lamindb 0.68.0__tar.gz → 0.68.2__tar.gz

{lamindb-0.68.0 → lamindb-0.68.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.68.0
+Version: 0.68.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,10 +9,10 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.62.0
-Requires-Dist: lamindb_setup==0.65.3
+Requires-Dist: lnschema_core==0.63.0
+Requires-Dist: lamindb_setup==0.66.1
 Requires-Dist: lamin_utils==0.13.0
-Requires-Dist: lamin_cli==0.8.1
+Requires-Dist: lamin_cli==0.9.3
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -24,8 +24,9 @@ Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: aiobotocore[boto3]>=2.5.4,<3.0.0 ; extra == "aws"
+Requires-Dist: s3fs==2023.12.2 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.12.2 ; extra == "aws"
-Requires-Dist: bionty==0.41.0 ; extra == "bionty"
+Requires-Dist: bionty==0.42.0 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
@@ -59,14 +60,11 @@ Provides-Extra: zarr
 
 # LaminDB - A data framework for biology
 
-LaminDB is an open-source Python framework to manage biological data & analyses:
-
-- Access data & metadata across storage & databases.
+- Access storage & databases with one Python API & CLI.
 - Track data lineage across notebooks & pipelines.
 - Manage registries for experimental metadata & in-house ontologies.
-- Validate, standardize & annotate data.
-- Organize and share data across a mesh of LaminDB instances.
-- Manage data access, leverage an auditable system of record.
+- Validate, standardize & annotate.
+- Collaborate across a mesh of distributed LaminDB instances.
 
 ## Documentation
 

{lamindb-0.68.0 → lamindb-0.68.2}/README.md

@@ -4,14 +4,11 @@
 
 # LaminDB - A data framework for biology
 
-LaminDB is an open-source Python framework to manage biological data & analyses:
-
-- Access data & metadata across storage & databases.
+- Access storage & databases with one Python API & CLI.
 - Track data lineage across notebooks & pipelines.
 - Manage registries for experimental metadata & in-house ontologies.
-- Validate, standardize & annotate data.
-- Organize and share data across a mesh of LaminDB instances.
-- Manage data access, leverage an auditable system of record.
+- Validate, standardize & annotate.
+- Collaborate across a mesh of distributed LaminDB instances.
 
 ## Documentation
 

{lamindb-0.68.0 → lamindb-0.68.2}/docs/bio-registries.ipynb

@@ -66,15 +66,9 @@
    "outputs": [],
    "source": [
     "import lamindb as ln\n",
-    "import bionty as bt"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "import bionty as bt\n",
+    "\n",
+    "ln.connect(\"test-registries\")\n",
     "ln.settings.verbosity = \"info\""
    ]
   },
@@ -939,16 +933,16 @@
    "name": "python3"
   },
   "language_info": {
-   "artifact_extension": ".py",
    "codemirror_mode": {
     "name": "ipython",
     "version": 3
    },
+   "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "s7F7PezA1HdQ",

{lamindb-0.68.0 → lamindb-0.68.2}/docs/changelog.md

@@ -6,7 +6,19 @@
 
 ## 0.68
 
-## 0.68.0 {small}`2024-03-01`
+### 0.68.2 {small}`2024-03-11`
+
+- 🚸 Move transform & run artifacts into cache before uploading [PR](https://github.com/laminlabs/lamindb/pull/1488) [@falexwolf](https://github.com/falexwolf)
+- 🚸 More sensible transform types [PR](https://github.com/laminlabs/lamindb/pull/1486) [@falexwolf](https://github.com/falexwolf)
+- 🚚 Rename `lnschema_lamin1` to `wetlab` [PR](https://github.com/laminlabs/lamindb/pull/1487) [@falexwolf](https://github.com/falexwolf)
+
+### 0.68.1 {small}`2024-03-08`
+
+- 🚸 You can now use `ln.connect()` to connect to a LaminDB instance [PR](https://github.com/laminlabs/lamindb/pull/1480) [@falexwolf](https://github.com/falexwolf)
+- 🚸 You can no longer delete data from non-default storage locations, as these might be tracked in other instances [PR](https://github.com/laminlabs/lamindb/pull/1484) [@sunnyosun](https://github.com/sunnyosun)
+- 🚸 Enable transferring data from local instances to remote instances [PR](https://github.com/laminlabs/lamindb/pull/1479) [@sunnyosun](https://github.com/sunnyosun)
+
+### 0.68.0 {small}`2024-03-01`
 
 🚸 Decouple features linking from Artifact construction [PR 1](https://github.com/laminlabs/lamindb/pull/1434) [2](https://github.com/laminlabs/lamindb/pull/1455) [3](https://github.com/laminlabs/lamindb/pull/1458) [@sunnyosun](https://github.com/sunnyosun).
 
@@ -43,7 +55,7 @@ artifact.labels.add(labels)
 
 ## 0.67
 
-## 0.67.3 {small}`2024-02-02`
+### 0.67.3 {small}`2024-02-02`
 
 - 🚸 Can now import `bionty` instead of `lnschema-bionty` [PR](https://github.com/laminlabs/lamindb/pull/1415) [@sunnyosun](https://github.com/sunnyosun)
 - ♻️ Use Click for CLI [PR](https://github.com/laminlabs/lamindb/pull/1420) [@chaichontat](https://github.com/chaichontat)

{lamindb-0.68.0 → lamindb-0.68.2}/docs/data.ipynb

@@ -63,6 +63,24 @@
     "!lamin init --storage s3://lamindb-ci/test-data --name test-data"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!lamin info"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!lamin set --auto-connect True"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -72,6 +90,15 @@
     "import lamindb as ln"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ln.connect(\"test-data\")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -322,16 +349,16 @@
    "name": "python3"
   },
   "language_info": {
-   "artifact_extension": ".py",
    "codemirror_mode": {
     "name": "ipython",
     "version": 3
    },
+   "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "YVUCtH4GfQOy",

{lamindb-0.68.0 → lamindb-0.68.2}/docs/faq/setup.ipynb

@@ -106,9 +106,7 @@
    "outputs": [],
    "source": [
     "with pytest.raises(RuntimeError):\n",
-    "    ln.setup.init(storage=\"./testsetup2\")\n",
-    "with pytest.raises(RuntimeError):\n",
-    "    ln.setup.load(\"testsetup\")"
+    "    ln.setup.init(storage=\"./testsetup2\")"
    ]
   },
   {

{lamindb-0.68.0 → lamindb-0.68.2}/docs/features-lamindb.md

@@ -1,16 +1,17 @@
 **Access data & metadata across storage (files, arrays) & database (SQL) backends.**
 
 - Query & search: {class}`~lamindb.core.Registry.filter`, {class}`~lamindb.core.Registry.search`
-- Stage, load or stream artifacts: {class}`~lamindb.Artifact.stage`, {class}`~lamindb.Artifact.load`, {class}`~lamindb.Artifact.backed`
-- Model data using {class}`~lamindb.Feature`, {class}`~lamindb.FeatureSet`, {class}`~lamindb.ULabel`
+- Stage, load & stream artifacts: {class}`~lamindb.Artifact.stage`, {class}`~lamindb.Artifact.load`, {class}`~lamindb.Artifact.backed`
+- Manage {class}`~lamindb.Feature`, {class}`~lamindb.FeatureSet`, {class}`~lamindb.ULabel`
 - Plug-in custom [schemas](/schemas) & manage schema migrations
 - Use array formats in memory & storage: [DataFrame](/tutorial), [AnnData](/data), [MuData](docs:multimodal), [SOMA](docs:cellxgene), ... backed by [parquet](/tutorial), [zarr](/data), [TileDB](docs:cellxgene), [HDF5](/data), [h5ad](/data), [DuckDB](docs:rxrx), ...
 - Bridge artifacts and warehousing: {class}`~lamindb.Artifact`, {class}`~lamindb.Collection`
+- Leverage out-of-the-box PyTorch data loaders: {meth}`~lamindb.Collection.mapped`
 - Version artifacts, collections & transforms
 
 **Track data lineage across notebooks, pipelines & UI: {meth}`~lamindb.track`, {class}`~lamindb.Transform` & {class}`~lamindb.Run`.**
 
-- Execution reports & source code for [notebooks & scripts](/track)
+- Execution reports, source code and Python environments for [notebooks & scripts](/track)
 - Integrate with workflow managers: [redun](docs:redun), [nextflow](docs:nextflow), [snakemake](docs:snakemake)
 
 **Manage registries for experimental metadata & in-house ontologies, import public ontologies.**
@@ -20,7 +21,7 @@
 - {class}`~bionty.ExperimentalFactor`, {class}`~bionty.CellType`, {class}`~bionty.CellLine`, {class}`~bionty.Tissue`, ...
 - Safeguards against typos & duplications
 
-**Validate, standardize & annotate data using registries: {class}`~lamindb.core.CanValidate.validate` & {class}`~lamindb.core.CanValidate.standardize`.**
+**Validate, standardize & annotate based on registries: {class}`~lamindb.core.CanValidate.validate` & {class}`~lamindb.core.CanValidate.standardize`.**
 
 - Inspect validation failures: {class}`~lamindb.core.CanValidate.inspect`
 - Annotate with untyped or typed labels: {class}`~lamindb.core.LabelManager.add`

{lamindb-0.68.0 → lamindb-0.68.2}/docs/introduction.ipynb

@@ -6,6 +6,8 @@
    "source": [
     "# Introduction\n",
     "\n",
+    "LaminDB is an open-source data framework for biology:\n",
+    "\n",
     "```{include} ../README.md\n",
     ":start-line: 6\n",
     ":end-line: -4\n",
@@ -39,7 +41,8 @@
     "Public beta: Close to having converged a stable API, but some breaking changes might still occur.\n",
     "\n",
     "```\n",
-    "In this Quickstart, you'll register a simple dataset into LaminDB, showcasing its data management and lineage tracking capabilities."
+    "\n",
+    "You'll ingest a small dataset while tracking data lineage, and learn how to validate, annotate, query & search."
    ]
   },
   {
@@ -53,43 +56,33 @@
     "pip install 'lamindb[jupyter,bionty]'\n",
     "```\n",
     "\n",
-    "Initialize a LaminDB instance:"
+    "Initialize a LaminDB instance mounting plug-in {py:mod}`bionty` for biological types:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "!lamin init --schema bionty --storage ./lamin-intro"
-   ]
-  },
-  {
-   "cell_type": "markdown",
    "metadata": {},
+   "outputs": [],
    "source": [
-    "To access public biological ontologies, we passed `--schema bionty`, which mounted plug-in {py:mod}`bionty`.\n",
+    "import lamindb as ln\n",
     "\n",
-    "Because we passed a local directory `./lamin-intro` to `--storage`, by default, artifacts are stored locally. You could pass an AWS or GCP bucket instead: `s3://my-bucket` `gs://my-bucket`."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Track data lineage"
+    "# artifacts are stored in a local directory `./lamin-intro`\n",
+    "ln.setup.init(schema=\"bionty\", storage=\"./lamin-intro\")\n",
+    "\n",
+    "# tag your code with auto-generated identifiers for a script or notebook\n",
+    "ln.transform.stem_uid = \"FPnfDtJz8qbE\"\n",
+    "ln.transform.version = \"1\"\n",
+    "\n",
+    "# track the execution of a transform with a global run context\n",
+    "ln.track()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Call {class}`~lamindb.track` to create a global run context:"
+    "### Manage artifacts"
    ]
   },
   {
@@ -98,20 +91,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import lamindb as ln\n",
     "import pandas as pd\n",
     "\n",
-    "# ln.track() prints transform settings if they're undefined\n",
-    "ln.transform.stem_uid = \"FPnfDtJz8qbE\"\n",
-    "ln.transform.version = \"1\"\n",
-    "ln.track()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Create artifacts"
+    "# dummy data\n",
+    "df = pd.DataFrame(\n",
+    "    {\"CD8A\": [1, 2, 3], \"CD4\": [3, 4, 5], \"CD14\": [5, 6, 7], \"perturbation\": [\"DMSO\", \"IFNG\", \"DMSO\"]},\n",
+    "    index=[\"observation1\", \"observation2\", \"observation3\"],\n",
+    ")"
    ]
   },
   {
@@ -129,10 +115,6 @@
    },
    "outputs": [],
    "source": [
-    "df = pd.DataFrame(\n",
-    "    {\"CD8A\": [1, 2, 3], \"CD4\": [3, 4, 5], \"CD14\": [5, 6, 7], \"perturbation\": [\"DMSO\", \"IFNG\", \"DMSO\"]},\n",
-    "    index=[\"observation1\", \"observation2\", \"observation3\"],\n",
-    ")\n",
     "artifact = ln.Artifact.from_df(df, description=\"my RNA-seq\", version=\"1\")"
    ]
   },
@@ -257,9 +239,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Because, under-the-hood, LaminDB is SQL & Django, you can write arbitrarily complex relational queries.\n",
-    "\n",
-    "This can give you a gist of it:"
+    "Because, under-the-hood, LaminDB is SQL & Django, you can write arbitrarily complex relational queries:"
    ]
   },
   {
@@ -279,7 +259,7 @@
     "\n",
     "If you work with a remote instance on LaminHub, you can compose queries as shown below.\n",
     "\n",
-    "Because LaminDB's metadata-management is based on SQL, you'll find that it scales to very large tables.\n",
+    "Because LaminDB's metadata-management is based on SQL, registries can easily have 10s of millions of rows.\n",
     "\n",
     "<img src=\"https://lamin-site-assets.s3.amazonaws.com/.lamindb/L188T2JjzZHWHfv2S0ib.png\" width=\"700px\">\n",
     "\n",
@@ -363,21 +343,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Validate & annotate"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "To define a validation framework for your data, you can define features and labels using their registries."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Features & labels"
+    "## Features & labels"
    ]
   },
   {
@@ -477,7 +443,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Validate & annotate data"
+    "## Validate & annotate"
    ]
   },
   {
@@ -563,13 +529,6 @@
     ":::"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Query for annotations"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -623,9 +582,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The generic {class}`~lamindb.Feature` and {class}`~lamindb.ULabel` will get you pretty far.\n",
+    "{class}`~lamindb.Feature` and {class}`~lamindb.ULabel` will get you pretty far.\n",
     "\n",
-    "But if you use an entity many times, you typically want a dedicated registry, which you can use to type your code & as an interface for public ontologies.\n",
+    "But if you use an entity many times, you typically want a dedicated registry.\n",
     "\n",
     "Let's do this with {class}`~bionty.Gene` and {class}`~bionty.Tissue` from plug-in {py:mod}`bionty`:"
    ]
@@ -668,16 +627,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To manage features of different types, let us use an `AnnData` object:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import anndata as ad"
+    "To manage features of different types, let us use an `AnnData` object, which comes with two slots for storing data & metadata:"
    ]
   },
   {
@@ -686,6 +636,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import anndata as ad\n",
+    "\n",
     "adata = ad.AnnData(df[[\"CD8A\", \"CD4\", \"CD14\"]], obs=df[[\"perturbation\"]])"
    ]
   },
@@ -765,15 +717,7 @@
     "artifact.features.add_from_anndata(var_field=bt.Gene.symbol, organism=\"human\")\n",
     "artifact.labels.add(study)\n",
     "artifact.labels.add(adata.obs.perturbation, feature=features_lookup.perturbation)\n",
-    "artifact.labels.add(tissue)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "artifact.labels.add(tissue)\n",
     "artifact.describe()"
    ]
   },
@@ -805,7 +749,37 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Append a new batch of data"
+    "### Manage biological registries\n",
+    "\n",
+    "Create a cell type registry and add a new cell state (from [here](bio-registries)):"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# create an ontology-coupled cell type record and save it\n",
+    "bt.CellType.from_public(name=\"neuron\").save()\n",
+    "\n",
+    "# create a record to track a new cell state\n",
+    "new_cell_state = bt.CellType(name=\"my neuron cell state\", description=\"explains X\")\n",
+    "new_cell_state.save()\n",
+    "\n",
+    "# express that it's a neuron state\n",
+    "cell_types = bt.CellType.lookup()\n",
+    "new_cell_state.parents.add(cell_types.neuron)\n",
+    "\n",
+    "# view ontological hierarchy\n",
+    "new_cell_state.view_parents(distance=2)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Collections of artifacts"
    ]
   },
   {
@@ -888,13 +862,6 @@
     "artifact2.describe()"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Collections of artifacts"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -950,7 +917,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Train a machine learning model"
+    "## Machine learning models"
    ]
   },
   {
@@ -980,9 +947,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## More examples\n",
-    "\n",
-    "### Understand data lineage\n",
+    "## Data lineage\n",
     "\n",
     "View the sequence of data transformations ({class}`~lamindb.Transform`) in a project (from [here](docs:project-flow), based on [Schmidt _et al._, 2022](https://pubmed.ncbi.nlm.nih.gov/35113687/)):\n",
     "\n",
@@ -1001,53 +966,14 @@
     "<img src=\"https://lamin-site-assets.s3.amazonaws.com/.lamindb/KQmzmmLOeBN0C8Ykitjn.svg\" width=\"800\">\n",
     "\n",
     "\n",
-    "Both figures are based on mere calls to `ln.track()` in notebooks, pipelines & app.\n",
-    "\n",
-    "\n",
-    "### Manage biological registries\n",
-    "\n",
-    "Create a cell type registry from public knowledge and add a new cell state (from [here](bio-registries)):"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "import bionty as bt\n",
-    "\n",
-    "# create an ontology-coupled cell type record and save it\n",
-    "bt.CellType.from_public(name=\"neuron\").save()\n",
-    "\n",
-    "# create a record to track a new cell state\n",
-    "new_cell_state = bt.CellType(name=\"my neuron cell state\", description=\"explains X\")\n",
-    "new_cell_state.save()\n",
-    "\n",
-    "# express that it's a neuron state\n",
-    "cell_types = bt.CellType.lookup()\n",
-    "new_cell_state.parents.add(cell_types.neuron)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# view ontological hierarchy\n",
-    "new_cell_state.view_parents(distance=2)"
+    "Both figures are based on mere calls to `ln.track()` in notebooks, pipelines & app."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Leverage a mesh of instances\n",
+    "## Mesh of databases\n",
     "\n",
     "LaminDB is a distributed system like git. Similar to cloning a repository, collaborators can load your instance on the command-line using:\n",
     "\n",
@@ -1057,18 +983,18 @@
     "\n",
     "If you run `lamin save <notebook_path>`, you will save the notebook to your default storage location.\n",
     "\n",
-    "You can explore the notebook report corresponding to the quickstart [here](https://lamin.ai/laminlabs/lamindata/record/core/Transform?id=FPnfDtJz8qbEz8) in LaminHub.\n",
+    "You can explore the notebook report corresponding to the quickstart [here](https://lamin.ai/laminlabs/lamindata/Transform?id=FPnfDtJz8qbEz8) in LaminHub.\n",
     "\n",
-    "### Manage custom schemas\n",
+    "## Custom schemas\n",
     "\n",
     "LaminDB can be customized & extended with schema & app plug-ins building on the [Django](https://github.com/django/django) ecosystem. Examples are\n",
     "\n",
     "- [bionty](./bionty): Registries for basic biological entities, coupled to public ontologies.\n",
-    "- [lnschema_lamin1](https://github.com/laminlabs/lnschema-lamin1): Exemplary custom schema to manage samples, treatments, etc. \n",
+    "- [wetlab](https://github.com/laminlabs/wetlab): Exemplary custom schema to manage samples, treatments, etc. \n",
     "\n",
     "If you'd like to create your own schema or app:\n",
     "\n",
-    "1. Create a git repository with registries similar to [lnschema_lamin1](https://github.com/laminlabs/lnschema-lamin1)\n",
+    "1. Create a git repository with registries similar to [wetlab](https://github.com/laminlabs/wetlab)\n",
     "2. Create & deploy migrations via `lamin migrate create` and `lamin migrate deploy`\n",
     "\n",
     "It's fastest if we do this for you based on our templates within an enterprise plan.\n",
@@ -1118,7 +1044,7 @@
     "\n",
     "- [lamindb](https://github.com/laminlabs/lamindb): Core API, which builds on the [core schema](https://github.com/laminlabs/lnschema-core).\n",
     "- [bionty](https://github.com/laminlabs/bionty): Registries for basic biological entities, coupled to public ontologies.\n",
-    "- [lnschema-lamin1](https://github.com/laminlabs/lnschema-lamin1): Exemplary custom schema to manage samples, treatments, etc.\n",
+    "- [wetlab](https://github.com/laminlabs/wetlab): Exemplary custom schema to manage samples, treatments, etc.\n",
     "- [lamindb-setup](https://github.com/laminlabs/lamindb-setup): Setup & configure LaminDB, client for LaminHub.\n",
     "- [lamin-cli](https://github.com/laminlabs/lamin-cli): CLI for `lamindb` and `lamindb-setup`.\n",
     "- [nbproject](https://github.com/laminlabs/nbproject): Metadata parser for Jupyter notebooks.\n",

{lamindb-0.68.0 → lamindb-0.68.2}/docs/schemas.ipynb

@@ -115,7 +115,7 @@
     "\n",
     "The only convention required by LaminDB for plugging in a valid (minimal) Django app.\n",
     "\n",
-    "You'll see how simple it is if you look at this example: [github.com/laminlabs/lnschema-lamin1](https://github.com/laminlabs/lnschema-lamin1).\n",
+    "You'll see how simple it is if you look at this example: [github.com/laminlabs/wetlab](https://github.com/laminlabs/wetlab).\n",
     "\n",
     "Schema management needs two CLI calls (see {doc}`/setup`):\n",
     "\n",