lamindb 0.71.2__tar.gz → 0.72.0__tar.gz

{lamindb-0.71.2 → lamindb-0.72.0}/.github/workflows/build.yml

@@ -22,7 +22,7 @@ jobs:
           - "faq"
           - "storage"
           - "cli"
-    timeout-minutes: 10
+    timeout-minutes: 6
 
     steps:
       - uses: actions/checkout@v4
@@ -50,10 +50,10 @@ jobs:
           path: ~/postgres.tar
           key: cache-postgres-0
       - name: cache postgres miss
-        if: ${{ steps.cache-postgres.outputs.cache-hit != 'true' && matrix.group == 'faq' || matrix.group == 'unit' }}
+        if: ${{ steps.cache-postgres.outputs.cache-hit != 'true' }}
         run: docker pull postgres:latest && docker image save postgres:latest --output ~/postgres.tar
       - name: cache postgres use
-        if: ${{ steps.cache-postgres.outputs.cache-hit == 'true' && matrix.group == 'faq' || matrix.group == 'unit' }}
+        if: ${{ steps.cache-postgres.outputs.cache-hit == 'true' }}
         run: docker image load --input ~/postgres.tar
       - run: pip install -U laminci
       - name: install postgres

{lamindb-0.71.2 → lamindb-0.72.0}/.gitmodules

@@ -13,3 +13,6 @@
 [submodule "sub/bionty"]
 	path = sub/bionty
 	url = https://github.com/laminlabs/bionty
+[submodule "sub/wetlab"]
+	path = sub/wetlab
+	url = https://github.com/laminlabs/wetlab

{lamindb-0.71.2 → lamindb-0.72.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.71.2
+Version: 0.72.0
 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==0.66.4
-Requires-Dist: lamindb_setup==0.71.3
+Requires-Dist: lnschema_core==0.67.1
+Requires-Dist: lamindb_setup==0.72.1
 Requires-Dist: lamin_utils==0.13.2
-Requires-Dist: lamin_cli==0.13.1
+Requires-Dist: lamin_cli==0.13.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -23,8 +23,9 @@ Requires-Dist: fsspec
 Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
+Requires-Dist: psutil
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.42.9 ; extra == "bionty"
+Requires-Dist: bionty==0.43.0 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
@@ -37,7 +38,7 @@ Requires-Dist: faker-biology ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=1.1.8 ; extra == "fcs"
 Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
-Requires-Dist: nbproject==0.10.2 ; extra == "jupyter"
+Requires-Dist: nbproject==0.10.3 ; extra == "jupyter"
 Requires-Dist: nbstripout==0.6.1 ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"

{lamindb-0.71.2 → lamindb-0.72.0}/docs/annotate-for-developers.ipynb

@@ -259,7 +259,7 @@
    "source": [
     "# external metadata features\n",
     "external_meta_features = [\n",
-    "    ln.Feature(name=name, type=\"category\") for name in external_meta.keys()\n",
+    "    ln.Feature(name=name, dtype=\"cat\") for name in external_meta.keys()\n",
     "]\n",
     "ln.save(external_meta_features)\n",
     "external_meta_features"

{lamindb-0.71.2 → lamindb-0.72.0}/docs/bio-registries.ipynb

@@ -149,7 +149,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "public.search(\"gamma delta T cell\").head(3)"
@@ -166,7 +170,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "lookup = public.lookup()\n",
@@ -192,18 +200,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "gdt_cell = bt.CellType(lookup.gamma_delta_t_cell)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
+    "gdt_cell = bt.CellType(lookup.gamma_delta_t_cell)\n",
     "gdt_cell"
    ]
   },
@@ -217,7 +221,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "bt.CellType.from_public(ontology_id=\"CL:0000798\")"
@@ -284,7 +292,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "gdt_cell.parents.df()"
@@ -339,7 +351,7 @@
    "source": [
     "When accessing data sources, one often encounters bulk references to entities that might be corrupted or standardized using different standardization schemes.\n",
     "\n",
-    "Let's consider an example based on an `AnnData` object:"
+    "Let's consider an example based on an `AnnData` object, in the `cell_type` annotations of this `AnnData` object, we find 4 references to cell types:"
    ]
   },
   {
@@ -352,22 +364,7 @@
    },
    "outputs": [],
    "source": [
-    "adata = ln.core.datasets.anndata_with_obs()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "In the `cell_type` annotations of this `AnnData` object, we find 4 references to cell types:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "adata = ln.core.datasets.anndata_with_obs()\n",
     "adata.obs.cell_type.value_counts()"
    ]
   },
@@ -383,7 +380,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "cell_types = bt.CellType.from_values(adata.obs.cell_type)\n",
@@ -444,7 +445,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "adata.obs.cell_type_id.unique().tolist()"
@@ -453,7 +458,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "bt.CellType.from_values(adata.obs.cell_type_id, field=bt.CellType.ontology_id)"
@@ -519,10 +528,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "bt.CellType.search(\"gamma delta T cell\").head(2)"
+    "bt.CellType.search(\"gamma delta T cell\").df().head(2)"
    ]
   },
   {
@@ -535,7 +548,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "cell_types = bt.CellType.lookup()\n",
@@ -562,7 +579,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "bt.CellType.validate([\"HSC\", \"blood forming stem cell\"])"
@@ -580,7 +601,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "bt.CellType.standardize([\"HSC\", \"blood forming stem cell\"])"
@@ -596,7 +621,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "bt.CellType.from_values([\"HSC\", \"blood forming stem cell\"])"
@@ -630,7 +659,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "bt.CellType.standardize([\"HSCs\"])"
@@ -662,7 +695,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "cell_types = bt.CellType.lookup(\"abbr\")\n",
@@ -720,13 +757,6 @@
     "bt.Gene.validate([\"TCF7\", \"ABC1\"], organism=\"human\")"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "You can also pass organism for validating features upon registering data, e.g., in `ln.Artifact.from_anndata(..., field=bionty.Gene.ensembl_gene_id, organism=...)`."
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -792,7 +822,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "hepatocyte = bt.CellType.filter(name=\"hepatocyte\").one()\n",
@@ -808,24 +842,6 @@
     "By default, records are created from the `\"currently_used\"` public sources which are configured during the instance initialization, e.g.:"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "bt.Phenotype.public()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Sometimes, the default source doesn't contain the ontology term you are looking for.\n",
-    "\n",
-    "You can then specify to create a record from a non-default source. For instance, instead of using untyped labels for iris organisms as {doc}`/tutorial2`, we can use the `ncbitaxon` ontology:"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -836,43 +852,7 @@
    },
    "outputs": [],
    "source": [
-    "public_source = bt.PublicSource.filter(entity=\"Organism\", source=\"ncbitaxon\").one()\n",
-    "iris_setosa = bt.Organism.from_public(name=\"iris setosa\", public_source=public_source)\n",
-    "iris_setosa.save()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "iris_setosa"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "iris_setosa.public_source"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "iris_setosa.parents.df()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Analogously, you can pass `public_source` to bulk-create records from a non-default source:"
+    "bt.Phenotype.public()"
    ]
   },
   {
@@ -885,28 +865,34 @@
    },
    "outputs": [],
    "source": [
-    "records = bt.Organism.from_values(\n",
-    "    [\"iris setosa\", \"iris versicolor\", \"iris virginica\"], public_source=public_source\n",
-    ")\n",
-    "ln.save(records)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "records"
+    "bt.Phenotype.sources(currently_used=True).df()"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "iris_setosa.parents.get(name=\"iris\").view_parents(with_children=True)"
+    "Sometimes, the default source doesn't contain the ontology term you are looking for.\n",
+    "\n",
+    "You can then specify to create a record from a non-default source. For instance, instead of using untyped labels for iris organisms as {doc}`/tutorial2`, we can use the `ncbitaxon` ontology:\n",
+    "\n",
+    "```python\n",
+    "\n",
+    "public_source = bt.PublicSource.filter(entity=\"Organism\", source=\"ncbitaxon\").one()\n",
+    "iris_setosa = bt.Organism.from_public(name=\"iris setosa\", public_source=public_source)\n",
+    "iris_setosa.save()\n",
+    "```\n",
+    "\n",
+    "Analogously, you can pass `public_source` to bulk-create records from a non-default source:\n",
+    "\n",
+    "```python\n",
+    "\n",
+    "records = bt.Organism.from_values(\n",
+    "    [\"iris setosa\", \"iris versicolor\", \"iris virginica\"], public_source=public_source\n",
+    ")\n",
+    "ln.save(records)\n",
+    "iris_setosa.parents.get(name=\"iris\").view_parents(with_children=True)\n",
+    "```"
    ]
   },
   {

{lamindb-0.71.2 → lamindb-0.72.0}/docs/changelog.md

@@ -12,8 +12,39 @@ LaminDB implements "migration-based versioning". When upgrading your LaminDB ins
 .. role:: small
 ```
 
+## 0.72
+
+### 0.72.0 {small}`2024-05-19`
+
+- ✨ Extend managed access for AWS S3 to arbitrary paths [PR](https://github.com/laminlabs/lamindb/pull/1668) [@Koncopd](https://github.com/Koncopd) [@fredericenard](https://github.com/fredericenard)
+- ✨ Extended data lineage tracking [PR](https://github.com/laminlabs/lamindb/pull/1667) [@falexwolf](https://github.com/falexwolf)
+    - Now store all _creating_ runs and all _updating_ runs for any entity, not just for `Artifact` & `Collection`, e.g., runs can now have `CellType` record outputs
+    - Code is simpler through inheritance from two new base classes: `TracksRun` and `TracksUpdates`
+- ♻️ Briefer and richer syntax for denoting feature types, renamed `Feature.type` to `Feature.dtype`, e.g., for categorical features, a valid type can be: `cat[ULabel|bionty.Drug]` [PR](https://github.com/laminlabs/lamindb/pull/1663) [@falexwolf](https://github.com/falexwolf)
+- ✨ Support non-categorical metadata [PR](https://github.com/laminlabs/lnschema-core/pull/379) [@falexwolf](https://github.com/falexwolf)
+    - Track non-categorical features: `int`, `float`, `bool`, `datetime`, lists & dictionaries stored in a `FeatureValue` registry
+    - Track arbitrary typed parameters for runs through a `Param` registry analogous to the `Feature` registry: this replaces the hard-to-validate, hard-to-migrate, and hard-to-query `json` field of `Run`
+- 🏗️ Refactor link models [PR](https://github.com/laminlabs/lamindb/pull/1666) [PR](https://github.com/laminlabs/lamindb/pull/1661) [@falexwolf](https://github.com/falexwolf)
+    - All annotation-related links are now stratified by `Feature`: what held for `ULabel` now also holds `CellType` and all other `Bionty` registries
+    - Indicate whether semantic keys were used during validation to enable warnings upon renames
+    - Protect artifact annotations rather than cascade delete them
+    - More consistent naming of link models, e.g., `ulabels.artifact_links` instead of `ulabels.artifactulabel_set`
+    - Dropped linking `Bionty` entities directly against `Collection`
+    - Pruned & squashed migrations for faster instance creation
+
 ## 0.71
 
+### 0.71.3 {small}`2024-05-14`
+
+- 🎨 Enable transfer when schema don't match [PR](https://github.com/laminlabs/lamindb/pull/1654) [@sunnyosun](https://github.com/sunnyosun)
+- ✨ Get artifacts through the CLI [PR](https://github.com/laminlabs/lamindb/pull/1642) [@falexwolf](https://github.com/falexwolf)
+- ⚡️ Improve the speed of describe [PR](https://github.com/laminlabs/lamindb/pull/1645) [@sunnyosun](https://github.com/sunnyosun)
+- ⚡️ Parallel hashing of directories [PR](https://github.com/laminlabs/lamindb/pull/1652) [@Koncopd](https://github.com/Koncopd)
+- ⚡️ Speed-up file hash [PR](https://github.com/laminlabs/lamindb/pull/1651) [@Koncopd](https://github.com/Koncopd)
+- ♻️ Refactor search [PR](https://github.com/laminlabs/lamindb/pull/1646) [@falexwolf](https://github.com/falexwolf)
+- ✨ Introduce bulk update [PR](https://github.com/laminlabs/lamindb/pull/1640) [@falexwolf](https://github.com/falexwolf)
+- 🚸 No need to pass organism if validating on ids [PR](https://github.com/laminlabs/lamindb/pull/1639) [@sunnyosun](https://github.com/sunnyosun)
+
 ### 0.71.2 {small}`2024-05-07`
 
 - ✨ Enable passing parameters to `ln.track()` [PR](https://github.com/laminlabs/lamindb/pull/1637) [@falexwolf](https://github.com/falexwolf)

{lamindb-0.71.2 → lamindb-0.72.0}/docs/faq/idempotency.ipynb

@@ -130,7 +130,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "label = ln.ULabel(name=\"My project 2\")"
+    "label = ln.ULabel(name=\"My project 1a\")"
    ]
   },
   {
@@ -197,7 +197,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "label = ln.ULabel(name=\"My project 3\")"
+    "label = ln.ULabel(name=\"My project 1b\")"
    ]
   },
   {
@@ -226,7 +226,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "label = ln.ULabel(name=\"My project 3\")"
+    "label = ln.ULabel(name=\"My project 1c\")"
    ]
   },
   {
@@ -401,7 +401,7 @@
     "artifact3 = ln.Artifact(filepath, description=\"My fcs artifact\")\n",
     "assert artifact3.id == artifact2.id\n",
     "assert artifact3.run != artifact2.run\n",
-    "assert artifact3.replicating_runs.first() == artifact2.run"
+    "assert artifact3.previous_runs.first() == artifact2.run"
    ]
   },
   {

{lamindb-0.71.2 → lamindb-0.72.0}/docs/introduction.ipynb

@@ -66,7 +66,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# store artifacts in a local directory `./lamin-intro`\n",
@@ -79,7 +83,9 @@
    "source": [
     "### Track\n",
     "\n",
-    "Run {meth}`~lamindb.track` to track the input and output data of your code ({class}`~lamindb.Transform`)."
+    "Run {meth}`~lamindb.track` to track the inputs and outputs of your code ({class}`~lamindb.Transform`).\n",
+    "\n",
+    "When you first run `ln.track()`, it creates a `stem_uid` & `version` to unambiguously identify your notebook or script."
    ]
   },
   {
@@ -94,11 +100,11 @@
    "source": [
     "import lamindb as ln\n",
     "\n",
-    "# auto-generated identifiers for your notebook or script\n",
-    "ln.settings.transform.stem_uid = \"FPnfDtJz8qbE\"\n",
-    "ln.settings.transform.version = \"1\"\n",
+    "# copy-pasted identifiers for your notebook or script\n",
+    "ln.settings.transform.stem_uid = \"FPnfDtJz8qbE\"  # <-- auto-generated by running ln.track()\n",
+    "ln.settings.transform.version = \"1\"  # <-- auto-generated by running ln.track()\n",
     "\n",
-    "# track the execution of your code\n",
+    "# track the execution of your notebook or script\n",
     "ln.track()"
    ]
   },
@@ -304,7 +310,7 @@
    "outputs": [],
    "source": [
     "# search in a registry\n",
-    "ln.Transform.search(\"intro\")\n",
+    "ln.Transform.search(\"intro\").df()\n",
     "\n",
     "# look up records with auto-complete\n",
     "labels = ln.ULabel.lookup()"
@@ -768,7 +774,7 @@
    "source": [
     "### Data lineage across entire projects\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",
+    "View the sequence of data transformations ({class}`~lamindb.Transform`) in a project (from [a use case](inv:docs#project-flow), based on [Schmidt _et al._, 2022](https://pubmed.ncbi.nlm.nih.gov/35113687/)):\n",
     "\n",
     "```python\n",
     "transform.view_parents()\n",
@@ -844,9 +850,12 @@
     "\n",
     "<img src=\"https://lamin-site-assets.s3.amazonaws.com/.lamindb/BunYmHkyFLITlM5MYQci.svg\" width=\"350px\" style=\"background: transparent\" align=\"right\">\n",
     "\n",
-    "The complexity of modern R&D data often blocks realizing the scientific progress it promises.\n",
+    "The complexity of modern R&D data often blocks realizing the scientific progress it promises: see this [blog post](https://lamin.ai/blog/problems).\n",
+    "\n",
+    "More basically: The pydata family of objects is at the heart of most data science, ML & comp bio workflows: `DataFrame`, `AnnData`, `pytorch.DataLoader`, `zarr.Array`, `pyarrow.Table`, `xarray.Collection`, etc. We couldn’t find a tool to link these objects to context so that they could be analyzed in context:\n",
     "\n",
-    "See this [blog post](https://lamin.ai/blog/problems).\n",
+    "- provenance: data sources, data transformations, models, users\n",
+    "- domain knowledge & experimental metadata: the features & labels derived from domain entities\n",
     "\n",
     "### Assumptions\n",
     "\n",
@@ -893,6 +902,11 @@
     "\n",
     "LaminDB was influenced by many other projects, see {doc}`docs:influences`."
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {

{lamindb-0.71.2 → lamindb-0.72.0}/docs/meta.ipynb

@@ -229,17 +229,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.Artifact.search(\"iris\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2aa66c4e",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "ln.Artifact.search(\"iris\", return_queryset=True).first()"
+    "ln.Artifact.search(\"iris\").df()"
    ]
   },
   {
@@ -282,7 +272,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.Transform.search(\"intestine\").head()"
+    "ln.Transform.search(\"intestine\").df().head()"
    ]
   },
   {

{lamindb-0.71.2 → lamindb-0.72.0}/docs/signup-login.md

@@ -12,7 +12,7 @@ Lamin does _not_ store or see any of your data, but only _basic_ metadata about
 
 If you register a LaminDB instance on LaminHub, Lamin only stores the storage location (AWS S3 or GCP bucket names, directory names).
 
-For more, see our guide on [access management & security](docs:access), [the source code](https://github.com/laminlabs/lamindb-setup), or the [privacy policy](https://lamin.ai/legal/privacy-policy).
+For more, see [doc](inv:docs#access), [the source code](https://github.com/laminlabs/lamindb-setup), or the [privacy policy](https://lamin.ai/legal/privacy-policy).
 
 ```