lamindb 0.67.0__tar.gz → 0.67.2__tar.gz

{lamindb-0.67.0 → lamindb-0.67.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.67.0
+Version: 0.67.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -12,7 +12,7 @@ Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: lnschema_core==0.61.1
 Requires-Dist: lamindb_setup==0.64.2
 Requires-Dist: lamin_utils==0.13.0
-Requires-Dist: lamin_cli==0.6.0
+Requires-Dist: lamin_cli==0.7.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -28,7 +28,7 @@ Requires-Dist: boto3==1.28.17 ; extra == "aws"
 Requires-Dist: aiobotocore==2.5.4 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.9.0 ; extra == "aws"
 Requires-Dist: s3fs>=2023.9.0 ; extra == "aws"
-Requires-Dist: lnschema_bionty==0.38.3 ; extra == "bionty"
+Requires-Dist: lnschema_bionty==0.39.0 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
@@ -42,7 +42,7 @@ Requires-Dist: lamin_vault ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=1.1.7 ; extra == "fcs"
 Requires-Dist: fsspec[gs]==2023.9.0 ; extra == "gcp"
-Requires-Dist: nbproject==0.9.2 ; extra == "jupyter"
+Requires-Dist: nbproject==0.10.0 ; extra == "jupyter"
 Requires-Dist: nbstripout ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"

{lamindb-0.67.0 → lamindb-0.67.2}/docs/changelog.md

@@ -7,6 +7,17 @@
 
 ## 0.67
 
+### 0.67.2 {small}`2024-01-14`
+
+- ✨ Enable staging notebooks & code using the CLI [PR](https://github.com/laminlabs/lamindb/pull/1403) [@falexwolf](https://github.com/falexwolf)
+
+### 0.67.1 {small}`2024-01-12`
+
+- 🐛 Fix idempotency of `collection.save()` [PR](https://github.com/laminlabs/lamindb/pull/1401) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Disallow bulk-delete for Artifact, Transform & Collection [PR](https://github.com/laminlabs/lamindb/pull/1398) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Init transform versions at 1 [PR](https://github.com/laminlabs/lamindb/pull/1397) [@falexwolf](https://github.com/falexwolf)
+- ✨ Load json and html files [PR](https://github.com/laminlabs/lamindb/pull/1396) [@falexwolf](https://github.com/falexwolf)
+
 ### 0.67.0 {small}`2024-01-11`
 
 - 🚚 Rename `.bionty` to `.public`, `.from_bionty` to `.from_public` [PR](https://github.com/laminlabs/lamindb/pull/1394) [@sunnyosun](https://github.com/sunnyosun)

{lamindb-0.67.0 → lamindb-0.67.2}/lamindb/__init__.py

@@ -54,7 +54,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.67.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.67.2"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 
@@ -102,20 +102,20 @@ if _INSTANCE_SETUP:
         User,
     )
 
-    File = Artifact  # backward compat
-    from . import _artifact  # noqa
-    from . import _collection
-    from . import _feature
-    from . import _feature_set
-    from . import _parents
-    from . import _registry
-    from . import _run
-    from . import _storage
-    from . import _transform
-    from . import _ulabel
-    from . import _validate
-    from . import dev
-    from ._delete import delete
+    from . import (
+        _artifact,
+        _collection,
+        _feature,
+        _feature_set,
+        _parents,
+        _registry,
+        _run,
+        _storage,
+        _transform,
+        _ulabel,
+        _validate,
+        dev,
+    )
     from ._save import save
     from ._view import view
     from .dev._run_context import run_context

{lamindb-0.67.0 → lamindb-0.67.2}/lamindb/_artifact.py

@@ -911,13 +911,13 @@ def delete(
     self, permanent: Optional[bool] = None, storage: Optional[bool] = None
 ) -> None:
     # by default, we only move artifacts into the trash
-    if self.visibility > VisibilityChoice.trash.value and permanent is not True:
+    if self.visibility > -1 and permanent is not True:
         if storage is not None:
             logger.warning("moving artifact to trash, storage arg is ignored")
         # move to trash
-        self.visibility = VisibilityChoice.trash.value
+        self.visibility = -1
         self.save()
-        logger.warning("moved artifact to trash")
+        logger.warning("moved artifact to trash (visibility = -1)")
         return
 
     # if the artifact is already in the trash
@@ -929,6 +929,7 @@ def delete(
         )
         delete_record = response == "y"
     else:
+        # this second option doesn't feel very intuitive
         delete_record = permanent
 
     if delete_record:

{lamindb-0.67.0 → lamindb-0.67.2}/lamindb/_collection.py

@@ -424,8 +424,12 @@ def save(self, *args, **kwargs) -> None:
         self.artifact.save()
     # we don't need to save feature sets again
     save_feature_sets(self)
+    state_was_adding = self._state.adding
     super(Collection, self).save()
-    if hasattr(self, "_artifacts"):
+    # we don't allow updating the collection of artifacts
+    # if users want to update the set of artifacts, they
+    # have to create a new collection
+    if state_was_adding and hasattr(self, "_artifacts"):
         if self._artifacts is not None and len(self._artifacts) > 0:
             links = [
                 CollectionArtifact(collection_id=self.id, artifact_id=artifact.id)

{lamindb-0.67.0 → lamindb-0.67.2}/lamindb/_from_values.py

@@ -173,20 +173,20 @@ def create_records_from_public(
 
     # create the corresponding bionty object from model
     try:
-        bionty_object = model.public(
+        public_ontology = model.public(
             organism=kwargs.get("organism"), public_source=kwargs.get("public_source")
         )
     except Exception:
         # for custom records that are not created from bionty sources
         return records, iterable_idx
     # add public_source record to the kwargs
-    kwargs.update({"public_source": get_public_source_record(bionty_object)})
+    kwargs.update({"public_source": get_public_source_record(public_ontology)})
 
     # filter the columns in bionty df based on fields
-    bionty_df = _filter_bionty_df_columns(model=model, bionty_object=bionty_object)
+    bionty_df = _filter_bionty_df_columns(model=model, public_ontology=public_ontology)
 
     # standardize in the bionty reference
-    result = bionty_object.inspect(iterable_idx, field=field.field.name, mute=True)
+    result = public_ontology.inspect(iterable_idx, field=field.field.name, mute=True)
     syn_mapper = result.synonyms_mapper
 
     msg_syn: str = ""
@@ -254,13 +254,13 @@ def _print_values(names: List, n: int = 20) -> str:
     return print_values
 
 
-def _filter_bionty_df_columns(model: Registry, bionty_object: Any) -> pd.DataFrame:
+def _filter_bionty_df_columns(model: Registry, public_ontology: Any) -> pd.DataFrame:
     bionty_df = pd.DataFrame()
-    if bionty_object is not None:
+    if public_ontology is not None:
         model_field_names = {i.name for i in model._meta.fields}
         # parents needs to be added here as relationships aren't in fields
         model_field_names.add("parents")
-        bionty_df = bionty_object.df().reset_index()
+        bionty_df = public_ontology.df().reset_index()
         if model.__name__ == "Gene":
             # groupby ensembl_gene_id and concat ncbi_gene_ids
             groupby_id_col = (

{lamindb-0.67.0 → lamindb-0.67.2}/lamindb/_query_manager.py

@@ -46,14 +46,11 @@ class QueryManager(models.Manager):
 
         Examples:
             >>> ln.save(ln.ULabel.from_values(["ULabel1", "ULabel2", "ULabel3"], field="name"))
-            >>> labels = ln.ULabel.filter(name__icontains = "label").all()
+            >>> labels = ln.ULabel.filter(name__icontains="label").all()
             >>> ln.ULabel(name="ULabel1").save()
             >>> label = ln.ULabel.filter(name="ULabel1").one()
             >>> label.parents.set(labels)
             >>> label.parents.list()
-            [ULabel(id=sFMcPepC, name=ULabel1, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
-            ULabel(id=2SscQvsM, name=ULabel2, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
-            ULabel(id=lecV87vi, name=ULabel3, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse)] # noqa
             >>> label.parents.list("name")
             ['ULabel1', 'ULabel2', 'ULabel3']
         """
@@ -76,7 +73,7 @@ class QueryManager(models.Manager):
         For `**kwargs`, see :meth:`lamindb.dev.QuerySet.df`.
         """
         self._track_run_input_manager()
-        return self.all_base_class()
+        return self._all_base_class()
 
     @doc_args(Registry.search.__doc__)
     def search(self, string: str, **kwargs):
@@ -115,5 +112,5 @@ models.Manager.__getitem__ = QueryManager.__getitem__
 models.Manager._track_run_input_manager = QueryManager._track_run_input_manager
 # the two lines below would be easy if we could actually inherit; like this,
 # they're suboptimal
-models.Manager.all_base_class = models.Manager.all
+models.Manager._all_base_class = models.Manager.all
 models.Manager.all = QueryManager.all

{lamindb-0.67.0 → lamindb-0.67.2}/lamindb/_query_set.py

@@ -4,7 +4,14 @@ from typing import Dict, Iterable, List, NamedTuple, Optional, Union
 import pandas as pd
 from django.db import models
 from lamindb_setup.dev._docs import doc_args
-from lnschema_core.models import CanValidate, IsTree, Registry
+from lnschema_core.models import (
+    Artifact,
+    CanValidate,
+    Collection,
+    IsTree,
+    Registry,
+    Transform,
+)
 from lnschema_core.types import ListLike, StrField
 
 
@@ -147,6 +154,13 @@ class QuerySet(models.QuerySet, CanValidate, IsTree):
                 df.rename(columns={values_expression: expression}, inplace=True)
         return df
 
+    def delete(self, *args, **kwargs):
+        if self.model in {Artifact, Collection, Transform}:
+            for record in self:
+                record.delete(*args, **kwargs)
+        else:
+            self._delete_base_class(*args, **kwargs)
+
     def list(self, field: Optional[str] = None) -> List[Registry]:
         """Populate a list with the results.
 
@@ -282,3 +296,5 @@ models.QuerySet.lookup = QuerySet.lookup
 models.QuerySet.validate = QuerySet.validate
 models.QuerySet.inspect = QuerySet.inspect
 models.QuerySet.standardize = QuerySet.standardize
+models.QuerySet._delete_base_class = models.QuerySet.delete
+models.QuerySet.delete = QuerySet.delete

{lamindb-0.67.0 → lamindb-0.67.2}/lamindb/_run.py

@@ -30,4 +30,27 @@ def __init__(run: Run, *args, **kwargs):
     )
 
 
+def delete_run_artifacts(run: Run) -> None:
+    environment = None
+    if run.environment is not None:
+        environment = run.environment
+        run.environment = None
+    report = None
+    if run.report is not None:
+        report = run.report
+        run.report = None
+    if environment is not None or report is not None:
+        run.save()
+    if environment is not None:
+        environment.delete(permanent=True)
+    if report is not None:
+        report.delete(permanent=True)
+
+
+def delete(self) -> None:
+    delete_run_artifacts(self)
+    super(Run, self).delete()
+
+
 Run.__init__ = __init__
+Run.delete = delete

{lamindb-0.67.0 → lamindb-0.67.2}/lamindb/_transform.py

@@ -1,7 +1,8 @@
 from typing import TYPE_CHECKING, Optional
 
-from lnschema_core.models import TRANSFORM_TYPE_DEFAULT, Transform
+from lnschema_core.models import TRANSFORM_TYPE_DEFAULT, Artifact, Run, Transform
 
+from ._run import delete_run_artifacts
 from .dev.versioning import get_uid_from_old_version, init_uid
 
 if TYPE_CHECKING:
@@ -63,4 +64,28 @@ def __init__(transform: Transform, *args, **kwargs):
     )
 
 
+def delete(self) -> None:
+    # set latest_report to None, it's tracked through the latest run
+    latest_report = None
+    if self.latest_report is not None:
+        latest_report = self.latest_report
+        self.latest_report = None
+    source_code = None
+    if self.source_code is not None:
+        source_code = self.source_code
+        self.source_code = None
+    if latest_report is not None or source_code is not None:
+        self.save()
+    if source_code is not None:
+        source_code.delete(permanent=True)
+    # query all runs and delete their artifacts
+    runs = Run.filter(transform=self)
+    for run in runs:
+        delete_run_artifacts(run)
+    # at this point, all artifacts have been taken care of
+    # we can now leverage CASCADE delete
+    super(Transform, self).delete()
+
+
 Transform.__init__ = __init__
+Transform.delete = delete

{lamindb-0.67.0 → lamindb-0.67.2}/lamindb/dev/_label_manager.py

@@ -23,7 +23,7 @@ def get_labels_as_dict(self: Data):
     ).items():
         if related_name in {
             "feature_sets",
-            "artifacts",
+            "unordered_artifacts",
             "input_of",
             "collections",
             "source_of",

{lamindb-0.67.0 → lamindb-0.67.2}/lamindb/dev/_run_context.py

@@ -27,9 +27,9 @@ msg_path_failed = (
 
 msg_manual_init = (
     "\n(1) save your notebook!"
-    "\n(2) attach metadata to the notebook by running the CLI:\n"
+    "\n(2) add stem_uid & version to your notebook file by running the CLI:\n"
     "lamin track {notebook_path}"
-    "\n(3) reload or re-open your notebook"
+    "\n(3) reload your notebook from disk"
 )
 
 

{lamindb-0.67.0 → lamindb-0.67.2}/lamindb/dev/storage/file.py

@@ -1,6 +1,8 @@
+import builtins
+import re
 import shutil
 from pathlib import Path
-from typing import Union
+from typing import Optional, Union
 
 import anndata as ad
 import pandas as pd
@@ -24,6 +26,7 @@ except ImportError:
 
 
 AUTO_KEY_PREFIX = ".lamindb/"
+is_run_from_ipython = getattr(builtins, "__IPYTHON__", False)
 
 
 # add type annotations back asap when re-organizing the module
@@ -143,6 +146,33 @@ def read_tsv(path: Union[str, Path, UPath]) -> pd.DataFrame:
     return pd.read_csv(path_sanitized, sep="\t")
 
 
+def load_html(path: Union[str, Path, UPath]):
+    if is_run_from_ipython:
+        with open(path, encoding="utf-8") as f:
+            html_content = f.read()
+        # Extract the body content using regular expressions
+        body_content = re.findall(
+            r"<body(?:.*?)>(?:.*?)</body>", html_content, re.DOTALL
+        )
+        # Remove any empty body tags
+        if body_content:
+            body_content = body_content[0]
+            body_content = body_content.strip()  # type: ignore
+        from IPython.display import HTML, display
+
+        display(HTML(data=body_content))
+    else:
+        return path
+
+
+def load_json(path: Union[str, Path, UPath]):
+    import json
+
+    with open(path) as f:
+        data = json.load(f)
+    return data
+
+
 def load_to_memory(filepath: Union[str, Path, UPath], stream: bool = False, **kwargs):
     """Load a file into memory.
 
@@ -170,6 +200,8 @@ def load_to_memory(filepath: Union[str, Path, UPath], stream: bool = False, **kw
         ".fcs": read_fcs,
         ".zarr": read_adata_zarr,
         ".zrad": read_adata_zarr,
+        ".html": load_html,
+        ".json": load_json,
     }
 
     reader = READER_FUNCS.get(filepath.suffix)

{lamindb-0.67.0 → lamindb-0.67.2}/noxfile.py

@@ -130,37 +130,41 @@ def docs(session):
         if group in {"tutorial", "guide", "biology"}:
             for path in Path(f"./docs/{group}").glob("*"):
                 path.rename(f"./docs/{path.name}")
-    login_testuser1(session)
     session.run(*"lamin init --storage ./docsbuild --schema bionty".split())
 
     def generate_cli_docs(main_parser):
         page = "# `lamin`\n\nFor a guide, see: {doc}`/setup`.\n\n"
-        commands = [
-            "login",
-            "init",
-            "load",
-            "close",
-            "delete",
-            "track",
-            "info",
-            "migrate",
-            "save",
-            "set",
-            "schema",
-        ]
+        command_groups = {
+            "General": ["login", "info"],
+            "Instances": [
+                "init",
+                "load",
+                "close",
+                "delete",
+                "migrate",
+                "set",
+                "schema",
+            ],
+            "Transforms": ["track", "save", "stage"],
+        }
         for action_group in main_parser._action_groups:
             for group_action in action_group._group_actions:
                 if type(group_action).__name__ == "_SubParsersAction":
-                    for command in commands:
-                        subparser = group_action.choices[command]
-                        # replace the "nox" command with the "lamin" command
-                        help_string = subparser.format_help().replace("nox", "lamin")
-                        page += f"## `lamin {command}`\n\n```\n{help_string}```\n\n"
+                    for command_group, commands in command_groups.items():
+                        page += f"## {command_group}\n\n"
+                        for command in commands:
+                            subparser = group_action.choices[command]
+                            # replace the "nox" command with the "lamin" command
+                            help_string = subparser.format_help().replace(
+                                "nox", "lamin"
+                            )
+                            page += (
+                                f"### `lamin {command}`\n\n```\n{help_string}```\n\n"
+                            )
         Path("./docs/cli.md").write_text(page)
 
     from lamin_cli import __main__
 
     generate_cli_docs(__main__.parser)
-
     build_docs(session, strip_prefix=True, strict=True)
     upload_docs_artifact(aws=True)

{lamindb-0.67.0 → lamindb-0.67.2}/pyproject.toml

@@ -19,7 +19,7 @@ dependencies = [
     "lnschema_core==0.61.1",
     "lamindb_setup==0.64.2",
     "lamin_utils==0.13.0",
-    "lamin_cli==0.6.0",
+    "lamin_cli==0.7.0",
     # others
     "rapidfuzz",
     "pyarrow",
@@ -37,7 +37,7 @@ Home = "https://github.com/laminlabs/lamindb"
 
 [project.optional-dependencies]
 bionty = [
-    "lnschema_bionty==0.38.3",
+    "lnschema_bionty==0.39.0",
 ]
 aws = [
     "botocore==1.31.17",  # for aiobotocore inside s3fs, to fix deps resolution
@@ -51,7 +51,7 @@ gcp = [
     "fsspec[gs]==2023.9.0"
 ]
 jupyter = [
-    "nbproject==0.9.2",  # keep pinning
+    "nbproject==0.10.0",  # keep pinning
     "nbstripout",
     "nbconvert",
 ]

lamindb-0.67.2/sub/lamin-cli/lamin_cli/__init__.py

@@ -0,0 +1,3 @@
+"""Lamin CLI."""
+
+__version__ = "0.7.0"

{lamindb-0.67.0 → lamindb-0.67.2}/sub/lamin-cli/lamin_cli/__main__.py

@@ -100,8 +100,12 @@ aa("--pypackage", type=str, metavar="pypackage", default=None, help=pypackage_he
 # save
 save_parser = subparsers.add_parser("save", help="save notebook or script")
 aa = save_parser.add_argument
-filepath_help = "A path to the notebook."
-aa("filepath", type=str, metavar="filepath", help=filepath_help)
+aa("filepath", type=str, metavar="filepath", help="filepath to notebook or script")
+
+# stage
+save_parser = subparsers.add_parser("stage", help="stage a notebook or script")
+aa = save_parser.add_argument
+aa("url", type=str, metavar="url", help="a lamin.ai url")
 
 # login and logout user
 login = subparsers.add_parser("login", help="log in")
@@ -219,6 +223,10 @@ def main():
         from lamin_cli._transform import save
 
         return save(args.filepath)
+    elif args.command == "stage":
+        from lamin_cli._stage import stage
+
+        return stage(args.url)
     elif args.command == "cache":
         from lamindb_setup._cache import clear_cache_dir, get_cache_dir, set_cache_dir
 

lamindb-0.67.2/sub/lamin-cli/lamin_cli/_stage.py

@@ -0,0 +1,29 @@
+from typing import Tuple
+from lamin_utils import logger
+
+
+def decompose_url(url: str) -> Tuple[str, str, str]:
+    assert "Transform" in url
+    uid = url.split("uid=")[1]
+    instance_identifier = "/".join(url.replace("https://lamin.ai/", "").split("/")[:2])
+    return instance_identifier, "transform", uid
+
+
+def stage(identifier: str):
+    import lamindb as ln
+
+    ln.settings.verbosity = "success"
+    if identifier.startswith("https://lamin.ai"):
+        instance_identifier, entity, uid = decompose_url(identifier)
+    else:
+        entity, uid = identifier.split()
+        instance_identifier = ln.setup.settings.instance.identifier
+
+    if entity == "transform":
+        transform = ln.Transform.using(instance_identifier).filter(uid=uid).one()
+        filepath_cache = transform.source_code.stage()
+        target_filename = f"{transform.short_name}.ipynb"
+        filepath_cache.rename(target_filename)
+        logger.success(f"staged source code of transform {uid} as {target_filename}")
+    else:
+        raise NotImplementedError

{lamindb-0.67.0 → lamindb-0.67.2}/sub/lamin-cli/lamin_cli/_transform.py

@@ -13,7 +13,7 @@ def init_script_metadata(script_path: str):
     from lnschema_core.ids import base62_12
 
     stem_uid = base62_12()
-    version = "0"
+    version = "1"
 
     with open(script_path) as f:
         content = f.read()
@@ -331,7 +331,7 @@ def save(filepath: str) -> Optional[str]:
         else:
             report_file = ln.Artifact(
                 filepath_html,
-                description=f"Report of transform {transform.uid}",
+                description=f"Report of run {run.uid}",
                 is_new_version_of=initial_report,
                 visibility=0,  # hidden file
             )

{lamindb-0.67.0 → lamindb-0.67.2}/sub/lamin-cli/tests/scripts/initialized.py

@@ -1,5 +1,5 @@
 __transform_stem_uid__ = "m5uCHTTpJnjQ"
-__version__ = "0"
+__version__ = "1"
 
 
 import lamindb as ln

{lamindb-0.67.0 → lamindb-0.67.2}/sub/lamin-cli/tests/test_scripts.py

@@ -7,6 +7,7 @@ scripts_dir = Path(__file__).parent.resolve() / "scripts"
 
 print(scripts_dir)
 
+
 def test_initialize():
     filepath = scripts_dir / "not-initialized.py"
     print(scripts_dir)
@@ -19,16 +20,16 @@ def test_initialize():
 
     with open(filepath) as f:
         content = f.read()
-    prepend = f'__transform_stem_uid__ = "'
+    prepend = '__transform_stem_uid__ = "'
     assert content.startswith(prepend)
 
 
-def test_run_and_save():
+def test_run_save_stage():
     env = os.environ
     env["LAMIN_TESTING"] = "true"
-    
+
     filepath = scripts_dir / "initialized.py"
-    # python sub/lamin-cli/tests/scripts/initialized.py     
+    # python sub/lamin-cli/tests/scripts/initialized.py
     result = subprocess.run(
         f"python {str(filepath)}",
         shell=True,
@@ -68,3 +69,11 @@ def test_run_and_save():
     )
     print(result)
     assert result.returncode == 0
+
+    result = subprocess.run(
+        "lamin stage 'transform m5uCHTTpJnjQ5zKv'",
+        shell=True,
+        capture_output=True,
+    )
+    print(result)
+    assert result.returncode == 0

lamindb-0.67.2/sub/lamin-cli/tests/test_stage.py

@@ -0,0 +1,21 @@
+from lamin_cli._stage import decompose_url
+import subprocess
+
+
+def test_decompose_url():
+    url = "https://lamin.ai/laminlabs/arrayloader-benchmarks/record/core/Transform?uid=1GCKs8zLtkc85zKv"  # noqa
+    instance_identifier, entity, uid = decompose_url(url)
+    assert instance_identifier == "laminlabs/arrayloader-benchmarks"
+    assert entity == "transform"
+    assert uid == "1GCKs8zLtkc85zKv"
+
+
+def test_stage():
+    result = subprocess.run(
+        "lamin stage"
+        " 'https://lamin.ai/laminlabs/arrayloader-benchmarks/record/core/Transform?uid=1GCKs8zLtkc85zKv'",  # noqa
+        shell=True,
+        capture_output=True,
+    )
+    print(result)
+    assert result.returncode == 0

{lamindb-0.67.0 → lamindb-0.67.2}/sub/lamindb-setup/docs/changelog.md

@@ -3,6 +3,8 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🐛 Fix option inheritance in create_path and add tests | [617](https://github.com/laminlabs/lamindb-setup/pull/617) | [Koncopd](https://github.com/Koncopd) | 2024-01-12 |
+✅ Update tests relying on laminhub-rest | [616](https://github.com/laminlabs/lamindb-setup/pull/616) | [fredericenard](https://github.com/fredericenard) | 2024-01-12 |
 🚚 Rename .bionty to .public | [615](https://github.com/laminlabs/lamindb-setup/pull/615) | [sunnyosun](https://github.com/sunnyosun) | 2024-01-10 | 0.64.2
 🚸 Fix connection timeout | [611](https://github.com/laminlabs/lamindb-setup/pull/611) | [falexwolf](https://github.com/falexwolf) | 2024-01-08 | 0.64.1
 🚸 Add anonymous access (now works without login) | [610](https://github.com/laminlabs/lamindb-setup/pull/610) | [falexwolf](https://github.com/falexwolf) | 2024-01-06 | 0.64.0