lamindb 0.69.3__py3-none-any.whl → 0.69.4__py3-none-any.whl

lamindb/__init__.py

@@ -15,7 +15,7 @@ Registries:
    Feature
    FeatureSet
 
-Functions:
+Key functionality:
 
 .. autosummary::
    :toctree: .
@@ -23,6 +23,7 @@ Functions:
    connect
    track
    finish
+   Annotate
    view
    save
 
@@ -31,7 +32,7 @@ Modules & settings:
 .. autosummary::
    :toctree: .
 
-   Annotate
+   integrations
    settings
    setup
    UPath
@@ -39,7 +40,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.69.3"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.69.4"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 
@@ -88,6 +89,7 @@ if _check_instance_setup(from_lamindb=True):
     )
 
     dev = core  # backward compat
+    from . import integrations
     from ._annotate import Annotate
     from ._finish import finish
     from ._save import save

lamindb/_annotate.py

@@ -81,7 +81,7 @@ class DataFrameAnnotator:
         self._collection = None
         self._validated = False
         self._kwargs: Dict = kwargs
-        self.register_features()
+        self.save_features()
 
     @property
     def fields(self) -> Dict:
@@ -99,7 +99,7 @@ class DataFrameAnnotator:
         fields = {**{"feature": self._feature_field}, **self.fields}
         return AnnotateLookup(fields=fields, using=using or self._using)
 
-    def register_features(self, validated_only: bool = True) -> None:
+    def save_features(self, validated_only: bool = True) -> None:
         """Register features records."""
         missing_columns = set(self.fields.keys()) - set(self._df.columns)
         if missing_columns:
@@ -141,7 +141,7 @@ class DataFrameAnnotator:
         if feature == "all":
             self._update_registry_all(validated_only=validated_only, **kwargs)
         elif feature == "feature":
-            self.register_features(validated_only=validated_only)
+            self.save_features(validated_only=validated_only)
         else:
             if feature not in self.fields:
                 raise ValueError(f"Feature {feature} is not part of the fields!")
@@ -175,7 +175,7 @@ class DataFrameAnnotator:
         )
         return self._validated
 
-    def register_artifact(self, description: str, **kwargs) -> Artifact:
+    def save_artifact(self, description: str, **kwargs) -> Artifact:
         """Register the validated DataFrame and metadata.
 
         Args:
@@ -199,7 +199,7 @@ class DataFrameAnnotator:
             settings.verbosity = "warning"
             self.update_registry("all")
 
-            self._artifact = register_artifact(
+            self._artifact = save_artifact(
                 self._df,
                 description=description,
                 fields=self.fields,
@@ -211,9 +211,9 @@ class DataFrameAnnotator:
 
         return self._artifact
 
-    def register_collection(
+    def save_collection(
         self,
-        artifact: Artifact | Iterable[Artifact],
+        artifact: Union[Artifact, Iterable[Artifact]],
         name: str,
         description: Optional[str] = None,
         reference: Optional[str] = None,
@@ -288,7 +288,7 @@ class AnnDataAnnotator(DataFrameAnnotator):
             **kwargs,
         )
         self._obs_fields = obs_fields
-        self._register_variables()
+        self._save_variables()
 
     @property
     def var_field(self) -> FieldAttr:
@@ -308,7 +308,7 @@ class AnnDataAnnotator(DataFrameAnnotator):
         }
         return AnnotateLookup(fields=fields, using=using or self._using)
 
-    def _register_variables(self, validated_only: bool = True, **kwargs):
+    def _save_variables(self, validated_only: bool = True, **kwargs):
         """Register variable records."""
         self._kwargs.update(kwargs)
         update_registry(
@@ -334,11 +334,11 @@ class AnnDataAnnotator(DataFrameAnnotator):
     def update_registry(self, feature: str, validated_only: bool = True, **kwargs):
         """Register labels for a feature."""
         if feature == "variables":
-            self._register_variables(validated_only=validated_only, **kwargs)
+            self._save_variables(validated_only=validated_only, **kwargs)
         else:
             super().update_registry(feature, validated_only, **kwargs)
 
-    def register_artifact(self, description: str, **kwargs) -> Artifact:
+    def save_artifact(self, description: str, **kwargs) -> Artifact:
         """Register the validated AnnData and metadata.
 
         Args:
@@ -352,7 +352,7 @@ class AnnDataAnnotator(DataFrameAnnotator):
         if not self._validated:
             raise ValidationError("Please run `validate()` first!")
 
-        self._artifact = register_artifact(
+        self._artifact = save_artifact(
             self._adata,
             description=description,
             feature_field=self.var_field,
@@ -536,7 +536,7 @@ def validate_anndata(
     return validated_var and validated_obs
 
 
-def register_artifact(
+def save_artifact(
     data: Union[pd.DataFrame, ad.AnnData],
     description: str,
     fields: Dict[str, FieldAttr],
@@ -669,7 +669,7 @@ def update_registry(
                 non_validated_records = Feature.from_df(df)
             else:
                 if "organism" in filter_kwargs:
-                    filter_kwargs["organism"] = _register_organism(name=organism)
+                    filter_kwargs["organism"] = _save_organism(name=organism)
                 for value in labels_registered["without reference"]:
                     filter_kwargs[field.field.name] = value
                     if registry == Feature:
@@ -678,7 +678,7 @@ def update_registry(
             ln_save(non_validated_records)
 
         if registry == ULabel and field.field.name == "name":
-            register_ulabels_with_parent(values, field=field, feature_name=feature_name)
+            save_ulabels_with_parent(values, field=field, feature_name=feature_name)
     finally:
         settings.verbosity = verbosity
 
@@ -710,7 +710,7 @@ def log_registered_labels(
             lookup_print = f".lookup().['{feature_name}']"
             msg += f"\n      → to lookup categories, use {lookup_print}"
             msg += (
-                f"\n      → to register, run {colors.yellow('register_features(validated_only=False)')}"
+                f"\n      → to register, run {colors.yellow('save_features(validated_only=False)')}"
                 if labels_type == "features"
                 else f"\n      → to register, set {colors.yellow('validated_only=False')}"
             )
@@ -722,7 +722,7 @@ def log_registered_labels(
             )
 
 
-def register_ulabels_with_parent(
+def save_ulabels_with_parent(
     values: List[str], field: FieldAttr, feature_name: str
 ) -> None:
     """Register a parent label for the given labels."""
@@ -774,7 +774,7 @@ def update_registry_from_using_instance(
     return labels_registered, not_registered
 
 
-def _register_organism(name: str):
+def _save_organism(name: str):
     """Register an organism record."""
     import bionty as bt
 

lamindb/_collection.py

@@ -64,7 +64,7 @@ def __init__(
     # now we proceed with the user-facing constructor
     if len(args) > 1:
         raise ValueError("Only one non-keyword arg allowed: data")
-    data: Union[pd.DataFrame, ad.AnnData, Artifact, Iterable[Artifact]] = (
+    data: Union[Artifact, Iterable[Artifact]] = (
         kwargs.pop("data") if len(args) == 0 else args[0]
     )
     meta: Optional[str] = kwargs.pop("meta") if "meta" in kwargs else None
@@ -108,57 +108,24 @@ def __init__(
         if name is None:
             name = is_new_version_of.name
     run = get_run(run)
-    data_init_complete = False
-    artifact = None
-    artifacts = None
-    # now handle potential metadata
+    if isinstance(data, Artifact):
+        data = [data]
+    else:
+        if not hasattr(data, "__getitem__"):
+            raise ValueError("Artifact or List[Artifact] is allowed.")
+        assert isinstance(data[0], Artifact)  # type: ignore
+    hash, feature_sets = from_artifacts(data)  # type: ignore
     if meta is not None:
-        if not isinstance(meta, (pd.DataFrame, ad.AnnData, Artifact)):
-            raise ValueError(
-                "meta has to be of type `(pd.DataFrame, ad.AnnData, Artifact)`"
-            )
-        data = meta
-    # init artifact - is either data or metadata
-    if isinstance(data, (pd.DataFrame, ad.AnnData, Artifact)):
-        if isinstance(data, Artifact):
-            artifact = data
-            if artifact._state.adding:
-                raise ValueError("Save artifact before creating collection!")
+        if not isinstance(meta, Artifact):
+            raise ValueError("meta has to be an Artifact")
+        if isinstance(meta, Artifact):
+            if meta._state.adding:
+                raise ValueError("Save meta artifact before creating collection!")
             if not feature_sets:
-                feature_sets = artifact.features._feature_set_by_slot
+                feature_sets = meta.features._feature_set_by_slot
             else:
-                if len(artifact.features._feature_set_by_slot) > 0:
+                if len(meta.features._feature_set_by_slot) > 0:
                     logger.info("overwriting feature sets linked to artifact")
-        else:
-            artifact_is_new_version_of = (
-                is_new_version_of.artifact if is_new_version_of is not None else None
-            )
-            artifact = Artifact(
-                data,
-                run=run,
-                description="tmp",
-                version=version,
-                is_new_version_of=artifact_is_new_version_of,
-                accessor=accessor,
-            )
-            # do we really want to update the artifact here?
-            if feature_sets:
-                artifact._feature_sets = feature_sets
-        hash = artifact.hash  # type: ignore
-        provisional_uid = artifact.uid  # type: ignore
-        if artifact.description is None or artifact.description == "tmp":
-            artifact.description = f"See collection {provisional_uid}"  # type: ignore
-        data_init_complete = True
-    if not data_init_complete:
-        if hasattr(data, "__getitem__"):
-            assert isinstance(data[0], Artifact)  # type: ignore
-            artifacts = data
-            hash, feature_sets = from_artifacts(artifacts)  # type: ignore
-            data_init_complete = True
-        else:
-            raise ValueError(
-                "Only DataFrame, AnnData, Artifact or list of artifacts is allowed."
-            )
     # we ignore collections in trash containing the same hash
     if hash is not None:
         existing_collection = Collection.filter(hash=hash).one_or_none()
@@ -183,88 +150,19 @@ def __init__(
             description=description,
             reference=reference,
             reference_type=reference_type,
-            artifact=artifact,
+            artifact=meta,
             hash=hash,
             run=run,
             version=version,
             visibility=visibility,
             **kwargs,
         )
-    collection._artifacts = artifacts
+    collection._artifacts = data
     collection._feature_sets = feature_sets
     # register provenance
     if is_new_version_of is not None:
         _track_run_input(is_new_version_of, run=run)
-    if artifact is not None and artifact.run != run:
-        _track_run_input(artifact, run=run)
-    elif artifacts is not None:
-        _track_run_input(artifacts, run=run)
-
-
-@classmethod  # type: ignore
-@doc_args(Collection.from_df.__doc__)
-def from_df(
-    cls,
-    df: "pd.DataFrame",
-    name: Optional[str] = None,
-    description: Optional[str] = None,
-    run: Optional[Run] = None,
-    reference: Optional[str] = None,
-    reference_type: Optional[str] = None,
-    version: Optional[str] = None,
-    is_new_version_of: Optional["Artifact"] = None,
-    **kwargs,
-) -> "Collection":
-    """{}."""
-    if isinstance(df, Artifact):
-        assert not df._state.adding
-        assert df.accessor == "DataFrame"
-    collection = Collection(
-        data=df,
-        name=name,
-        run=run,
-        description=description,
-        reference=reference,
-        reference_type=reference_type,
-        version=version,
-        is_new_version_of=is_new_version_of,
-        accessor="DataFrame",
-        **kwargs,
-    )
-    return collection
-
-
-@classmethod  # type: ignore
-@doc_args(Collection.from_anndata.__doc__)
-def from_anndata(
-    cls,
-    adata: "AnnData",
-    name: Optional[str] = None,
-    description: Optional[str] = None,
-    run: Optional[Run] = None,
-    reference: Optional[str] = None,
-    reference_type: Optional[str] = None,
-    version: Optional[str] = None,
-    is_new_version_of: Optional["Artifact"] = None,
-    **kwargs,
-) -> "Collection":
-    """{}."""
-    if isinstance(adata, Artifact):
-        assert not adata._state.adding
-        assert adata.accessor == "AnnData"
-    collection = Collection(
-        data=adata,
-        run=run,
-        name=name,
-        description=description,
-        reference=reference,
-        reference_type=reference_type,
-        version=version,
-        is_new_version_of=is_new_version_of,
-        accessor="AnnData",
-        **kwargs,
-    )
-    return collection
+    _track_run_input(data, run=run)
 
 
 # internal function, not exposed to user
@@ -373,18 +271,6 @@ def stage(self, is_run_input: Optional[bool] = None) -> List[UPath]:
     return path_list
 
 
-# docstring handled through attach_func_to_class_method
-def backed(
-    self, is_run_input: Optional[bool] = None
-) -> Union["AnnDataAccessor", "BackedAccessor"]:
-    _track_run_input(self, is_run_input)
-    if self.artifact is None:
-        raise RuntimeError(
-            "Can only call backed() for collections with a single artifact"
-        )
-    return self.artifact.backed()
-
-
 # docstring handled through attach_func_to_class_method
 def load(
     self,
@@ -393,29 +279,25 @@ def load(
     **kwargs,
 ) -> DataLike:
     # cannot call _track_run_input here, see comment further down
-    if self.artifact is not None:
-        _track_run_input(self, is_run_input)
-        return self.artifact.load()
-    else:
-        all_artifacts = self.artifacts.all()
-        suffixes = [artifact.suffix for artifact in all_artifacts]
-        if len(set(suffixes)) != 1:
-            raise RuntimeError(
-                "Can only load collections where all artifacts have the same suffix"
-            )
-        # because we're tracking data flow on the collection-level, here, we don't
-        # want to track it on the artifact-level
-        objects = [artifact.load(is_run_input=False) for artifact in all_artifacts]
-        artifact_uids = [artifact.uid for artifact in all_artifacts]
-        if isinstance(objects[0], pd.DataFrame):
-            concat_object = pd.concat(objects, join=join)
-        elif isinstance(objects[0], ad.AnnData):
-            concat_object = ad.concat(
-                objects, join=join, label="artifact_uid", keys=artifact_uids
-            )
-        # only call it here because there might be errors during concat
-        _track_run_input(self, is_run_input)
-        return concat_object
+    all_artifacts = self.artifacts.all()
+    suffixes = [artifact.suffix for artifact in all_artifacts]
+    if len(set(suffixes)) != 1:
+        raise RuntimeError(
+            "Can only load collections where all artifacts have the same suffix"
+        )
+    # because we're tracking data flow on the collection-level, here, we don't
+    # want to track it on the artifact-level
+    objects = [artifact.load(is_run_input=False) for artifact in all_artifacts]
+    artifact_uids = [artifact.uid for artifact in all_artifacts]
+    if isinstance(objects[0], pd.DataFrame):
+        concat_object = pd.concat(objects, join=join)
+    elif isinstance(objects[0], ad.AnnData):
+        concat_object = ad.concat(
+            objects, join=join, label="artifact_uid", keys=artifact_uids
+        )
+    # only call it here because there might be errors during concat
+    _track_run_input(self, is_run_input)
+    return concat_object
 
 
 # docstring handled through attach_func_to_class_method
@@ -484,11 +366,8 @@ def artifacts(self) -> QuerySet:
 
 METHOD_NAMES = [
     "__init__",
-    "from_anndata",
-    "from_df",
     "mapped",
     "stage",
-    "backed",
     "load",
     "delete",
     "save",

lamindb/core/_data.py

@@ -36,9 +36,7 @@ from ._label_manager import LabelManager, print_labels
 from ._run_context import run_context
 from .exceptions import ValidationError
 
-WARNING_RUN_TRANSFORM = (
-    "no run & transform get linked, consider passing a `run` or calling ln.track()"
-)
+WARNING_RUN_TRANSFORM = "no run & transform get linked, consider calling ln.track()"
 
 
 def get_run(run: Optional[Run]) -> Optional[Run]:

lamindb/core/_feature_manager.py

@@ -253,8 +253,7 @@ class FeatureManager:
         if isinstance(self._host, Artifact):
             assert self._host.accessor == "AnnData"
         else:
-            # Collection
-            assert self._host.artifact.accessor == "AnnData"
+            raise NotImplementedError()
 
         # parse and register features
         adata = self._host.load()

lamindb/integrations/__init__.py

@@ -0,0 +1,8 @@
+"""Integrations.
+
+.. autosummary::
+   :toctree: .
+
+   save_vitessce_config
+"""
+from ._vitessce import save_vitessce_config

lamindb/integrations/_vitessce.py

@@ -0,0 +1,36 @@
+import json
+from datetime import datetime, timezone
+
+import lamindb_setup as ln_setup
+from lamin_utils import logger
+
+from lamindb._artifact import Artifact
+
+
+# tested in lamin-spatial
+# can't type vitessce_config because can't assume it's installed
+def save_vitessce_config(vitessce_config, description: str) -> Artifact:
+    """Takes a ``VitessceConfig`` object and saves it as an artifact.
+
+    Args:
+        vitessce_config (``VitessceConfig``): A VitessceConfig object.
+        description: A description for the artifact.
+    """
+    from vitessce import VitessceConfig
+
+    assert isinstance(vitessce_config, VitessceConfig)
+    timestamp = datetime.now(timezone.utc).isoformat().split(".")[0]
+    vitesse_export = f"./vitessce_export_{timestamp}.vitessce"
+    vitessce_config.export(to="files", base_url="", out_dir=vitesse_export)
+    logger.important(f"local export: {vitesse_export}")
+    artifact = Artifact(vitesse_export, description=description)
+    artifact.save()
+    config_dict = vitessce_config.to_dict(base_url=artifact.path.to_url())
+    config_filename = "vitessce_config.json"
+    config_file_local_path = f"{vitesse_export}/{config_filename}"
+    with open(config_file_local_path, "w") as file:
+        json.dump(config_dict, file)
+    (artifact.path / config_filename).upload_from(config_file_local_path)
+    slug = ln_setup.settings.instance.slug
+    logger.important(f"go to: https://lamin.ai/{slug}/artifact/{artifact.uid}")
+    return artifact

{lamindb-0.69.3.dist-info → lamindb-0.69.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.69.3
+Version: 0.69.4
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -10,7 +10,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: lnschema_core==0.64.1
-Requires-Dist: lamindb_setup==0.68.1
+Requires-Dist: lamindb_setup==0.68.2
 Requires-Dist: lamin_utils==0.13.1
 Requires-Dist: lamin_cli==0.10.2
 Requires-Dist: rapidfuzz

{lamindb-0.69.3.dist-info → lamindb-0.69.4.dist-info}/RECORD

@@ -1,8 +1,8 @@
-lamindb/__init__.py,sha256=Xy8yw0Woc26c9DxrgHP5c_UvVJpocigGwfCj8Ho_VZo,2108
-lamindb/_annotate.py,sha256=k9Is43plKcQaMvGnzVw6OeWvZDWcSxw3FQ7nsQVDHzw,27744
+lamindb/__init__.py,sha256=3kVakyBIty4I2C-69S114uW3z9lnEOgpnOz3LsZb2ro,2163
+lamindb/_annotate.py,sha256=BopvJvzUlNKiTzOELg6MXeXQNUVMUTk-FcRoV9mfZdo,27682
 lamindb/_artifact.py,sha256=RV36tcHMZ6wH6u65jOAQ_H4rfmFiIzZmAr8IY7kFhm0,35817
 lamindb/_can_validate.py,sha256=w7lrUGTWldpvwaRiXBRrjfU_ZRidA7CooOu_r5MbocY,14569
-lamindb/_collection.py,sha256=03CQ0u8eCY_dx31pIT5ZMZsmxbbj6J5dJ9zUqJLrDGY,18427
+lamindb/_collection.py,sha256=SdNNhhMh2O4q0hG4Hf_y1bcwcbkMF_sqk6MIYc-hLZo,14525
 lamindb/_feature.py,sha256=ahRv87q1tcRLQ0UM5FA3KtcMQvIjW__fZq1yAdRAV7s,6728
 lamindb/_feature_set.py,sha256=G_Ss6mKh4D0Eji-xSfLRbKVFXwgUE82YOqIUmkV0CAA,8767
 lamindb/_filter.py,sha256=_PjyQWQBR3ohDAvJbR3hMvZ-2p2GvzFxLfKGC-gPnHI,1320
@@ -21,8 +21,8 @@ lamindb/_ulabel.py,sha256=euXsDPD7wC99oopLXVkT-vq7f3E6-zP4Z4akI-yh0aM,1913
 lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
 lamindb/_view.py,sha256=yFMu4vnt0YqvN1q11boAkwigxCH1gdliDUSbzh3IuDw,2175
 lamindb/core/__init__.py,sha256=Mw4sI-xgnMXNsu84oYFQBZOF8mxxxhp6-e3BjTQqjlA,1131
-lamindb/core/_data.py,sha256=Q8w1I8pXXOaLVIxfjWBkLV6GGnzaQxCXamu9tplFgsA,17287
-lamindb/core/_feature_manager.py,sha256=II0nuxtjOdEtU_9a7eB18_Clw9d1n5k1JOqk_vHisRw,13940
+lamindb/core/_data.py,sha256=SCyUjS9bL7MMqyZTJl8PxnNtLKL7eNiUcLvmwFrqP-k,17260
+lamindb/core/_feature_manager.py,sha256=_Bicjal2DQbpl6tR7p5o7Alb9rq0XYzAxrF_bV9sTjE,13894
 lamindb/core/_label_manager.py,sha256=zrWDSd2AkR6fKsGDxLSWqHC9fz9BcGlavPZEh92Wzjg,9063
 lamindb/core/_mapped_collection.py,sha256=e4P3AoykIMjD4_88BWbISWvKyWWTklwHl-_WLa72ZG4,16841
 lamindb/core/_run_context.py,sha256=EK0lFJWx32NY2FdqFR1YozR9zioC-BjA394nPu-KwLQ,17510
@@ -44,9 +44,11 @@ lamindb/core/storage/_backed_access.py,sha256=DUJIDjkGkemjmKLD05blndP_rO5DpUD0EZ
 lamindb/core/storage/_zarr.py,sha256=bMQSCsTOCtQy4Yo3KwCVpbUkKdWRApN9FM1rM-d2_G0,2839
 lamindb/core/storage/file.py,sha256=WTeC4ENn_O6HEoinmTviB89W81UrJT3bSGtnpqPpIyE,7242
 lamindb/core/storage/object.py,sha256=MPUb2M8Fleq2j9x1Ryqr3BETmvsDKyf11Ifvbxd3NpA,1097
+lamindb/integrations/__init__.py,sha256=aH2PmO2m4-vwIifMYTB0Fyyr_gZWtVnV71jT0tVWSw0,123
+lamindb/integrations/_vitessce.py,sha256=NHOiDJzn2QtzfkThhHEuDJuTTcSkem9x5d_wrQ-8nPI,1474
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=LqIIvJNcONxkqjbnP6CUaP4d45Lbd6TSMAcXFp4C7_8,231
-lamindb-0.69.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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