lamindb 1.12.0__tar.gz → 1.13.0__tar.gz

{lamindb-1.12.0 → lamindb-1.13.0}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.12.0
-Summary: A data lakehouse for biology.
+Version: 1.13.0
+Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10,<3.14
 Description-Content-Type: text/markdown
@@ -10,13 +10,14 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: lamin_utils==0.15.0
-Requires-Dist: lamin_cli==1.8.0
-Requires-Dist: lamindb_setup[aws]==1.11.0
+Requires-Dist: lamin_cli==1.8.1
+Requires-Dist: lamindb_setup[aws]==1.12.0
 Requires-Dist: bionty==1.8.1
 Requires-Dist: wetlab==1.6.1
 Requires-Dist: nbproject==0.11.1
 Requires-Dist: jupytext
 Requires-Dist: nbconvert>=7.2.1
+Requires-Dist: ipykernel<7.0.0
 Requires-Dist: pyyaml
 Requires-Dist: pyarrow
 Requires-Dist: pandera>=0.24.0
@@ -56,38 +57,41 @@ Provides-Extra: zarr
 [![pypi](https://img.shields.io/pypi/v/lamindb?color=blue&label=pypi%20package)](https://pypi.org/project/lamindb)
 [![PyPI Downloads](https://img.shields.io/pepy/dt/lamindb?logo=pypi)](https://pepy.tech/project/lamindb)
 
-# LaminDB - A data lakehouse for biology
+# LaminDB - A data framework for biology
 
-LaminDB organizes datasets through validation & annotation and provides data lineage, queryability & reproducibility on top of [FAIR](https://en.wikipedia.org/wiki/FAIR_data) data.
+Makes your data queryable, traceable, reproducible, and FAIR. One API: lakehouse, lineage, feature store, ontologies, LIMS, ELN.
 
 <details>
 <summary>Why?</summary>
 
 Reproducing analytical results or understanding how a dataset or model was created can be a pain.
-Let alone training models on historical data, LIMS & ELN systems, orthogonal assays, or datasets generated by other teams.
-Even maintaining a mere overview of a project's or team's datasets & analyses is harder than it sounds.
+Training models on historical data, LIMS & ELN systems, orthogonal assays, or datasets from other teams is even harder.
+Even maintaining an overview of a project's datasets & analyses is more difficult than it should be.
 
-Biological datasets are typically managed with versioned storage systems, GUI-focused community or SaaS platforms, structureless data lakes, rigid data warehouses (SQL, monolithic arrays), and data lakehouses for tabular data.
+Biological datasets are typically managed with versioned storage systems, GUI-focused platforms, structureless data lakes, rigid data warehouses (SQL, monolithic arrays), or tabular lakehouses.
 
 LaminDB extends the lakehouse architecture to biological registries & datasets beyond tables (`DataFrame`, `AnnData`, `.zarr`, `.tiledbsoma`, ...) with enough structure to enable queries and enough freedom to keep the pace of R&D high.
 Moreover, it provides context through data lineage -- tracing data and code, scientists and models -- and abstractions for biological domain knowledge and experimental metadata.
 
 </details>
 
-**Highlights.**
+<img width="800px" src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/BunYmHkyFLITlM5M0005.png">
 
-- **data lineage:** track inputs & outputs of notebooks, scripts, functions & pipelines with a single line of code
-- **unified access:** storage locations (local, S3, GCP, ...), SQL databases (Postgres, SQLite) & ontologies
-- **lakehouse**: manage, monitor & validate features, labels & dataset schemas; distributed queries and batch loading
-- **biological formats:** validate & annotate `DataFrame`, `AnnData`, `SpatialData`, ... backed by `parquet`, `zarr`, HDF5, LanceDB, ...
-- **biological entities**: manage experimental metadata & ontologies based on the Django ORM
-- **reproducible & auditable:** auto-version & timestamp execution reports, source code & compute environments, attribute records to users
-- **zero lock-in & scalable:** runs in your infrastructure; is _not_ a client for a rate-limited REST API
-- **extendable:** create custom plug-ins for your own applications based on the Django ecosystem
-- **integrations:** visualization tools like [vitessce](https://docs.lamin.ai/vitessce), workflow managers like [nextflow](https://docs.lamin.ai/nextflow) & [redun](https://docs.lamin.ai/redun), and [other tools](https://docs.lamin.ai/integrations)
-- **production-ready:** used in BigPharma, BioTech, hospitals & top labs
+Highlights:
 
-LaminDB can be connected to LaminHub to serve as a [LIMS](https://en.wikipedia.org/wiki/Laboratory_information_management_system) for wetlab scientists, closing the drylab-wetlab feedback loop: [lamin.ai](https://lamin.ai).
+- **lineage** → track inputs & outputs of notebooks, scripts, functions & pipelines with a single line of code
+- **lakehouse** → manage, monitor & validate schemas; query across many datasets
+- **feature store** → manage features & labels; leverage batch loading
+- **FAIR datasets** → validate & annotate `DataFrame`, `AnnData`, `SpatialData`, `parquet`, `.h5ad`, `zarr`, ...
+- **LIMS & ELN** → manage experimental metadata, ontologies & markdown notes
+- **unified access** → storage locations (local, S3, GCP, ...), SQL databases (Postgres, SQLite) & ontologies
+- **reproducible & auditable** → auto-version & timestamp execution reports, source code & environments; attribute records to users
+- **integrations** → [vitessce](https://docs.lamin.ai/vitessce), [nextflow](https://docs.lamin.ai/nextflow), [redun](https://docs.lamin.ai/redun), and [more](https://docs.lamin.ai/integrations)
+- **zero lock-in & scalable** → runs in your infrastructure; not a client for a rate-limited REST API
+- **extendable** → create custom plug-ins based on the Django ORM
+- **production-ready** → used in BigPharma, BioTech, hospitals & top labs
+
+If you want a GUI, you can connect your LaminDB instance to LaminHub and close the drylab-wetlab feedback loop: [lamin.ai](https://lamin.ai).
 
 ## Docs
 
@@ -159,7 +163,7 @@ You can organize datasets with validation & annotation of any kind of metadata t
 To annotate an artifact with a label, use:
 
 ```python
-my_experiment = ln.Record(name="My experiment").save()  # create a label in the universal label ontology
+my_experiment = ln.Record(name="My experiment").save()  # create a label record
 artifact.records.add(my_experiment)  # annotate the artifact with the label
 ```
 

{lamindb-1.12.0 → lamindb-1.13.0}/README.md

@@ -5,38 +5,41 @@
 [![pypi](https://img.shields.io/pypi/v/lamindb?color=blue&label=pypi%20package)](https://pypi.org/project/lamindb)
 [![PyPI Downloads](https://img.shields.io/pepy/dt/lamindb?logo=pypi)](https://pepy.tech/project/lamindb)
 
-# LaminDB - A data lakehouse for biology
+# LaminDB - A data framework for biology
 
-LaminDB organizes datasets through validation & annotation and provides data lineage, queryability & reproducibility on top of [FAIR](https://en.wikipedia.org/wiki/FAIR_data) data.
+Makes your data queryable, traceable, reproducible, and FAIR. One API: lakehouse, lineage, feature store, ontologies, LIMS, ELN.
 
 <details>
 <summary>Why?</summary>
 
 Reproducing analytical results or understanding how a dataset or model was created can be a pain.
-Let alone training models on historical data, LIMS & ELN systems, orthogonal assays, or datasets generated by other teams.
-Even maintaining a mere overview of a project's or team's datasets & analyses is harder than it sounds.
+Training models on historical data, LIMS & ELN systems, orthogonal assays, or datasets from other teams is even harder.
+Even maintaining an overview of a project's datasets & analyses is more difficult than it should be.
 
-Biological datasets are typically managed with versioned storage systems, GUI-focused community or SaaS platforms, structureless data lakes, rigid data warehouses (SQL, monolithic arrays), and data lakehouses for tabular data.
+Biological datasets are typically managed with versioned storage systems, GUI-focused platforms, structureless data lakes, rigid data warehouses (SQL, monolithic arrays), or tabular lakehouses.
 
 LaminDB extends the lakehouse architecture to biological registries & datasets beyond tables (`DataFrame`, `AnnData`, `.zarr`, `.tiledbsoma`, ...) with enough structure to enable queries and enough freedom to keep the pace of R&D high.
 Moreover, it provides context through data lineage -- tracing data and code, scientists and models -- and abstractions for biological domain knowledge and experimental metadata.
 
 </details>
 
-**Highlights.**
+<img width="800px" src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/BunYmHkyFLITlM5M0005.png">
 
-- **data lineage:** track inputs & outputs of notebooks, scripts, functions & pipelines with a single line of code
-- **unified access:** storage locations (local, S3, GCP, ...), SQL databases (Postgres, SQLite) & ontologies
-- **lakehouse**: manage, monitor & validate features, labels & dataset schemas; distributed queries and batch loading
-- **biological formats:** validate & annotate `DataFrame`, `AnnData`, `SpatialData`, ... backed by `parquet`, `zarr`, HDF5, LanceDB, ...
-- **biological entities**: manage experimental metadata & ontologies based on the Django ORM
-- **reproducible & auditable:** auto-version & timestamp execution reports, source code & compute environments, attribute records to users
-- **zero lock-in & scalable:** runs in your infrastructure; is _not_ a client for a rate-limited REST API
-- **extendable:** create custom plug-ins for your own applications based on the Django ecosystem
-- **integrations:** visualization tools like [vitessce](https://docs.lamin.ai/vitessce), workflow managers like [nextflow](https://docs.lamin.ai/nextflow) & [redun](https://docs.lamin.ai/redun), and [other tools](https://docs.lamin.ai/integrations)
-- **production-ready:** used in BigPharma, BioTech, hospitals & top labs
+Highlights:
 
-LaminDB can be connected to LaminHub to serve as a [LIMS](https://en.wikipedia.org/wiki/Laboratory_information_management_system) for wetlab scientists, closing the drylab-wetlab feedback loop: [lamin.ai](https://lamin.ai).
+- **lineage** → track inputs & outputs of notebooks, scripts, functions & pipelines with a single line of code
+- **lakehouse** → manage, monitor & validate schemas; query across many datasets
+- **feature store** → manage features & labels; leverage batch loading
+- **FAIR datasets** → validate & annotate `DataFrame`, `AnnData`, `SpatialData`, `parquet`, `.h5ad`, `zarr`, ...
+- **LIMS & ELN** → manage experimental metadata, ontologies & markdown notes
+- **unified access** → storage locations (local, S3, GCP, ...), SQL databases (Postgres, SQLite) & ontologies
+- **reproducible & auditable** → auto-version & timestamp execution reports, source code & environments; attribute records to users
+- **integrations** → [vitessce](https://docs.lamin.ai/vitessce), [nextflow](https://docs.lamin.ai/nextflow), [redun](https://docs.lamin.ai/redun), and [more](https://docs.lamin.ai/integrations)
+- **zero lock-in & scalable** → runs in your infrastructure; not a client for a rate-limited REST API
+- **extendable** → create custom plug-ins based on the Django ORM
+- **production-ready** → used in BigPharma, BioTech, hospitals & top labs
+
+If you want a GUI, you can connect your LaminDB instance to LaminHub and close the drylab-wetlab feedback loop: [lamin.ai](https://lamin.ai).
 
 ## Docs
 
@@ -108,7 +111,7 @@ You can organize datasets with validation & annotation of any kind of metadata t
 To annotate an artifact with a label, use:
 
 ```python
-my_experiment = ln.Record(name="My experiment").save()  # create a label in the universal label ontology
+my_experiment = ln.Record(name="My experiment").save()  # create a label record
 artifact.records.add(my_experiment)  # annotate the artifact with the label
 ```
 

{lamindb-1.12.0 → lamindb-1.13.0}/docs/curate.ipynb

@@ -780,7 +780,7 @@
    },
    "outputs": [],
    "source": [
-    "adata = ln.core.datasets.mini_immuno.get_dataset1(\n",
+    "adata = ln.examples.datasets.mini_immuno.get_dataset1(\n",
     "    with_gene_typo=True, with_cell_type_typo=True, otype=\"AnnData\"\n",
     ")\n",
     "adata"

{lamindb-1.12.0 → lamindb-1.13.0}/docs/faq/acid.ipynb

@@ -145,7 +145,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert len(ln.Artifact.filter().all()) == 0"
+    "assert len(ln.Artifact.filter()) == 0"
    ]
   },
   {
@@ -203,7 +203,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifacts = ln.Artifact.filter().all()\n",
+    "artifacts = ln.Artifact.filter()\n",
     "assert len(artifacts) == 0"
    ]
   },

{lamindb-1.12.0 → lamindb-1.13.0}/docs/faq/pydantic-pandera.ipynb

@@ -49,7 +49,7 @@
     "\n",
     "from typing import Literal, Any\n",
     "\n",
-    "df = ln.examples.datasets.small_dataset1()\n",
+    "df = ln.examples.datasets.mini_immuno.get_dataset1()\n",
     "df"
    ]
   },

lamindb-1.12.0/docs/faq/visibility.ipynb → lamindb-1.13.0/docs/faq/trash-archive.ipynb

@@ -4,16 +4,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# When does visibility of artifacts and collections change?\n",
+    "# How do I trash or archive records?\n",
     "\n",
-    "Any record in LaminDB has the following 3 levels of visibility:\n",
+    "Any record in LaminDB has the following 3 levels of visibility through 3 default branches:\n",
     "- 1: \"default\", visible by default\n",
     "- 0: \"archive\", excluded from query & search by default\n",
-    "- -1: \"trash\", excluded from the query results, set with `.delete()`\n",
-    "\n",
-    "These values are represented in the database via a private integer field `branch_id` that also models the branches involved in merge requests.\n",
-    "\n",
-    "However, `.filter()` also accepts the `visibility` keyword, see below."
+    "- -1: \"trash\", excluded from query & search by default"
    ]
   },
   {
@@ -22,8 +18,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# !pip install lamindb\n",
-    "!lamin init --storage test-branch_id"
+    "# pip install lamindb\n",
+    "!lamin init --storage test-branch"
    ]
   },
   {
@@ -43,16 +39,15 @@
    "outputs": [],
    "source": [
     "artifact = ln.Artifact.from_dataframe(\n",
-    "    pd.DataFrame({\"a\": [1, 2], \"b\": [3, 4]}), description=\"mydf\"\n",
-    ")\n",
-    "artifact.save()"
+    "    pd.DataFrame({\"a\": [1, 2], \"b\": [3, 4]}), key=\"dataset.parquet\"\n",
+    ").save()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "A new artifact has default visibility 1 via `branch_id`:"
+    "An artifact is by default created on the `main` branch and then visible."
    ]
   },
   {
@@ -61,23 +56,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert artifact.branch_id == 1"
+    "assert artifact.branch.name == \"main\""
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "When you delete an artifact, its `branch_id` is set to -1 (\"trash\"):"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "artifact.delete()"
+    "If you delete an artifact, it gets moved into the `trash` branch."
    ]
   },
   {
@@ -86,14 +72,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert artifact.branch_id == -1"
+    "artifact.delete()\n",
+    "assert artifact.branch.name == \"trash\""
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Files in trash won't be returned from default queries:"
+    "Artifacts in trash won't via default queries:"
    ]
   },
   {
@@ -102,14 +89,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.Artifact.filter(description=\"mydf\").all()"
+    "ln.Artifact.filter(key=\"dataset.parquet\").to_dataframe()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Unless you specify `visibility=None` to see all hidden and trashed artifacts."
+    "You can query for them by adding the `trash` branch to the filter."
    ]
   },
   {
@@ -118,7 +105,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.Artifact.filter(description=\"mydf\", visibility=None).all()"
+    "ln.Artifact.filter(key=\"dataset.parquet\", branch__name=\"trash\").to_dataframe()"
    ]
   },
   {
@@ -134,50 +121,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifact.restore()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "assert artifact.branch_id == 1"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "ln.Artifact.filter(description=\"mydf\").all()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Delete test artifact and instance:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "artifact.delete(permanent=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!lamin delete --force test-branch_id"
+    "artifact.restore()\n",
+    "assert artifact.branch.name == \"main\"\n",
+    "ln.Artifact.filter(key=\"dataset.parquet\").to_dataframe()"
    ]
   }
  ],

{lamindb-1.12.0 → lamindb-1.13.0}/docs/faq.md

@@ -7,11 +7,10 @@ faq/pydantic-pandera
 faq/idempotency
 faq/acid
 faq/track-run-inputs
-faq/setup
 faq/curate-any
 faq/import-modules
 faq/reference-field
-faq/visibility
+faq/trash-archive
 faq/delete
 faq/keep-artifacts-local
 faq/validate-fields

{lamindb-1.12.0 → lamindb-1.13.0}/docs/registries.ipynb

@@ -293,7 +293,7 @@
    "id": "25",
    "metadata": {},
    "source": [
-    "Filter for all artifacts annotated by a record:"
+    "Filter for all artifacts annotated by a record and get the result as a dataframe:"
    ]
   },
   {
@@ -315,12 +315,15 @@
    "id": "27",
    "metadata": {},
    "source": [
+    "{meth}`~lamindb.models.SQLRecord.filter` returns a {class}`~lamindb.models.QuerySet`. \n",
+    "\n",
     "To access the results encoded in a filter statement, execute its return value with one of:\n",
     "\n",
     "- {meth}`~lamindb.models.QuerySet.to_dataframe`: A pandas `DataFrame` with each record in a row.\n",
-    "- {meth}`~lamindb.models.QuerySet.all`: A {class}`~lamindb.models.QuerySet`.\n",
     "- {meth}`~lamindb.models.QuerySet.one`: Exactly one record. Will raise an error if there is none. Is equivalent to the `.get()` method shown above.\n",
-    "- {meth}`~lamindb.models.QuerySet.one_or_none`: Either one record or `None` if there is no query result."
+    "- {meth}`~lamindb.models.QuerySet.one_or_none`: Either one record or `None` if there is no query result.\n",
+    "\n",
+    "You can also use it as an iterator or get individual records via `__getitem__` (`[0]`, `[1]` etc.)."
    ]
   },
   {
@@ -330,8 +333,6 @@
    "source": [
     "```{note}\n",
     "\n",
-    "{meth}`~lamindb.models.SQLRecord.filter` returns a {class}`~lamindb.models.QuerySet`.\n",
-    "\n",
     "The registries in LaminDB are Django Models and any [Django query](https://docs.djangoproject.com/en/stable/topics/db/queries/) works.\n",
     "\n",
     "LaminDB re-interprets Django's API for data scientists.\n",
@@ -540,7 +541,7 @@
    "source": [
     "cd8a = bt.Gene.get(symbol=\"CD8A\")\n",
     "# query for all feature sets that contain CD8A\n",
-    "feature_sets_with_cd8a = ln.Schema.filter(genes=cd8a).all()\n",
+    "feature_sets_with_cd8a = ln.Schema.filter(genes=cd8a)\n",
     "# get all artifacts\n",
     "ln.Artifact.filter(feature_sets__in=feature_sets_with_cd8a).to_dataframe()"
    ]

{lamindb-1.12.0 → lamindb-1.13.0}/docs/scripts/curate_dataframe_external_features.py

@@ -1,6 +1,6 @@
 import lamindb as ln
 
-df = ln.examples.datasets.small_dataset1(otype="DataFrame")
+df = ln.examples.datasets.mini_immuno.get_dataset1(otype="DataFrame")
 
 species = ln.Feature(name="species", dtype="str").save()
 split = ln.Feature(name="split", dtype="str").save()

{lamindb-1.12.0 → lamindb-1.13.0}/docs/scripts/curate_dataframe_flexible.py

@@ -2,7 +2,7 @@ import lamindb as ln
 
 ln.examples.datasets.mini_immuno.define_features_labels()
 schema = ln.examples.schemas.valid_features()
-df = ln.examples.datasets.small_dataset1(otype="DataFrame")
+df = ln.examples.datasets.mini_immuno.get_dataset1(otype="DataFrame")
 artifact = ln.Artifact.from_dataframe(
     df, key="examples/dataset1.parquet", schema=schema
 ).save()

{lamindb-1.12.0 → lamindb-1.13.0}/docs/scripts/curate_dataframe_minimal_errors.py

@@ -1,7 +1,7 @@
 import lamindb as ln
 
 schema = ln.examples.datasets.mini_immuno.define_mini_immuno_schema_flexible()
-df = ln.examples.datasets.small_dataset1(otype="DataFrame")
+df = ln.examples.datasets.mini_immuno.get_dataset1(otype="DataFrame")
 df.pop("donor")  # remove donor column to trigger validation error
 try:
     artifact = ln.Artifact.from_dataframe(

{lamindb-1.12.0 → lamindb-1.13.0}/docs/scripts/run_track_with_params.py

@@ -11,7 +11,7 @@ if __name__ == "__main__":
         "input_dir": args.input_dir,
         "learning_rate": args.learning_rate,
         "preprocess_params": {
-            "downsample": args.downsample,  # nested parameter names & values in dictionaries are not validated
+            "downsample": args.downsample,
             "normalization": "the_good_one",
         },
     }

{lamindb-1.12.0 → lamindb-1.13.0}/docs/scripts/run_workflow.py

@@ -1,8 +1,6 @@
 import argparse
 import lamindb as ln
 
-ln.Param(name="run_workflow_subset", dtype=bool).save()
-
 
 @ln.tracked()
 def subset_dataframe(
@@ -22,12 +20,12 @@ if __name__ == "__main__":
     p.add_argument("--subset", action="store_true")
     args = p.parse_args()
 
-    params = {"run_workflow_subset": args.subset}
+    params = {"is_subset": args.subset}
 
     ln.track(params=params)
 
     if args.subset:
-        df = ln.examples.datasets.small_dataset1(otype="DataFrame")
+        df = ln.examples.datasets.mini_immuno.get_dataset1(otype="DataFrame")
         artifact = ln.Artifact.from_dataframe(
             df, key="my_analysis/dataset.parquet"
         ).save()

{lamindb-1.12.0 → lamindb-1.13.0}/docs/storage/prepare-transfer-local-to-cloud.ipynb

@@ -13,7 +13,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!lamin settings set auto-connect false"
+    "!lamin disconnect"
    ]
   },
   {
@@ -48,16 +48,12 @@
     ").save()\n",
     "features = bt.CellMarker.from_values(\n",
     "    [\"PD1\", \"CD21\"], field=bt.CellMarker.name, organism=\"human\"\n",
-    ")\n",
-    "ln.save(features)\n",
-    "artifact.features._add_schema(ln.FeatureSet(features), slot=\"var\")\n",
-    "\n",
+    ").save()\n",
+    "artifact.features._add_schema(ln.Schema(features), slot=\"var\")\n",
     "organism = bt.Organism.from_source(name=\"human\").save()\n",
     "artifact.labels.add(organism)\n",
-    "\n",
     "experiment = wl.Experiment(name=\"experiment-test-transfer-to-cloud\").save()\n",
     "artifact.experiments.add(experiment)\n",
-    "\n",
     "artifact.describe()"
    ]
   },
@@ -67,7 +63,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert artifact.features[\"var\"].count() == 2"
+    "assert artifact.features.slots[\"var\"].members.count() == 2"
    ]
   }
  ],

{lamindb-1.12.0 → lamindb-1.13.0}/docs/storage/transfer-local-to-cloud.ipynb

@@ -14,10 +14,8 @@
    "outputs": [],
    "source": [
     "import lamindb as ln\n",
-    "import bionty as bt\n",
     "\n",
-    "ln.connect(\"laminlabs/lamin-dev\")\n",
-    "bt.settings.organism = \"human\""
+    "ln.connect(\"laminlabs/lamin-dev\")"
    ]
   },
   {
@@ -38,7 +36,7 @@
     "    experiments.delete()\n",
     "\n",
     "\n",
-    "artifacts = ln.Artifact.filter(description=\"test-transfer-to-cloud\").all()\n",
+    "artifacts = ln.Artifact.filter(description=\"test-transfer-to-cloud\")\n",
     "for artifact in artifacts:\n",
     "    cleanup(artifact)"
    ]
@@ -102,7 +100,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "py312",
    "language": "python",
    "name": "python3"
   },
@@ -116,7 +114,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,