lamindb 1.11a1__tar.gz → 1.11.2__tar.gz

{lamindb-1.11a1 → lamindb-1.11.2}/.gitignore

@@ -66,7 +66,9 @@ run-tests
 test-django-validation/
 curate.tiledbsoma
 small_dataset.tiledbsoma
+nonregistered_storage
 registered_storage
+tests/core/notebooks/no-uid-renamed.ipynb
 
 # General
 .DS_Store

{lamindb-1.11a1 → lamindb-1.11.2}/.gitmodules

@@ -10,9 +10,6 @@
 [submodule "sub/wetlab"]
 	path = sub/wetlab
 	url = https://github.com/laminlabs/wetlab
-[submodule "sub/clinicore"]
-	path = sub/clinicore
-	url = https://github.com/laminlabs/clinicore
 [submodule "sub/cellxgene-lamin"]
 	path = sub/cellxgene-lamin
 	url = https://github.com/laminlabs/cellxgene-lamin.git

{lamindb-1.11a1 → lamindb-1.11.2}/.pre-commit-config.yaml

@@ -68,5 +68,6 @@ repos:
               tests/writelog/conftest.py|
               tests/writelog_sqlite/conftest.py|
               tests/curators/test_curators_examples.py|
-              tests/core/conftest.py
+              tests/core/conftest.py|
+              docs/scripts/
           )

lamindb-1.11.2/PKG-INFO

@@ -0,0 +1,180 @@
+Metadata-Version: 2.3
+Name: lamindb
+Version: 1.11.2
+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
+Classifier: Programming Language :: Python :: 3.10
+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==1.7.1
+Requires-Dist: lamindb_setup[aws]==1.10.1
+Requires-Dist: bionty>=1.7a1
+Requires-Dist: wetlab>=1.5a1
+Requires-Dist: nbproject==0.11.1
+Requires-Dist: jupytext
+Requires-Dist: nbconvert>=7.2.1
+Requires-Dist: mistune!=3.1.0
+Requires-Dist: pyyaml
+Requires-Dist: pyarrow
+Requires-Dist: pandera>=0.24.0
+Requires-Dist: typing_extensions!=4.6.0
+Requires-Dist: python-dateutil
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: scipy<1.15.0
+Requires-Dist: anndata>=0.8.0,<=0.12.1
+Requires-Dist: fsspec
+Requires-Dist: graphviz
+Requires-Dist: psycopg2-binary
+Requires-Dist: tomlkit ; extra == "dev"
+Requires-Dist: line_profiler ; extra == "dev"
+Requires-Dist: pre-commit ; extra == "dev"
+Requires-Dist: nox ; extra == "dev"
+Requires-Dist: laminci>=0.3 ; extra == "dev"
+Requires-Dist: pytest>=6.0 ; extra == "dev"
+Requires-Dist: coverage ; extra == "dev"
+Requires-Dist: pytest-cov<7.0.0 ; extra == "dev"
+Requires-Dist: mudata ; extra == "dev"
+Requires-Dist: nbproject_test>=0.6.0 ; extra == "dev"
+Requires-Dist: faker-biology ; extra == "dev"
+Requires-Dist: pronto ; extra == "dev"
+Requires-Dist: readfcs>=2.0.1 ; extra == "fcs"
+Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
+Requires-Dist: numcodecs<0.16.0 ; extra == "zarr"
+Requires-Dist: zarr>=2.16.0,<3.0.0a0 ; extra == "zarr"
+Project-URL: Home, https://github.com/laminlabs/lamindb
+Provides-Extra: dev
+Provides-Extra: fcs
+Provides-Extra: gcp
+Provides-Extra: zarr
+
+[![Stars](https://img.shields.io/github/stars/laminlabs/lamindb?logo=GitHub)](https://github.com/laminlabs/lamindb)
+[![codecov](https://codecov.io/gh/laminlabs/lamindb/branch/main/graph/badge.svg?token=VKMRJ7OWR3)](https://codecov.io/gh/laminlabs/lamindb)
+[![Docs](https://img.shields.io/badge/docs-humans-yellow)](https://docs.lamin.ai)
+[![DocsLLMs](https://img.shields.io/badge/docs-LLMs-yellow)](https://docs.lamin.ai/summary.md)
+[![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 is an open-source data lakehouse to enable learning at scale in biology.
+It organizes datasets through validation & annotation and provides data lineage, queryability, and reproducibility on top of [FAIR](https://en.wikipedia.org/wiki/FAIR_data) data.
+
+<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.
+
+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.
+
+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.**
+
+- **data lineage:** track inputs & outputs of notebooks, scripts, functions & pipelines with a single line of code
+- **unified infrastructure:** access diverse storage locations (local, S3, GCP, ...), SQL databases (Postgres, SQLite) & ontologies
+- **lakehouse capabilities**: manage, monitor & validate features, labels & dataset schemas; perform distributed queries and batch loading
+- **biological data formats:** validate & annotate formats like `DataFrame`, `AnnData`, `MuData`, ... backed by `parquet`, `zarr`, HDF5, LanceDB, DuckDB, ...
+- **biological entities**: organize experimental metadata & extensible ontologies in registries 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
+
+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)
+
+## Docs
+
+Copy [summary.md](https://docs.lamin.ai/summary.md) into an LLM chat and let AI explain or read the [docs](https://docs.lamin.ai).
+
+## Setup
+
+<!-- copied from quick-setup-lamindb.md -->
+
+Install the `lamindb` Python package:
+
+```shell
+pip install lamindb
+```
+
+Create a LaminDB instance:
+
+```shell
+lamin init --storage ./quickstart-data  # or s3://my-bucket, gs://my-bucket
+```
+
+Or if you have write access to an instance, connect to it:
+
+```shell
+lamin connect account/name
+```
+
+## Quickstart
+
+<!-- copied from preface.md -->
+
+Track a script or notebook run with source code, inputs, outputs, logs, and environment.
+
+<!-- copied from py-quickstart.py -->
+
+```python
+import lamindb as ln
+
+ln.track()  # track a run
+open("sample.fasta", "w").write(">seq1\nACGT\n")
+ln.Artifact("sample.fasta", key="sample.fasta").save()  # create an artifact
+ln.finish()  # finish the run
+```
+
+<!-- from here on, slight deviation from preface.md, where all this is treated in the walk through in more depth -->
+
+This code snippet creates an artifact, which can store a dataset or model as a file or folder in various formats.
+Running the snippet as a script (`python create-fasta.py`) produces the following data lineage.
+
+```python
+artifact = ln.Artifact.get(key="sample.fasta")  # query artifact by key
+artifact.view_lineage()
+```
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/EkQATsQL5wqC95Wj0005.png" width="250">
+
+You'll know how that artifact was created and what it's used for ([interactive visualization](https://lamin.ai/laminlabs/lamindata/artifact/8incOOgjn6F0K1TS)) in addition to capturing basic metadata:
+
+```python
+artifact.describe()
+```
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/BOTCBgHDAvwglN3U0002.png" width="550">
+
+You can organize datasets with validation & annotation of any kind of metadata to then access them via queries & search. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/9K1dteZ6Qx0EXK8g).
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/6sofuDVvTANB0f480002.png" width="850">
+
+To annotate an artifact with a label, use:
+
+```python
+my_experiment = ln.ULabel(name="My experiment").save()  # create a label in the universal label ontology
+artifact.ulabels.add(my_experiment)  # annotate the artifact with the label
+```
+
+To query for a set of artifacts, use the `filter()` statement.
+
+```python
+ln.Artifact.filter(ulabels=my_experiment, suffix=".fasta").to_dataframe()  # query by suffix and the ulabel we just created
+ln.Artifact.filter(transform__key="create-fasta.py").to_dataframe()  # query by the name of the script we just ran
+```
+
+If you have a structured dataset like a `DataFrame`, an `AnnData`, or another array, you can validate the content of the dataset (and parse annotations).
+Here is an example for a dataframe: [docs.lamin.ai/introduction#validate-an-artifact](https://docs.lamin.ai/introduction#validate-an-artifact).
+
+With a large body of validated datasets, you can then access data through distributed queries & batch streaming, see here: [docs.lamin.ai/arrays](https://docs.lamin.ai/arrays).
+

lamindb-1.11.2/README.md

@@ -0,0 +1,126 @@
+[![Stars](https://img.shields.io/github/stars/laminlabs/lamindb?logo=GitHub)](https://github.com/laminlabs/lamindb)
+[![codecov](https://codecov.io/gh/laminlabs/lamindb/branch/main/graph/badge.svg?token=VKMRJ7OWR3)](https://codecov.io/gh/laminlabs/lamindb)
+[![Docs](https://img.shields.io/badge/docs-humans-yellow)](https://docs.lamin.ai)
+[![DocsLLMs](https://img.shields.io/badge/docs-LLMs-yellow)](https://docs.lamin.ai/summary.md)
+[![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 is an open-source data lakehouse to enable learning at scale in biology.
+It organizes datasets through validation & annotation and provides data lineage, queryability, and reproducibility on top of [FAIR](https://en.wikipedia.org/wiki/FAIR_data) data.
+
+<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.
+
+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.
+
+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.**
+
+- **data lineage:** track inputs & outputs of notebooks, scripts, functions & pipelines with a single line of code
+- **unified infrastructure:** access diverse storage locations (local, S3, GCP, ...), SQL databases (Postgres, SQLite) & ontologies
+- **lakehouse capabilities**: manage, monitor & validate features, labels & dataset schemas; perform distributed queries and batch loading
+- **biological data formats:** validate & annotate formats like `DataFrame`, `AnnData`, `MuData`, ... backed by `parquet`, `zarr`, HDF5, LanceDB, DuckDB, ...
+- **biological entities**: organize experimental metadata & extensible ontologies in registries 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
+
+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)
+
+## Docs
+
+Copy [summary.md](https://docs.lamin.ai/summary.md) into an LLM chat and let AI explain or read the [docs](https://docs.lamin.ai).
+
+## Setup
+
+<!-- copied from quick-setup-lamindb.md -->
+
+Install the `lamindb` Python package:
+
+```shell
+pip install lamindb
+```
+
+Create a LaminDB instance:
+
+```shell
+lamin init --storage ./quickstart-data  # or s3://my-bucket, gs://my-bucket
+```
+
+Or if you have write access to an instance, connect to it:
+
+```shell
+lamin connect account/name
+```
+
+## Quickstart
+
+<!-- copied from preface.md -->
+
+Track a script or notebook run with source code, inputs, outputs, logs, and environment.
+
+<!-- copied from py-quickstart.py -->
+
+```python
+import lamindb as ln
+
+ln.track()  # track a run
+open("sample.fasta", "w").write(">seq1\nACGT\n")
+ln.Artifact("sample.fasta", key="sample.fasta").save()  # create an artifact
+ln.finish()  # finish the run
+```
+
+<!-- from here on, slight deviation from preface.md, where all this is treated in the walk through in more depth -->
+
+This code snippet creates an artifact, which can store a dataset or model as a file or folder in various formats.
+Running the snippet as a script (`python create-fasta.py`) produces the following data lineage.
+
+```python
+artifact = ln.Artifact.get(key="sample.fasta")  # query artifact by key
+artifact.view_lineage()
+```
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/EkQATsQL5wqC95Wj0005.png" width="250">
+
+You'll know how that artifact was created and what it's used for ([interactive visualization](https://lamin.ai/laminlabs/lamindata/artifact/8incOOgjn6F0K1TS)) in addition to capturing basic metadata:
+
+```python
+artifact.describe()
+```
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/BOTCBgHDAvwglN3U0002.png" width="550">
+
+You can organize datasets with validation & annotation of any kind of metadata to then access them via queries & search. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/9K1dteZ6Qx0EXK8g).
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/6sofuDVvTANB0f480002.png" width="850">
+
+To annotate an artifact with a label, use:
+
+```python
+my_experiment = ln.ULabel(name="My experiment").save()  # create a label in the universal label ontology
+artifact.ulabels.add(my_experiment)  # annotate the artifact with the label
+```
+
+To query for a set of artifacts, use the `filter()` statement.
+
+```python
+ln.Artifact.filter(ulabels=my_experiment, suffix=".fasta").to_dataframe()  # query by suffix and the ulabel we just created
+ln.Artifact.filter(transform__key="create-fasta.py").to_dataframe()  # query by the name of the script we just ran
+```
+
+If you have a structured dataset like a `DataFrame`, an `AnnData`, or another array, you can validate the content of the dataset (and parse annotations).
+Here is an example for a dataframe: [docs.lamin.ai/introduction#validate-an-artifact](https://docs.lamin.ai/introduction#validate-an-artifact).
+
+With a large body of validated datasets, you can then access data through distributed queries & batch streaming, see here: [docs.lamin.ai/arrays](https://docs.lamin.ai/arrays).

{lamindb-1.11a1 → lamindb-1.11.2}/docs/api.md

@@ -1,4 +1,4 @@
-# API
+# API Reference
 
 <meta http-equiv="Refresh" content="0; url=./lamindb.html" />
 
@@ -18,5 +18,4 @@ lamindb
 
 bionty
 wetlab
-clinicore
 ```

{lamindb-1.11a1 → lamindb-1.11.2}/docs/curate.ipynb

@@ -955,13 +955,88 @@
    "id": "73",
    "metadata": {},
    "source": [
-    "## MuData"
+    "## Unstructured dictionaries"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "74",
    "metadata": {},
+   "source": [
+    "Most datastructures support unstructured metadata stored as dictionaries:\n",
+    "\n",
+    "- Pandas DataFrames: `.attrs`\n",
+    "- AnnData: `.uns`\n",
+    "- MuData: `.uns` and `modality:uns`\n",
+    "- SpatialData: `.attrs`\n",
+    "\n",
+    "Here, we exemplary show how to curate such metadata for AnnData:"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "75",
+   "metadata": {},
+   "source": [
+    "```{eval-rst}\n",
+    ".. literalinclude:: scripts/define_schema_anndata_uns.py\n",
+    "   :language: python\n",
+    "   :caption: define_schema_anndata_uns.py\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "76",
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "!python scripts/define_schema_anndata_uns.py"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "77",
+   "metadata": {},
+   "source": [
+    "```{eval-rst}\n",
+    ".. literalinclude:: scripts/curate_anndata_uns.py\n",
+    "   :language: python\n",
+    "   :caption: curate_anndata_uns.py\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "78",
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "!python scripts/curate_anndata_uns.py"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "79",
+   "metadata": {},
+   "source": [
+    "## MuData"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "80",
+   "metadata": {},
    "source": [
     "```{eval-rst}\n",
     ".. literalinclude:: scripts/curate_mudata.py\n",
@@ -973,7 +1048,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "75",
+   "id": "81",
    "metadata": {
     "tags": [
      "hide-output"
@@ -986,7 +1061,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "76",
+   "id": "82",
    "metadata": {},
    "source": [
     "## SpatialData"
@@ -994,7 +1069,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "77",
+   "id": "83",
    "metadata": {},
    "source": [
     "```{eval-rst}\n",
@@ -1007,7 +1082,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "78",
+   "id": "84",
    "metadata": {
     "tags": [
      "hide-output"
@@ -1020,7 +1095,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "79",
+   "id": "85",
    "metadata": {},
    "source": [
     "```{eval-rst}\n",
@@ -1033,7 +1108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "80",
+   "id": "86",
    "metadata": {
     "tags": [
      "hide-output"
@@ -1046,7 +1121,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "81",
+   "id": "87",
    "metadata": {},
    "source": [
     "## TiledbsomaExperiment"
@@ -1054,7 +1129,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "82",
+   "id": "88",
    "metadata": {},
    "source": [
     "```{eval-rst}\n",
@@ -1067,7 +1142,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "83",
+   "id": "89",
    "metadata": {
     "tags": [
      "hide-output"
@@ -1080,7 +1155,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "84",
+   "id": "90",
    "metadata": {},
    "source": [
     "## Other data structures"
@@ -1088,7 +1163,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "85",
+   "id": "91",
    "metadata": {},
    "source": [
     "If you have other data structures, read: {doc}`/faq/curate-any`."
@@ -1097,7 +1172,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "86",
+   "id": "92",
    "metadata": {
     "tags": [
      "hide-cell"

{lamindb-1.11a1 → lamindb-1.11.2}/docs/faq/acid.ipynb

@@ -23,7 +23,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# !pip install 'lamindb[jupyter,aws]'\n",
+    "# pip install lamindb\n",
     "from laminci.db import setup_local_test_postgres\n",
     "\n",
     "pgurl = setup_local_test_postgres()"

{lamindb-1.11a1 → lamindb-1.11.2}/docs/faq/idempotency.ipynb

@@ -43,7 +43,7 @@
    },
    "outputs": [],
    "source": [
-    "# pip install 'lamindb[jupyter]'\n",
+    "# pip install lamindb\n",
     "!lamin init --storage ./test-idempotency"
    ]
   },

{lamindb-1.11a1 → lamindb-1.11.2}/docs/faq/keep-artifacts-local.ipynb

@@ -47,10 +47,10 @@
    },
    "outputs": [],
    "source": [
-    "# pip install 'lamindb[jupyter]'\n",
+    "# pip install lamindb\n",
     "import lamindb as ln\n",
     "\n",
-    "ln.track(\"l9lFf83aPwRc0000\")"
+    "ln.track(\"l9lFf83aPwRc\")"
    ]
   },
   {

{lamindb-1.11a1 → lamindb-1.11.2}/docs/faq/setup.ipynb

@@ -30,7 +30,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# pip install 'lamindb[jupyter]'\n",
+    "# pip install lamindb\n",
     "import lamindb as ln\n",
     "import pytest"
    ]

{lamindb-1.11a1 → lamindb-1.11.2}/docs/faq/track-run-inputs.ipynb

@@ -26,7 +26,7 @@
    },
    "outputs": [],
    "source": [
-    "# !pip install 'lamindb[jupyter]'\n",
+    "# pip install lamindb\n",
     "!lamin init --storage test-run-inputs"
    ]
   },

{lamindb-1.11a1 → lamindb-1.11.2}/docs/includes/installation.md

@@ -7,15 +7,12 @@ pip install lamindb
 You can configure the installation using `extras`, e.g.,
 
 ```shell
-pip install 'lamindb[jupyter,bionty]'
+pip install 'lamindb[gcp]'
 ```
 
 Supported `extras` are:
 
 ```yaml
-# commonly used
-jupyter   # parse Jupyter notebook metadata
-bionty    # basic biological ontologies
 # cloud backends (AWS is assumed)
 gcp       # Google Cloud (gcfs, etc.)
 # biological artifact formats

{lamindb-1.11a1 → lamindb-1.11.2}/docs/query-search.md

@@ -1,4 +1,4 @@
-# Query & search
+# Query, search & stream
 
 ```{toctree}
 :maxdepth: 1