lamindb 0.70.1__tar.gz → 0.70.2__tar.gz

{lamindb-0.70.1 → lamindb-0.70.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.70.1
+Version: 0.70.2
 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==0.69.4
+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-0.70.2}/docs/changelog.md

@@ -14,9 +14,14 @@ 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)
+- 🐛 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-0.70.2/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-0.70.1 → 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-0.70.1 → lamindb-0.70.2}/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__ = "0.70.2"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

{lamindb-0.70.1 → 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-0.70.1 → 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-0.70.1 → lamindb-0.70.2}/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-0.70.2}/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-0.70.2/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-0.70.2/lamindb/integrations/_vitessce.py

@@ -0,0 +1,70 @@
+from __future__ import annotations
+
+import json
+from datetime import datetime, timezone
+from typing import TYPE_CHECKING
+
+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
+
+
+# tested & context in https://github.com/laminlabs/lamin-spatial
+def save_vitessce_config(vitessce_config: VitessceConfig, description: str) -> Artifact:
+    """Validates and saves a ``VitessceConfig`` object.
+
+    Example: :doc:`docs:vitessce`.
+
+    Args:
+        vitessce_config (``VitessceConfig``): A VitessceConfig object.
+        description: A description for the artifact.
+
+    .. 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(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-0.70.1 → lamindb-0.70.2}/noxfile.py

@@ -74,6 +74,7 @@ def install(session, group):
         session.run(
             *"uv pip install --system --no-deps git+https://github.com/laminlabs/wetlab".split()
         )
+        session.run(*"uv pip install --system vitessce".split())
     elif group == "docs":
         extras += "bionty"
         session.run(*"uv pip install --system mudata".split())

{lamindb-0.70.1 → lamindb-0.70.2}/pyproject.toml

@@ -17,8 +17,8 @@ classifiers = [
 dependencies = [
     # Lamin PINNED packages
     "lnschema_core==0.65.1",
-    "lamindb_setup==0.69.2",
-    "lamin_utils==0.13.1",
+    "lamindb_setup==0.69.4",
+    "lamin_utils==0.13.2",
     "lamin_cli==0.12.3",
     # others
     "rapidfuzz",

{lamindb-0.70.1 → lamindb-0.70.2}/sub/lamindb-setup/docs/changelog.md

@@ -3,6 +3,8 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+♻️ Do not always read from local cache | [720](https://github.com/laminlabs/lamindb-setup/pull/720) | [falexwolf](https://github.com/falexwolf) | 2024-04-19 | 0.69.4
+♻️ Improve suffix handling | [718](https://github.com/laminlabs/lamindb-setup/pull/718) | [falexwolf](https://github.com/falexwolf) | 2024-04-19 | 0.69.3
 ✨ Enable hybrid storage mode | [717](https://github.com/laminlabs/lamindb-setup/pull/717) | [falexwolf](https://github.com/falexwolf) | 2024-04-16 | 0.69.1
 🚸 Better migrations warning | [716](https://github.com/laminlabs/lamindb-setup/pull/716) | [falexwolf](https://github.com/falexwolf) | 2024-04-16 |
 🚸 Refresh token also upon access-aws | [715](https://github.com/laminlabs/lamindb-setup/pull/715) | [falexwolf](https://github.com/falexwolf) | 2024-04-15 |

{lamindb-0.70.1 → lamindb-0.70.2}/sub/lamindb-setup/lamindb_setup/__init__.py

@@ -36,7 +36,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.69.2"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.69.4"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import sys
 from os import name as _os_name

{lamindb-0.70.1 → lamindb-0.70.2}/sub/lamindb-setup/lamindb_setup/_connect_instance.py

@@ -50,8 +50,11 @@ def update_db_using_local(
             if os.getenv("LAMINDB_INSTANCE_DB") is not None:
                 logger.important("loading db URL from env variable LAMINDB_INSTANCE_DB")
                 db_dsn_local = LaminDsnModel(db=os.getenv("LAMINDB_INSTANCE_DB"))
-            # read from a cached settings file
-            elif settings_file.exists():
+            # read from a cached settings file in case the hub result is only
+            # read level or inexistent
+            elif settings_file.exists() and (
+                "read" in db_dsn_hub.db.user or db_dsn_hub.db.user is None
+            ):
                 isettings = load_instance_settings(settings_file)
                 db_dsn_local = LaminDsnModel(db=isettings.db)
             else:

{lamindb-0.70.1 → lamindb-0.70.2}/sub/lamindb-setup/lamindb_setup/core/upath.py

@@ -21,7 +21,8 @@ LocalPathClasses = (PosixUPath, WindowsUPath, LocalPath)
 
 # also see https://gist.github.com/securifera/e7eed730cbe1ce43d0c29d7cd2d582f4
 #    ".gz" is not listed here as it typically occurs with another suffix
-KNOWN_SUFFIXES = {
+# the complete list is at lamindb.core.storage._suffixes
+VALID_SUFFIXES = {
     #
     # without readers
     #
@@ -47,7 +48,7 @@ KNOWN_SUFFIXES = {
     ".fcs",
     ".xslx",
     ".zarr",
-    ".zrad",
+    ".json",
 }
 
 
@@ -56,13 +57,17 @@ TRAILING_SEP = (os.sep, os.altsep) if os.altsep is not None else os.sep
 
 def extract_suffix_from_path(path: Path, arg_name: Optional[str] = None) -> str:
     def process_digits(suffix: str):
-        if suffix[1:].isdigit():
+        if suffix[1:].isdigit():  # :1 to skip the dot
             return ""  # digits are no valid suffixes
         else:
             return suffix
 
     if len(path.suffixes) <= 1:
         return process_digits(path.suffix)
+
+    total_suffix = "".join(path.suffixes)
+    if total_suffix in VALID_SUFFIXES:
+        return total_suffix
     else:
         print_hint = True
         arg_name = "file" if arg_name is None else arg_name  # for the warning
@@ -73,18 +78,18 @@ def extract_suffix_from_path(path: Path, arg_name: Optional[str] = None) -> str:
         # in COMPRESSION_SUFFIXES to detect something like .random.gz and then
         # add ".random.gz" but concluded it's too dangerous it's safer to just
         # use ".gz" in such a case
-        if path.suffixes[-2] in KNOWN_SUFFIXES:
+        if path.suffixes[-2] in VALID_SUFFIXES:
             suffix = "".join(path.suffixes[-2:])
             msg += f"inferring: '{suffix}'"
             # do not print a warning for things like .tar.gz, .fastq.gz
             if path.suffixes[-1] == ".gz":
                 print_hint = False
         else:
-            suffix = path.suffixes[-1]  # this is equivalent to path.suffix!!!
+            suffix = path.suffixes[-1]  # this is equivalent to path.suffix
             msg += (
-                f"using only last suffix: '{suffix}' - if you want your file format to"
-                " be recognized, make an issue:"
-                " https://github.com/laminlabs/lamindb/issues/new"
+                f"using only last suffix: '{suffix}' - if you want your composite"
+                " suffix to be recognized add it to"
+                " lamindb.core.storage.VALID_SUFFIXES.add()"
             )
         if print_hint:
             logger.hint(msg)

{lamindb-0.70.1 → lamindb-0.70.2}/sub/lamindb-setup/tests/hub-cloud/test_connect_instance.py

@@ -116,16 +116,31 @@ def test_load_after_private_public_switch():
 
 def test_load_with_db_parameter():
     if os.getenv("LAMIN_ENV") == "prod":
-        ln_setup.login("static-testuser1@lamin.ai", key="static-testuser1-password")
+        # take a write-level access collaborator
+        ln_setup.login("testuser1")
         # test load from hub
         ln_setup.connect("laminlabs/lamindata", _test=True)
+        assert "root" in ln_setup.settings.instance.db
         # test load from provided db argument
-        db = "postgresql://testuser:testpwd@database2.cmyfs24wugc3.us-east-1.rds.amazonaws.com:5432/db1"  # noqa
+        db = "postgresql://testdbuser:testpwd@database2.cmyfs24wugc3.us-east-1.rds.amazonaws.com:5432/db1"  # noqa
         ln_setup.connect("laminlabs/lamindata", db=db, _test=True)
-        assert "testuser" in ln_setup.settings.instance.db
-        # test load from cache (no db arg)
+        assert "testdbuser" in ln_setup.settings.instance.db
+        # test ignore loading from cache because hub result has >read access
         ln_setup.connect("laminlabs/lamindata", _test=True)
-        assert "testuser" in ln_setup.settings.instance.db
+        assert "root" in ln_setup.settings.instance.db
+
+        # now take a user that has no collaborator status
+        ln_setup.login("testuser2")
+        # the cached high priviledge connection string remains active
+        ln_setup.connect("laminlabs/lamindata", _test=True)
+        assert "root" in ln_setup.settings.instance.db
+        # now pass the connection string
+        ln_setup.connect("laminlabs/lamindata", db=db, _test=True)
+        assert "testdbuser" in ln_setup.settings.instance.db
+        # now the cache is used
+        ln_setup.connect("laminlabs/lamindata", _test=True)
+        assert "testdbuser" in ln_setup.settings.instance.db
+
         # test corrupted input
         db_corrupted = "postgresql://testuser:testpwd@wrongserver:5432/db1"
         with pytest.raises(ValueError) as error:
@@ -133,4 +148,3 @@ def test_load_with_db_parameter():
         assert error.exconly().startswith(
             "ValueError: The local differs from the hub database information"
         )
-        ln_setup.login("testuser2")

{lamindb-0.70.1 → lamindb-0.70.2}/tests/notebooks/with-title-initialized-consecutive-finish-not-last-cell.ipynb

@@ -14,8 +14,7 @@
    "outputs": [],
    "source": [
     "import lamindb as ln\n",
-    "import pytest\n",
-    "from lamindb._finish import CallFinishInLastCell"
+    "import pytest"
    ]
   },
   {
@@ -44,7 +43,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.finish(i_saved_the_notebook=True)"
+    "ln.finish()"
    ]
   },
   {

{lamindb-0.70.1 → lamindb-0.70.2}/tests/notebooks/with-title-initialized-consecutive-finish.ipynb

@@ -51,7 +51,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.finish(i_saved_the_notebook=True)"
+    "ln.finish()"
    ]
   }
  ],