lamindb 0.49.3__py3-none-any.whl → 0.50.1__py3-none-any.whl

{lamindb-0.49.3.dist-info → lamindb-0.50.1.dist-info}/METADATA

@@ -1,16 +1,16 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.49.3
-Summary: Open-source data lake & feature store for biology.
+Version: 0.50.1
+Summary: Open-source data platform for biology.
 Author-email: Lamin Labs <laminlabs@gmail.com>
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
-Requires-Dist: lnschema_core==0.43.3
-Requires-Dist: lamindb_setup==0.49.4
-Requires-Dist: lamin_utils==0.9.3
+Requires-Dist: lnschema_core==0.44.3
+Requires-Dist: lamindb_setup==0.49.6
+Requires-Dist: lamin_utils==0.9.6
 Requires-Dist: erdiagram>=0.1.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pydantic[dotenv]
@@ -24,7 +24,7 @@ Requires-Dist: botocore==1.29.76 ; extra == "aws"
 Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: boto3==1.26.76 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.5.0 ; extra == "aws"
-Requires-Dist: lnschema_bionty==0.29.0 ; extra == "bionty"
+Requires-Dist: lnschema_bionty==0.29.2 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"
@@ -39,7 +39,7 @@ Requires-Dist: fsspec[gs]==2023.5.0 ; extra == "gcp"
 Requires-Dist: nbproject==0.9.0 ; extra == "jupyter"
 Requires-Dist: nbproject==0.9.0 ; extra == "nbproject"
 Requires-Dist: psycopg2-binary ; extra == "postgres"
-Requires-Dist: zarr ; extra == "zarr"
+Requires-Dist: zarr>=2.16.0 ; extra == "zarr"
 Project-URL: Home, https://github.com/laminlabs/lamindb
 Provides-Extra: aws
 Provides-Extra: bionty
@@ -58,27 +58,27 @@ Provides-Extra: zarr
 
 # LaminDB
 
-Open-source data lake & feature store for biology.
+Open-source data platform for biology.
 
 ```{warning}
 
-Public beta: Currently only recommended for collaborators as we still make breaking changes.
+Public beta: Close to having converged a stable API, but some breaking changes might still occur.
 
-Update 2023-06-14:
-
-- We completed a major migration from SQLAlchemy/SQLModel to Django, available in 0.42.0.
-- The last version before the migration is 0.41.2.
 ```
 
 ## Introduction
 
-LaminDB is an open-source Python library to:
+LaminDB is an open-source Python library to manage files & datasets while
+
+- tracking provenance across pipelines, notebooks & app uploads
+- validating & linking data batches using biological registries & ontologies
+
+You can
 
-- Manage files & datasets while tracking provenance across pipelines, notebooks & app uploads.
-- Manage biological registries, ontologies, features & schemas.
-- Enhance integrity through built-in data validation and [idempotent](https://lamin.ai/docs/faq/idempotency), [ACID](https://lamin.ai/docs/faq/acid) operations.
+- Manage features & labels schema-less or schema-full.
 - Query, search, look up, save, load and stream with one API.
 - Collaborate across a mesh of LaminDB instances.
+- Enjoy [idempotent](https://lamin.ai/docs/faq/idempotency) & [ACID](https://lamin.ai/docs/faq/acid) operations.
 
 LaminApp is a data management app built on LaminDB. If LaminDB ~ git, LaminApp ~ GitHub.
 
@@ -101,17 +101,22 @@ import lamindb as ln
 # import lnschema_bionty as lb # optional, for bionty schema
 ```
 
-### Manage data objects
+### Manage files and data objects
 
 ```python
-# Store a DataFrame object
+# Store and register a file
+ln.File("s3://my-bucket/images/image001.jpg").save()  # or a local path
+
+# Store and register a DataFrame object
 df = pd.DataFrame({"feat1": [1, 2], "feat2": [3, 4]})  # AnnData works, too
 ln.File(df, description="Data batch 1").save()  # create a File object and save/upload it
 
 # To find it, if you don't have specific metadata in mind, run a search
 ln.File.search("batch 1")
-# Or filter (under-the-hood, you have the full power of SQL to query)
+# Or query (under-the-hood, you have the full power of SQL to query)
 file = ln.File.filter(description="Data batch 1").one()  # get exactly one result
+# Query by `key` (the relative path within your storage)
+ln.File.filter(key__startswith="images/").df()  # get query results as a DataFrame
 
 # Load a file back into memory
 df = file.load()
@@ -119,27 +124,19 @@ df = file.load()
 backed = file.backed()  # currently works for AnnData, zarr, HDF5, not yet for DataFrame
 ```
 
-### Manage files
-
-```python
-# Store a file
-file = ln.File("s3://my-bucket/images/image001.jpg")  # or a local path
-file.save()  # register the file
-
-# Query by `key` (the relative path within your storage) and load into memory
-file.filter(key__startswith="images/").df()  # all files in folder "images/" in default storage
-```
-
 ### Auto-complete categoricals and search
 
 ```python
-# When you're unsure about spellings, use a lookup object:
-users = ln.User.lookup()
+# When you're unsure about spellings, use a lookup object
+users = ln.User.lookup() # by default uses handle field
 ln.File.filter(created_by=users.lizlemon)
+users = ln.User.lookup("name") # a lookup object of the name field
+users.liz_lemon
 
 # Or search
-ln.User.search("liz lemon", field="name")
+ln.User.search("liz lemon") # by default searches the handle field
 user = ln.User.search("liz lemon", return_queryset=True).first() # grab the top search result as a record
+ln.User.search("liz lemon", field=["name", "handle"]) # search against multiple fields
 ```
 
 ### Track & query data lineage
@@ -161,11 +158,12 @@ file.view_lineage()
 Track a Jupyter Notebook:
 
 ```python
+# my-analysis.ipynb
 ln.track()  # auto-detect & save notebook metadata
 ln.File("my_artifact.parquet").save()  # this file is now aware that it was saved in this notebook
 ```
 
-When you query the file, later on, you'll know from which notebook it came:
+When you query the file, later on, you'll know which notebook it came from:
 
 ```python
 file = ln.File.filter(description="my_artifact.parquet").one()  # query for a file
@@ -314,7 +312,7 @@ We do _not_ store any of your data, but only basic metadata about you (email add
 
 LaminDB builds semantics of R&D and biology onto well-established tools:
 
-- SQLite & Postgres for SQL databases using Django ORM (previously: SQLModel)
+- SQLite & Postgres for SQL databases using Django Registry (previously: SQLModel)
 - S3, GCP & local storage for object storage using fsspec
 - Configurable storage formats: pyarrow, anndata, zarr, etc.
 - Biological knowledge sources & ontologies: see [Bionty](https://lamin.ai/docs/bionty)

lamindb-0.50.1.dist-info/RECORD

@@ -0,0 +1,47 @@
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+lamindb/_delete.py,sha256=jvzDM_hbraBvOMhulibRziyDhoM1mqIX_MSLeC42c1M,1917
+lamindb/_feature.py,sha256=B3U9q-v_Bu9o3xrl2ScYefMEkNnDrlWpLzL4sdN4izQ,5479
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+lamindb/_filter.py,sha256=Rf5RSkglIhJhSdk3AIPfc83F5NIfZrdCZDpgcYNj5KY,351
+lamindb/_from_values.py,sha256=mezvC4d_b8ndRF8NNPl1vEj3O70qLv92b9ZjII5Qa3E,10532
+lamindb/_label.py,sha256=-gLa8WvD1mycruDEB67Zx_oewhO85KvOwVZ3SsKvSvs,1544
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+lamindb/_registry.py,sha256=Jd0qb9sK1CO8ONMSN8MnF9UYofd-vvM1XszJQvNETNA,16486
+lamindb/_save.py,sha256=jC2a9JzQBZYVHHuq6NyIovFQI1Y6WT1q2C1dfiXKv_E,9216
+lamindb/_storage.py,sha256=a0ofo106NHNY2RBF3MB1PeeONZMc28aHFG2fbndn_80,246
+lamindb/_synonym.py,sha256=I7qL57F5a_Z3a_5hVIQKz5w55HGKEpgpBY9s-35Bg80,5870
+lamindb/_transform.py,sha256=K-Y37UqQPu06lsA3Jfnkyt5dssRpuMnpCDDHDbT40Z4,1251
+lamindb/_validate.py,sha256=W374jmKFvAy1wIfibz-C4sftxxtlWVwBHliIBy_YD1w,3606
+lamindb/_view.py,sha256=dxZ7BPrMAf0rJ8aKSprkQiO1O2OJsjtSaHBJfpKvVT4,2187
+lamindb/types.py,sha256=svg5S_aynuGfbEOsbmqkR_gF9d9YMzfOkcvGN37Rzvg,232
+lamindb/dev/__init__.py,sha256=K8cgi474J2uIxbnQZeeeMrsDcWIPdsRXwjIrWcJ_qaQ,656
+lamindb/dev/_data.py,sha256=M5AGGCAvw7e_cDooAWA8_hUQFjxAC62QPs-vEQFqpD4,7806
+lamindb/dev/_feature_manager.py,sha256=laJRqKiL8Qlm5Jq60RoXXX6xYwgyL2MPd6OgS8eXs6A,3526
+lamindb/dev/_settings.py,sha256=WLweWZNAvBquybQYUlYyIehIlv3t5llgYhyNpL0obdg,2926
+lamindb/dev/_view_parents.py,sha256=pF0qTZirLwzgWFtqzRe-KksqASHjpFWLRkNK-0GsyGU,8590
+lamindb/dev/exc.py,sha256=xJ0QCeineZccjYKq-W-RXhU6fJH6JyFLtDyHKZTOoyU,96
+lamindb/dev/hashing.py,sha256=oYHDSEjINsmDYgCLasnhh_VHbB1dLag27ufVUwDgLyQ,1385
+lamindb/dev/utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
+lamindb/dev/datasets/__init__.py,sha256=0ObE_PmGsxOaCvMYZYkLQLo7zYD6Hr17Ixh53A-jqNs,1310
+lamindb/dev/datasets/_core.py,sha256=6GsgLPavWQPI0K7EIKJ5xq9JXKIxiF1ZNf_1GOABvD0,12426
+lamindb/dev/datasets/_fake.py,sha256=S8mNho-oSh1M9x9oOSsUBLLHmBAegsOLlFk6LnF81EA,942
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+lamindb/dev/storage/_anndata_sizes.py,sha256=0XVzA6AQeVGPaGPrhGusKyxFgFjeo3qSN29hxb8D5E8,993
+lamindb/dev/storage/_backed_access.py,sha256=PSyVDGwkaZ1xpo0JJXSQS0HJyR72QIec2hiuvlMIVBY,20126
+lamindb/dev/storage/_zarr.py,sha256=7W1Jos1QOOF3f41uML_arQoDTNPZVpRyP2m3SLWaCAo,2766
+lamindb/dev/storage/file.py,sha256=-pWYLfS5HDyAX-KyomyHnngmTX8PaD2WRs1zIbsrjs4,6988
+lamindb/dev/storage/object.py,sha256=x8sy23WqkGir2sg2c3AngQPgv0RbErEA6cpvVN0Zc4I,945
+lamindb/schema/__init__.py,sha256=PznznlFvbeNSZKpn1RS6Gv0JMXFkLmU2_ej_1hVLSTs,796
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+lamindb/setup/__init__.py,sha256=8-0F2C4Glx23-b8-D_1CBGgRBM5PppVhazhoXZYOLsg,275
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+lamindb-0.50.1.dist-info/entry_points.txt,sha256=MioM8vSpKwXxY3geNBwjo1wnwy1l15WjJYlI3lpKuZI,53
+lamindb-0.50.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.50.1.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.50.1.dist-info/METADATA,sha256=It6LNQR9QYgxitisJK1KcWhRfDhOq5CkcLpqpDhjLuY,12570
+lamindb-0.50.1.dist-info/RECORD,,

lamindb/_feature_manager.py

@@ -1,237 +0,0 @@
-from collections import defaultdict
-from typing import Dict, List, Optional, Union
-
-import pandas as pd
-from lamin_utils import logger
-from lnschema_core.models import ORM, Dataset, Feature, FeatureSet, File, Label
-
-from ._queryset import QuerySet
-from ._save import save
-
-
-def validate_and_cast_feature(
-    feature: Union[str, Feature], records: List[ORM]
-) -> Feature:
-    if isinstance(feature, str):
-        feature_name = feature
-        feature = Feature.filter(name=feature_name).one_or_none()
-        if feature is None:
-            orm_types = set([record.__class__ for record in records])
-            feature = Feature(
-                name=feature_name, type="category", registries=list(orm_types)
-            )
-            logger.warning(f"Created & saved: {feature}")
-            feature.save()
-    return feature
-
-
-def create_features_df(
-    file: File, feature_sets: List[FeatureSet], exclude: bool = True
-):
-    features = []
-    for feature_set in feature_sets:
-        if exclude:
-            features_df = feature_set.features.exclude(registries__isnull=True).df()
-        else:
-            features_df = feature_set.features.df()
-        slots = file.feature_sets.through.objects.filter(
-            file=file, feature_set=feature_set
-        ).list("slot")
-        for slot in slots:
-            features_df["slot"] = slot
-            features.append(features_df)
-    features_df = pd.concat(features)
-    return features_df.sort_values(["slot", "registries"])
-
-
-def get_accessor_by_orm(host: Union[File, Dataset]) -> Dict:
-    dictionary = {
-        field.related_model.__get_name_with_schema__(): field.name
-        for field in host._meta.related_objects
-    }
-    dictionary["core.Feature"] = "features"
-    dictionary["core.Label"] = "labels"
-    return dictionary
-
-
-def get_feature_set_by_slot(host) -> Dict:
-    feature_set_links = host.feature_sets.through.objects.filter(file_id=host.id)
-    return {
-        feature_set_link.slot: FeatureSet.objects.get(
-            id=feature_set_link.feature_set_id
-        )
-        for feature_set_link in feature_set_links
-    }
-
-
-class FeatureManager:
-    """Feature manager."""
-
-    def __init__(self, host: Union[File, Dataset]):
-        self._host = host
-        self._feature_set_by_slot = get_feature_set_by_slot(host)
-        self._accessor_by_orm = get_accessor_by_orm(host)
-
-    def __repr__(self) -> str:
-        if len(self._feature_set_by_slot) > 0:
-            msg = "slots:\n"
-            for slot, feature_set in self._feature_set_by_slot.items():
-                msg += f"    {slot}: {feature_set}\n"
-            return msg
-        else:
-            return "No linked features."
-
-    def __getitem__(self, slot) -> QuerySet:
-        feature_set = self._feature_set_by_slot[slot]
-        orm_name = ".".join(feature_set.ref_field.split(".")[:2])
-        return getattr(feature_set, self._accessor_by_orm[orm_name]).all()
-
-    def get_labels(
-        self,
-        feature: Optional[Union[str, ORM]] = None,
-        mute: bool = False,
-        flat_names: bool = False,
-    ) -> Union[QuerySet, Dict[str, QuerySet], List]:
-        """Get labels given a feature."""
-        if isinstance(feature, str):
-            feature_name = feature
-            feature = Feature.filter(name=feature_name).one_or_none()
-            if feature is None:
-                raise ValueError("Feature doesn't exist")
-        if feature.registries is None:
-            raise ValueError("Feature does not have linked labels")
-        registries_to_check = feature.registries.split("|")
-        if len(registries_to_check) > 1 and not mute:
-            logger.warning("Labels come from multiple registries!")
-        qs_by_registry = {}
-        for registry in registries_to_check:
-            # currently need to distinguish between Label and non-Label, because
-            # we only have the feature information for Label
-            if registry == "core.Label":
-                links_to_labels = getattr(
-                    self._host, self._accessor_by_orm[registry]
-                ).through.objects.filter(file_id=self._host.id, feature_id=feature.id)
-                label_ids = [link.label_id for link in links_to_labels]
-                qs_by_registry[registry] = Label.objects.filter(id__in=label_ids)
-            else:
-                qs_by_registry[registry] = getattr(
-                    self._host, self._accessor_by_orm[registry]
-                ).all()
-        if flat_names:
-            # returns a flat list of names
-            from ._orm import get_default_str_field
-
-            values = []
-            for v in qs_by_registry.values():
-                values += v.list(get_default_str_field(v))
-            return values
-        if len(registries_to_check) == 1:
-            return qs_by_registry[registry]
-        else:
-            return qs_by_registry
-
-    def add_labels(
-        self,
-        records: Union[ORM, List[ORM], QuerySet],
-        feature: Optional[Union[str, ORM]] = None,
-    ) -> None:
-        """Add one or several labels and associate them with a feature."""
-        if isinstance(records, (QuerySet, QuerySet.__base__)):  # need to have both
-            records = records.list()
-        if isinstance(records, str) or not isinstance(records, List):
-            records = [records]
-        if isinstance(records[0], str):  # type: ignore
-            raise ValueError(
-                "Please pass a record (an ORM object), not a string, e.g., via: label"
-                f" = ln.Label(name='{records[0]}')"  # type: ignore
-            )
-        if self._host._state.adding:
-            raise ValueError("Please save the file or dataset before adding a label!")
-        feature = validate_and_cast_feature(feature, records)
-        records_by_feature_orm = defaultdict(list)
-        for record in records:
-            if feature is None:
-                error_msg = (
-                    "Please pass feature: add_labels(labels, feature='myfeature')"
-                )
-                record_feature = feature
-                if hasattr(record, "_feature"):
-                    record_feature = record._feature
-                if record_feature is None:
-                    raise ValueError(error_msg)
-                # TODO: refactor so that we don't call the following line
-                # repeatedly for the same feature
-                record_feature = validate_and_cast_feature(record_feature, [record])
-            else:
-                record_feature = feature
-            records_by_feature_orm[
-                (record_feature, record.__class__.__get_name_with_schema__())
-            ].append(record)
-        # ensure all labels are saved
-        save(records)
-        for (feature, orm_name), records in records_by_feature_orm.items():
-            getattr(self._host, self._accessor_by_orm[orm_name]).add(
-                *records, through_defaults={"feature_id": feature.id}
-            )
-        feature_set_links = self._host.feature_sets.through.objects.filter(
-            file_id=self._host.id
-        )
-        feature_set_ids = [link.feature_set_id for link in feature_set_links.all()]
-        # get all linked features of type Feature
-        feature_sets = FeatureSet.filter(id__in=feature_set_ids).all()
-        linked_features_by_slot = {
-            feature_set_links.filter(feature_set_id=feature_set.id)
-            .one()
-            .slot: feature_set.features.all()
-            for feature_set in feature_sets
-            if "core.Feature" in feature_set.ref_field
-        }
-        for (feature, orm_name), records in records_by_feature_orm.items():
-            feature = validate_and_cast_feature(feature, records)
-            logger.info(f"Linking feature {feature.name} to {orm_name}")
-            if feature.registries is None:
-                feature.registries = orm_name
-            elif orm_name not in feature.registries:
-                feature.registries += f"|{orm_name}"
-            feature.save()
-            # check whether we have to update the feature set that manages labels
-            # (Feature) to account for a new feature
-            found_feature = False
-            for _, linked_features in linked_features_by_slot.items():
-                if feature in linked_features:
-                    found_feature = True
-            if not found_feature:
-                if "ext" not in linked_features_by_slot:
-                    logger.info("Creating feature_set for slot 'ext' (external)")
-                    feature_set = FeatureSet([feature], modality="meta")
-                    feature_set.save()
-                    self.add_feature_set(feature_set, slot="ext")
-                else:
-                    feature_set = self._feature_set_by_slot["ext"]
-                    logger.info(
-                        f"Linking feature {feature.name} to feature set {feature_set}"
-                    )
-                    feature_set.features.add(feature)
-                    feature_set.n += 1
-                    feature_set.save()
-
-    def add_feature_set(self, feature_set: FeatureSet, slot: str):
-        """Add new feature set to a slot.
-
-        Args:
-            feature_set: `FeatureSet` A feature set object.
-            slot: `str` The access slot.
-        """
-        if self._host._state.adding:
-            raise ValueError(
-                "Please save the file or dataset before adding a feature set!"
-            )
-        feature_set.save()
-        link_record = self._host.feature_sets.through.objects.filter(
-            file=self._host, feature_set=feature_set, slot=slot
-        ).one_or_none()
-        if link_record is None:
-            self._host.feature_sets.through(
-                file=self._host, feature_set=feature_set, slot=slot
-            ).save()
-            self._feature_set_by_slot[slot] = feature_set

lamindb-0.49.3.dist-info/RECORD

@@ -1,43 +0,0 @@
-lamindb/__init__.py,sha256=WlX04-h-0nICmekfxd0IZdSzqnM6kBiYApNvsY7RDFw,2712
-lamindb/_context.py,sha256=RhzZXlfiNS4JRjTrVfZKSCM9lSl-PSzOFWSyYR-wU7c,17837
-lamindb/_dataset.py,sha256=w5Byx-9IwVsi2rZx1lKy-HuxTHq3f_Q-MF7t3zb0Msw,4884
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