lamindb 1.5.0__tar.gz → 1.5.2__tar.gz

{lamindb-1.5.0 → lamindb-1.5.2}/.github/workflows/build.yml

@@ -106,8 +106,8 @@ jobs:
         if: ${{ matrix.group == 'tutorial' || matrix.group == 'guide' || matrix.group == 'biology' || matrix.group == 'faq'}}
         run: sudo apt-get -y install graphviz
 
-      - run: nox -s lint
-        if: ${{ matrix.group == 'tutorial' }}
+      # - run: nox -s lint
+      #   if: ${{ matrix.group == 'tutorial' }}
 
       - run: nox -s "install_ci(group='${{ matrix.group }}')"
 

{lamindb-1.5.0 → lamindb-1.5.2}/.pre-commit-config.yaml

@@ -59,5 +59,6 @@ repos:
               script-to-test-versioning.py|
               tests/storage/conftest.py|
               tests/curators/conftest.py|
-              tests/permissions/conftest.py
+              tests/permissions/conftest.py|
+              tests/curators/test_curators_examples.py
           )

{lamindb-1.5.0 → lamindb-1.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.5.0
+Version: 1.5.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10,<3.14

{lamindb-1.5.0 → lamindb-1.5.2}/docs/arrays.ipynb

@@ -56,7 +56,14 @@
    "outputs": [],
    "source": [
     "!lamin login testuser1\n",
-    "!lamin init --storage s3://lamindb-ci/test-array-notebook --name test-array-notebook"
+    "!lamin init --storage s3://lamindb-ci/test-arrays"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Import lamindb and track this notebook."
    ]
   },
   {
@@ -91,8 +98,8 @@
    },
    "outputs": [],
    "source": [
-    "ln.Artifact(\"s3://lamindb-ci/lndb-storage/pbmc68k.h5ad\").save()\n",
-    "ln.Artifact(\"s3://lamindb-ci/lndb-storage/testfile.hdf5\").save()"
+    "ln.Artifact(\"s3://lamindb-ci/test-arrays/pbmc68k.h5ad\").save()\n",
+    "ln.Artifact(\"s3://lamindb-ci/test-arrays/testfile.hdf5\").save()"
    ]
   },
   {
@@ -171,7 +178,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifact = ln.Artifact.get(key=\"lndb-storage/pbmc68k.h5ad\")"
+    "artifact = ln.Artifact.get(key=\"pbmc68k.h5ad\")"
    ]
   },
   {
@@ -320,7 +327,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifact = ln.Artifact.get(key=\"lndb-storage/testfile.hdf5\")"
+    "artifact = ln.Artifact.get(key=\"testfile.hdf5\")"
    ]
   },
   {
@@ -550,13 +557,13 @@
    "outputs": [],
    "source": [
     "# clean up test instance\n",
-    "!lamin delete --force test-array-notebook"
+    "!lamin delete --force test-arrays"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "py312",
    "language": "python",
    "name": "python3"
   },
@@ -570,7 +577,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.16"
+   "version": "3.12.8"
   },
   "nbproject": {
    "id": "YVUCtH4GfQOy",

{lamindb-1.5.0 → lamindb-1.5.2}/docs/curate.ipynb

@@ -308,7 +308,7 @@
    "id": "27",
    "metadata": {},
    "source": [
-    "The {meth}`~lamindb.curators.Curator.validate` method validates that your dataset adheres to the criteria defined by the `schema`. It identifies which values are already validated (exist in the registries) and which are potentially problematic (do not yet exist in our registries)."
+    "The {meth}`~lamindb.curators.core.Curator.validate` method validates that your dataset adheres to the criteria defined by the `schema`. It identifies which values are already validated (exist in the registries) and which are potentially problematic (do not yet exist in our registries)."
    ]
   },
   {

{lamindb-1.5.0 → lamindb-1.5.2}/docs/storage/anndata-accessor.ipynb

@@ -34,7 +34,7 @@
    },
    "outputs": [],
    "source": [
-    "ln.Artifact(\"s3://lamindb-ci/lndb-storage/pbmc68k.h5ad\").save()"
+    "ln.Artifact(\"s3://lamindb-ci/test-anndata/pbmc68k.h5ad\").save()"
    ]
   },
   {
@@ -50,7 +50,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifact = ln.Artifact.filter(key=\"lndb-storage/pbmc68k.h5ad\").one()"
+    "artifact = ln.Artifact.filter(key=\"pbmc68k.h5ad\").one()"
    ]
   },
   {

{lamindb-1.5.0 → lamindb-1.5.2}/lamindb/__init__.py

@@ -94,7 +94,7 @@ Low-level functionality.
 
 # ruff: noqa: I001
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "1.5.0"
+__version__ = "1.5.2"
 
 import warnings
 

{lamindb-1.5.0 → lamindb-1.5.2}/lamindb/core/_context.py

@@ -259,8 +259,8 @@ class Context:
         self,
         transform: str | Transform | None = None,
         *,
-        project: str | None = None,
-        space: str | None = None,
+        project: str | Project | None = None,
+        space: str | Space | None = None,
         params: dict | None = None,
         new_run: bool | None = None,
         path: str | None = None,
@@ -273,9 +273,10 @@ class Context:
 
         Args:
             transform: A transform (stem) `uid` (or record). If `None`, auto-creates a `transform` with its `uid`.
-            project: A project `name` or `uid` for labeling entities created during the run.
-            space: A space `name` or `uid` to identify where potentially sensitive entities are created during the run.
-                This doesn't affect `Storage`, `ULabel`, `Feature`, `Schema`, `Param` and bionty entities as these provide mere structure that should typically be commonly accessible.
+            project: A project, its `name` or `uid` for labeling entities created during the run.
+            space: A restricted space, its `name` or `uid` for creating sensitive entities are created during the run.
+                The default is the common `"All"` space that every LaminDB instance has.
+                The `space` argument doesn't affect `Storage`, `ULabel`, `Feature`, `Schema`, `Param` and bionty entities as these provide structure that should typically be commonly accessible.
                 If you want to manually move entities to a different space, set the `.space` field (:doc:`docs:access`).
             params: A dictionary of parameters to track for the run.
             new_run: If `False`, loads the latest run of transform
@@ -309,20 +310,32 @@ class Context:
         if project is None:
             project = os.environ.get("LAMIN_CURRENT_PROJECT")
         if project is not None:
-            project_record = Project.filter(
-                Q(name=project) | Q(uid=project)
-            ).one_or_none()
-            if project_record is None:
-                raise InvalidArgument(
-                    f"Project '{project}' not found, either create it with `ln.Project(name='...').save()` or fix typos."
+            if isinstance(project, Project):
+                assert project._state.adding is False, (  # noqa: S101
+                    "Project must be saved before passing it to track()"
                 )
+                project_record = project
+            else:
+                project_record = Project.filter(
+                    Q(name=project) | Q(uid=project)
+                ).one_or_none()
+                if project_record is None:
+                    raise InvalidArgument(
+                        f"Project '{project}' not found, either create it with `ln.Project(name='...').save()` or fix typos."
+                    )
             self._project = project_record
         if space is not None:
-            space_record = Space.filter(Q(name=space) | Q(uid=space)).one_or_none()
-            if space_record is None:
-                raise InvalidArgument(
-                    f"Space '{space}', please check on the hub UI whether you have the correct `uid` or `name`."
+            if isinstance(space, Space):
+                assert space._state.adding is False, (  # noqa: S101
+                    "Space must be saved before passing it to track()"
                 )
+                space_record = space
+            else:
+                space_record = Space.filter(Q(name=space) | Q(uid=space)).one_or_none()
+                if space_record is None:
+                    raise InvalidArgument(
+                        f"Space '{space}', please check on the hub UI whether you have the correct `uid` or `name`."
+                    )
             self._space = space_record
         self._logging_message_track = ""
         self._logging_message_imports = ""

{lamindb-1.5.0 → lamindb-1.5.2}/lamindb/core/storage/_tiledbsoma.py

@@ -110,7 +110,7 @@ def save_tiledbsoma_experiment(
 ) -> Artifact:
     """Write `AnnData` to `tiledbsoma.Experiment`.
 
-    Reads `AnnData` objects, writes them to `tiledbsoma.Experiment`, creates & saves an {class}`~lamindb.Artifact`.
+    Reads `AnnData` objects, writes them to `tiledbsoma.Experiment`, creates & saves an :class:`~lamindb.Artifact`.
 
     Populates a column `lamin_run_uid` column in `obs` with the current `run.uid`.
 
@@ -202,28 +202,44 @@ def save_tiledbsoma_experiment(
             context=ctx,
         )
 
+    prepare_experiment = False
     resize_experiment = False
     if registration_mapping is not None:
-        if version.parse(soma.__version__) < version.parse("1.15.0rc4"):
+        soma_version_parsed = version.parse(soma.__version__)
+        if soma_version_parsed < version.parse("1.15.0rc4"):
             n_observations = len(registration_mapping.obs_axis.data)
         else:
             n_observations = registration_mapping.get_obs_shape()
-            resize_experiment = True
+            prepare_experiment = soma_version_parsed >= version.parse("1.16.2")
+            resize_experiment = not prepare_experiment
     else:  # happens only if not appending and only one adata passed
         assert len(adata_objects) == 1  # noqa: S101
         n_observations = adata_objects[0].n_obs
 
     logger.important(f"Writing the tiledbsoma store to {storepath_str}")
+    experiment_exists: bool | None = None
     for adata_obj in adata_objects:
-        if resize_experiment and soma.Experiment.exists(storepath_str, context=ctx):
-            # can only happen if registration_mapping is not None
-            soma_io.resize_experiment(
-                storepath_str,
-                nobs=n_observations,
-                nvars=registration_mapping.get_var_shapes(),
-                context=ctx,
-            )
-            resize_experiment = False
+        # do not recheck if True
+        if not experiment_exists and (resize_experiment or prepare_experiment):
+            experiment_exists = soma.Experiment.exists(storepath_str, context=ctx)
+        if experiment_exists:
+            # both can only happen if registration_mapping is not None
+            if resize_experiment:
+                soma_io.resize_experiment(
+                    storepath_str,
+                    nobs=n_observations,
+                    nvars=registration_mapping.get_var_shapes(),
+                    context=ctx,
+                )
+                resize_experiment = False
+            elif prepare_experiment:
+                registration_mapping.prepare_experiment(storepath_str, context=ctx)
+                prepare_experiment = False
+        registration_mapping_write = (
+            registration_mapping.subset_for_anndata(adata_obj)
+            if hasattr(registration_mapping, "subset_for_anndata")
+            else registration_mapping
+        )
         soma_io.from_anndata(
             storepath_str,
             adata_obj,
@@ -231,7 +247,7 @@ def save_tiledbsoma_experiment(
             context=ctx,
             obs_id_name=obs_id_name,
             var_id_name=var_id_name,
-            registration_mapping=registration_mapping,
+            registration_mapping=registration_mapping_write,
             **kwargs,
         )
 

{lamindb-1.5.0 → lamindb-1.5.2}/lamindb/curators/core.py

@@ -305,6 +305,8 @@ class SlotsCurator(Curator):
         for slot, curator in self._slots.items():
             logger.info(f"validating slot {slot} ...")
             curator.validate()
+        # set _is_validated to True as no slot raised an error
+        self._is_validated = True
 
     @doc_args(SAVE_ARTIFACT_DOCSTRING)
     def save_artifact(
@@ -510,7 +512,7 @@ class DataFrameCurator(Curator):
             categoricals=categoricals,
             index=schema.index,
             slot=slot,
-            schema_maximal_set=schema.maximal_set,
+            maximal_set=schema.maximal_set,
         )
 
     @property
@@ -836,7 +838,7 @@ class SpatialDataCurator(SlotsCurator):
                     sub_slot = split_result[1]
                     data_object = self._dataset.attrs[split_result[1]]
                 data_object = pd.DataFrame([data_object])
-            self._slots[slot] = DataFrameCurator(data_object, slot_schema)
+            self._slots[slot] = DataFrameCurator(data_object, slot_schema, slot)
             _assign_var_fields_categoricals_multimodal(
                 modality=table_key,
                 slot_type=sub_slot,
@@ -850,27 +852,20 @@ class SpatialDataCurator(SlotsCurator):
 
 
 class CatVector:
-    """Categorical vector for `DataFrame`.
-
-    Args:
-        values_getter: A callable or iterable that returns the values to validate.
-        field: The field to validate against.
-        key: The name of the column to validate. Only used for logging.
-        values_setter: A callable that sets the values.
-        source: The source to validate against.
-    """
+    """Vector with categorical values."""
 
     def __init__(
         self,
-        values_getter: Callable | Iterable[str],
-        field: FieldAttr,
-        key: str,
-        values_setter: Callable | None = None,
-        source: Record | None = None,
+        values_getter: Callable
+        | Iterable[str],  # A callable or iterable that returns the values to validate.
+        field: FieldAttr,  # The field to validate against.
+        key: str,  # The name of the vector to validate. Only used for logging.
+        values_setter: Callable | None = None,  # A callable that sets the values.
+        source: Record | None = None,  # The ontology source to validate against.
         feature: Feature | None = None,
         cat_manager: DataFrameCatManager | None = None,
         subtype_str: str = "",
-        maximal_set: bool = False,  # Passed during validation. Whether unvalidated categoricals cause validation failure.
+        maximal_set: bool = True,  # whether unvalidated categoricals cause validation failure.
     ) -> None:
         self._values_getter = values_getter
         self._values_setter = values_setter
@@ -912,18 +907,20 @@ class CatVector:
     @property
     def is_validated(self) -> bool:
         """Whether the vector is validated."""
-        # ensembl gene IDs pass even if they were not validated
-        # this is a simple solution to the ensembl gene version problem
-        if self._field.field.attname == "ensembl_gene_id":
-            # if none of the ensembl gene ids were validated, we are probably not looking at ensembl gene IDs
-            if len(self.values) == len(self._non_validated):
-                return False
-            # if maximal set, we do not allow additional unvalidated genes
-            elif len(self._non_validated) != 0 and self._maximal_set:
-                return False
-            return True
-        else:
-            return len(self._non_validated) == 0
+        # if nothing was validated, something likely is fundamentally wrong
+        # should probably add a setting `at_least_one_validated`
+        result = True
+        if len(self.values) > 0 and len(self.values) == len(self._non_validated):
+            result = False
+        # len(self._non_validated) != 0
+        #     if maximal_set is True, return False
+        #     if maximal_set is False, return True
+        # len(self._non_validated) == 0
+        #     return True
+        if len(self._non_validated) != 0:
+            if self._maximal_set:
+                result = False
+        return result
 
     def _replace_synonyms(self) -> list[str]:
         """Replace synonyms in the vector with standardized values."""
@@ -1078,11 +1075,6 @@ class CatVector:
         field_name = self._field.field.name
         model_field = f"{registry.__name__}.{field_name}"
 
-        def _log_mapping_info():
-            logger.indent = ""
-            logger.info(f'mapping "{self._key}" on {colors.italic(model_field)}')
-            logger.indent = "  "
-
         kwargs_current = get_current_filter_kwargs(
             registry, {"organism": self._organism, "source": self._source}
         )
@@ -1121,7 +1113,6 @@ class CatVector:
         non_validated = [i for i in non_validated if i not in values_validated]
         n_non_validated = len(non_validated)
         if n_non_validated == 0:
-            logger.indent = ""
             logger.success(
                 f'"{self._key}" is validated against {colors.italic(model_field)}'
             )
@@ -1143,14 +1134,12 @@ class CatVector:
                 warning_message += f"    → fix typos, remove non-existent values, or save terms via: {colors.cyan(non_validated_hint_print)}"
                 if self._subtype_query_set is not None:
                     warning_message += f"\n    → a valid label for subtype '{self._subtype_str}' has to be one of {self._subtype_query_set.list('name')}"
-            if logger.indent == "":
-                _log_mapping_info()
+            logger.info(f'mapping "{self._key}" on {colors.italic(model_field)}')
             logger.warning(warning_message)
             if self._cat_manager is not None:
                 self._cat_manager._validate_category_error_messages = strip_ansi_codes(
                     warning_message
                 )
-            logger.indent = ""
             return non_validated, syn_mapper
 
     def validate(self) -> None:
@@ -1218,7 +1207,7 @@ class DataFrameCatManager:
         sources: dict[str, Record] | None = None,
         index: Feature | None = None,
         slot: str | None = None,
-        schema_maximal_set: bool = False,
+        maximal_set: bool = False,
     ) -> None:
         self._non_validated = None
         self._index = index
@@ -1235,7 +1224,7 @@ class DataFrameCatManager:
         self._validate_category_error_messages: str = ""
         self._cat_vectors: dict[str, CatVector] = {}
         self._slot = slot
-        self._maximal_set = schema_maximal_set
+        self._maximal_set = maximal_set
 
         if columns_names is None:
             columns_names = []
@@ -1280,7 +1269,6 @@ class DataFrameCatManager:
                 feature=feature,
                 cat_manager=self,
                 subtype_str=subtype_str,
-                maximal_set=self._maximal_set,
             )
         if index is not None and index.dtype.startswith("cat"):
             result = parse_dtype(index.dtype)[0]
@@ -1292,7 +1280,6 @@ class DataFrameCatManager:
                 key=key,
                 feature=index,
                 cat_manager=self,
-                maximal_set=self._maximal_set,
             )
 
     @property
@@ -1330,7 +1317,7 @@ class DataFrameCatManager:
 
         validated = True
         for key, cat_vector in self._cat_vectors.items():
-            logger.info(f"validating column {key}")
+            logger.info(f"validating vector {key}")
             cat_vector.validate()
             validated &= cat_vector.is_validated
         self._is_validated = validated
@@ -1493,6 +1480,9 @@ def annotate_artifact(
                 else "columns"
             )
             features = slot_curator.cat._cat_vectors[name].records
+            if features is None:
+                logger.warning(f"no features found for slot {slot}")
+                continue
             itype = parse_cat_dtype(artifact.schema.slots[slot].itype, is_itype=True)[
                 "field"
             ]

lamindb-1.5.2/lamindb/migrations/0093_alter_schemacomponent_unique_together.py

@@ -0,0 +1,16 @@
+# Generated by Django 5.2 on 2025-05-07 12:16
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("lamindb", "0092_alter_artifactfeaturevalue_artifact_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterUniqueTogether(
+            name="schemacomponent",
+            unique_together={("composite", "slot"), ("composite", "slot", "component")},
+        ),
+    ]

{lamindb-1.5.0 → lamindb-1.5.2}/lamindb/models/_feature_manager.py

@@ -49,7 +49,7 @@ from ._label_manager import _get_labels, describe_labels
 from ._relations import (
     dict_related_model_to_related_name,
 )
-from .feature import Feature, FeatureValue
+from .feature import Feature, FeatureValue, parse_dtype
 from .record import Record
 from .run import Param, ParamManager, ParamManagerRun, ParamValue, Run
 from .ulabel import ULabel
@@ -649,13 +649,22 @@ def filter_base(cls, _skip_validation: bool = True, **expression) -> QuerySet:
                 if cls == FeatureManager:
                     from .artifact import ArtifactFeatureValue
 
-                    return Artifact.objects.exclude(
-                        id__in=Subquery(
-                            ArtifactFeatureValue.objects.filter(
-                                featurevalue__feature=feature
-                            ).values("artifact_id")
+                    if value:  # True
+                        return Artifact.objects.exclude(
+                            id__in=Subquery(
+                                ArtifactFeatureValue.objects.filter(
+                                    featurevalue__feature=feature
+                                ).values("artifact_id")
+                            )
+                        )
+                    else:
+                        return Artifact.objects.exclude(
+                            id__in=Subquery(
+                                ArtifactFeatureValue.objects.filter(
+                                    featurevalue__feature=feature
+                                ).values("artifact_id")
+                            )
                         )
-                    )
             if comparator in {"__startswith", "__contains"}:
                 logger.important(
                     f"currently not supporting `{comparator}`, using `__icontains` instead"
@@ -667,7 +676,14 @@ def filter_base(cls, _skip_validation: bool = True, **expression) -> QuerySet:
         elif isinstance(value, (str, Record, bool)):
             if comparator == "__isnull":
                 if cls == FeatureManager:
-                    return Artifact.objects.exclude(links_ulabel__feature=feature)
+                    result = parse_dtype(feature.dtype)[0]
+                    kwargs = {
+                        f"links_{result['registry'].__name__.lower()}__feature": feature
+                    }
+                    if value:  # True
+                        return Artifact.objects.exclude(**kwargs)
+                    else:
+                        return Artifact.objects.filter(**kwargs)
             else:
                 # because SQL is sensitive to whether querying with __in or not
                 # and might return multiple equivalent records for the latter

{lamindb-1.5.0 → lamindb-1.5.2}/lamindb/models/artifact.py

@@ -17,7 +17,6 @@ from django.db.models import CASCADE, PROTECT, Q
 from lamin_utils import colors, logger
 from lamindb_setup import settings as setup_settings
 from lamindb_setup._init_instance import register_storage_in_instance
-from lamindb_setup.core import doc_args
 from lamindb_setup.core._settings_storage import init_storage
 from lamindb_setup.core.hashing import HASH_LENGTH, hash_dir, hash_file
 from lamindb_setup.core.types import UPathStr
@@ -99,8 +98,6 @@ WARNING_RUN_TRANSFORM = "no run & transform got linked, call `ln.track()` & re-r
 
 WARNING_NO_INPUT = "run input wasn't tracked, call `ln.track()` and re-run"
 
-DEBUG_KWARGS_DOC = "**kwargs: Internal arguments for debugging."
-
 try:
     from ..core.storage._zarr import identify_zarr_type
 except ImportError:
@@ -914,7 +911,7 @@ def add_labels(
         for registry_name, records in records_by_registry.items():
             if not from_curator and feature.name in internal_features:
                 raise ValidationError(
-                    "Cannot manually annotate internal feature with label. Please use ln.Curator"
+                    "Cannot manually annotate a feature measured *within* the dataset. Please use a Curator."
                 )
             if registry_name not in feature.dtype:
                 if not feature.dtype.startswith("cat"):
@@ -1236,7 +1233,7 @@ class Artifact(Record, IsVersioned, TracksRun, TracksUpdates):
         default=None,
         related_name="validated_artifacts",
     )
-    """The schema that validated this artifact in a :class:`~lamindb.curators.Curator`."""
+    """The schema that validated this artifact in a :class:`~lamindb.curators.core.Curator`."""
     feature_sets: Schema = models.ManyToManyField(
         Schema, related_name="artifacts", through="ArtifactSchema"
     )
@@ -2363,6 +2360,11 @@ class Artifact(Record, IsVersioned, TracksRun, TracksUpdates):
 
         if hasattr(self, "_memory_rep") and self._memory_rep is not None:
             access_memory = self._memory_rep
+            # SpatialData objects zarr stores are moved when saved
+            # SpatialData's __repr__ method attempts to access information from the old path
+            # Therefore, we need to update the in-memory path to the now moved Artifact storage path
+            if access_memory.__class__.__name__ == "SpatialData":
+                access_memory.path = self._cache_path
         else:
             filepath, cache_key = filepath_cache_key_from_artifact(
                 self, using_key=settings._using_key
@@ -2395,9 +2397,9 @@ class Artifact(Record, IsVersioned, TracksRun, TracksUpdates):
                 access_memory = load_to_memory(cache_path, **kwargs)
         # only call if load is successfull
         _track_run_input(self, is_run_input)
+
         return access_memory
 
-    @doc_args(DEBUG_KWARGS_DOC)
     def cache(
         self, *, is_run_input: bool | None = None, mute: bool = False, **kwargs
     ) -> Path:
@@ -2410,7 +2412,6 @@ class Artifact(Record, IsVersioned, TracksRun, TracksUpdates):
         Args:
             mute: Silence logging of caching progress.
             is_run_input: Whether to track this artifact as run input.
-            {}
 
         Example::
 
@@ -2560,13 +2561,11 @@ class Artifact(Record, IsVersioned, TracksRun, TracksUpdates):
                 if delete_msg != "did-not-delete":
                     logger.success(f"deleted {colors.yellow(f'{path}')}")
 
-    @doc_args(DEBUG_KWARGS_DOC)
     def save(self, upload: bool | None = None, **kwargs) -> Artifact:
         """Save to database & storage.
 
         Args:
             upload: Trigger upload to cloud storage in instances with hybrid storage mode.
-            {}
 
         Example::
 
@@ -2763,8 +2762,8 @@ def _track_run_input(
                 # record is on another db
                 # we have to save the record into the current db with
                 # the run being attached to a transfer transform
-                logger.important(
-                    f"completing transfer to track {data.__class__.__name__}('{data.uid[:8]}') as input"
+                logger.info(
+                    f"completing transfer to track {data.__class__.__name__}('{data.uid[:8]}...') as input"
                 )
                 data.save()
                 is_valid = True