lamindb 0.70.1__tar.gz → 0.70.3__tar.gz

{lamindb-0.70.1 → lamindb-0.70.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.70.1
+Version: 0.70.3
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -10,8 +10,8 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: lnschema_core==0.65.1
-Requires-Dist: lamindb_setup==0.69.2
-Requires-Dist: lamin_utils==0.13.1
+Requires-Dist: lamindb_setup==0.69.5
+Requires-Dist: lamin_utils==0.13.2
 Requires-Dist: lamin_cli==0.12.3
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow

{lamindb-0.70.1 → lamindb-0.70.3}/docs/changelog.md

@@ -14,9 +14,20 @@ When upgrading your LaminDB installation to a new `minor` version in `major.mino
 
 ## 0.70
 
+### 0.70.3 {small}`2024-04-22`
+
+- 🚸 Update metadata like description upon re-running [PR](https://github.com/laminlabs/lamindb/pull/1588) [@falexwolf](https://github.com/falexwolf)
+- 🐛 Fix detection of AnnData in zarr and h5ad, refactor directory upload [PR](https://github.com/laminlabs/lamindb/pull/1587) [@Koncopd](https://github.com/Koncopd)
+- 🚸 Raise error if transforms of type notebook or script are passed manually [PR](https://github.com/laminlabs/lamindb/pull/1584) [@falexwolf](https://github.com/falexwolf)
+
+### 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)
+- 🐛 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`
 

lamindb-0.70.3/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-0.70.1 → lamindb-0.70.3}/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-0.70.1 → lamindb-0.70.3}/lamindb/__init__.py

@@ -40,7 +40,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.70.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.70.3"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

{lamindb-0.70.1 → lamindb-0.70.3}/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-0.70.1 → lamindb-0.70.3}/lamindb/_artifact.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from pathlib import Path, PurePath, PurePosixPath
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, Mapping
 
 import fsspec
 import lamindb_setup as ln_setup
@@ -26,7 +26,7 @@ from lnschema_core.types import (
 )
 
 from lamindb._utils import attach_func_to_class_method
-from lamindb.core._data import _track_run_input
+from lamindb.core._data import Data, _track_run_input
 from lamindb.core._settings import settings
 from lamindb.core.storage import (
     LocalPathClasses,
@@ -53,6 +53,14 @@ from .core._data import (
 from .core.storage.objects import _mudata_is_installed
 from .core.storage.paths import AUTO_KEY_PREFIX
 
+try:
+    from .core.storage._zarr import zarr_is_adata
+except ImportError:
+
+    def zarr_is_adata(storepath):  # type: ignore
+        raise ImportError("Please install zarr: pip install zarr")
+
+
 if TYPE_CHECKING:
     from lamindb_setup.core.types import UPathStr
     from mudata import MuData
@@ -329,16 +337,17 @@ def get_artifact_kwargs_from_data(
         using_key=using_key,
     )
     if isinstance(stat_or_artifact, Artifact):
+        artifact = stat_or_artifact
         # update the run of the existing artifact
         if run is not None:
             # save the information that this artifact was previously
             # produced by another run
-            if stat_or_artifact.run is not None:
-                stat_or_artifact.run.replicated_output_artifacts.add(stat_or_artifact)
+            if artifact.run is not None:
+                artifact.run.replicated_output_artifacts.add(artifact)
             # update the run of the artifact with the latest run
             stat_or_artifact.run = run
             stat_or_artifact.transform = run.transform
-        return stat_or_artifact, None
+        return artifact, None
     else:
         size, hash, hash_type, n_objects = stat_or_artifact
 
@@ -446,12 +455,19 @@ def data_is_anndata(data: AnnData | UPathStr):
     if isinstance(data, AnnData):
         return True
     if isinstance(data, (str, Path, UPath)):
-        if Path(data).suffix == ".h5ad":
+        data_path = UPath(data)
+        if data_path.suffix == ".h5ad":
             return True
-        elif Path(data).suffix == ".zarr":
-            raise NotImplementedError(
-                "auto-detecting AnnData from Zarr is not yet supported"
-            )
+        elif data_path.suffix == ".zarr":
+            # ".anndata.zarr" is a valid suffix (core.storage._valid_suffixes)
+            if ".anndata" in data_path.suffixes:
+                return True
+            # check only for local, expensive for cloud
+            if fsspec.utils.get_protocol(data_path) == "file":
+                return zarr_is_adata(data_path)
+            else:
+                logger.warning("We do not check if cloud zarr is AnnData or not.")
+                return False
     return False
 
 
@@ -461,27 +477,39 @@ def data_is_mudata(data: MuData | UPathStr):
 
         if isinstance(data, MuData):
             return True
-    if isinstance(data, (str, Path, UPath)):
-        return Path(data).suffix in {".h5mu"}
+    if isinstance(data, (str, Path)):
+        return UPath(data).suffix in {".h5mu"}
     return False
 
 
 def _check_accessor_artifact(data: Any, accessor: str | None = None):
-    if accessor is None and not isinstance(data, (str, Path, UPath)):
+    if accessor is None:
         if isinstance(data, pd.DataFrame):
             logger.warning("data is a DataFrame, please use .from_df()")
             accessor = "DataFrame"
-        elif data_is_anndata(data):
-            logger.warning("data is an AnnData, please use .from_anndata()")
+            return accessor
+
+        data_is_path = isinstance(data, (str, Path))
+        if data_is_anndata(data):
+            if not data_is_path:
+                logger.warning("data is an AnnData, please use .from_anndata()")
             accessor = "AnnData"
         elif data_is_mudata(data):
-            logger.warning("data is a MuData, please use .from_mudata()")
+            if not data_is_path:
+                logger.warning("data is a MuData, please use .from_mudata()")
             accessor = "MuData"
-        else:
+        elif not data_is_path:  # UPath is a subclass of Path
             raise TypeError("data has to be a string, Path, UPath")
     return accessor
 
 
+def update_attributes(data: Data, attributes: Mapping[str, str]):
+    for key, value in attributes.items():
+        if getattr(data, key) != value:
+            logger.warning(f"updated {key} from {getattr(data, key)} to {value}")
+            setattr(data, key, value)
+
+
 def __init__(artifact: Artifact, *args, **kwargs):
     # Below checks for the Django-internal call in from_db()
     # it'd be better if we could avoid this, but not being able to create a Artifact
@@ -558,8 +586,13 @@ def __init__(artifact: Artifact, *args, **kwargs):
     if isinstance(kwargs_or_artifact, Artifact):
         from ._registry import init_self_from_db
 
-        # kwargs_or_artifact is an existing file
         init_self_from_db(artifact, kwargs_or_artifact)
+        # adding "key" here is dangerous because key might be auto-populated
+        update_attributes(artifact, {"description": description})
+        if artifact.key != key:
+            logger.warning(
+                f"key {artifact.key} on existing artifact differs from passed key {key}"
+            )
         return None
     else:
         kwargs = kwargs_or_artifact

{lamindb-0.70.1 → lamindb-0.70.3}/lamindb/_collection.py

@@ -18,13 +18,13 @@ from lamindb_setup.core.hashing import hash_set
 from lnschema_core.models import Collection, CollectionArtifact, FeatureSet
 from lnschema_core.types import VisibilityChoice
 
+from lamindb._artifact import update_attributes
 from lamindb._utils import attach_func_to_class_method
 from lamindb.core._data import _track_run_input
 from lamindb.core._mapped_collection import MappedCollection
 from lamindb.core.versioning import get_uid_from_old_version, init_uid
 
 from . import Artifact, Run
-from ._artifact import data_is_anndata
 from ._registry import init_self_from_db
 from .core._data import (
     add_transform_to_kwargs,
@@ -128,6 +128,7 @@ def __init__(
             existing_collection.run = run
             existing_collection.transform = run.transform
         init_self_from_db(collection, existing_collection)
+        update_attributes(collection, {"description": description, "name": name})
         for slot, feature_set in collection.features._feature_set_by_slot.items():
             if slot in feature_sets:
                 if not feature_sets[slot] == feature_set:

{lamindb-0.70.1 → lamindb-0.70.3}/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-0.70.1 → lamindb-0.70.3}/lamindb/core/_run_context.py

@@ -306,6 +306,11 @@ class run_context:
             if not is_tracked:
                 raise_transform_settings_error()
         else:
+            if transform.type in {"notebook", "script"}:
+                raise ValueError(
+                    "Use ln.track() without passing transform in a notebook or script"
+                    " - metadata is automatically parsed"
+                )
             transform_exists = None
             if transform.id is not None:
                 # transform has an id but unclear whether already saved

{lamindb-0.70.1 → lamindb-0.70.3}/lamindb/core/storage/__init__.py

@@ -10,5 +10,6 @@ from lamindb_setup.core.upath import LocalPathClasses, UPath, infer_filesystem
 
 from ._anndata_sizes import size_adata
 from ._backed_access import AnnDataAccessor, BackedAccessor
+from ._valid_suffixes import VALID_SUFFIXES
 from .objects import infer_suffix, write_to_file
 from .paths import delete_storage, load_to_memory

{lamindb-0.70.1 → lamindb-0.70.3}/lamindb/core/storage/_backed_access.py

@@ -733,7 +733,7 @@ class BackedAccessor:
 
 
 def backed_access(
-    artifact_or_filepath: Artifact | Path, using_key: str | None
+    artifact_or_filepath: Artifact | Path, using_key: str | None = None
 ) -> AnnDataAccessor | BackedAccessor:
     if isinstance(artifact_or_filepath, Artifact):
         filepath = filepath_from_artifact(artifact_or_filepath, using_key=using_key)
@@ -747,11 +747,11 @@ def backed_access(
         conn, storage = registry.open("zarr", filepath)
     else:
         raise ValueError(
-            "file should have .h5, .hdf5, .h5ad, .zarr suffix, not"
+            "object should have .h5, .hdf5, .h5ad, .zarr suffix, not"
             f" {filepath.suffix}."
         )
 
-    if filepath.suffix in (".h5ad", ".zarr"):
+    if filepath.suffix == ".h5ad":
         return AnnDataAccessor(conn, storage, name)
     else:
         if get_spec(storage).encoding_type == "anndata":

lamindb-0.70.3/lamindb/core/storage/_valid_suffixes.py

@@ -0,0 +1,3 @@
+from lamindb_setup.core.upath import VALID_SUFFIXES
+
+VALID_SUFFIXES.update({".vitessce.json", ".anndata.zarr", ".spatialdata.zarr"})

{lamindb-0.70.1 → lamindb-0.70.3}/lamindb/core/storage/_zarr.py

@@ -7,28 +7,44 @@ import scipy.sparse as sparse
 import zarr
 from anndata._io import read_zarr
 from anndata._io.specs import write_elem
+from anndata._io.specs.registry import get_spec
+from fsspec.implementations.local import LocalFileSystem
 from lamindb_setup.core.upath import create_mapper, infer_filesystem
 
 from ._anndata_sizes import _size_elem, _size_raw, size_adata
 
 if TYPE_CHECKING:
     from anndata import AnnData
-
-
-def read_adata_zarr(storepath) -> AnnData:
-    fs, storepath = infer_filesystem(storepath)
-    store = create_mapper(fs, storepath, check=True)
-
-    adata = read_zarr(store)
-
+    from lamindb_setup.core.types import UPathStr
+
+
+def zarr_is_adata(storepath: UPathStr) -> bool:
+    fs, storepath_str = infer_filesystem(storepath)
+    if isinstance(fs, LocalFileSystem):
+        # this is faster than through an fsspec mapper for local
+        open_obj = storepath_str
+    else:
+        open_obj = create_mapper(fs, storepath_str, check=True)
+    storage = zarr.open(open_obj, mode="r")
+    return get_spec(storage).encoding_type == "anndata"
+
+
+def read_adata_zarr(storepath: UPathStr) -> AnnData:
+    fs, storepath_str = infer_filesystem(storepath)
+    if isinstance(fs, LocalFileSystem):
+        # this is faster than through an fsspec mapper for local
+        open_obj = storepath_str
+    else:
+        open_obj = create_mapper(fs, storepath_str, check=True)
+    adata = read_zarr(open_obj)
     return adata
 
 
 def write_adata_zarr(
-    adata: AnnData, storepath, callback=None, chunks=None, **dataset_kwargs
+    adata: AnnData, storepath: UPathStr, callback=None, chunks=None, **dataset_kwargs
 ):
-    fs, storepath = infer_filesystem(storepath)
-    store = create_mapper(fs, storepath, create=True)
+    fs, storepath_str = infer_filesystem(storepath)
+    store = create_mapper(fs, storepath_str, create=True)
 
     f = zarr.open(store, mode="w")
 

{lamindb-0.70.1 → lamindb-0.70.3}/lamindb/core/storage/paths.py

@@ -29,7 +29,7 @@ try:
     from ._zarr import read_adata_zarr
 except ImportError:
 
-    def read_adata_zarr(filepath):  # type: ignore
+    def read_adata_zarr(storepath):  # type: ignore
         raise ImportError("Please install zarr: pip install zarr")
 
 
@@ -114,7 +114,7 @@ def store_file_or_folder(local_path: UPathStr, storage_path: UPath) -> None:
     local_path = Path(local_path)
     if not isinstance(storage_path, LocalPathClasses):
         # this uploads files and directories
-        storage_path.upload_from(local_path, recursive=True, print_progress=True)
+        storage_path.upload_from(local_path, dir_inplace=True, print_progress=True)
     else:  # storage path is local
         storage_path.parent.mkdir(parents=True, exist_ok=True)
         if local_path.is_file():