lamindb 0.71.1__py3-none-any.whl → 0.71.2__py3-none-any.whl

lamindb/__init__.py

@@ -41,7 +41,7 @@ Modules & settings:
 """
 
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "0.71.1"
+__version__ = "0.71.2"
 
 import os as _os
 

lamindb/_run.py

@@ -13,6 +13,7 @@ def __init__(run: Run, *args, **kwargs):
     transform: Transform = None
     if "transform" in kwargs or len(args) == 1:
         transform = kwargs.pop("transform") if len(args) == 0 else args[0]
+    params: str | None = kwargs.pop("params") if "params" in kwargs else None
     reference: str | None = kwargs.pop("reference") if "reference" in kwargs else None
     reference_type: str | None = (
         kwargs.pop("reference_type") if "reference_type" in kwargs else None
@@ -25,6 +26,7 @@ def __init__(run: Run, *args, **kwargs):
         transform=transform,
         reference=reference,
         reference_type=reference_type,
+        json=params,
     )
 
 

lamindb/_transform.py

@@ -1,10 +1,10 @@
 from __future__ import annotations
 
-from lnschema_core.models import Artifact, Run, Transform
+from lnschema_core.models import Run, Transform
 from lnschema_core.types import TransformType
 
 from ._run import delete_run_artifacts
-from .core.versioning import get_uid_from_old_version, init_uid
+from .core.versioning import process_is_new_version_of
 
 
 def __init__(transform: Transform, *args, **kwargs):
@@ -32,15 +32,9 @@ def __init__(transform: Transform, *args, **kwargs):
             "Only name, key, version, type, is_new_version_of, reference, "
             f"reference_type can be passed, but you passed: {kwargs}"
         )
-    if is_new_version_of is None:
-        new_uid = init_uid(version=version, n_full_id=Transform._len_full_uid)
-    else:
-        if not isinstance(is_new_version_of, Transform):
-            raise TypeError("is_new_version_of has to be of type ln.Transform")
-        new_uid, version = get_uid_from_old_version(is_new_version_of, version)
-        if name is None:
-            name = is_new_version_of.name
-
+    new_uid, version, name = process_is_new_version_of(
+        is_new_version_of, version, name, Transform
+    )
     # this is only because the user-facing constructor allows passing an id
     # most others don't
     if uid is None:

lamindb/core/_run_context.py

@@ -201,6 +201,7 @@ class run_context:
     def _track(
         cls,
         *,
+        params: dict | None = None,
         transform: Transform | None = None,
         new_run: bool | None = None,
         path: str | None = None,
@@ -216,6 +217,7 @@ class run_context:
         whether the script exists in the git repository and add a link.
 
         Args:
+            params: A dictionary of parameters to track for the run.
             transform: Can be of type `"pipeline"` or `"notebook"`
                 (:class:`~lamindb.core.types.TransformType`).
             new_run: If `False`, loads latest run of transform
@@ -310,11 +312,13 @@ class run_context:
             )
             if run is not None:  # loaded latest run
                 run.started_at = datetime.now(timezone.utc)  # update run time
+                run.json = params  # update run params
                 logger.important(f"loaded: {run}")
 
         if run is None:  # create new run
             run = Run(
                 transform=cls.transform,
+                params=params,
             )
             logger.important(f"saved: {run}")
         # can only determine at ln.finish() if run was consecutive in

lamindb/core/versioning.py

@@ -42,10 +42,7 @@ def init_uid(
     if is_new_version_of is not None:
         stem_uid = is_new_version_of.stem_uid
     else:
-        if n_full_id == 20:
-            stem_uid = ids.base62_16()
-        elif n_full_id == 16:
-            stem_uid = ids.base62_12()
+        stem_uid = ids.base62(n_full_id - 4)
     if version is not None:
         if not isinstance(version, str):
             raise ValueError(
@@ -90,3 +87,20 @@ def get_new_path_from_uid(old_path: UPath, old_uid: str, new_uid: str):
         # for cloud path, the rename target must be the last part of the path
         new_path = old_path.name.replace(old_uid, new_uid)
     return new_path
+
+
+def process_is_new_version_of(
+    is_new_version_of: IsVersioned,
+    version: str | None,
+    name: str | None,
+    type: type[IsVersioned],
+) -> tuple[str, str, str]:
+    if is_new_version_of is not None and not isinstance(is_new_version_of, type):
+        raise TypeError(f"is_new_version_of has to be of type {type}")
+    if is_new_version_of is None:
+        uid = init_uid(version=version, n_full_id=type._len_stem_uid)
+    else:
+        uid, version = get_uid_from_old_version(is_new_version_of, version)
+        if name is None:
+            name = is_new_version_of.name
+    return uid, version, name

{lamindb-0.71.1.dist-info → lamindb-0.71.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.71.1
+Version: 0.71.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,7 +9,7 @@ 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==0.66.3
+Requires-Dist: lnschema_core==0.66.4
 Requires-Dist: lamindb_setup==0.71.3
 Requires-Dist: lamin_utils==0.13.2
 Requires-Dist: lamin_cli==0.13.1

{lamindb-0.71.1.dist-info → lamindb-0.71.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lamindb/__init__.py,sha256=PbZGEkozIsD8RM3XLafkYGo4iPJy7FJFdzVr0VW7Zy0,2182
+lamindb/__init__.py,sha256=GKrW6unkqBBwwpxTXjuUv-5k4c4unimsV-vGFSWt68I,2182
 lamindb/_annotate.py,sha256=kgbilILfgzoS-GEpjxzVwRMs7CoSa9BNEcIWXFBW69I,43915
 lamindb/_artifact.py,sha256=8uBW-dhuWyBUQGs728sAPCnuhTic-NKjSbaneF07aMo,40106
 lamindb/_can_validate.py,sha256=nvoZG-35n3HofkY4Xc6hBv9AV54_RDan7Hzp5TuqY9I,14709
@@ -13,10 +13,10 @@ lamindb/_parents.py,sha256=N9T8jbd3eaoHDLE9TD1y1QgGcO81E6Brapy8LILzRCQ,14790
 lamindb/_query_manager.py,sha256=3zokXqxgj9vTJBnN2sbYKS-q69fyDDPF_aGq_rFHzXU,4066
 lamindb/_query_set.py,sha256=n0owd74cTzGz6-mIv8SlDz0wcyRz7Xw3Ke1LhE8UlIg,10784
 lamindb/_registry.py,sha256=fmX-BUnan3Y0WrEAx3qNwRYCIJwJgjoKnRnpgcXujEI,19358
-lamindb/_run.py,sha256=b7A52M1On3QzFgIYyfQoz5Kk7V3wcu9p_Prq5bzd8v8,1838
+lamindb/_run.py,sha256=We50MUeGH778begutDGoNFM-n5_81_BfMCnZS1bdkt0,1937
 lamindb/_save.py,sha256=_7r3TUV3B6Hp75r5O_ymu3fKWyBHbGa5vmE_pxrtsVI,10923
 lamindb/_storage.py,sha256=VW8xq3VRv58-ciholvOdlcgvp_OIlLxx5GxLt-e2Irs,614
-lamindb/_transform.py,sha256=rxojJ91qQSkeYDHYbwqjFAYxBMgJd3cq_K7Z0n5g8Aw,3482
+lamindb/_transform.py,sha256=E9C7psuOnsNrUQpWRuGgEUM8_pc7YhDn7n4ieHzB4X0,3169
 lamindb/_ulabel.py,sha256=e5dw9h1tR0_u-DMn7Gzx0WhUhV5w7j4v3QbnLWQV7eI,1941
 lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
 lamindb/_view.py,sha256=GV1FrqIMmdooEkA-5zvcTWgV1nqx1sehi6WdWEaFpxM,2171
@@ -25,7 +25,7 @@ lamindb/core/_data.py,sha256=Lico6-Vx15bNpGLl1bqFqEsh62pD4YKOOBnmahse1tI,17673
 lamindb/core/_feature_manager.py,sha256=uTzZZ7-qqEAmdwi48Holy2j5VGTgmoQxhb21r6mLShI,15824
 lamindb/core/_label_manager.py,sha256=0RtegYnK3zIisOnd970EobOrHMpp7OCH-mEoPrPXw2c,9075
 lamindb/core/_mapped_collection.py,sha256=_OwFZh5SePDUD70XIK5kngv3we_Z5-YdGHNfpUSatSQ,19469
-lamindb/core/_run_context.py,sha256=3Pa9DQRR9_OZTMJyezi4p_ZIdL6JsKnQ8gM57whFpMo,16926
+lamindb/core/_run_context.py,sha256=7iCCOB2z154puBI7ZKzcaEZ5l6_9S8aSYBOBJI65lyc,17117
 lamindb/core/_settings.py,sha256=rW1KfEXfT56XErwcnSuQxaCytpOy1kJ-u7tVmkmNmxY,6131
 lamindb/core/_sync_git.py,sha256=06Te35UZj2QBaHNcc59VSC9vJgcFct7Z2sK78NLkZBs,4119
 lamindb/core/_track_environment.py,sha256=xLZ6kgzxWS6MWZ5LQ_wkbJX99vmYOT8iQ-Fz4OHCgWw,754
@@ -33,7 +33,7 @@ lamindb/core/_transform_settings.py,sha256=eV96QKX9jOojjzF-a0oo0wXQsMXN2F6QV7orE
 lamindb/core/exceptions.py,sha256=PHk5lyBdJPrrEQcid3ItfdNzz3fgiQsUmsEDdz063F0,197
 lamindb/core/fields.py,sha256=Jgi_XI-iTe6cT7oD8FV_JqEpjN1Q9rZWwL8VLtj4jkA,164
 lamindb/core/types.py,sha256=xeQF2x40p2pR9eIVQrXT74RrS810z2fbjmTRTSQUqPM,230
-lamindb/core/versioning.py,sha256=DsEHpCueNwhRiIaRH5-O8H_1fJVNtWslCRx30YiIS5o,3080
+lamindb/core/versioning.py,sha256=T9d28erodCUmFlRA7InralbRoffdniPQxBE7qWqs2u8,3601
 lamindb/core/datasets/__init__.py,sha256=zRP98oqUAaXhqWyKMiH0s_ImVIuNeziQQ2kQ_t0f-DI,1353
 lamindb/core/datasets/_core.py,sha256=9bcDfVfMZ1h1WAS88ZBjy-R91xbP2KIm_ofHguXAKpY,20177
 lamindb/core/datasets/_fake.py,sha256=BZF9R_1iF0HDnvtZNqL2FtsjSMuqDIfuFxnw_LJYIh4,953
@@ -48,7 +48,7 @@ lamindb/integrations/__init__.py,sha256=aH2PmO2m4-vwIifMYTB0Fyyr_gZWtVnV71jT0tVW
 lamindb/integrations/_vitessce.py,sha256=b0FqTBsP-M6Q7xCYXVwFwM8DOIeeOBZEhYbryhtq4gk,2535
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
-lamindb-0.71.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.71.1.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.71.1.dist-info/METADATA,sha256=fmFFlU4FrVwO0ON6JVCs8qCh8_HLWyt9WyYs_zyIZgo,2674
-lamindb-0.71.1.dist-info/RECORD,,
+lamindb-0.71.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.71.2.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.71.2.dist-info/METADATA,sha256=l49_xPwqfUDB6jUvUQoAVeQu8Tj3JUNCfTPB9cqOq_Y,2674
+lamindb-0.71.2.dist-info/RECORD,,