lamindb 0.45.0__py3-none-any.whl → 0.46a1__py3-none-any.whl

lamindb/dev/storage/{_file.py → file.py}

@@ -6,11 +6,11 @@ from typing import Union
 import anndata as ad
 import fsspec
 import pandas as pd
+from lamin_logger import logger
 from lamindb_setup import settings
+from lamindb_setup.dev import StorageSettings
 from lamindb_setup.dev.upath import UPath, infer_filesystem
-from lnschema_core.models import File
-
-from lamindb._file_access import attempt_accessing_path
+from lnschema_core.models import File, Storage
 
 try:
     from ._zarr import read_adata_zarr
@@ -20,6 +20,51 @@ except ImportError:
         raise ImportError("Please install zarr: pip install zarr")
 
 
+AUTO_KEY_PREFIX = ".lamindb/"
+
+
+# add type annotations back asap when re-organizing the module
+def auto_storage_key_from_file(file: File):
+    if file.key is None:
+        return f"{AUTO_KEY_PREFIX}{file.id}{file.suffix}"
+    else:
+        return file.key
+
+
+def attempt_accessing_path(file: File, storage_key: str):
+    if file.storage_id == settings.storage.id:
+        path = settings.storage.key_to_filepath(storage_key)
+    else:
+        logger.warning(
+            "file.path() is slower for files outside the currently configured storage"
+            " location"
+        )
+        storage = Storage.select(id=file.storage_id).one()
+        # find a better way than passing None to instance_settings in the future!
+        storage_settings = StorageSettings(storage.root, instance_settings=None)
+        path = storage_settings.key_to_filepath(storage_key)
+    # the following is for backward compat
+    if storage_key.startswith(AUTO_KEY_PREFIX) and not path.exists():
+        logger.warning(
+            "You have auto-keyed files in your storage root, please move them into"
+            f" {AUTO_KEY_PREFIX} within your storage location"
+        )
+        # try legacy_storage_key in root
+        for previous_prefix in ["", "lndb/"]:
+            legacy_storage_key = storage_key.replace(AUTO_KEY_PREFIX, previous_prefix)
+            path = settings.storage.key_to_filepath(legacy_storage_key)
+            if path.exists():
+                return path
+    return path
+
+
+# add type annotations back asap when re-organizing the module
+def filepath_from_file(file: File):
+    storage_key = auto_storage_key_from_file(file)
+    path = attempt_accessing_path(file, storage_key)
+    return path
+
+
 def read_adata_h5ad(filepath, **kwargs) -> ad.AnnData:
     fs, filepath = infer_filesystem(filepath)
 

lamindb/dev/storage/{_object.py → object.py}

@@ -9,6 +9,7 @@ def infer_suffix(dmem, adata_format: Optional[str] = None):
     """Infer LaminDB storage file suffix from a data object."""
     if isinstance(dmem, AnnData):
         if adata_format is not None:
+            # below should be zrad, not zarr
             if adata_format not in ("h5ad", "zarr"):
                 raise ValueError
             return "." + adata_format

lamindb/dev/utils.py

@@ -0,0 +1,9 @@
+def attach_func_to_class_method(func_name, cls, globals):
+    implementation = globals[func_name]
+    target = getattr(cls, func_name)
+    # assigning the original class definition docstring
+    # to the implementation only has an effect for regular methods
+    # not for class methods
+    # this is why we need @doc_args for class methods
+    implementation.__doc__ = target.__doc__
+    setattr(cls, func_name, implementation)

lamindb/types.py

@@ -5,6 +5,14 @@
 
    PathLike
    DataLike
+   StrField
+   ListLike
    TransformType
 """
-from lnschema_core.types import DataLike, PathLike, TransformType  # noqa
+from lnschema_core.types import (  # noqa
+    DataLike,
+    ListLike,
+    PathLike,
+    StrField,
+    TransformType,
+)

{lamindb-0.45.0.dist-info → lamindb-0.46a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.45.0
+Version: 0.46a1
 Summary: LaminDB: Manage R&D data & analyses.
 Author-email: Lamin Labs <laminlabs@gmail.com>
 Requires-Python: >=3.8
@@ -8,9 +8,9 @@ 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==0.36.1
-Requires-Dist: lamindb_setup==0.47.11
-Requires-Dist: lamin_logger==0.7.1
+Requires-Dist: lnschema_core==0.38.0
+Requires-Dist: lamindb_setup==0.48.1
+Requires-Dist: lamin_logger==0.7.4
 Requires-Dist: erdiagram>=0.1.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pydantic[dotenv]
@@ -24,7 +24,7 @@ Requires-Dist: pandas
 Requires-Dist: botocore==1.29.76 ; extra == "aws"
 Requires-Dist: boto3==1.26.76 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.5.0 ; extra == "aws"
-Requires-Dist: lnschema_bionty==0.24.0 ; extra == "bionty"
+Requires-Dist: lnschema_bionty==0.25.5 ; extra == "bionty"
 Requires-Dist: readfcs>=1.1.3 ; extra == "fcs"
 Requires-Dist: fsspec[gs]==2023.5.0 ; extra == "gcp"
 Requires-Dist: nbproject>=0.9.0 ; extra == "jupyter"
@@ -57,7 +57,9 @@ Provides-Extra: zarr
 
 # LaminDB
 
-Open-source data lake to manage your existing data in your existing infrastructure.
+Open-source data lake, warehouse & feature store for biology.
+
+Manage your existing data & analyses in your existing infrastructure.
 
 ```{warning}
 
@@ -69,21 +71,22 @@ Update 2023-06-14:
 - The last version before the migration is 0.41.2.
 ```
 
-## Features
+## What?
 
-Free:
+LaminDB is a free & open-source Python library allowing you to:
 
-- Track [data lineage](https://lamin.ai/docs/guide/data-lineage) across notebooks, pipelines & apps.
-- Manage [biological registries, ontologies & features](https://lamin.ai/docs/biology/registries).
-- [Query, search & look up anything](https://lamin.ai/docs/guide/select), [manage & migrate custom schemas](https://lamin.ai/docs/setup/migrate).
-- [Persist, load](https://lamin.ai/docs/guide/files-records#in-memory-objects) & [stream data objects](https://lamin.ai/docs/guide/stream) with a single line of code.
-- [Idempotent](https://lamin.ai/docs/faq/idempotency) and [ACID](https://lamin.ai/docs/faq/acid) operations.
-- Use a mesh of LaminDB instances and [share them in a hub](https://lamin.ai/laminlabs) akin to GitHub.
+- Manage files & datasets while tracking [provenance](https://lamin.ai/docs/guide/data-lineage) across pipelines, notebooks & apps.
+- Manage biological [registries](https://lamin.ai/docs/biology/registries), [ontologies](https://lamin.ai/docs/bionty/) & features.
+- Rely on integrity & quality through largely automated data validation and [idempotent](https://lamin.ai/docs/faq/idempotency) & [ACID](https://lamin.ai/docs/faq/acid) operations.
+- Use a simple API for common tasks like:
+  - [Queries, searches & look ups](https://lamin.ai/docs/guide/select).
+  - Saving, loading & [streaming](https://lamin.ai/docs/guide/stream) of data objects.
+- Collaborate across a mesh of LaminDB instances ([share them in a hub](https://lamin.ai/laminlabs) akin to GitHub).
 
-Enterprise:
+You can combine LaminDB with LaminApp & consulting services on an enterprise plan:
 
-- Explore, share data & submit samples with LaminApp (deployable in your infrastructure).
-- Receive support, code templates & services for a BioTech data & analytics platform.
+- LaminApp: Explore & collaborate on data in a UI (deployable in your infrastructure).
+- Services: Support & code templates for a BioTech data & analytics platform.
 
 ## Usage overview
 

lamindb-0.46a1.dist-info/RECORD

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+lamindb/_file.py,sha256=AR4EVjHnF-vnGxC_101ms1DGbK8NEwHeLNue0S14FFg,24407
+lamindb/_from_values.py,sha256=vbxTujbmmX6zSTBhOwrt6k-VGgA-QGAtjvYbzqEHNnw,8188
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