lamindb 0.76.0__py3-none-any.whl → 0.76.2__py3-none-any.whl

lamindb/core/versioning.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 from typing import TYPE_CHECKING, Literal
 
 from lamin_utils import logger
+from lamin_utils._base62 import CHARSET_DEFAULT as BASE62_CHARS
 from lamindb_setup.core.upath import LocalPathClasses, UPath
 from lnschema_core import ids
 
@@ -10,6 +11,28 @@ if TYPE_CHECKING:
     from lnschema_core.models import IsVersioned
 
 
+def message_update_key_in_version_family(
+    *,
+    suid: str,
+    existing_key: str,
+    registry: str,
+    new_key: str,
+) -> str:
+    return f'Or update key "{existing_key}" in your existing family:\n\nln.{registry}.filter(uid__startswith="{suid}").update(key="{new_key}")'
+
+
+def increment_base62(s: str) -> str:
+    # we don't need to throw an error for zzzz because uids are enforced to be unique
+    # on the db level and have an enforced maximum length
+    value = sum(BASE62_CHARS.index(c) * (62**i) for i, c in enumerate(reversed(s)))
+    value += 1
+    result = ""
+    while value:
+        value, remainder = divmod(value, 62)
+        result = BASE62_CHARS[remainder] + result
+    return result.zfill(len(s))
+
+
 def bump_version(
     version: str,
     bump_type: str = "minor",
@@ -65,57 +88,43 @@ def set_version(version: str | None = None, previous_version: str | None = None)
         version: Version string.
         previous_version: Previous version string.
     """
-    if version == previous_version:
-        raise ValueError(f"Please increment the previous version: '{previous_version}'")
     if version is None and previous_version is not None:
         version = bump_version(previous_version, bump_type="major")
     return version
 
 
-def init_uid(
+def create_uid(
     *,
     version: str | None = None,
     n_full_id: int = 20,
-    is_new_version_of: IsVersioned | None = None,
-) -> str:
-    if is_new_version_of is not None:
-        stem_uid = is_new_version_of.stem_uid
+    revises: IsVersioned | None = None,
+) -> tuple[str, IsVersioned | None]:
+    if revises is not None:
+        if not revises.is_latest:
+            # need one more request
+            revises = revises.__class__.objects.get(
+                is_latest=True, uid__startswith=revises.stem_uid
+            )
+            logger.warning(
+                f"didn't pass the latest version in `revises`, retrieved it: {revises}"
+            )
+        suid = revises.stem_uid
+        vuid = increment_base62(revises.uid[-4:])
     else:
-        stem_uid = ids.base62(n_full_id - 4)
+        suid = ids.base62(n_full_id - 4)
+        vuid = "0000"
     if version is not None:
         if not isinstance(version, str):
             raise ValueError(
                 "`version` parameter must be `None` or `str`, e.g., '0.1', '1', '2',"
                 " etc."
             )
-    return stem_uid + ids.base62_4()
-
-
-def get_uid_from_old_version(
-    is_new_version_of: IsVersioned,
-    version: str | None = None,
-    using_key: str | None = None,
-) -> tuple[str, str]:
-    """{}"""  # noqa: D415
-    msg = ""
-    if is_new_version_of.version is None:
-        previous_version = "1"
-        msg = f"setting previous version to '{previous_version}'"
-    else:
-        previous_version = is_new_version_of.version
-    version = set_version(version, previous_version)
-    new_uid = init_uid(
-        version=version,
-        n_full_id=is_new_version_of._len_full_uid,
-        is_new_version_of=is_new_version_of,
-    )
-    # the following covers the edge case where the old file was unversioned
-    if is_new_version_of.version is None:
-        is_new_version_of.version = previous_version
-        is_new_version_of.save(using=using_key)
-        if msg != "":
-            msg += f"& new version to '{version}'"
-    return new_uid, version
+        if revises is not None:
+            if version == revises.version:
+                raise ValueError(
+                    f"Please increment the previous version: '{revises.version}'"
+                )
+    return suid + vuid, revises
 
 
 def get_new_path_from_uid(old_path: UPath, old_uid: str, new_uid: str):
@@ -128,18 +137,18 @@ def get_new_path_from_uid(old_path: UPath, old_uid: str, new_uid: str):
     return new_path
 
 
-def process_is_new_version_of(
-    is_new_version_of: IsVersioned,
+def process_revises(
+    revises: IsVersioned | None,
     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.__name__}")
-    if is_new_version_of is None:
-        uid = init_uid(version=version, n_full_id=type._len_full_uid)
-    else:
-        uid, version = get_uid_from_old_version(is_new_version_of, version)
+) -> tuple[str, str, str, IsVersioned | None]:
+    if revises is not None and not isinstance(revises, type):
+        raise TypeError(f"`revises` has to be of type `{type.__name__}`")
+    uid, revises = create_uid(
+        revises=revises, version=version, n_full_id=type._len_full_uid
+    )
+    if revises is not None:
         if name is None:
-            name = is_new_version_of.name
-    return uid, version, name
+            name = revises.name
+    return uid, version, name, revises

lamindb/integrations/_vitessce.py

@@ -109,4 +109,6 @@ def save_vitessce_config(
     logger.important(
         f"go to: https://lamin.ai/{slug}/artifact/{vitessce_config_artifact.uid}"
     )
+    run.finished_at = datetime.now(timezone.utc)
+    run.save()
     return vitessce_config_artifact

{lamindb-0.76.0.dist-info → lamindb-0.76.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.76.0
+Version: 0.76.2
 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==0.73.0
-Requires-Dist: lamindb_setup==0.76.4
-Requires-Dist: lamin_utils==0.13.2
-Requires-Dist: lamin_cli==0.16.1
+Requires-Dist: lnschema_core==0.73.2
+Requires-Dist: lamindb_setup==0.76.6
+Requires-Dist: lamin_utils==0.13.4
+Requires-Dist: lamin_cli==0.16.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -24,7 +24,7 @@ Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.48.1 ; extra == "bionty"
+Requires-Dist: bionty==0.48.3 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"
@@ -57,13 +57,5 @@ Provides-Extra: zarr
 
 # LaminDB - A data framework for biology
 
-- Manage data & metadata with a unified Python API ("lakehouse").
-- Track data lineage across notebooks & pipelines.
-- Integrate registries for experimental metadata & in-house ontologies.
-- Validate, standardize & annotate.
-- Collaborate across distributed databases.
-
-## Documentation
-
-Read the [docs](https://lamin.ai/docs).
+Read the [docs](https://docs.lamin.ai).
 

lamindb-0.76.2.dist-info/RECORD

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