lamindb 0.71.1__tar.gz → 0.71.2__tar.gz

{lamindb-0.71.1 → lamindb-0.71.2}/PKG-INFO

@@ -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 → lamindb-0.71.2}/docs/changelog.md

@@ -14,6 +14,10 @@ LaminDB implements "migration-based versioning". When upgrading your LaminDB ins
 
 ## 0.71
 
+### 0.71.2 {small}`2024-05-07`
+
+- ✨ Enable passing parameters to `ln.track()` [PR](https://github.com/laminlabs/lamindb/pull/1637) [@falexwolf](https://github.com/falexwolf)
+
 ### 0.71.1 {small}`2024-05-07`
 
 - 🚸  Upload source code of scripts upon `ln.finish()` and no longer upon `ln.track()` [PR](https://github.com/laminlabs/lamindb/pull/1624) [@falexwolf](https://github.com/falexwolf)

{lamindb-0.71.1 → lamindb-0.71.2}/docs/tutorial.ipynb

@@ -895,7 +895,7 @@
    "source": [
     "Most functionality that you just learned about artifacts - e.g., queries & provenance - also applies to {class}`~lamindb.Collection`.\n",
     "\n",
-    "Collections become powerful if you directly leverage them for training models: {class}`docs:scrna5`."
+    "Collections become powerful if you directly leverage them for training models: {doc}`docs:scrna5`."
    ]
   },
   {

{lamindb-0.71.1 → lamindb-0.71.2}/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-0.71.1 → lamindb-0.71.2}/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-0.71.1 → lamindb-0.71.2}/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-0.71.1 → lamindb-0.71.2}/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-0.71.1 → lamindb-0.71.2}/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 → lamindb-0.71.2}/pyproject.toml

@@ -16,7 +16,7 @@ classifiers = [
 ]
 dependencies = [
     # Lamin PINNED packages
-    "lnschema_core==0.66.3",
+    "lnschema_core==0.66.4",
     "lamindb_setup==0.71.3",
     "lamin_utils==0.13.2",
     "lamin_cli==0.13.1",

{lamindb-0.71.1 → lamindb-0.71.2}/sub/lnschema-bionty/docs/changelog.md

@@ -3,6 +3,7 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+:sparkles: Add links to all specific bionty registry tutorials | [233](https://github.com/laminlabs/lnschema-bionty/pull/233) | [Zethson](https://github.com/Zethson) | 2024-05-07 |
 🚑️ Fix public_source in inspect | [232](https://github.com/laminlabs/lnschema-bionty/pull/232) | [sunnyosun](https://github.com/sunnyosun) | 2024-04-18 |
 :bug: Remove repr | [231](https://github.com/laminlabs/lnschema-bionty/pull/231) | [Zethson](https://github.com/Zethson) | 2024-04-11 |
 🐛 Fix syncing public sources | [230](https://github.com/laminlabs/lnschema-bionty/pull/230) | [sunnyosun](https://github.com/sunnyosun) | 2024-04-11 |

{lamindb-0.71.1 → lamindb-0.71.2}/sub/lnschema-bionty/lnschema_bionty/models.py

@@ -227,6 +227,10 @@ class BioRegistry(Registry, HasParents, CanValidate):
 class Organism(BioRegistry):
     """Organism - `NCBI Taxonomy <https://www.ncbi.nlm.nih.gov/taxonomy/>`__, `Ensembl Organism <https://useast.ensembl.org/info/about/species.html>`__.
 
+    Notes:
+        For more info, see tutorials :doc:`bio-registries` and :doc:`/organism`.
+
+
     Examples:
         >>> record = bionty.Organism.from_public(name="rabbit")
     """
@@ -295,6 +299,8 @@ class Gene(BioRegistry):
     """Genes - `Ensembl <https://ensembl.org/>`__, `NCBI Gene <https://www.ncbi.nlm.nih.gov/gene/>`__.
 
     Notes:
+        For more info, see tutorials :doc:`bio-registries` and :doc:`/gene`.
+
         Bulk create Gene records via :class:`~lamindb.core.Registry.from_values`.
 
     Examples:
@@ -386,6 +392,8 @@ class Protein(BioRegistry):
     """Proteins - `Uniprot <https://www.uniprot.org/>`__.
 
     Notes:
+        For more info, see tutorials :doc:`bio-registries` and :doc:`/protein`.
+
         Bulk create Protein records via :class:`~lamindb.core.Registry.from_values`.
 
     Examples:
@@ -478,6 +486,8 @@ class CellMarker(BioRegistry):
     """Cell markers - `CellMarker <http://xteam.xbio.top/CellMarker>`__.
 
     Notes:
+        For more info, see tutorials :doc:`bio-registries` and :doc:`/cell_marker`.
+
         Bulk create CellMarker records via :class:`~lamindb.core.Registry.from_values`.
 
     Examples:
@@ -568,7 +578,7 @@ class Tissue(BioRegistry):
     """Tissues - `Uberon <http://obophenotype.github.io/uberon/>`__.
 
     Notes:
-        For more info, see tutorial :doc:`bio-registries`
+        For more info, see tutorials :doc:`bio-registries` :doc:`/tissue`.
 
         Bulk create Tissue records via :class:`~lamindb.core.Registry.from_values`.
 
@@ -650,7 +660,7 @@ class CellType(BioRegistry):
     """Cell types - `Cell Ontology <https://obophenotype.github.io/cell-ontology/>`__.
 
     Notes:
-        For more info, see tutorial :doc:`bio-registries`
+        For more info, see tutorials :doc:`bio-registries` and :doc:`/cell_type`.
 
         Bulk create CellType records via :class:`~lamindb.core.Registry.from_values`.
 
@@ -737,10 +747,10 @@ class Disease(BioRegistry):
     """Diseases - `Mondo <https://mondo.monarchinitiative.org/>`__, `Human Disease <https://disease-ontology.org/>`__.
 
     Notes:
-        For more info, see tutorial :doc:`bio-registries`
-
         Bulk create Disease records via :class:`~lamindb.core.Registry.from_values`.
 
+        For more info, see tutorials: :doc:`/disease`.
+
     Examples:
         >>> record = bionty.Disease.from_public(name="Alzheimer disease")
     """
@@ -824,7 +834,7 @@ class CellLine(BioRegistry):
     """Cell lines - `Cell Line Ontology <https://github.com/CLO-ontology/CLO>`__.
 
     Notes:
-        For more info, see tutorial :doc:`bio-registries`
+        For more info, see tutorials :doc:`bio-registries` and :doc:`/cell_line`.
 
         Bulk create CellLine records via :class:`~lamindb.core.Registry.from_values`.
 
@@ -915,7 +925,7 @@ class Phenotype(BioRegistry):
     `Zebrafish Phenotype <http://obofoundry.org/ontology/zp.html>`__.
 
     Notes:
-        For more info, see tutorial :doc:`bio-registries`
+        For more info, see tutorials :doc:`bio-registries` and :doc:`/phenotype`.
 
         Bulk create Phenotype records via :class:`~lamindb.core.Registry.from_values`.
 
@@ -1004,7 +1014,7 @@ class Pathway(BioRegistry):
     `Pathway Ontology <https://bioportal.bioontology.org/ontologies/PW>`__.
 
     Notes:
-        For more info, see tutorial :doc:`bio-registries`
+        For more info, see tutorials :doc:`bio-registries` and :doc:`/pathway`.
 
         Bulk create Pathway records via :class:`~lamindb.core.Registry.from_values`.
 
@@ -1098,7 +1108,7 @@ class ExperimentalFactor(BioRegistry):
     """Experimental factors - `Experimental Factor Ontology <https://www.ebi.ac.uk/ols/ontologies/efo>`__.
 
     Notes:
-        For more info, see tutorial :doc:`bio-registries`
+        For more info, see tutorials :doc:`bio-registries` and :doc:`/experimental_factor`.
 
         Bulk create ExperimentalFactor records via :class:`~lamindb.core.Registry.from_values`.
 
@@ -1193,7 +1203,7 @@ class DevelopmentalStage(BioRegistry):
     `Mouse Developmental Stages <https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv>`__.  # noqa.
 
     Notes:
-        For more info, see tutorial :doc:`bio-registries`
+        For more info, see tutorials :doc:`bio-registries` and :doc:`/developmental_stage`.
 
         Bulk create DevelopmentalStage records via :class:`~lamindb.core.Registry.from_values`.
 
@@ -1281,7 +1291,7 @@ class Ethnicity(BioRegistry):
     """Ethnicity - `Human Ancestry Ontology <https://github.com/EBISPOT/hancestro>`__.
 
     Notes:
-        For more info, see tutorial :doc:`bio-registries`
+        For more info, see tutorials :doc:`bio-registries` and :doc:`/ethnicity`.
 
         Bulk create Ethnicity records via :class:`~lamindb.core.Registry.from_values`.
 

{lamindb-0.71.1 → lamindb-0.71.2}/sub/lnschema-core/CHANGELOG.md

@@ -3,6 +3,8 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+Add using docstring | [378](https://github.com/laminlabs/lnschema-core/pull/378) | [Zethson](https://github.com/Zethson) | 2024-05-07 |
+♻️ Move `version` field into `IsVersioned` base model | [377](https://github.com/laminlabs/lnschema-core/pull/377) | [falexwolf](https://github.com/falexwolf) | 2024-05-07 |
 📝 Better examples for FeatureSet | [375](https://github.com/laminlabs/lnschema-core/pull/375) | [sunnyosun](https://github.com/sunnyosun) | 2024-05-06 |
 ✨ Add an `instance_uid` field to Storage | [374](https://github.com/laminlabs/lnschema-core/pull/374) | [falexwolf](https://github.com/falexwolf) | 2024-04-28 | 0.66.0
 ✨ Allow passing path to .from_anndata | [373](https://github.com/laminlabs/lnschema-core/pull/373) | [sunnyosun](https://github.com/sunnyosun) | 2024-04-23 |

{lamindb-0.71.1 → lamindb-0.71.2}/sub/lnschema-core/lnschema_core/__init__.py

@@ -1,6 +1,6 @@
 """LaminDB's core registries."""
 
-__version__ = "0.66.3"
+__version__ = "0.66.4"
 
 
 from lamindb_setup import _check_instance_setup

{lamindb-0.71.1 → lamindb-0.71.2}/sub/lnschema-core/lnschema_core/models.py

@@ -8,7 +8,6 @@ from typing import (
     Iterable,
     Literal,
     NamedTuple,
-    Optional,
     overload,
 )
 
@@ -57,11 +56,23 @@ if TYPE_CHECKING or _INSTANCE_SETUP or RUNNING_SPHINX:
     pass
 
 
-class IsVersioned:
+class IsVersioned(models.Model):
     """Base class for versioned models."""
 
+    class Meta:
+        abstract = True
+
     _len_stem_uid: int
 
+    version = CharField(max_length=10, default=None, null=True, db_index=True)
+    """Version (default `None`).
+
+    Defines version of a family of records characterized by the same `stem_uid`.
+
+    Consider using `semantic versioning <https://semver.org>`__
+    with `Python versioning <https://peps.python.org/pep-0440/>`__.
+    """
+
     @property
     def stem_uid(self) -> str:
         return self.uid[: self._len_stem_uid]  # type: ignore
@@ -588,6 +599,14 @@ class Registry(models.Model):
 
         Args:
             instance: An instance identifier of form "account_handle/instance_name".
+
+        Examples:
+            >>> ln.ULabel.using("account_handle/instance_name").search("ULabel7", field="name")
+                        uid    score
+            name
+            ULabel7  g7Hk9b2v  100.0
+            ULabel5  t4Jm6s0q   75.0
+            ULabel6  r2Xw8p1z   75.0
         """
         pass
 
@@ -896,6 +915,9 @@ class Transform(Registry, HasParents, IsVersioned):
         >>> transform.view_parents()
     """
 
+    class Meta(Registry.Meta, IsVersioned.Meta):
+        abstract = False
+
     _len_stem_uid: int = 12
     _len_full_uid: int = 16
 
@@ -907,14 +929,6 @@ class Transform(Registry, HasParents, IsVersioned):
     """A name or title. For instance, a pipeline name, notebook title, etc."""
     key = CharField(max_length=120, db_index=True, null=True, default=None)
     """A key for concise reference & versioning (optional)."""
-    version = CharField(max_length=10, default=None, null=True, db_index=True)
-    """Version (default `None`).
-
-    Defines version of a family of records characterized by the same `stem_uid`.
-
-    Consider using `semantic versioning <https://semver.org>`__
-    with `Python versioning <https://peps.python.org/pep-0440/>`__.
-    """
     description = CharField(max_length=255, null=True, default=None)
     """A description (optional)."""
     type = CharField(
@@ -1592,6 +1606,9 @@ class Artifact(Registry, Data, IsVersioned):
 
     """
 
+    class Meta(Registry.Meta, IsVersioned.Meta):
+        abstract = False
+
     _len_full_uid: int = 20
     _len_stem_uid: int = 16
 
@@ -1617,14 +1634,6 @@ class Artifact(Registry, Data, IsVersioned):
     """
     description = CharField(max_length=255, db_index=True, null=True, default=None)
     """A description."""
-    version = CharField(max_length=10, null=True, default=None, db_index=True)
-    """Version (default `None`).
-
-    Defines version of a family of records characterized by the same `stem_uid`.
-
-    Consider using `semantic versioning <https://semver.org>`__
-    with `Python versioning <https://peps.python.org/pep-0440/>`__.
-    """
     size = models.BigIntegerField(null=True, db_index=True)
     """Size in bytes.
 
@@ -2079,6 +2088,9 @@ class Collection(Registry, Data, IsVersioned):
         >>> assert new_collection.version == "2"
     """
 
+    class Meta(Registry.Meta, IsVersioned.Meta):
+        abstract = False
+
     _len_full_uid: int = 20
     _len_stem_uid: int = 16
 
@@ -2092,14 +2104,6 @@ class Collection(Registry, Data, IsVersioned):
     """Name or title of collection (required)."""
     description = TextField(null=True, default=None)
     """A description."""
-    version = CharField(max_length=10, null=True, default=None, db_index=True)
-    """Version (default `None`).
-
-    Defines version of a family of records characterized by the same `stem_uid`.
-
-    Consider using `semantic versioning <https://semver.org>`__
-    with `Python versioning <https://peps.python.org/pep-0440/>`__.
-    """
     hash = CharField(max_length=86, db_index=True, null=True, default=None)
     """Hash of collection content. 86 base64 chars allow to store 64 bytes, 512 bits."""
     reference = CharField(max_length=255, db_index=True, null=True, default=None)

{lamindb-0.71.1 → lamindb-0.71.2}/tests/test_run_context.py

@@ -13,7 +13,10 @@ def test_track_with_multi_parents():
     child = ln.Transform(name="Child")
     child.save()
     child.parents.set([parent1, parent2])
-    ln.track(transform=child)
+    params = {"param1": 1, "param2": "my-string", "param3": 3.14}
+    ln.track(transform=child, params=params)
+
+    assert ln.core.run_context.run.json == params
     # unset to remove side effects
     ln.core.run_context.run = None
     ln.core.run_context.transform = None

{lamindb-0.71.1 → lamindb-0.71.2}/tests/test_transform.py

@@ -41,9 +41,7 @@ def test_is_new_version_of_versioned_transform():
     # wrong transform type
     with pytest.raises(TypeError) as error:
         ln.Transform(is_new_version_of=ln.ULabel(name="x"))
-    assert (
-        error.exconly() == "TypeError: is_new_version_of has to be of type ln.Transform"
-    )
+    assert error.exconly().startswith("TypeError: is_new_version_of has to be of type")
 
     # wrong kwargs
     with pytest.raises(ValueError) as error: