PyPI - lamindb - Versions diffs - 1.0.5__py3-none-any.whl → 1.1.1__py3-none-any.whl - Mend

lamindb 1.0.5py3-none-any.whl → 1.1.1py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (80) hide show

lamindb/__init__.py +17 -6
lamindb/_artifact.py +202 -87
lamindb/_can_curate.py +27 -8
lamindb/_collection.py +86 -52
lamindb/_feature.py +177 -41
lamindb/_finish.py +21 -7
lamindb/_from_values.py +83 -98
lamindb/_parents.py +4 -4
lamindb/_query_set.py +78 -18
lamindb/_record.py +170 -53
lamindb/_run.py +4 -4
lamindb/_save.py +42 -11
lamindb/_schema.py +135 -38
lamindb/_storage.py +1 -1
lamindb/_tracked.py +129 -0
lamindb/_transform.py +21 -8
lamindb/_ulabel.py +5 -14
lamindb/base/users.py +1 -4
lamindb/base/validation.py +2 -6
lamindb/core/__init__.py +13 -14
lamindb/core/_context.py +14 -9
lamindb/core/_data.py +29 -25
lamindb/core/_describe.py +1 -1
lamindb/core/_django.py +1 -1
lamindb/core/_feature_manager.py +53 -43
lamindb/core/_label_manager.py +4 -4
lamindb/core/_mapped_collection.py +24 -9
lamindb/core/_track_environment.py +2 -1
lamindb/core/datasets/__init__.py +6 -1
lamindb/core/datasets/_core.py +12 -11
lamindb/core/datasets/_small.py +67 -21
lamindb/core/exceptions.py +1 -90
lamindb/core/loaders.py +21 -15
lamindb/core/relations.py +6 -4
lamindb/core/storage/_anndata_accessor.py +49 -3
lamindb/core/storage/_backed_access.py +12 -7
lamindb/core/storage/_pyarrow_dataset.py +40 -15
lamindb/core/storage/_tiledbsoma.py +56 -12
lamindb/core/storage/paths.py +30 -24
lamindb/core/subsettings/_creation_settings.py +4 -16
lamindb/curators/__init__.py +2193 -846
lamindb/curators/_cellxgene_schemas/__init__.py +26 -0
lamindb/curators/_cellxgene_schemas/schema_versions.yml +104 -0
lamindb/errors.py +96 -0
lamindb/integrations/_vitessce.py +3 -3
lamindb/migrations/0069_squashed.py +76 -75
lamindb/migrations/0075_lamindbv1_part5.py +4 -5
lamindb/migrations/0082_alter_feature_dtype.py +21 -0
lamindb/migrations/0083_alter_feature_is_type_alter_flextable_is_type_and_more.py +94 -0
lamindb/migrations/0084_alter_schemafeature_feature_and_more.py +35 -0
lamindb/migrations/0085_alter_feature_is_type_alter_flextable_is_type_and_more.py +63 -0
lamindb/migrations/0086_various.py +95 -0
lamindb/migrations/0087_rename__schemas_m2m_artifact_feature_sets_and_more.py +41 -0
lamindb/migrations/0088_schema_components.py +273 -0
lamindb/migrations/0088_squashed.py +4372 -0
lamindb/models.py +475 -168
{lamindb-1.0.5.dist-info → lamindb-1.1.1.dist-info}/METADATA +9 -7
lamindb-1.1.1.dist-info/RECORD +95 -0
lamindb/curators/_spatial.py +0 -528
lamindb/migrations/0052_squashed.py +0 -1261
lamindb/migrations/0053_alter_featureset_hash_alter_paramvalue_created_by_and_more.py +0 -57
lamindb/migrations/0054_alter_feature_previous_runs_and_more.py +0 -35
lamindb/migrations/0055_artifact_type_artifactparamvalue_and_more.py +0 -61
lamindb/migrations/0056_rename_ulabel_ref_is_name_artifactulabel_label_ref_is_name_and_more.py +0 -22
lamindb/migrations/0057_link_models_latest_report_and_others.py +0 -356
lamindb/migrations/0058_artifact__actions_collection__actions.py +0 -22
lamindb/migrations/0059_alter_artifact__accessor_alter_artifact__hash_type_and_more.py +0 -31
lamindb/migrations/0060_alter_artifact__actions.py +0 -22
lamindb/migrations/0061_alter_collection_meta_artifact_alter_run_environment_and_more.py +0 -45
lamindb/migrations/0062_add_is_latest_field.py +0 -32
lamindb/migrations/0063_populate_latest_field.py +0 -45
lamindb/migrations/0064_alter_artifact_version_alter_collection_version_and_more.py +0 -33
lamindb/migrations/0065_remove_collection_feature_sets_and_more.py +0 -22
lamindb/migrations/0066_alter_artifact__feature_values_and_more.py +0 -352
lamindb/migrations/0067_alter_featurevalue_unique_together_and_more.py +0 -20
lamindb/migrations/0068_alter_artifactulabel_unique_together_and_more.py +0 -20
lamindb/migrations/0069_alter_artifact__accessor_alter_artifact__hash_type_and_more.py +0 -1294
lamindb-1.0.5.dist-info/RECORD +0 -102
{lamindb-1.0.5.dist-info → lamindb-1.1.1.dist-info}/LICENSE +0 -0
{lamindb-1.0.5.dist-info → lamindb-1.1.1.dist-info}/WHEEL +0 -0

lamindb/migrations/0063_populate_latest_field.py DELETED Viewed

@@ -1,45 +0,0 @@
-# Generated by Django 5.2 on 2024-08-12 07:46
-from django.db import migrations
-SQL_TEMPLATE = """\
--- First, set all is_latest to False
-UPDATE {table_name} SET is_latest = false;
--- Then, set is_latest to True for the latest records
-UPDATE {table_name}
-SET is_latest = true
-WHERE id IN (
-    SELECT t.id
-    FROM {table_name} t
-    INNER JOIN (
-        SELECT substr(uid, 1, {stem_uid_len}) AS stem_uid, MAX(created_at) AS max_created_at
-        FROM {table_name}
-        GROUP BY substr(uid, 1, {stem_uid_len})
-    ) latest ON substr(t.uid, 1, {stem_uid_len}) = latest.stem_uid AND t.created_at = latest.max_created_at
-);
-"""
-class Migration(migrations.Migration):
-    dependencies = [
-        (
-            "lamindb",
-            "0062_add_is_latest_field",
-        ),
-    ]
-    operations = []  # type: ignore
-# add data migration
-for table_name, stem_uid_len in [
-    ("lamindb_transform", 12),
-    ("lamindb_artifact", 16),
-    ("lamindb_collection", 16),
-]:
-    Migration.operations.append(
-        migrations.RunSQL(
-            sql=SQL_TEMPLATE.format(table_name=table_name, stem_uid_len=stem_uid_len)
-        )
-    )

lamindb/migrations/0064_alter_artifact_version_alter_collection_version_and_more.py DELETED Viewed

@@ -1,33 +0,0 @@
-# Generated by Django 5.2 on 2024-08-28 16:09
-from django.db import migrations, models
-class Migration(migrations.Migration):
-    dependencies = [
-        ("lamindb", "0063_populate_latest_field"),
-    ]
-    operations = [
-        migrations.AlterField(
-            model_name="artifact",
-            name="version",
-            field=models.CharField(
-                db_index=True, default=None, max_length=30, null=True
-            ),
-        ),
-        migrations.AlterField(
-            model_name="collection",
-            name="version",
-            field=models.CharField(
-                db_index=True, default=None, max_length=30, null=True
-            ),
-        ),
-        migrations.AlterField(
-            model_name="transform",
-            name="version",
-            field=models.CharField(
-                db_index=True, default=None, max_length=30, null=True
-            ),
-        ),
-    ]

lamindb/migrations/0065_remove_collection_feature_sets_and_more.py DELETED Viewed

@@ -1,22 +0,0 @@
-# Generated by Django 5.2 on 2024-09-08 11:37
-from django.db import migrations
-class Migration(migrations.Migration):
-    dependencies = [
-        (
-            "lamindb",
-            "0064_alter_artifact_version_alter_collection_version_and_more",
-        ),
-    ]
-    operations = [
-        migrations.RemoveField(
-            model_name="collection",
-            name="feature_sets",
-        ),
-        migrations.DeleteModel(
-            name="CollectionFeatureSet",
-        ),
-    ]

lamindb/migrations/0066_alter_artifact__feature_values_and_more.py DELETED Viewed

@@ -1,352 +0,0 @@
-# Generated by Django 5.2 on 2024-09-09 07:52
-import django.db.models.deletion
-from django.db import migrations, models
-import lamindb.base.users
-import lamindb.models
-class Migration(migrations.Migration):
-    dependencies = [
-        ("lamindb", "0065_remove_collection_feature_sets_and_more"),
-    ]
-    operations = [
-        migrations.AlterField(
-            model_name="artifact",
-            name="_feature_values",
-            field=models.ManyToManyField(
-                related_name="artifacts",
-                through="lamindb.ArtifactFeatureValue",
-                to="lamindb.featurevalue",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="artifact",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="artifactfeatureset",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="artifactfeatureset",
-            name="run",
-            field=models.ForeignKey(
-                default=lamindb.models.current_run,
-                null=True,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="artifactfeaturevalue",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="artifactfeaturevalue",
-            name="run",
-            field=models.ForeignKey(
-                default=lamindb.models.current_run,
-                null=True,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="artifactulabel",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="artifactulabel",
-            name="run",
-            field=models.ForeignKey(
-                default=lamindb.models.current_run,
-                null=True,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="collection",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="collectionartifact",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="collectionartifact",
-            name="run",
-            field=models.ForeignKey(
-                default=lamindb.models.current_run,
-                null=True,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="collectionulabel",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="collectionulabel",
-            name="run",
-            field=models.ForeignKey(
-                default=lamindb.models.current_run,
-                null=True,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="feature",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="feature",
-            name="run",
-            field=models.ForeignKey(
-                default=lamindb.models.current_run,
-                null=True,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="featureset",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="featureset",
-            name="run",
-            field=models.ForeignKey(
-                default=lamindb.models.current_run,
-                null=True,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="featurevalue",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="featurevalue",
-            name="run",
-            field=models.ForeignKey(
-                default=lamindb.models.current_run,
-                null=True,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="param",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="param",
-            name="run",
-            field=models.ForeignKey(
-                default=lamindb.models.current_run,
-                null=True,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="storage",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="storage",
-            name="run",
-            field=models.ForeignKey(
-                default=lamindb.models.current_run,
-                null=True,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="ulabel",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="ulabel",
-            name="run",
-            field=models.ForeignKey(
-                default=lamindb.models.current_run,
-                null=True,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="artifact",
-            name="_previous_runs",
-            field=models.ManyToManyField(
-                related_name="_output_artifacts_with_later_updates",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="artifact",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="created_artifacts",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="collection",
-            name="_previous_runs",
-            field=models.ManyToManyField(
-                related_name="_output_collections_with_later_updates",
-                to="lamindb.run",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="featurevalue",
-            name="feature",
-            field=models.ForeignKey(
-                default=None,
-                null=True,
-                on_delete=django.db.models.deletion.CASCADE,
-                related_name="values",
-                to="lamindb.feature",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="paramvalue",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="+",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="paramvalue",
-            name="param",
-            field=models.ForeignKey(
-                on_delete=django.db.models.deletion.CASCADE,
-                related_name="values",
-                to="lamindb.param",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="run",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.CASCADE,
-                related_name="created_runs",
-                to="lamindb.user",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="transform",
-            name="created_by",
-            field=models.ForeignKey(
-                default=lamindb.base.users.current_user_id,
-                on_delete=django.db.models.deletion.PROTECT,
-                related_name="created_transforms",
-                to="lamindb.user",
-            ),
-        ),
-    ]

lamindb/migrations/0067_alter_featurevalue_unique_together_and_more.py DELETED Viewed

@@ -1,20 +0,0 @@
-# Generated by Django 5.1.1 on 2024-10-02 23:29
-from django.db import migrations
-class Migration(migrations.Migration):
-    dependencies = [
-        ("lamindb", "0066_alter_artifact__feature_values_and_more"),
-    ]
-    operations = [
-        migrations.AlterUniqueTogether(
-            name="featurevalue",
-            unique_together=set(),
-        ),
-        migrations.AlterUniqueTogether(
-            name="paramvalue",
-            unique_together=set(),
-        ),
-    ]

lamindb/migrations/0068_alter_artifactulabel_unique_together_and_more.py DELETED Viewed

@@ -1,20 +0,0 @@
-# Generated by Django 5.1.1 on 2024-10-18 14:31
-from django.db import migrations
-class Migration(migrations.Migration):
-    dependencies = [
-        ("lamindb", "0067_alter_featurevalue_unique_together_and_more"),
-    ]
-    operations = [
-        migrations.AlterUniqueTogether(
-            name="artifactulabel",
-            unique_together={("artifact", "ulabel", "feature")},
-        ),
-        migrations.AlterUniqueTogether(
-            name="featuresetfeature",
-            unique_together={("featureset", "feature")},
-        ),
-    ]

lamindb 1.0.5__py3-none-any.whl → 1.1.1__py3-none-any.whl

lamindb 1.0.5py3-none-any.whl → 1.1.1py3-none-any.whl