lamindb 0.70.0__tar.gz → 0.70.1__tar.gz

{lamindb-0.70.0 → lamindb-0.70.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.70.0
+Version: 0.70.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,7 +9,7 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.65.0
+Requires-Dist: lnschema_core==0.65.1
 Requires-Dist: lamindb_setup==0.69.2
 Requires-Dist: lamin_utils==0.13.1
 Requires-Dist: lamin_cli==0.12.3
@@ -27,7 +27,7 @@ Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: aiobotocore[boto3]>=2.5.4,<3.0.0 ; extra == "aws"
 Requires-Dist: s3fs==2023.12.2 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.12.2 ; extra == "aws"
-Requires-Dist: bionty==0.42.8 ; extra == "bionty"
+Requires-Dist: bionty==0.42.9 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"

{lamindb-0.70.0 → lamindb-0.70.1}/docs/changelog.md

@@ -14,6 +14,10 @@ When upgrading your LaminDB installation to a new `minor` version in `major.mino
 
 ## 0.70
 
+### 0.70.1 {small}`2024-04-18`
+
+- 🚑️ Fix public_source in inspect [PR](https://github.com/laminlabs/lamindb/pull/1578) [@sunnyosun](https://github.com/sunnyosun)
+
 ### 0.70.0 {small}`2024-04-17`
 
 - 🚸 Update data source in case transform is re-run [PR](https://github.com/laminlabs/lamindb/pull/1571) [@falexwolf](https://github.com/falexwolf)

{lamindb-0.70.0 → lamindb-0.70.1}/docs/introduction.ipynb

@@ -675,7 +675,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# if it's small enough, you can load the entire collection into memory as if it was one\n",

{lamindb-0.70.0 → lamindb-0.70.1}/docs/storage/add-replace-stage.ipynb

@@ -37,7 +37,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "AUTO_KEY_PREFIX = ln.core.storage.file.AUTO_KEY_PREFIX\n",
+    "AUTO_KEY_PREFIX = ln.core.storage.paths.AUTO_KEY_PREFIX\n",
     "root = ln.settings.storage"
    ]
   },

{lamindb-0.70.0 → lamindb-0.70.1}/lamindb/__init__.py

@@ -40,7 +40,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.70.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.70.1"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

{lamindb-0.70.0 → lamindb-0.70.1}/lamindb/_artifact.py

@@ -37,7 +37,7 @@ from lamindb.core.storage import (
     size_adata,
     write_to_file,
 )
-from lamindb.core.storage.file import (
+from lamindb.core.storage.paths import (
     auto_storage_key_from_artifact,
     auto_storage_key_from_artifact_uid,
     filepath_from_artifact,
@@ -50,8 +50,8 @@ from .core._data import (
     save_feature_set_links,
     save_feature_sets,
 )
-from .core.storage.file import AUTO_KEY_PREFIX
-from .core.storage.object import _mudata_is_installed
+from .core.storage.objects import _mudata_is_installed
+from .core.storage.paths import AUTO_KEY_PREFIX
 
 if TYPE_CHECKING:
     from lamindb_setup.core.types import UPathStr
@@ -167,7 +167,7 @@ def process_data(
         # Alex: I don't understand the line below
         if path.suffixes == []:
             path = path.with_suffix(suffix)
-        if suffix not in {".zarr", ".zrad"}:
+        if suffix != ".zarr":
             write_to_file(data, path)
         use_existing_storage_key = False
     else:
@@ -188,11 +188,7 @@ def get_stat_or_artifact(
     n_objects = None
     if settings.upon_file_create_skip_size_hash:
         return None, None, None, n_objects
-    if (
-        suffix in {".zarr", ".zrad"}
-        and memory_rep is not None
-        and isinstance(memory_rep, AnnData)
-    ):
+    if suffix == ".zarr" and memory_rep is not None and isinstance(memory_rep, AnnData):
         size = size_adata(memory_rep)
         return size, None, None, n_objects
     stat = path.stat()  # one network request
@@ -450,7 +446,12 @@ def data_is_anndata(data: AnnData | UPathStr):
     if isinstance(data, AnnData):
         return True
     if isinstance(data, (str, Path, UPath)):
-        return Path(data).suffix in {".h5ad", ".zrad"}
+        if Path(data).suffix == ".h5ad":
+            return True
+        elif Path(data).suffix == ".zarr":
+            raise NotImplementedError(
+                "auto-detecting AnnData from Zarr is not yet supported"
+            )
     return False
 
 
@@ -832,7 +833,7 @@ def replace(
 
 # docstring handled through attach_func_to_class_method
 def backed(self, is_run_input: bool | None = None) -> AnnDataAccessor | BackedAccessor:
-    suffixes = (".h5", ".hdf5", ".h5ad", ".zrad", ".zarr")
+    suffixes = (".h5", ".hdf5", ".h5ad", ".zarr")
     if self.suffix not in suffixes:
         raise ValueError(
             "Artifact should have a zarr or h5 object as the underlying data, please"

{lamindb-0.70.0 → lamindb-0.70.1}/lamindb/_can_validate.py

@@ -30,6 +30,7 @@ def inspect(
     *,
     mute: bool = False,
     organism: str | Registry | None = None,
+    public_source: Registry | None = None,
 ) -> InspectResult:
     """{}."""
     return _inspect(
@@ -38,6 +39,7 @@ def inspect(
         field=field,
         mute=mute,
         organism=organism,
+        public_source=public_source,
     )
 
 
@@ -63,6 +65,7 @@ def _inspect(
     mute: bool = False,
     using_key: str | None = None,
     organism: str | Registry | None = None,
+    public_source: Registry | None = None,
 ) -> pd.DataFrame | dict[str, list[str]]:
     """{}."""
     from lamin_utils._inspect import inspect
@@ -86,9 +89,9 @@ def _inspect(
 
     if len(nonval) > 0 and orm.__get_schema_name__() == "bionty":
         try:
-            bionty_result = orm.public(organism=organism).inspect(
-                values=nonval, field=field, mute=True
-            )
+            bionty_result = orm.public(
+                organism=organism, public_source=public_source
+            ).inspect(values=nonval, field=field, mute=True)
             bionty_validated = bionty_result.validated
             bionty_mapper = bionty_result.synonyms_mapper
             hint = False

{lamindb-0.70.0 → lamindb-0.70.1}/lamindb/_collection.py

@@ -234,7 +234,7 @@ def mapped(
 ) -> MappedCollection:
     path_list = []
     for artifact in self.artifacts.all():
-        if artifact.suffix not in {".h5ad", ".zrad", ".zarr"}:
+        if artifact.suffix not in {".h5ad", ".zarr"}:
             logger.warning(f"Ignoring artifact with suffix {artifact.suffix}")
             continue
         elif not stream:

{lamindb-0.70.0 → lamindb-0.70.1}/lamindb/_from_values.py

@@ -21,6 +21,7 @@ def get_or_create_records(
     from_public: bool = False,
     organism: Registry | str | None = None,
     public_source: Registry | None = None,
+    mute: bool = False,
 ) -> list[Registry]:
     """Get or create records from iterables."""
     upon_create_search_names = settings.upon_create_search_names
@@ -38,14 +39,18 @@ def get_or_create_records(
 
         # returns existing records & non-existing values
         records, nonexist_values, msg = get_existing_records(
-            iterable_idx=iterable_idx, field=field, **kwargs
+            iterable_idx=iterable_idx, field=field, mute=mute, **kwargs
         )
 
         # new records to be created based on new values
         if len(nonexist_values) > 0:
             if from_public:
                 records_bionty, unmapped_values = create_records_from_public(
-                    iterable_idx=nonexist_values, field=field, msg=msg, **kwargs
+                    iterable_idx=nonexist_values,
+                    field=field,
+                    msg=msg,
+                    mute=mute,
+                    **kwargs,
                 )
                 if len(records_bionty) > 0:
                     msg = ""
@@ -56,16 +61,17 @@ def get_or_create_records(
                 unmapped_values = nonexist_values
             # unmapped new_ids will NOT create records
             if len(unmapped_values) > 0:
-                if len(msg) > 0:
+                if len(msg) > 0 and not mute:
                     logger.success(msg)
                 s = "" if len(unmapped_values) == 1 else "s"
                 print_values = colors.yellow(_print_values(unmapped_values))
                 name = Registry.__name__
                 n_nonval = colors.yellow(f"{len(unmapped_values)} non-validated")
-                logger.warning(
-                    f"{colors.red('did not create')} {name} record{s} for "
-                    f"{n_nonval} {colors.italic(f'{field.field.name}{s}')}: {print_values}"
-                )
+                if not mute:
+                    logger.warning(
+                        f"{colors.red('did not create')} {name} record{s} for "
+                        f"{n_nonval} {colors.italic(f'{field.field.name}{s}')}: {print_values}"
+                    )
         if Registry.__module__.startswith("lnschema_bionty.") or Registry == ULabel:
             if isinstance(iterable, pd.Series):
                 feature = iterable.name
@@ -85,6 +91,7 @@ def get_or_create_records(
 def get_existing_records(
     iterable_idx: pd.Index,
     field: StrField,
+    mute: bool = False,
     **kwargs,
 ):
     model = field.field.model
@@ -96,7 +103,11 @@ def get_existing_records(
     # standardize based on the DB reference
     # log synonyms mapped terms
     result = model.inspect(
-        iterable_idx, field=field, organism=kwargs.get("organism"), mute=True
+        iterable_idx,
+        field=field,
+        organism=kwargs.get("organism"),
+        public_source=kwargs.get("public_source"),
+        mute=True,
     )
     syn_mapper = result.synonyms_mapper
 
@@ -146,9 +157,10 @@ def get_existing_records(
     # no logging if all values are validated
     # logs if there are synonyms
     if len(syn_msg) > 0:
-        if len(msg) > 0:
+        if len(msg) > 0 and not mute:
             logger.success(msg)
-        logger.success(syn_msg)
+        if not mute:
+            logger.success(syn_msg)
         msg = ""
 
     existing_values = iterable_idx.intersection(
@@ -163,6 +175,7 @@ def create_records_from_public(
     iterable_idx: pd.Index,
     field: StrField,
     msg: str = "",
+    mute: bool = False,
     **kwargs,
 ):
     model = field.field.model
@@ -219,19 +232,20 @@ def create_records_from_public(
             s = "" if len(validated) == 1 else "s"
             print_values = colors.purple(_print_values(validated))
             # this is the success msg for existing records in the DB
-            if len(msg) > 0:
+            if len(msg) > 0 and not mute:
                 logger.success(msg)
-            logger.success(
-                "created"
-                f" {colors.purple(f'{len(validated)} {model.__name__} record{s} from Bionty')}"
-                f" matching {colors.italic(f'{field.field.name}')}: {print_values}"
-            )
+            if not mute:
+                logger.success(
+                    "created"
+                    f" {colors.purple(f'{len(validated)} {model.__name__} record{s} from Bionty')}"
+                    f" matching {colors.italic(f'{field.field.name}')}: {print_values}"
+                )
 
     # make sure that synonyms logging appears after the field logging
-    if len(msg_syn) > 0:
+    if len(msg_syn) > 0 and not mute:
         logger.success(msg_syn)
     # warning about multi matches
-    if len(multi_msg) > 0:
+    if len(multi_msg) > 0 and not mute:
         logger.warning(multi_msg)
 
     # return the values that are not found in the bionty reference

{lamindb-0.70.0 → lamindb-0.70.1}/lamindb/_registry.py

@@ -134,6 +134,7 @@ def from_values(
     field: StrField | None = None,
     organism: Registry | str | None = None,
     public_source: Registry | None = None,
+    mute: bool = False,
 ) -> list[Registry]:
     """{}."""
     from_public = True if cls.__module__.startswith("lnschema_bionty.") else False
@@ -144,6 +145,7 @@ def from_values(
         from_public=from_public,
         organism=organism,
         public_source=public_source,
+        mute=mute,
     )
 
 

{lamindb-0.70.0 → lamindb-0.70.1}/lamindb/_save.py

@@ -16,11 +16,11 @@ from lamindb_setup.core.upath import UPath, print_hook
 from lnschema_core.models import Artifact, Registry
 
 from lamindb.core._settings import settings
-from lamindb.core.storage.file import (
+from lamindb.core.storage.paths import (
     attempt_accessing_path,
     auto_storage_key_from_artifact,
     delete_storage_using_key,
-    store_artifact,
+    store_file_or_folder,
 )
 
 try:
@@ -286,7 +286,7 @@ def upload_artifact(
     )
     msg = f"storing artifact '{artifact.uid}' at '{storage_path}'"
     if (
-        artifact.suffix in {".zarr", ".zrad"}
+        artifact.suffix == ".zarr"
         and hasattr(artifact, "_memory_rep")
         and artifact._memory_rep is not None
     ):
@@ -295,6 +295,5 @@ def upload_artifact(
         write_adata_zarr(artifact._memory_rep, storage_path, callback=print_progress)
     elif hasattr(artifact, "_to_store") and artifact._to_store:
         logger.save(msg)
-        store_artifact(artifact._local_filepath, storage_path)
-
+        store_file_or_folder(artifact._local_filepath, storage_path)
     return storage_path

{lamindb-0.70.0 → lamindb-0.70.1}/lamindb/core/storage/__init__.py

@@ -10,5 +10,5 @@ from lamindb_setup.core.upath import LocalPathClasses, UPath, infer_filesystem
 
 from ._anndata_sizes import size_adata
 from ._backed_access import AnnDataAccessor, BackedAccessor
-from .file import delete_storage, load_to_memory
-from .object import infer_suffix, write_to_file
+from .objects import infer_suffix, write_to_file
+from .paths import delete_storage, load_to_memory

{lamindb-0.70.0 → lamindb-0.70.1}/lamindb/core/storage/_backed_access.py

@@ -22,7 +22,7 @@ from lamindb_setup.core.upath import UPath, create_mapper, infer_filesystem
 from lnschema_core import Artifact
 from packaging import version
 
-from lamindb.core.storage.file import filepath_from_artifact
+from lamindb.core.storage.paths import filepath_from_artifact
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -743,15 +743,15 @@ def backed_access(
 
     if filepath.suffix in (".h5", ".hdf5", ".h5ad"):
         conn, storage = registry.open("h5py", filepath)
-    elif filepath.suffix in (".zarr", ".zrad"):
+    elif filepath.suffix == ".zarr":
         conn, storage = registry.open("zarr", filepath)
     else:
         raise ValueError(
-            "file should have .h5, .hdf5, .h5ad, .zarr or .zrad suffix, not"
+            "file should have .h5, .hdf5, .h5ad, .zarr suffix, not"
             f" {filepath.suffix}."
         )
 
-    if filepath.suffix in (".h5ad", ".zrad"):
+    if filepath.suffix in (".h5ad", ".zarr"):
         return AnnDataAccessor(conn, storage, name)
     else:
         if get_spec(storage).encoding_type == "anndata":

lamindb-0.70.0/lamindb/core/storage/object.py → lamindb-0.70.1/lamindb/core/storage/objects.py

@@ -21,11 +21,10 @@ def infer_suffix(dmem, adata_format: str | None = 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", "zrad"):
+            if adata_format not in ("h5ad", "zarr"):
                 raise ValueError(
                     "Error when specifying AnnData storage format, it should be"
-                    f" 'h5ad', 'zarr' or 'zrad', not '{adata_format}'. Check 'format'"
+                    f" 'h5ad', 'zarr', not '{adata_format}'. Check 'format'"
                     " or the suffix of 'key'."
                 )
             return "." + adata_format

lamindb-0.70.0/lamindb/core/storage/file.py → lamindb-0.70.1/lamindb/core/storage/paths.py

@@ -109,23 +109,23 @@ def read_adata_h5ad(filepath, **kwargs) -> ad.AnnData:
         return adata
 
 
-def store_artifact(localpath: UPathStr, storagepath: UPath) -> None:
-    """Store directory or file to configured storage location."""
-    localpath = Path(localpath)
-    if not isinstance(storagepath, LocalPathClasses):
+def store_file_or_folder(local_path: UPathStr, storage_path: UPath) -> None:
+    """Store file or folder (localpath) at storagepath."""
+    local_path = Path(local_path)
+    if not isinstance(storage_path, LocalPathClasses):
         # this uploads files and directories
-        storagepath.upload_from(localpath, recursive=True, print_progress=True)
+        storage_path.upload_from(local_path, recursive=True, print_progress=True)
     else:  # storage path is local
-        storagepath.parent.mkdir(parents=True, exist_ok=True)
-        if localpath.is_file():
+        storage_path.parent.mkdir(parents=True, exist_ok=True)
+        if local_path.is_file():
             try:
-                shutil.copyfile(localpath, storagepath)
+                shutil.copyfile(local_path, storage_path)
             except shutil.SameFileError:
                 pass
         else:
-            if storagepath.exists():
-                shutil.rmtree(storagepath)
-            shutil.copytree(localpath, storagepath)
+            if storage_path.exists():
+                shutil.rmtree(storage_path)
+            shutil.copytree(local_path, storage_path)
 
 
 def delete_storage_using_key(
@@ -212,7 +212,7 @@ def load_to_memory(filepath: UPathStr, stream: bool = False, **kwargs):
     """
     filepath = create_path(filepath)
 
-    if filepath.suffix not in {".h5ad", ".zarr", ".zrad"}:
+    if filepath.suffix not in {".h5ad", ".zarr"}:
         stream = False
 
     if not stream:
@@ -229,7 +229,6 @@ def load_to_memory(filepath: UPathStr, stream: bool = False, **kwargs):
         ".parquet": pd.read_parquet,
         ".fcs": read_fcs,
         ".zarr": read_adata_zarr,
-        ".zrad": read_adata_zarr,
         ".html": load_html,
         ".json": load_json,
         ".h5mu": read_mdata_h5mu,

{lamindb-0.70.0 → lamindb-0.70.1}/pyproject.toml

@@ -16,7 +16,7 @@ classifiers = [
 ]
 dependencies = [
     # Lamin PINNED packages
-    "lnschema_core==0.65.0",
+    "lnschema_core==0.65.1",
     "lamindb_setup==0.69.2",
     "lamin_utils==0.13.1",
     "lamin_cli==0.12.3",
@@ -38,7 +38,7 @@ Home = "https://github.com/laminlabs/lamindb"
 
 [project.optional-dependencies]
 bionty = [
-    "bionty==0.42.8",
+    "bionty==0.42.9",
 ]
 aws = [
     "urllib3<2", # for botocore, TODO: check that really required

{lamindb-0.70.0 → lamindb-0.70.1}/sub/bionty/bionty/__init__.py

@@ -122,7 +122,7 @@ Developer API:
    core
 """
 
-__version__ = "0.42.8"
+__version__ = "0.42.9"
 
 from lamindb_setup._check_setup import InstanceNotSetupError, _check_instance_setup
 from lnschema_bionty import ids

{lamindb-0.70.0 → lamindb-0.70.1}/sub/bionty/pyproject.toml

@@ -8,7 +8,7 @@ authors = [{name = "Lamin Labs", email = "open-source@lamin.ai"}]
 readme = "README.md"
 dynamic = ["version", "description"]
 dependencies = [
-    "lnschema-bionty==0.41.8",
+    "lnschema-bionty==0.41.9",
 ]
 
 [project.urls]

{lamindb-0.70.0 → lamindb-0.70.1}/sub/lnschema-bionty/docs/changelog.md

@@ -3,6 +3,7 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🚑️ Fix public_source in inspect | [232](https://github.com/laminlabs/lnschema-bionty/pull/232) | [sunnyosun](https://github.com/sunnyosun) | 2024-04-18 |
 :bug: Remove repr | [231](https://github.com/laminlabs/lnschema-bionty/pull/231) | [Zethson](https://github.com/Zethson) | 2024-04-11 |
 🐛 Fix syncing public sources | [230](https://github.com/laminlabs/lnschema-bionty/pull/230) | [sunnyosun](https://github.com/sunnyosun) | 2024-04-11 |
 Upgrade bionty-base | [229](https://github.com/laminlabs/lnschema-bionty/pull/229) | [Zethson](https://github.com/Zethson) | 2024-04-05 |

{lamindb-0.70.0 → lamindb-0.70.1}/sub/lnschema-bionty/lnschema_bionty/__init__.py

@@ -4,7 +4,7 @@ Since version 0.40.0, `bionty` replaces `lnschema-bionty` as the user-facing pac
 
 """
 
-__version__ = "0.41.8"  # Denote a release candidate of version 0.1.0 with 0.1rc1
+__version__ = "0.41.9"  # Denote a release candidate of version 0.1.0 with 0.1rc1
 
 from lamindb_setup import _check_instance_setup
 

{lamindb-0.70.0 → lamindb-0.70.1}/sub/lnschema-bionty/lnschema_bionty/models.py

@@ -149,7 +149,9 @@ class BioRegistry(Registry, HasParents, CanValidate):
             )
 
     @classmethod
-    def from_public(cls, **kwargs) -> BioRegistry | list[BioRegistry] | None:
+    def from_public(
+        cls, mute: bool = False, **kwargs
+    ) -> BioRegistry | list[BioRegistry] | None:
         """Create a record or records from public reference based on a single field value.
 
         Notes:
@@ -183,7 +185,7 @@ class BioRegistry(Registry, HasParents, CanValidate):
         else:
             k = next(iter(kv))
             v = kwargs.pop(k)
-            results = cls.from_values([v], field=getattr(cls, k), **kwargs)
+            results = cls.from_values([v], field=getattr(cls, k), mute=mute, **kwargs)
             if len(results) == 1:
                 return results[0]
             elif len(results) == 0:

{lamindb-0.70.0 → lamindb-0.70.1}/sub/lnschema-core/CHANGELOG.md

@@ -3,6 +3,7 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🚑️ Fix public_source in inspect | [372](https://github.com/laminlabs/lnschema-core/pull/372) | [sunnyosun](https://github.com/sunnyosun) | 2024-04-18 |
 🐛 Fix replicated outputs slot | [371](https://github.com/laminlabs/lnschema-core/pull/371) | [falexwolf](https://github.com/falexwolf) | 2024-04-17 | 0.65.0
 🚚 Rename `.stage()` to `.cache()`, add `.save(upload=None)` | [369](https://github.com/laminlabs/lnschema-core/pull/369) | [falexwolf](https://github.com/falexwolf) | 2024-04-16 |
 🚚 Add `Run.replicated_outputs` & `Transform.ulabels` | [370](https://github.com/laminlabs/lnschema-core/pull/370) | [falexwolf](https://github.com/falexwolf) | 2024-04-16 |

{lamindb-0.70.0 → lamindb-0.70.1}/sub/lnschema-core/lnschema_core/__init__.py

@@ -1,6 +1,6 @@
 """LaminDB's core registries."""
 
-__version__ = "0.65.0"
+__version__ = "0.65.1"
 
 
 from lamindb_setup import _check_instance_setup

{lamindb-0.70.0 → lamindb-0.70.1}/sub/lnschema-core/lnschema_core/models.py

@@ -122,6 +122,7 @@ class CanValidate:
         *,
         mute: bool = False,
         organism: str | Registry | None = None,
+        public_source: Registry | None = None,
     ) -> InspectResult:
         """Inspect if values are mappable to a field.
 
@@ -135,6 +136,7 @@ class CanValidate:
                 field names.
             mute: Mute logging.
             organism: An Organism name or record.
+            public_source: A PublicSource record.
 
         See Also:
             :meth:`~lamindb.core.CanValidate.validate`
@@ -407,6 +409,7 @@ class Registry(models.Model):
         field: StrField | None = None,
         organism: Registry | str | None = None,
         public_source: Registry | None = None,
+        mute: bool = False,
     ) -> list[Registry]:
         """Bulk create validated records by parsing values for an identifier (a name, an id, etc.).
 

{lamindb-0.70.0 → lamindb-0.70.1}/tests/test_artifact.py

@@ -17,7 +17,7 @@ from lamindb._artifact import (
 )
 from lamindb.core._settings import settings
 from lamindb.core.storage._zarr import write_adata_zarr
-from lamindb.core.storage.file import (
+from lamindb.core.storage.paths import (
     AUTO_KEY_PREFIX,
     auto_storage_key_from_artifact_uid,
     delete_storage,
@@ -71,14 +71,6 @@ def tsv_file():
     filepath.unlink()
 
 
-@pytest.fixture(scope="module")
-def zrad_file():
-    filepath = Path("test.zrad")
-    pd.DataFrame([1, 2]).to_csv(filepath, sep="\t")
-    yield filepath
-    filepath.unlink()
-
-
 @pytest.fixture(scope="module")
 def zip_file():
     filepath = Path("test.zip")
@@ -722,16 +714,13 @@ def test_serialize_paths():
     assert isinstance(filepath, CloudPath)
 
 
-def test_load_to_memory(tsv_file, zrad_file, zip_file, fcs_file):
+def test_load_to_memory(tsv_file, zip_file, fcs_file):
     # tsv
     df = read_tsv(tsv_file)
     assert isinstance(df, pd.DataFrame)
     # fcs
     adata = read_fcs(fcs_file)
     assert isinstance(adata, ad.AnnData)
-    # other
-    with pytest.raises(NotADirectoryError):
-        load_to_memory(zrad_file)
     # none
     load_to_memory(zip_file)
 
@@ -753,10 +742,10 @@ def test_folder_upload_cache(adata):
     def callback(*args, **kwargs):
         pass
 
-    zarr_path = Path("./test_adata.zrad")
+    zarr_path = Path("./test_adata.zarr")
     write_adata_zarr(adata, zarr_path, callback)
 
-    artifact = ln.Artifact(zarr_path, key="test_adata.zrad")
+    artifact = ln.Artifact(zarr_path, key="test_adata.zarr")
     artifact.save()
 
     assert isinstance(artifact.path, CloudPath) and artifact.path.exists()
@@ -794,10 +783,6 @@ def test_adata_suffix(adata):
     assert artifact.suffix == ".h5ad"
     artifact = ln.Artifact.from_anndata(adata, key="test_.zarr")
     assert artifact.suffix == ".zarr"
-    artifact = ln.Artifact.from_anndata(adata, key="test_.zrad")
-    assert artifact.suffix == ".zrad"
-    artifact = ln.Artifact.from_anndata(adata, format="zrad", key="test_.zrad")
-    assert artifact.suffix == ".zrad"
 
     with pytest.raises(ValueError) as error:
         artifact = ln.Artifact.from_anndata(adata, key="test_.def")
@@ -806,13 +791,6 @@ def test_adata_suffix(adata):
         == "ValueError: Error when specifying AnnData storage format"
     )
 
-    # with pytest.raises(ValueError) as error:
-    #     artifact = ln.Artifact.from_anndata(adata, format="h5ad", key="test.zrad")
-    # assert (
-    #     error.exconly().partition(",")[0]
-    #     == "ValueError: The suffix '.zrad' of the provided key is incorrect"
-    # )
-
     with pytest.raises(ValueError) as error:
         artifact = ln.Artifact.from_anndata(adata, key="test_")
     assert (