lamindb 0.70.0__tar.gz → 0.70.2__tar.gz

{lamindb-0.70.0 → lamindb-0.70.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.70.0
+Version: 0.70.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,9 +9,9 @@ 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: lamindb_setup==0.69.2
-Requires-Dist: lamin_utils==0.13.1
+Requires-Dist: lnschema_core==0.65.1
+Requires-Dist: lamindb_setup==0.69.4
+Requires-Dist: lamin_utils==0.13.2
 Requires-Dist: lamin_cli==0.12.3
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
@@ -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-0.70.2}/docs/changelog.md

@@ -14,6 +14,15 @@ When upgrading your LaminDB installation to a new `minor` version in `major.mino
 
 ## 0.70
 
+### 0.70.2 {small}`2024-04-19`
+
+- ♻️ In Vitessce integration, separate `VitessceConfig` from its referenced artifacts [PR](https://github.com/laminlabs/lamindb/pull/1582) [@falexwolf](https://github.com/falexwolf)
+- 🚸 In `ln.finish()`, remove flag `i_saved_the_notebook` [PR](https://github.com/laminlabs/lamindb/pull/1581) [@falexwolf](https://github.com/falexwolf)
+
+### 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-0.70.2}/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-0.70.2}/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-0.70.2/docs/storage/vitessce.ipynb

@@ -0,0 +1,157 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Vitessce integration"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "For more comprehensive integration tests, see: https://github.com/laminlabs/lamin-spatial"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pytest\n",
+    "import lamindb as ln\n",
+    "\n",
+    "INSTANCE_NAME = \"test-vitessce\"\n",
+    "ln.setup.init(storage=f\"s3://lamindb-ci/{INSTANCE_NAME}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pbmc68k = ln.core.datasets.anndata_pbmc68k_reduced()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pbmc68k = pbmc68k[:100, :200].copy()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "zarr_filepath = \"my_test.zarr\"\n",
+    "pbmc68k.write_zarr(zarr_filepath)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "zarr_artifact = ln.Artifact(zarr_filepath, description=\"Test dataset\")\n",
+    "zarr_artifact.save()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from vitessce import (\n",
+    "    VitessceConfig,\n",
+    "    Component as cm,\n",
+    "    AnnDataWrapper,\n",
+    ")\n",
+    "vc = VitessceConfig(\n",
+    "    schema_version=\"1.0.15\",\n",
+    "    name=\"Test dataset\",\n",
+    "    description=\"Test description\",\n",
+    ")\n",
+    "dataset = vc.add_dataset(name=\"test1\").add_object(\n",
+    "    AnnDataWrapper(adata_url=zarr_artifact.path.to_url()),\n",
+    ")\n",
+    "obs_sets = vc.add_view(cm.OBS_SETS, dataset=dataset)\n",
+    "obs_sets_sizes = vc.add_view(cm.OBS_SET_SIZES, dataset=dataset)\n",
+    "scatterplot = vc.add_view(cm.SCATTERPLOT, dataset=dataset, mapping=\"UMAP\")\n",
+    "heatmap = vc.add_view(cm.HEATMAP, dataset=dataset)\n",
+    "genes = vc.add_view(cm.FEATURE_LIST, dataset=dataset)\n",
+    "vc.layout(((scatterplot | obs_sets) / heatmap) | (obs_sets_sizes / genes))\n",
+    "\n",
+    "# inspect the config\n",
+    "vc.to_dict()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from lamindb.integrations import save_vitessce_config"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vc_artifact = save_vitessce_config(vc, description=\"View Habib17 in Vitessce\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "zarr_artifact.delete(permanent=True)\n",
+    "vc_artifact.delete(permanent=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!lamin delete --force test-vitessce"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "py310",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

{lamindb-0.70.0 → lamindb-0.70.2}/docs/storage.md

@@ -8,4 +8,5 @@ storage/add-replace-stage
 storage/anndata-accessor
 storage/prepare-transfer-local-to-cloud
 storage/transfer-local-to-cloud
+storage/vitessce
 ```

{lamindb-0.70.0 → lamindb-0.70.2}/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__ = "0.70.2"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

{lamindb-0.70.0 → lamindb-0.70.2}/lamindb/_annotate.py

@@ -351,7 +351,7 @@ class AnnDataAnnotator(DataFrameAnnotator):
         self,
         adata: ad.AnnData,
         var_index: FieldAttr,
-        categoricals: dict[str, FieldAttr],
+        categoricals: dict[str, FieldAttr] | None = None,
         using: str = "default",
         verbosity: str = "hint",
         organism: str | None = None,
@@ -494,7 +494,7 @@ class MuDataAnnotator:
         self,
         mdata: MuData,
         var_index: dict[str, dict[str, FieldAttr]],
-        categoricals: dict[str, FieldAttr],
+        categoricals: dict[str, FieldAttr] | None = None,
         using: str = "default",
         verbosity: str = "hint",
         organism: str | None = None,
@@ -751,7 +751,7 @@ class Annotate:
         cls,
         adata: ad.AnnData,
         var_index: FieldAttr,
-        categoricals: dict[str, FieldAttr],
+        categoricals: dict[str, FieldAttr] | None = None,
         using: str = "default",
         verbosity: str = "hint",
         organism: str | None = None,
@@ -772,7 +772,7 @@ class Annotate:
         cls,
         mdata: MuData,
         var_index: dict[str, dict[str, FieldAttr]],
-        categoricals: dict[str, dict[str, FieldAttr]],
+        categoricals: dict[str, FieldAttr] | None = None,
         using: str = "default",
         verbosity: str = "hint",
         organism: str | None = None,

{lamindb-0.70.0 → lamindb-0.70.2}/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-0.70.2}/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-0.70.2}/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-0.70.2}/lamindb/_finish.py

@@ -20,37 +20,40 @@ if TYPE_CHECKING:
     from ._query_set import QuerySet
 
 
-class CallFinishInLastCell(SystemExit):
+class TrackNotCalled(SystemExit):
     pass
 
 
-def finish(i_saved_the_notebook: bool = False):
-    """Mark a tracked run as finished.
+class NotebookNotSaved(SystemExit):
+    pass
 
-    When run in notebooks, save the run report to your default storage location.
 
-    Args:
-        i_saved_the_notebook: Indicate that you saved the notebook in your
-            editor (JupyterLab, VSCode, etc.).
-    """
-    if is_run_from_ipython:
-        # notebooks
-        from nbproject.dev import read_notebook
-        from nbproject.dev._check_last_cell import check_last_cell
+def get_seconds_since_modified(filepath) -> float:
+    return datetime.now().timestamp() - filepath.stat().st_mtime
 
-        if not i_saved_the_notebook and not ln_setup._TESTING:
-            logger.error(
-                "Please pass `i_saved_the_notebook=True` to `ln.finish()`, save the notebook, and re-run this cell."
+
+def finish():
+    """Mark a tracked run as finished.
+
+    If run in a notebook, it saves the run report & source code to your default storage location.
+    """
+    if run_context.path is None:
+        raise TrackNotCalled("Please run `ln.track()` before `ln.finish()`")
+    if is_run_from_ipython:  # notebooks
+        if (
+            get_seconds_since_modified(run_context.path) > 3
+            and os.getenv("LAMIN_TESTING") is None
+        ):
+            raise NotebookNotSaved(
+                "Please save the notebook in your editor right before running `ln.finish()`"
             )
-            return None
         save_run_context_core(
             run=run_context.run,
             transform=run_context.transform,
             filepath=run_context.path,
             finished_at=True,
         )
-    else:
-        # scripts
+    else:  # scripts
         # save_run_context_core was already called during ln.track()
         run_context.run.finished_at = datetime.now(timezone.utc)  # update run time
         run_context.run.save()
@@ -98,7 +101,7 @@ def save_run_context_core(
         # log_level is set to 40 to silence the nbconvert logging
         subprocess.run(
             "jupyter nbconvert --to html"
-            f" {filepath.as_posix()} --Application.log_level=40",
+            f" '{filepath.as_posix()}' --Application.log_level=40",
             shell=True,
             check=True,
         )
@@ -118,7 +121,7 @@ def save_run_context_core(
         # first, copy the notebook file to a temporary file in the cache
         source_code_path = ln_setup.settings.storage.cache_dir / filepath.name
         shutil.copy2(filepath, source_code_path)  # copy
-        subprocess.run(f"nbstripout {source_code_path}", shell=True, check=True)
+        subprocess.run(f"nbstripout '{source_code_path}'", shell=True, check=True)
     # find initial versions of source codes and html reports
     prev_report = None
     prev_source = None
@@ -139,9 +142,8 @@ def save_run_context_core(
             if os.getenv("LAMIN_TESTING") is None:
                 # in test, auto-confirm overwrite
                 response = input(
-                    "You try to save a new notebook source code with the same version"
-                    f" '{transform.version}'; do you want to replace the content of the"
-                    f" existing source code {transform.source_code}? (y/n)"
+                    f"You are about to overwrite existing source code (hash {transform.source_code.hash}) for transform version"
+                    f" '{transform.version}'. Proceed? (y/n)"
                 )
             else:
                 response = "y"
@@ -149,10 +151,7 @@ def save_run_context_core(
                 transform.source_code.replace(source_code_path)
                 transform.source_code.save()
             else:
-                logger.warning(
-                    "Please create a new version of the notebook via `lamin track"
-                    " <filepath>` and re-run the notebook"
-                )
+                logger.warning("Please re-run `ln.track()` to make a new version")
                 return "rerun-the-notebook"
     else:
         source_code = ln.Artifact(
@@ -207,8 +206,11 @@ def save_run_context_core(
     transform.save()
     if transform.type == TransformType.notebook:
         logger.success(f"saved transform.latest_report: {transform.latest_report}")
-    identifier = ln_setup.settings.instance.slug
-    logger.success(f"go to: https://lamin.ai/{identifier}/transform/{transform.uid}")
+    if ln_setup.settings.instance.is_remote:
+        identifier = ln_setup.settings.instance.slug
+        logger.success(
+            f"go to: https://lamin.ai/{identifier}/transform/{transform.uid}"
+        )
     # because run & transform changed, update the global run_context
     run_context.run = run
     run_context.transform = transform

{lamindb-0.70.0 → lamindb-0.70.2}/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-0.70.2}/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-0.70.2}/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