lamindb 1.4.0__py3-none-any.whl → 1.5.1__py3-none-any.whl

lamindb/errors.py

@@ -94,3 +94,14 @@ class UpdateContext(SystemExit):
     """Transform settings require update."""
 
     pass
+
+
+# -------------------------------------------------------------------------------------
+# record
+# -------------------------------------------------------------------------------------
+
+
+class NoWriteAccess(Exception):
+    """No write access to a space."""
+
+    pass

lamindb/examples/__init__.py

@@ -0,0 +1,27 @@
+"""Examples.
+
+.. autosummary::
+   :toctree: .
+
+   ingest_mini_immuno_datasets
+   schemas
+
+"""
+
+from . import schemas
+
+
+def ingest_mini_immuno_datasets():
+    """Ingest mini immuno datasets.
+
+    .. literalinclude:: scripts/ingest_mini_immuno_datasets.py
+        :language: python
+    """
+    import sys
+    from pathlib import Path
+
+    docs_path = Path(__file__).parent.parent.parent / "docs" / "scripts"
+    if str(docs_path) not in sys.path:
+        sys.path.append(str(docs_path))
+
+    import ingest_mini_immuno_datasets  # noqa

lamindb/examples/schemas/__init__.py

@@ -0,0 +1,12 @@
+"""Example schemas.
+
+.. autosummary::
+   :toctree: .
+
+   valid_features
+   anndata_ensembl_gene_ids_and_valid_features_in_obs
+
+"""
+
+from ._anndata import anndata_ensembl_gene_ids_and_valid_features_in_obs
+from ._simple import valid_features

lamindb/examples/schemas/_anndata.py

@@ -0,0 +1,25 @@
+from ... import Schema
+
+
+def anndata_ensembl_gene_ids_and_valid_features_in_obs() -> Schema:
+    """Return a schema for an AnnData with Ensembl gene IDs and valid features in obs.
+
+    .. literalinclude:: scripts/define_schema_anndata_ensembl_gene_ids_and_valid_features_in_obs.py
+        :language: python
+    """
+    import subprocess
+    from pathlib import Path
+
+    docs_path = Path(__file__).parent.parent.parent.parent / "docs" / "scripts"
+    subprocess.run(
+        [
+            "python",
+            str(
+                docs_path
+                / "define_schema_anndata_ensembl_gene_ids_and_valid_features_in_obs.py"
+            ),
+        ],
+        check=True,
+    )
+
+    return Schema.get(name="anndata_ensembl_gene_ids_and_valid_features_in_obs")

lamindb/examples/schemas/_simple.py

@@ -0,0 +1,19 @@
+from ... import Schema
+
+
+def valid_features() -> Schema:
+    """Return a schema for an AnnData with Ensembl gene IDs and valid features in obs.
+
+    .. literalinclude:: scripts/define_schema_anndata_ensembl_gene_ids_and_valid_features_in_obs.py
+        :language: python
+    """
+    import subprocess
+    from pathlib import Path
+
+    docs_path = Path(__file__).parent.parent.parent.parent / "docs" / "scripts"
+    subprocess.run(
+        ["python", str(docs_path / "define_valid_features.py")],
+        check=True,
+    )
+
+    return Schema.get(name="valid_features")

lamindb/integrations/_vitessce.py

@@ -19,7 +19,9 @@ if TYPE_CHECKING:
 # "unit test": https://github.com/laminlabs/lamindb/blob/main/docs/storage/vitessce.ipynb
 # integration test & context: https://github.com/laminlabs/lamin-spatial/blob/main/docs/vitessce.ipynb
 def save_vitessce_config(
-    vitessce_config: VitessceConfig, description: str | None = None
+    vitessce_config: VitessceConfig,
+    key: str | None = None,
+    description: str | None = None,
 ) -> Artifact:
     """Validates and saves a `VitessceConfig` object.
 
@@ -30,9 +32,10 @@ def save_vitessce_config(
 
     Args:
         vitessce_config: A `VitessceConfig` object.
-        description: A description for the `VitessceConfig` object. Is used as
-            `key` for a `Collection` in case the `VitessceConfig` object
-            references multiple artifacts.
+        key: A key for the `VitessceConfig` object. Is used as `key` for a
+            `Collection` in case the `VitessceConfig` object references
+            multiple artifacts.
+        description: A description for the `VitessceConfig` object.
 
     .. versionchanged:: 0.76.12
         Now assumes `vitessce-python >= 3.4.0`, which allows passing artifacts within `VitessceConfig`.
@@ -77,7 +80,7 @@ def save_vitessce_config(
     with open(config_file_local_path, "w") as file:
         json.dump(vc_dict, file)
     vitessce_config_artifact = Artifact(
-        config_file_local_path, description=description, run=run
+        config_file_local_path, key=key, description=description, run=run
     ).save()
     slug = ln_setup.settings.instance.slug
     logger.important(

lamindb/migrations/0091_alter_featurevalue_options_alter_space_options_and_more.py

@@ -0,0 +1,24 @@
+# Generated by Django 5.1.4 on 2025-04-30 09:11
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("lamindb", "0090_squashed"),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name="featurevalue",
+            options={"base_manager_name": "objects"},
+        ),
+        migrations.AlterModelOptions(
+            name="space",
+            options={"base_manager_name": "objects"},
+        ),
+        migrations.AlterModelOptions(
+            name="user",
+            options={"base_manager_name": "objects"},
+        ),
+    ]

lamindb/migrations/0092_alter_artifactfeaturevalue_artifact_and_more.py

@@ -0,0 +1,75 @@
+# Generated by Django 5.2 on 2025-05-06 20:34
+
+import django.db.models.deletion
+from django.db import migrations
+
+import lamindb.base.fields
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("lamindb", "0091_alter_featurevalue_options_alter_space_options_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="artifactfeaturevalue",
+            name="artifact",
+            field=lamindb.base.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="links_featurevalue",
+                to="lamindb.artifact",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="artifactfeaturevalue",
+            name="featurevalue",
+            field=lamindb.base.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="links_artifact",
+                to="lamindb.featurevalue",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="artifactparamvalue",
+            name="artifact",
+            field=lamindb.base.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="links_paramvalue",
+                to="lamindb.artifact",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="artifactparamvalue",
+            name="paramvalue",
+            field=lamindb.base.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="links_artifact",
+                to="lamindb.paramvalue",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="runparamvalue",
+            name="paramvalue",
+            field=lamindb.base.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="links_run",
+                to="lamindb.paramvalue",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="runparamvalue",
+            name="run",
+            field=lamindb.base.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="links_paramvalue",
+                to="lamindb.run",
+            ),
+        ),
+    ]

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/models/__init__.py

@@ -6,7 +6,9 @@
    BasicRecord
    Record
    Registry
+   BasicQuerySet
    QuerySet
+   ArtifactSet
    QueryManager
    RecordList
    FeatureManager
@@ -55,7 +57,8 @@ from .collection import Collection, CollectionArtifact
 from .project import Person, Project, Reference
 from .flextable import FlexTable, RunData
 from .query_manager import QueryManager
-from .query_set import QuerySet, RecordList
+from .query_set import BasicQuerySet, QuerySet, RecordList
+from .artifact_set import ArtifactSet
 from .has_parents import HasParents
 from datetime import datetime as _datetime
 

lamindb/models/_describe.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import datetime
+import re
 from typing import TYPE_CHECKING
 
 from lamin_utils import logger
@@ -35,7 +36,9 @@ TYPE_WIDTH = 25
 VALUES_WIDTH = 40
 
 
-def print_rich_tree(tree: Tree, fallback=str):
+def format_rich_tree(
+    tree: Tree, fallback: str = "", return_str: bool = False, strip_ansi: bool = True
+) -> str | None:
     from rich.console import Console
 
     # If tree has no children, return fallback
@@ -45,6 +48,20 @@ def print_rich_tree(tree: Tree, fallback=str):
     console = Console(force_terminal=True)
     printed = False
 
+    if return_str:
+        from io import StringIO
+
+        string_io = StringIO()
+        str_console = Console(file=string_io, force_terminal=True)
+        str_console.print(tree)
+        result = string_io.getvalue()
+        if strip_ansi:
+            ansi_escape = re.compile(r"\x1b(?:\[[0-9;]*[a-zA-Z]|\(B)")
+            result = ansi_escape.sub("", result)
+        # rstrip trailing whitespace on every line
+        result = "\n".join(line.rstrip() for line in result.splitlines())
+        return result
+
     try:
         if not is_run_from_ipython:
             from IPython import get_ipython
@@ -55,16 +72,16 @@ def print_rich_tree(tree: Tree, fallback=str):
             if isinstance(shell, InteractiveShell):
                 display(tree)
                 printed = True
-                return ""
+                return None
     except (NameError, ImportError):
         pass
 
-    # If not printed through IPython
     if not printed:
         # be careful to test this on a terminal
         console = Console(force_terminal=True)
         console.print(tree)
-        return ""
+
+    return None
 
 
 def describe_header(self: Artifact | Collection | Run) -> Tree: