.urlsafe_b64encode(bstr).decode().strip("=")
-    return b64
-
-
-def b16_to_b64(s: str):
-    return to_b64_str(base64.b16decode(s.strip('"'), casefold=True))
-
-
-# a lot to read about this: lamin-notes/2022/hashing
-def hash_set(s: Set[str]) -> str:
-    bstr = ":".join(sorted(s)).encode("utf-8")
-    # as we're truncating at 20 b64, we choose md5 over sha512
-    return to_b64_str(hashlib.md5(bstr).digest())[:20]
-
-
-def hash_md5s_from_dir(etags: List[str]) -> Tuple[str, str]:
-    # need to sort below because we don't want the order of parsing the dir to
-    # affect the hash
-    digests = b"".join(
-        hashlib.md5(etag.encode("utf-8")).digest() for etag in sorted(etags)
-    )
-    digest = hashlib.md5(digests).digest()
-    return to_b64_str(digest)[:22], "md5-d"
-
-
-def hash_file(file_path, chunk_size=50 * 1024 * 1024) -> Tuple[str, str]:
-    chunks = []
-    with open(file_path, "rb") as fp:
-        # read first chunk
-        chunks = [fp.read(chunk_size)]
-        # try reading the 2nd chunk
-        data = fp.read(chunk_size)
-        if data:
-            # go to end of file
-            fp.seek(-chunk_size, 2)
-            # read last chunk
-            data = fp.read(chunk_size)
-            chunks.append(data)
-    if len(chunks) == 1:
-        digest = hashlib.md5(chunks[0]).digest()
-        hash_type = "md5"
-    else:
-        digests = b"".join(hashlib.sha1(chunk).digest() for chunk in chunks)
-        digest = hashlib.sha1(digests).digest()
-        hash_type = "sha1-fl"  # sha1 first last chunk
-    return to_b64_str(digest)[:22], hash_type

lamindb-0.68.0.dist-info/RECORD

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