lamindb 0.70.0__py3-none-any.whl → 0.70.2__py3-none-any.whl

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/_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/_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/_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/_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/_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/_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/_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/_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/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 .file import delete_storage, load_to_memory
-from .object import infer_suffix, write_to_file
+from ._valid_suffixes import VALID_SUFFIXES
+from .objects import infer_suffix, write_to_file
+from .paths import delete_storage, load_to_memory

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
@@ -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)
@@ -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"
+            "object should have .h5, .hdf5, .h5ad, .zarr suffix, not"
             f" {filepath.suffix}."
         )
 
-    if filepath.suffix in (".h5ad", ".zrad"):
+    if filepath.suffix == ".h5ad":
         return AnnDataAccessor(conn, storage, name)
     else:
         if get_spec(storage).encoding_type == "anndata":

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/core/storage/{object.py → 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/core/storage/{file.py → 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/integrations/_vitessce.py

@@ -8,6 +8,8 @@ import lamindb_setup as ln_setup
 from lamin_utils import logger
 
 from lamindb._artifact import Artifact
+from lamindb._run import Run
+from lamindb._transform import Transform
 
 if TYPE_CHECKING:
     from vitessce import VitessceConfig
@@ -15,36 +17,54 @@ if TYPE_CHECKING:
 
 # tested & context in https://github.com/laminlabs/lamin-spatial
 def save_vitessce_config(vitessce_config: VitessceConfig, description: str) -> Artifact:
-    """Takes a ``VitessceConfig`` object and saves it as an artifact.
+    """Validates and saves a ``VitessceConfig`` object.
+
+    Example: :doc:`docs:vitessce`.
 
     Args:
         vitessce_config (``VitessceConfig``): A VitessceConfig object.
         description: A description for the artifact.
-    """
-    # can't assume vitessce is installed
-    from vitessce import VitessceConfig
 
-    # create a local _data export_ in a folder
-    timestamp = datetime.now(timezone.utc).isoformat().split(".")[0]
-    vitesse_export_folder = f"./vitessce_export_{timestamp}.vitessce"
-    vitessce_config.export(to="files", base_url="", out_dir=vitesse_export_folder)
-    logger.important(f"local export: {vitesse_export_folder}")
-    # create an artifact and store the local export in th cloud
-    artifact = Artifact(vitesse_export_folder, description=description)
-    artifact.save()
-    # create a JSON export that points to the data in the cloud
-    config_dict = vitessce_config.to_dict(base_url=artifact.path.to_url())
-    logger.important(f"base url: {artifact.path.to_url()}")
-    # manually place that JSON export into the local data export folder
-    config_filename = "vitessce_config.json"
-    config_file_local_path = f"{vitesse_export_folder}/{config_filename}"
+    .. versionchanged:: 0.70.2
+        This function no longer saves the dataset. It only saves the VitessceConfig object.
+    """
+    vc_dict = vitessce_config.to_dict()
+    # validate
+    datasets = vc_dict["datasets"]
+    input_artifacts = []
+    for dataset in datasets:
+        if "files" not in dataset:
+            raise ValueError("Each dataset must have a 'files' key.")
+        for file in dataset["files"]:
+            if "url" not in file:
+                raise ValueError("Each file must have a 'url' key.")
+            filename = file["url"].split("/")[-1]
+            assert filename.endswith((".anndata.zarr", ".spatialdata.zarr", ".zarr"))
+            filestem = (
+                filename.replace(".anndata.zarr", "")
+                .replace(".spatialdata.zarr", "")
+                .replace(".zarr", "")
+            )
+            artifact = Artifact.filter(uid__startswith=filestem).one_or_none()
+            if artifact is None:
+                logger.warning(f"could not find dataset in lamindb: {dataset}")
+            else:
+                input_artifacts.append(artifact)
+    # link inputs
+    with logger.mute():
+        transform = Transform(name="save_vitessce_config", type="function", version="1")
+        transform.save()
+    run = Run(transform=transform)
+    run.save()
+    run.input_artifacts.set(input_artifacts)
+    # create a JSON export
+    config_file_local_path = (
+        ln_setup.settings.storage.cache_dir / "config.vitessce.json"
+    )
     with open(config_file_local_path, "w") as file:
-        json.dump(config_dict, file)
-    # manually place that JSON export into the previously registered artifact folder
-    config_file_path = artifact.path / config_filename
-    config_file_path.upload_from(config_file_local_path)
-    # log the the URLs
-    logger.important(f"config url: {config_file_path.to_url()}")
+        json.dump(vc_dict, file)
+    artifact = Artifact(config_file_local_path, description=description, run=run)
+    artifact.save()
     slug = ln_setup.settings.instance.slug
     logger.important(f"go to: https://lamin.ai/{slug}/artifact/{artifact.uid}")
     return artifact

{lamindb-0.70.0.dist-info → lamindb-0.70.2.dist-info}/METADATA

@@ -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.dist-info → lamindb-0.70.2.dist-info}/RECORD

@@ -1,20 +1,20 @@
-lamindb/__init__.py,sha256=BT6UZlIvg7VG1sTaQ_k81e1b2ATVgR3eTSMjFitNerA,2163
-lamindb/_annotate.py,sha256=BXYWFATifbfRVmLFIgE4cZ4Fls4lkH2WXAEL2o7v-XM,43035
-lamindb/_artifact.py,sha256=eUh0_dCD_wLMUL7HxWTKjk7WGeyFh1olJVMkQETzLUU,37193
-lamindb/_can_validate.py,sha256=qA6Ni9scObcIeYzuudVymgOjQVLLxnGNofBSDNDaqfY,14557
-lamindb/_collection.py,sha256=Yo72YdmAKP4O6awoJAFhRKKzM6rKelS0inII8sKk0ls,14545
+lamindb/__init__.py,sha256=JHrhBHkihUcLRbreh9xyafsWang75NJxz9CVIWx6Bc0,2163
+lamindb/_annotate.py,sha256=B0KSvo5S2kJPeMMqy2SSFkqRJCS2QRC4NtI0_vWEZMs,43080
+lamindb/_artifact.py,sha256=BUl_3WYwrZ28P93Pb9AiwriVFBSLvBUEQjYEyYCrkZ0,37307
+lamindb/_can_validate.py,sha256=nvoZG-35n3HofkY4Xc6hBv9AV54_RDan7Hzp5TuqY9I,14709
+lamindb/_collection.py,sha256=wf7ClfiD3vsetts_iSUk4UihWsHq0IdOF8LdIIHS7JU,14536
 lamindb/_feature.py,sha256=srAKchY7gqD-h-cWlEiAWuHlpFKFwv0PWIA-JX0Go8c,6758
 lamindb/_feature_set.py,sha256=AzjOcHzQajpeikPOAic-aj0z_C5b7VpHVegg3ThRSLw,9045
 lamindb/_filter.py,sha256=xnjJzjF3Zj4dK_Kfymvhgczk27MhhXz5ZYc7XINbgHY,1331
-lamindb/_finish.py,sha256=SIPIIMAXM2d00L6VHMf2qFiOHuTyAlLy-5qRJ-BYaIQ,8107
-lamindb/_from_values.py,sha256=Mupz-mW_aftlhSktH1cgSD4hVaQJW93VehoFJhD15h4,12207
+lamindb/_finish.py,sha256=oR7oe6By3vEhF0twDBqSdT1EF28MPhyiS_cfZP0CcCw,8040
+lamindb/_from_values.py,sha256=DVXjnQ2wwNw-2bFzy0uXLdVlqoprrn95hTnrXwn-KqM,12638
 lamindb/_is_versioned.py,sha256=0PgRCmxEmYDcAjllLSOYZm132B1lW6QgmBBERhRyFt0,1341
 lamindb/_parents.py,sha256=N9T8jbd3eaoHDLE9TD1y1QgGcO81E6Brapy8LILzRCQ,14790
 lamindb/_query_manager.py,sha256=3zokXqxgj9vTJBnN2sbYKS-q69fyDDPF_aGq_rFHzXU,4066
 lamindb/_query_set.py,sha256=fy6xMK9MPGbD8D_i5iNzR8XA009W05ud4tbgrzd5-Vg,11287
-lamindb/_registry.py,sha256=CL-KlCC23HPWQgSeYg7Od2kbZdNViAjFqqdiGpKJKw8,19293
+lamindb/_registry.py,sha256=-Bv10zSr6IY7QM5pu_35NiVjQDJnBcXRECVe9h7GEuY,19336
 lamindb/_run.py,sha256=b7A52M1On3QzFgIYyfQoz5Kk7V3wcu9p_Prq5bzd8v8,1838
-lamindb/_save.py,sha256=aqvE0ryZs4-sDk6DZPn-Ki724gHeLyA9w-1oN5m_XMU,11425
+lamindb/_save.py,sha256=x16FBwltaTd1tnXm_zCxkvuVxyon6vRtekf37CfepXg,11426
 lamindb/_storage.py,sha256=VW8xq3VRv58-ciholvOdlcgvp_OIlLxx5GxLt-e2Irs,614
 lamindb/_transform.py,sha256=rxojJ91qQSkeYDHYbwqjFAYxBMgJd3cq_K7Z0n5g8Aw,3482
 lamindb/_ulabel.py,sha256=e5dw9h1tR0_u-DMn7Gzx0WhUhV5w7j4v3QbnLWQV7eI,1941
@@ -38,17 +38,18 @@ lamindb/core/versioning.py,sha256=DsEHpCueNwhRiIaRH5-O8H_1fJVNtWslCRx30YiIS5o,30
 lamindb/core/datasets/__init__.py,sha256=zRP98oqUAaXhqWyKMiH0s_ImVIuNeziQQ2kQ_t0f-DI,1353
 lamindb/core/datasets/_core.py,sha256=36vUOYFkX_4hBAnM_BujV5BRARMI5b9iI_SM9qS7wGc,20191
 lamindb/core/datasets/_fake.py,sha256=BZF9R_1iF0HDnvtZNqL2FtsjSMuqDIfuFxnw_LJYIh4,953
-lamindb/core/storage/__init__.py,sha256=9alBNtyH59VnoWJS-IdjLwFKlK-kgeCGl6jXk0_wGeQ,369
+lamindb/core/storage/__init__.py,sha256=6jnbFj-eBV3xZt04qP-kTsMWoP8YwpM50wlnnxDYsZU,415
 lamindb/core/storage/_anndata_sizes.py,sha256=aXO3OB--tF5MChenSsigW6Q-RuE8YJJOUTVukkLrv9A,1029
-lamindb/core/storage/_backed_access.py,sha256=uW0zaeKune6k2zYJcLazIA7Xux9TS2tAHDNdz1syYZw,24557
+lamindb/core/storage/_backed_access.py,sha256=eManrLsu3pSSQAyAKy47FDBm-iHgjaNfHA-zLy59uDs,24536
+lamindb/core/storage/_valid_suffixes.py,sha256=sewRRU3I6fJ-Jd5ACNcco_o3hic9zmqTs8BuZui-450,133
 lamindb/core/storage/_zarr.py,sha256=0i9-cJPjieIsp5UpK-IyRPkHAF-iKkWgpkWviSni2MM,2900
-lamindb/core/storage/file.py,sha256=AEMbrC6oWoIp3vs4F2bgm50EVBxkCGbN9R4na7Wanaw,7754
-lamindb/core/storage/object.py,sha256=37p8CSlfSlWPVuuD3MFcwQRj1n_kovLKVImh9SCR4Eg,1601
+lamindb/core/storage/objects.py,sha256=5LbBeZVKuOOB8DceSE-PN8elKY0N9OhFXZPQJE4lK48,1538
+lamindb/core/storage/paths.py,sha256=XWfSHK5b3_TFiK-IMvH-srvxO0bZStzA_rwjNaTxQU4,7725
 lamindb/integrations/__init__.py,sha256=aH2PmO2m4-vwIifMYTB0Fyyr_gZWtVnV71jT0tVWSw0,123
-lamindb/integrations/_vitessce.py,sha256=l3GPkzQXcwnMypbm8vDkITjognELjX8ucLaiqy99Jgg,2131
+lamindb/integrations/_vitessce.py,sha256=Ii2YhGwXH_tNDS9MXzxNekthWoDmDGpgGxAOVcTIbB4,2550
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
-lamindb-0.70.0.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.70.0.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.70.0.dist-info/METADATA,sha256=Mj16sNRVTgeMpFSL9mNUzF9HBaGo1RzERYp2ejiW8Xk,2835
-lamindb-0.70.0.dist-info/RECORD,,
+lamindb-0.70.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.70.2.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.70.2.dist-info/METADATA,sha256=KqXBjKMhKMBbx7VYeaWWfP0Xot_OyRRjpFO9vZotb7c,2835
+lamindb-0.70.2.dist-info/RECORD,,