lamindb 1.5.2__py3-none-any.whl → 1.6a2__py3-none-any.whl

lamindb/models/transform.py

@@ -18,23 +18,21 @@ from lamindb.base.users import current_user_id
 
 from ..models._is_versioned import process_revises
 from ._is_versioned import IsVersioned
-from .record import Record, init_self_from_db, update_attributes
 from .run import Run, User, delete_run_artifacts
+from .sqlrecord import SQLRecord, init_self_from_db, update_attributes
 
 if TYPE_CHECKING:
     from datetime import datetime
 
     from lamindb.base.types import TransformType
 
-    from .artifact import Artifact
-    from .collection import Collection
     from .project import Project, Reference
     from .ulabel import ULabel
 
 
 # does not inherit from TracksRun because the Transform
 # is needed to define a run
-class Transform(Record, IsVersioned):
+class Transform(SQLRecord, IsVersioned):
     """Data transformations such as scripts, notebooks, functions, or pipelines.
 
     A "transform" can refer to a Python function, a script, a notebook, or a
@@ -95,8 +93,9 @@ class Transform(Record, IsVersioned):
         >>> transform.view_lineage()
     """
 
-    class Meta(Record.Meta, IsVersioned.Meta):
+    class Meta(SQLRecord.Meta, IsVersioned.Meta):
         abstract = False
+        unique_together = ("key", "hash")
 
     _len_stem_uid: int = 12
     _len_full_uid: int = 16
@@ -108,6 +107,9 @@ class Transform(Record, IsVersioned):
         editable=False, unique=True, db_index=True, max_length=_len_full_uid
     )
     """Universal id."""
+    # the fact that key is nullable is consistent with Artifact
+    # it might turn out that there will never really be a use case for this
+    # but there likely also isn't much harm in it except for the mixed type
     key: str | None = CharField(db_index=True, null=True)
     """A name or "/"-separated path-like string.
 
@@ -122,16 +124,8 @@ class Transform(Record, IsVersioned):
     )
     """:class:`~lamindb.base.types.TransformType` (default `"pipeline"`)."""
     source_code: str | None = TextField(null=True)
-    """Source code of the transform.
-
-    .. versionchanged:: 0.75
-       The `source_code` field is no longer an artifact, but a text field.
-    """
-    # we have a unique constraint here but not on artifact because on artifact, we haven't yet
-    # settled how we model the same artifact in different storage locations
-    hash: str | None = CharField(
-        max_length=HASH_LENGTH, db_index=True, null=True, unique=True
-    )
+    """Source code of the transform."""
+    hash: str | None = CharField(max_length=HASH_LENGTH, db_index=True, null=True)
     """Hash of the source code."""
     reference: str | None = CharField(max_length=255, db_index=True, null=True)
     """Reference for the transform, e.g., a URL."""
@@ -148,29 +142,14 @@ class Transform(Record, IsVersioned):
     )
     """Preceding transforms.
 
-    These are auto-populated whenever an artifact or collection serves as a run
-    input, e.g., `artifact.run` and `artifact.transform` get populated & saved.
-
-    The table provides a more convenient method to query for the predecessors that
-    bypasses querying the :class:`~lamindb.Run`.
-
-    It also allows to manually add predecessors whose outputs are not tracked in a run.
+    Allows to _manually_ define predecessors. Is typically not necessary as data lineage is
+    automatically tracked via runs whenever an artifact or collection serves as an input for a run.
     """
     successors: Transform
     """Subsequent transforms.
 
     See :attr:`~lamindb.Transform.predecessors`.
     """
-    output_artifacts: Artifact
-    """The artifacts generated by all runs of this transform.
-
-    If you're looking for the outputs of a single run, see :attr:`lamindb.Run.output_artifacts`.
-    """
-    output_collections: Collection
-    """The collections generated by all runs of this transform.
-
-    If you're looking for the outputs of a single run, see :attr:`lamindb.Run.output_collections`.
-    """
     projects: Project
     """Linked projects."""
     references: Reference
@@ -339,7 +318,12 @@ class Transform(Record, IsVersioned):
         super().delete()
 
     def view_lineage(self, with_successors: bool = False, distance: int = 5):
-        """View lineage of transforms."""
+        """View lineage of transforms.
+
+        Note that this only accounts for manually defined predecessors and successors.
+
+        Auto-generate lineage through inputs and outputs of runs is not included.
+        """
         from .has_parents import view_parents
 
         return view_parents(

lamindb/models/ulabel.py

@@ -5,6 +5,7 @@ from typing import TYPE_CHECKING, overload
 from django.db import models
 from django.db.models import CASCADE, PROTECT
 
+from lamindb.base import deprecated
 from lamindb.base.fields import (
     BooleanField,
     CharField,
@@ -17,8 +18,8 @@ from ..base.ids import base62_8
 from .can_curate import CanCurate
 from .feature import Feature
 from .has_parents import HasParents
-from .record import BasicRecord, LinkORM, Record, _get_record_kwargs
 from .run import Run, TracksRun, TracksUpdates, User, current_user_id
+from .sqlrecord import BaseSQLRecord, IsLink, SQLRecord, _get_record_kwargs
 from .transform import Transform
 
 if TYPE_CHECKING:
@@ -29,7 +30,7 @@ if TYPE_CHECKING:
     from .project import Project
 
 
-class ULabel(Record, HasParents, CanCurate, TracksRun, TracksUpdates):
+class ULabel(SQLRecord, HasParents, CanCurate, TracksRun, TracksUpdates):
     """Universal labels.
 
     Args:
@@ -41,8 +42,7 @@ class ULabel(Record, HasParents, CanCurate, TracksRun, TracksUpdates):
     A `ULabel` record provides the easiest way to annotate a dataset
     with a label: `"My project"`, `"curated"`, or `"Batch X"`:
 
-        >>> my_project = ULabel(name="My project")
-        >>> my_project.save()
+        >>> my_project = ULabel(name="My project").save()
         >>> artifact.ulabels.add(my_project)
 
     Often, a ulabel is measured *within* a dataset. For instance, an artifact
@@ -68,11 +68,11 @@ class ULabel(Record, HasParents, CanCurate, TracksRun, TracksUpdates):
 
     Examples:
 
-        Create a new label:
+        Create a ulabel:
 
         >>> train_split = ln.ULabel(name="train").save()
 
-        Organize labels in a hierarchy:
+        Organize ulabels in a hierarchy:
 
         >>> split_type = ln.ULabel(name="Split", is_type=True).save()
         >>> train_split = ln.ULabel(name="train", type="split_type").save()
@@ -81,12 +81,12 @@ class ULabel(Record, HasParents, CanCurate, TracksRun, TracksUpdates):
 
         >>> artifact.ulabels.add(ulabel)
 
-        Query an artifact by label:
+        Query an artifact by ulabel:
 
         >>> ln.Artifact.filter(ulabels=train_split).df()
     """
 
-    class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
+    class Meta(SQLRecord.Meta, TracksRun.Meta, TracksUpdates.Meta):
         abstract = False
 
     _name_field: str = "name"
@@ -99,13 +99,13 @@ class ULabel(Record, HasParents, CanCurate, TracksRun, TracksUpdates):
     """A universal random id, valid across DB instances."""
     name: str = CharField(max_length=150, db_index=True)
     """Name or title of ulabel."""
-    type: ULabel | None = ForeignKey("self", PROTECT, null=True, related_name="records")
+    type: ULabel | None = ForeignKey("self", PROTECT, null=True, related_name="ulabels")
     """Type of ulabel, e.g., `"donor"`, `"split"`, etc.
 
     Allows to group ulabels by type, e.g., all donors, all split ulabels, etc.
     """
-    records: ULabel
-    """Records of this type."""
+    ulabels: ULabel
+    """ULabels of this type (can only be non-empty if `is_type` is `True`)."""
     is_type: bool = BooleanField(default=False, db_index=True, null=True)
     """Distinguish types from instances of the type.
 
@@ -193,8 +193,14 @@ class ULabel(Record, HasParents, CanCurate, TracksRun, TracksUpdates):
             _aux=_aux,
         )
 
+    @property
+    @deprecated("ulabels")
+    def records(self) -> list[ULabel]:
+        """Return all instances of this type."""
+        return self.ulabels
 
-class ArtifactULabel(BasicRecord, LinkORM, TracksRun):
+
+class ArtifactULabel(BaseSQLRecord, IsLink, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
     artifact: Artifact = ForeignKey("Artifact", CASCADE, related_name="links_ulabel")
     ulabel: ULabel = ForeignKey(ULabel, PROTECT, related_name="links_artifact")
@@ -210,7 +216,7 @@ class ArtifactULabel(BasicRecord, LinkORM, TracksRun):
         unique_together = ("artifact", "ulabel", "feature")
 
 
-class TransformULabel(BasicRecord, LinkORM, TracksRun):
+class TransformULabel(BaseSQLRecord, IsLink, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
     transform: Transform = ForeignKey(Transform, CASCADE, related_name="links_ulabel")
     ulabel: ULabel = ForeignKey(ULabel, PROTECT, related_name="links_transform")
@@ -219,7 +225,7 @@ class TransformULabel(BasicRecord, LinkORM, TracksRun):
         unique_together = ("transform", "ulabel")
 
 
-class RunULabel(BasicRecord, LinkORM):
+class RunULabel(BaseSQLRecord, IsLink):
     id: int = models.BigAutoField(primary_key=True)
     run: Run = ForeignKey(Run, CASCADE, related_name="links_ulabel")
     ulabel: ULabel = ForeignKey(ULabel, PROTECT, related_name="links_run")
@@ -236,7 +242,7 @@ class RunULabel(BasicRecord, LinkORM):
         unique_together = ("run", "ulabel")
 
 
-class CollectionULabel(BasicRecord, LinkORM, TracksRun):
+class CollectionULabel(BaseSQLRecord, IsLink, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
     collection: Collection = ForeignKey(
         "Collection", CASCADE, related_name="links_ulabel"

{lamindb-1.5.2.dist-info → lamindb-1.6a2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.5.2
+Version: 1.6a2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10,<3.14
@@ -10,21 +10,20 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: lamin_utils==0.14.0
-Requires-Dist: lamin_cli==1.4.0
-Requires-Dist: lamindb_setup[aws]==1.5.2
+Requires-Dist: lamin_cli==1.4.1
+Requires-Dist: lamindb_setup[aws]==1.6.0
 Requires-Dist: pyyaml
 Requires-Dist: pyarrow
-Requires-Dist: pandera
+Requires-Dist: pandera>=0.24.0
 Requires-Dist: typing_extensions!=4.6.0
 Requires-Dist: python-dateutil
-Requires-Dist: scipy<1.15.0
 Requires-Dist: pandas>=2.0.0
+Requires-Dist: scipy<1.15.0
 Requires-Dist: anndata>=0.8.0,<=0.11.4
 Requires-Dist: fsspec
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
-Requires-Dist: bionty>=1.3.2 ; extra == "bionty"
-Requires-Dist: cellregistry ; extra == "cellregistry"
+Requires-Dist: bionty>=1.4a1 ; extra == "bionty"
 Requires-Dist: clinicore ; extra == "clinicore"
 Requires-Dist: tomlkit ; extra == "dev"
 Requires-Dist: line_profiler ; extra == "dev"
@@ -37,7 +36,6 @@ Requires-Dist: pytest-cov ; extra == "dev"
 Requires-Dist: mudata ; extra == "dev"
 Requires-Dist: nbproject_test>=0.6.0 ; extra == "dev"
 Requires-Dist: faker-biology ; extra == "dev"
-Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=2.0.1 ; extra == "fcs"
 Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
 Requires-Dist: nbproject==0.11.1 ; extra == "jupyter"
@@ -45,15 +43,13 @@ Requires-Dist: jupytext ; extra == "jupyter"
 Requires-Dist: nbconvert>=7.2.1 ; extra == "jupyter"
 Requires-Dist: mistune!=3.1.0 ; extra == "jupyter"
 Requires-Dist: omop ; extra == "omop"
-Requires-Dist: wetlab ; extra == "wetlab"
+Requires-Dist: wetlab>=1.3a1 ; extra == "wetlab"
 Requires-Dist: numcodecs<0.16.0 ; extra == "zarr"
 Requires-Dist: zarr>=2.16.0,<3.0.0a0 ; extra == "zarr"
 Project-URL: Home, https://github.com/laminlabs/lamindb
 Provides-Extra: bionty
-Provides-Extra: cellregistry
 Provides-Extra: clinicore
 Provides-Extra: dev
-Provides-Extra: erdiagram
 Provides-Extra: fcs
 Provides-Extra: gcp
 Provides-Extra: jupyter

lamindb-1.6a2.dist-info/RECORD

@@ -0,0 +1,118 @@
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lamindb/core/storage/_anndata_sizes.py

@@ -1,41 +0,0 @@
-from __future__ import annotations
-
-import warnings
-
-import scipy.sparse as sparse
-from pandas import DataFrame
-
-
-def _size_val(val):
-    with warnings.catch_warnings():
-        warnings.filterwarnings("ignore", category=FutureWarning)
-
-        if sparse.issparse(val):
-            val_csr = sparse.csr_matrix(val)
-            return val_csr.data.nbytes + val_csr.indptr.nbytes + val_csr.indices.nbytes
-        else:
-            return val.__sizeof__()
-
-
-def _size_elem(elem):
-    if hasattr(elem, "keys") and not isinstance(elem, DataFrame):
-        return sum([_size_val(elem[k]) for k in elem.keys()])
-    else:
-        return _size_val(elem)
-
-
-def _size_raw(raw):
-    return _size_val(raw.X) + _size_val(raw.var) + _size_elem(raw.varm)
-
-
-def size_adata(adata):
-    with warnings.catch_warnings():
-        warnings.filterwarnings("ignore", category=FutureWarning)
-
-        total_size = adata.__sizeof__()
-
-        raw = adata.raw
-        if raw is not None:
-            total_size += _size_raw(raw)
-
-        return total_size

lamindb/models/flextable.py

@@ -1,163 +0,0 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING
-
-from django.db import models
-from django.db.models import PROTECT, ManyToManyField
-
-from lamindb.base.fields import (
-    BooleanField,
-    CharField,
-    ForeignKey,
-    IntegerField,
-)
-
-from .artifact import Artifact
-from .feature import Feature
-from .record import (
-    BasicRecord,
-    Record,
-)
-from .run import Param, TracksRun, TracksUpdates
-
-if TYPE_CHECKING:
-    from .project import Project
-
-from django.core.exceptions import ValidationError
-
-from ..base.ids import base62_12
-from .collection import Collection
-from .project import Person, Project
-from .record import Space
-from .schema import Schema
-from .ulabel import ULabel
-
-
-class DataMixin(models.Model):
-    space: Space = ForeignKey(Space, PROTECT, default=1, db_default=1)
-    feature = ForeignKey(
-        Feature, null=True, blank=True, on_delete=models.CASCADE, related_name="+"
-    )
-    param = ForeignKey(
-        Param, null=True, blank=True, on_delete=models.CASCADE, related_name="+"
-    )
-    row = IntegerField(help_text="Use -1 for result data")
-
-    # Value fields
-    value_int = models.BigIntegerField(null=True, blank=True)
-    value_float = models.FloatField(null=True, blank=True)
-    value_str = models.TextField(null=True, blank=True)
-    value_datetime = models.DateTimeField(null=True, blank=True)
-    value_ulabel = models.ForeignKey(
-        ULabel, null=True, blank=True, on_delete=models.CASCADE, related_name="+"
-    )
-    value_person = models.ForeignKey(
-        Person, null=True, blank=True, on_delete=models.CASCADE, related_name="+"
-    )
-    value_artifact = models.ForeignKey(
-        Artifact, null=True, blank=True, on_delete=models.CASCADE, related_name="+"
-    )
-    value_collection = models.ForeignKey(
-        Collection, null=True, blank=True, on_delete=models.CASCADE, related_name="+"
-    )
-    value_project = models.ForeignKey(
-        Project, null=True, blank=True, on_delete=models.CASCADE, related_name="+"
-    )
-    value_json = models.JSONField(null=True, blank=True)
-
-    class Meta:
-        abstract = True
-
-    def clean(self):
-        # Validate feature/param mutual exclusivity
-        if (self.feature is not None) == (self.param is not None):
-            raise ValidationError("Exactly one of feature or param must be set")
-
-        # Validate value fields
-        values = [
-            self.value_int,
-            self.value_float,
-            self.value_str,
-            self.value_datetime,
-            self.value_ulabel,
-            self.value_artifact,
-            self.value_json,
-        ]
-        non_null_count = sum(1 for v in values if v is not None)
-
-        if non_null_count != 1:
-            raise ValidationError("Exactly one value field must be set")
-
-
-class RunData(BasicRecord, DataMixin):
-    run = models.ForeignKey("Run", on_delete=models.CASCADE, related_name="_rundata")
-
-    class Meta:
-        constraints = [
-            models.CheckConstraint(
-                condition=(
-                    models.Q(feature__isnull=False, param__isnull=True)
-                    | models.Q(feature__isnull=True, param__isnull=False)
-                ),
-                name="run_data_feature_param_mutex",
-            ),
-            models.UniqueConstraint(
-                fields=["run", "row", "feature", "param"], name="run_data_unique"
-            ),
-        ]
-        indexes = [
-            models.Index(fields=["run", "row"]),
-            models.Index(fields=["feature"]),
-            models.Index(fields=["param"]),
-        ]
-
-
-class FlexTable(Record, TracksRun, TracksUpdates):
-    uid: str = CharField(
-        editable=False, unique=True, max_length=12, db_index=True, default=base62_12
-    )
-    name = CharField()
-    schema: Schema | None = ForeignKey(
-        Schema, null=True, on_delete=models.SET_NULL, related_name="_tidytables"
-    )
-    type: FlexTable | None = ForeignKey(
-        "self", PROTECT, null=True, related_name="records"
-    )
-    """Type of tidy table, e.g., `Cell`, `SampleSheet`, etc."""
-    records: ULabel
-    """Records of this type."""
-    is_type: bool = BooleanField(default=False, db_index=True, null=True)
-    """Distinguish types from instances of the type."""
-    description: str = CharField(null=True, db_index=True)
-    """A description."""
-    projects: Project = ManyToManyField(Project, related_name="_tidytables")
-    ulabels: Project = ManyToManyField(ULabel, related_name="_tidytables")
-
-    class Meta:
-        indexes = [models.Index(fields=["uid"]), models.Index(fields=["name"])]
-
-
-class FlexTableData(BasicRecord, DataMixin):
-    tidytable = models.ForeignKey(
-        FlexTable, on_delete=models.CASCADE, related_name="data"
-    )
-
-    class Meta:
-        constraints = [
-            models.CheckConstraint(
-                condition=(
-                    models.Q(feature__isnull=False, param__isnull=True)
-                    | models.Q(feature__isnull=True, param__isnull=False)
-                ),
-                name="tidy_table_data_feature_param_mutex",
-            ),
-            models.UniqueConstraint(
-                fields=["tidytable", "row", "feature", "param"],
-                name="tidy_table_data_unique",
-            ),
-        ]
-        indexes = [
-            models.Index(fields=["tidytable", "row"]),
-            models.Index(fields=["feature"]),
-            models.Index(fields=["param"]),
-        ]