lamindb 0.64.2__tar.gz → 0.65.1__tar.gz

{lamindb-0.64.2 → lamindb-0.65.1}/.github/workflows/build.yml

@@ -63,7 +63,7 @@ jobs:
         if: ${{ matrix.group == 'tutorial' }} # choose a fast-running a group
       - run: nox -s "install(group='${{ matrix.group }}')"
       - uses: aws-actions/configure-aws-credentials@v1
-        if: ${{ matrix.group == 'unit' || matrix.group == 'guide' || matrix.group == 'storage' }}
+        if: ${{ matrix.group == 'unit' || matrix.group == 'guide' || matrix.group == 'storage' || matrix.group == 'cli' }}
         # in particular, the tutorial should be run on an anonymous worker *without* AWS credentials
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}

{lamindb-0.64.2 → lamindb-0.65.1}/.github/workflows/latest-changes.jinja2

@@ -1 +1 @@
-- {{pr.title}} [PR{{pr.number}}]({{pr.html_url}}) [@{{pr.user.login}}]({{pr.user.html_url}})
+- {{pr.title}} [PR{{pr.number}}]({{pr.html_url}}) [@{{pr.user.login}}]({{pr.user.html_url}})

{lamindb-0.64.2 → lamindb-0.65.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.64.2
+Version: 0.65.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -8,10 +8,11 @@ Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
-Requires-Dist: lnschema_core==0.58.1
-Requires-Dist: lamindb_setup==0.61.4
-Requires-Dist: lamin_utils==0.12.0
-Requires-Dist: lamin_cli==0.3.0
+Classifier: Programming Language :: Python :: 3.11
+Requires-Dist: lnschema_core==0.60.0
+Requires-Dist: lamindb_setup==0.63.1
+Requires-Dist: lamin_utils==0.13.0
+Requires-Dist: lamin_cli==0.5.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -27,7 +28,7 @@ Requires-Dist: boto3==1.28.17 ; extra == "aws"
 Requires-Dist: aiobotocore==2.5.4 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.9.0 ; extra == "aws"
 Requires-Dist: s3fs>=2023.9.0 ; extra == "aws"
-Requires-Dist: lnschema_bionty==0.36.1 ; extra == "bionty"
+Requires-Dist: lnschema_bionty==0.37.0 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"

{lamindb-0.64.2 → lamindb-0.65.1}/docs/annotate.ipynb

@@ -67,7 +67,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Register a dataset"
+    "## Register a collection"
    ]
   },
   {
@@ -111,7 +111,7 @@
     "    index=[\"sample1\", \"sample2\", \"sample3\"],\n",
     ")\n",
     "\n",
-    "# external metadata (describes the entire dataset)\n",
+    "# external metadata (describes the entire collection)\n",
     "external_meta = {\n",
     "    \"organism\": \"human\",\n",
     "    \"assay\": \"scRNA-seq\",\n",
@@ -157,15 +157,15 @@
    "source": [
     "ln.track()\n",
     "\n",
-    "dataset = ln.Dataset(adata, name=\"my RNA-seq\")\n",
-    "dataset.save()"
+    "collection = ln.Collection(adata, name=\"my RNA-seq\")\n",
+    "collection.save()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We don't see any metadata in the registered dataset yet:"
+    "We don't see any metadata in the registered collection yet:"
    ]
   },
   {
@@ -174,7 +174,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.describe()"
+    "collection.describe()"
    ]
   },
   {
@@ -230,7 +230,7 @@
    "source": [
     "Metadata features refer to descriptive or contextual information about the data. They don't directly describe the content of the data but rather its characteristics.\n",
     "\n",
-    "In this example, the metadata features are \"cell_type\", \"tissue\" that describe observations (stored in `adata.obs.columns`) and \"organism\", \"assay\", \"experiment\" that describe the entire dataset.\n",
+    "In this example, the metadata features are \"cell_type\", \"tissue\" that describe observations (stored in `adata.obs.columns`) and \"organism\", \"assay\", \"experiment\" that describe the entire collection.\n",
     "\n",
     "Here we define them using the {class}`~lamindb.Feature` registry:"
    ]
@@ -353,7 +353,7 @@
    "source": [
     "## Annotate with features\n",
     "\n",
-    "Non-external features are annotated when registering datasets using `.from_df` or `.from_anndata` methods:\n",
+    "Non-external features are annotated when registering collections using `.from_df` or `.from_anndata` methods:\n",
     "\n",
     "(See the below \"Annotate with labels stratified by metadata features\" session for adding external features.)"
    ]
@@ -368,19 +368,19 @@
    },
    "outputs": [],
    "source": [
-    "dataset = ln.Dataset.from_anndata(\n",
+    "collection = ln.Collection.from_anndata(\n",
     "    adata,\n",
     "    name=\"my RNA-seq\",\n",
     "    field=lb.Gene.symbol,  # the registry field to use for the data features\n",
     ")\n",
-    "dataset.save()"
+    "collection.save()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This dataset is now annotated with features:"
+    "This collection is now annotated with features:"
    ]
   },
   {
@@ -389,7 +389,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.describe()"
+    "collection.describe()"
    ]
   },
   {
@@ -407,7 +407,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.features"
+    "collection.features"
    ]
   },
   {
@@ -423,7 +423,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.features[\"var\"].df()"
+    "collection.features[\"var\"].df()"
    ]
   },
   {
@@ -432,7 +432,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.features[\"obs\"].df()"
+    "collection.features[\"obs\"].df()"
    ]
   },
   {
@@ -441,7 +441,7 @@
    "source": [
     "## Annotate with labels\n",
     "\n",
-    "If you simply want to tag a dataset with some descriptive labels, you can pass them to `.labels.add`. For example, let's add the experiment label \"EXP0001\" and project label \"PRJ0001\" to the dataset:"
+    "If you simply want to tag a collection with some descriptive labels, you can pass them to `.labels.add`. For example, let's add the experiment label \"EXP0001\" and project label \"PRJ0001\" to the collection:"
    ]
   },
   {
@@ -450,15 +450,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.labels.add(experiment)\n",
-    "dataset.labels.add(project)"
+    "collection.labels.add(experiment)\n",
+    "collection.labels.add(project)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now you see the dataset is annotated with 'EXP0001', 'PRJ0001' labels:"
+    "Now you see the collection is annotated with 'EXP0001', 'PRJ0001' labels:"
    ]
   },
   {
@@ -467,7 +467,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.describe()"
+    "collection.describe()"
    ]
   },
   {
@@ -483,7 +483,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.labels"
+    "collection.labels"
    ]
   },
   {
@@ -501,7 +501,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.ulabels.df()"
+    "collection.ulabels.df()"
    ]
   },
   {
@@ -512,7 +512,7 @@
     "\n",
     "For labels associated with metadata features, you can pass \"feature\" to `.labels.add` to stratified them by feature. (Another way to stratify labels is through ontological hierarchy, which is covered in the [Quickstart](/introduction))\n",
     "\n",
-    "Let's add the experiment label \"EXP0001\" and project label \"PRJ0001\" to the dataset again, this time specifying their features:"
+    "Let's add the experiment label \"EXP0001\" and project label \"PRJ0001\" to the collection again, this time specifying their features:"
    ]
   },
   {
@@ -528,15 +528,15 @@
     "# an auto-complete object of registered features\n",
     "features = ln.Feature.lookup()\n",
     "\n",
-    "dataset.labels.add(experiment, feature=features.experiment)\n",
-    "dataset.labels.add(project, feature=features.project)"
+    "collection.labels.add(experiment, feature=features.experiment)\n",
+    "collection.labels.add(project, feature=features.project)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "You now see a 3rd featureset is added to the dataset at slot \"external\", and the labels are stratified by two features:"
+    "You now see a 3rd featureset is added to the collection at slot \"external\", and the labels are stratified by two features:"
    ]
   },
   {
@@ -545,7 +545,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.describe()"
+    "collection.describe()"
    ]
   },
   {
@@ -561,7 +561,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.labels.get(features.experiment).df()"
+    "collection.labels.get(features.experiment).df()"
    ]
   },
   {
@@ -581,7 +581,7 @@
    },
    "outputs": [],
    "source": [
-    "dataset.labels.add(assay, feature=features.assay)"
+    "collection.labels.add(assay, feature=features.assay)"
    ]
   },
   {
@@ -591,7 +591,7 @@
    "outputs": [],
    "source": [
     "# access labels directly via default accessor \"experimental_factors\"\n",
-    "dataset.experimental_factors.df()"
+    "collection.experimental_factors.df()"
    ]
   },
   {
@@ -601,7 +601,7 @@
    "outputs": [],
    "source": [
     "# access labels via feature\n",
-    "dataset.labels.get(features.assay).df()"
+    "collection.labels.get(features.assay).df()"
    ]
   },
   {
@@ -622,18 +622,18 @@
    "outputs": [],
    "source": [
     "# labels of obs metadata features\n",
-    "dataset.labels.add(cell_types, feature=features.cell_type)\n",
-    "dataset.labels.add(tissues, feature=features.tissue)\n",
+    "collection.labels.add(cell_types, feature=features.cell_type)\n",
+    "collection.labels.add(tissues, feature=features.tissue)\n",
     "\n",
     "# labels of external metadata features\n",
-    "dataset.labels.add(organism, feature=features.organism)"
+    "collection.labels.add(organism, feature=features.organism)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now you've annotated your dataset with all features and labels:"
+    "Now you've annotated your collection with all features and labels:"
    ]
   },
   {
@@ -642,7 +642,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dataset.describe()"
+    "collection.describe()"
    ]
   },
   {

{lamindb-0.64.2 → lamindb-0.65.1}/docs/changelog.md

@@ -4,6 +4,25 @@
 .. role:: small
 ```
 
+## 0.65
+
+### 0.65.1 {small}`2024-01-05`
+
+- 🩹 Prepare a potential migration of the hub to Django [PR1385](https://github.com/laminlabs/lamindb/pull/1385) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Various improvements [PR1384](https://github.com/laminlabs/lamindb/pull/1384) [@falexwolf](https://github.com/falexwolf)
+- 🩹 Track suffix of requirements.txt [PR1383](https://github.com/laminlabs/lamindb/pull/1383) [@falexwolf](https://github.com/falexwolf)
+- ✨ Add outer join and categories caching to Collection.mapped [PR1380](https://github.com/laminlabs/lamindb/pull/1380) [@Koncopd](https://github.com/Koncopd)
+- ♻️ Except memory error [PR1382](https://github.com/laminlabs/lamindb/pull/1382) [@falexwolf](https://github.com/falexwolf)
+
+### 0.65.0 {small}`2024-01-02`
+
+- 🚚 Rename `Dataset` to `Collection` [PR1377](https://github.com/laminlabs/lamindb/pull/1377) [@falexwolf](https://github.com/falexwolf)
+- ✨ Track run environment [PR1368](https://github.com/laminlabs/lamindb/pull/1368) [@falexwolf](https://github.com/falexwolf)
+- ✨ Allow transfer from private instances [PR1370](https://github.com/laminlabs/lamindb/pull/1370) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Speed up transfer and enable transfer parents [PR1371](https://github.com/laminlabs/lamindb/pull/1371) [@sunnyosun](https://github.com/sunnyosun)
+- 🎨 Version based on `stem_uid` instead of `initial_version_id` and replace `__lamindb_uid_prefix__` with `__transform_stem_uid__` [PR1369](https://github.com/laminlabs/lamindb/pull/1369) [PR1375](https://github.com/laminlabs/lamindb/pull/1375) [PR1373](https://github.com/laminlabs/lamindb/pull/1373) [@bpenteado](https://github.com/bpenteado) [@falexwolf](https://github.com/falexwolf)
+- 🎨 Name `.lndb` files by instance id [PR1372](https://github.com/laminlabs/lamindb/pull/1372) [@falexwolf](https://github.com/falexwolf)
+
 ## 0.64
 
 ### 0.64.2 {small}`2023-12-18`

{lamindb-0.64.2 → lamindb-0.65.1}/docs/data.ipynb

@@ -20,7 +20,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We saw how LaminDB allows to query & search across artifacts & datasets using registries: {doc}`meta`.\n",
+    "We saw how LaminDB allows to query & search across artifacts & collections using registries: {doc}`meta`.\n",
     "\n",
     "Let us now look at the following case:\n",
     "\n",
@@ -35,12 +35,12 @@
     "\n",
     "Because the artifact was validated, querying the `DataFrame` is guaranteed to succeed!\n",
     "\n",
-    "Such within-dataset queries are also possible for cloud-backed datasets using DuckDB, TileDB, zarr, HDF5, parquet, and other storage backends.\n",
+    "Such within-collection queries are also possible for cloud-backed collections using DuckDB, TileDB, zarr, HDF5, parquet, and other storage backends.\n",
     "\n",
     "- For a use case with TileDB, see: {doc}`docs:cellxgene`\n",
     "- For a use case with DuckDB, see: {doc}`docs:rxrx`\n",
     "\n",
-    "In this notebook, we show how to subset an `AnnData` and generic `HDF5` and `zarr` datasets accessed in the cloud."
+    "In this notebook, we show how to subset an `AnnData` and generic `HDF5` and `zarr` collections accessed in the cloud."
    ]
   },
   {

{lamindb-0.64.2 → lamindb-0.65.1}/docs/faq/delete.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "Registry records can be deleted with `record.delete()`, which will **permanently remove** them from your database.\n",
     "\n",
-    "When it comes to **records of `File` and `Dataset`**, they are **\"moved into trash\"** when you first call `record.delete()`.\n",
+    "When it comes to **records of `File` and `Collection`**, they are **\"moved into trash\"** when you first call `record.delete()`.\n",
     "- Trashed records are invisible in the UI and excluded from the query results, see [visibility faq](/faq/visibility).\n",
     "- If a record is already in the trash or `permanent=True` is passed, calling `record.delete()` triggers permanent delete.\n",
     "- During permanent deletion of a record, its artifact in storage is also deleted unless it has a semantic `key`."

{lamindb-0.64.2 → lamindb-0.65.1}/docs/faq/key.ipynb

@@ -11,8 +11,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "LaminDB is designed around associating biological metadata to artifacts and datasets.\n",
-    "This enables querying for them in storage by metadata and removes the requirement for semantic artifact and dataset names.\n",
+    "LaminDB is designed around associating biological metadata to artifacts and collections.\n",
+    "This enables querying for them in storage by metadata and removes the requirement for semantic artifact and collection names.\n",
     "\n",
     "Here, we will discuss trade-offs for using the `key` parameter, which allows for semantic keys, in various scenarios."
    ]
@@ -65,12 +65,12 @@
     "                f.write(random_text)\n",
     "\n",
     "        for i in range(1, 3):\n",
-    "            dataset_folder = raw_folder / f\"Dataset_{i}\"\n",
-    "            dataset_folder.mkdir()\n",
+    "            collection_folder = raw_folder / f\"Collection_{i}\"\n",
+    "            collection_folder.mkdir()\n",
     "\n",
     "            for j in range(1, 5):\n",
     "                artifact_name = f\"raw_data_{j}.txt\"\n",
-    "                with (dataset_folder / artifact_name).open(\"w\") as f:\n",
+    "                with (collection_folder / artifact_name).open(\"w\") as f:\n",
     "                    random_text = \"\".join(\n",
     "                        random.choice(string.ascii_letters) for _ in range(10)\n",
     "                    )\n",
@@ -132,7 +132,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Storing artifacts using `Storage`, `File`, and `Dataset`"
+    "## Storing artifacts using `Storage`, `File`, and `Collection`"
    ]
   },
   {
@@ -143,7 +143,7 @@
     "\n",
     "1. {class}`~lamindb.Storage`: Manages the default storage root that can be either local or in the cloud. For more details we refer to {doc}`docs:faq/storage`.\n",
     "2. {class}`~lamindb.Artifact`: Manages data batches with an optional `key` that acts as a relative path within the current default storage root (see {class}`~lamindb.Storage`). An example is a single h5 artifact.\n",
-    "3. {class}`~lamindb.Dataset`: Manages a collection of data batches with an optional `key` that acts as a relative path within the current default storage root (see {class}`~lamindb.Storage`). An example is a collection of h5 artifacts.\n",
+    "3. {class}`~lamindb.Collection`: Manages a collection of data batches with an optional `key` that acts as a relative path within the current default storage root (see {class}`~lamindb.Storage`). An example is a collection of h5 artifacts.\n",
     "\n",
     "For more details we refer to {doc}`docs:tutorial`."
    ]
@@ -186,7 +186,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We will now create `File` objects with and without semantic keys using `key` and also save them as `Datasets`."
+    "We will now create `File` objects with and without semantic keys using `key` and also save them as `Collections`."
    ]
   },
   {
@@ -253,8 +253,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "`Dataset` does not have a `key` parameter because it does not store any additional data in `Storage`.\n",
-    "In contrast, it has a `name` parameter that serves as a semantic identifier of the dataset."
+    "`Collection` does not have a `key` parameter because it does not store any additional data in `Storage`.\n",
+    "In contrast, it has a `name` parameter that serves as a semantic identifier of the collection."
    ]
   },
   {
@@ -263,8 +263,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds_1 = ln.Dataset(data=[artifact_no_key_1, artifact_no_key_2], name=\"no key collection\")\n",
-    "ds_2 = ln.Dataset(data=[artifact_key_3, artifact_key_4], name=\"sample collection\")\n",
+    "ds_1 = ln.Collection(data=[artifact_no_key_1, artifact_no_key_2], name=\"no key collection\")\n",
+    "ds_2 = ln.Collection(data=[artifact_key_3, artifact_key_4], name=\"sample collection\")\n",
     "ds_1"
    ]
   },
@@ -283,7 +283,7 @@
     "\n",
     "### Advantages:\n",
     "\n",
-    "- Simple: It can be easier to refer to specific datasets in conversations\n",
+    "- Simple: It can be easier to refer to specific collections in conversations\n",
     "- Familiarity: Most people are familiar with the concept of semantic names\n",
     "\n",
     "### Disadvantages\n",
@@ -600,8 +600,8 @@
     "It can be useful to resemble the artifact structure in \"complex_biological_project\" from above also in LaminDB to allow for queries for artifacts that were stored in specific folders.\n",
     "Common examples of this are folders specifying different processing stages such as `raw`, `preprocessed`, or `annotated`.\n",
     "\n",
-    "Note that this use-case may also be overlapping with `Dataset` which also allows for grouping `Files`.\n",
-    "However, `Dataset` cannot model hierarchical groupings."
+    "Note that this use-case may also be overlapping with `Collection` which also allows for grouping `Files`.\n",
+    "However, `Collection` cannot model hierarchical groupings."
    ]
   },
   {
@@ -640,14 +640,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Dataset"
+    "### Collection"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Alternatively, it would have been possible to create a `Dataset` with a corresponding name:"
+    "Alternatively, it would have been possible to create a `Collection` with a corresponding name:"
    ]
   },
   {
@@ -666,7 +666,7 @@
     "for path in all_data_paths:\n",
     "    all_data_artifacts.append(ln.Artifact(path))\n",
     "\n",
-    "data_ds = ln.Dataset(all_data_artifacts, name=\"data\")\n",
+    "data_ds = ln.Collection(all_data_artifacts, name=\"data\")\n",
     "data_ds.save()"
    ]
   },
@@ -676,7 +676,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.Dataset.filter(name__icontains=\"data\").df()"
+    "ln.Collection.filter(name__icontains=\"data\").df()"
    ]
   },
   {
@@ -748,7 +748,7 @@
    "metadata": {},
    "source": [
     "Due to the chance of clashes for the aforementioned approaches being rather high, we generally recommend not to store hierarchical data with solely semantic keys.\n",
-    "Biological metadata makes `Files` and `Datasets` unambiguous and easily queryable.\n"
+    "Biological metadata makes `Files` and `Collections` unambiguous and easily queryable.\n"
    ]
   },
   {
@@ -762,7 +762,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Distributed Datasets"
+    "### Distributed Collections"
    ]
   },
   {
@@ -771,7 +771,7 @@
    "source": [
     "LaminDB can ingest legacy data that already had a structure in their storage.\n",
     "In such cases, it disables `artifact_use_virtual_keys` and the artifacts are ingested with their actual storage location.\n",
-    "It might be therefore be possible that `Files` stored in different storage roots may be associated with a single `Dataset`.\n",
+    "It might be therefore be possible that `Files` stored in different storage roots may be associated with a single `Collection`.\n",
     "To simulate this, we are disabling `artifact_use_virtual_keys` and ingest artifacts stored in a different path (the \"legacy data\")."
    ]
   },
@@ -817,7 +817,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifact_from_raw = ln.Artifact.filter(key__icontains=\"Dataset_2/raw_data_1\").first()\n",
+    "artifact_from_raw = ln.Artifact.filter(key__icontains=\"Collection_2/raw_data_1\").first()\n",
     "artifact_from_preprocessed = ln.Artifact.filter(\n",
     "    key__icontains=\"preprocessed/result_1\"\n",
     ").first()\n",
@@ -830,7 +830,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Let's create our `Dataset`:"
+    "Let's create our `Collection`:"
    ]
   },
   {
@@ -839,8 +839,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds = ln.Dataset(\n",
-    "    [artifact_from_raw, artifact_from_preprocessed], name=\"raw_and_processed_dataset_2\"\n",
+    "ds = ln.Collection(\n",
+    "    [artifact_from_raw, artifact_from_preprocessed], name=\"raw_and_processed_collection_2\"\n",
     ")\n",
     "ds.save()"
    ]
@@ -1010,12 +1010,12 @@
     "\n",
     "Question: Does the rxrx1 use-case work well with our current `key` design?\n",
     "\n",
-    "Answer: The rxrx1 use-case currently has an immutable parquet file with metadata associated with the `Dataset`.\n",
+    "Answer: The rxrx1 use-case currently has an immutable parquet file with metadata associated with the `Collection`.\n",
     "Since we did not register the `File` objects themselves, we have to query for the artifacts and their paths through the parquet file.\n",
     "This requires the paths to be stable remote URLs that are kept sync with the metadata parquet `File`.\n",
     "https://github.com/laminlabs/rxrx-lamin/blob/main/docs/notebooks/02-rxrx1.ipynb describes the curation for the images.\n",
-    "Here, a `Dataset` is created without any `File` objects.\n",
-    "The `Dataset` does not have `key`, solely `File` objects, which are not created here.\n",
+    "Here, a `Collection` is created without any `File` objects.\n",
+    "The `Collection` does not have `key`, solely `File` objects, which are not created here.\n",
     "Any hierarchy that is resembled in the `paths` and `path` (why 2?) columns of the metadata DataFrame is not reflected in `Storage` (via `key`) due to the lack of `Files`."
    ]
   },

{lamindb-0.64.2 → lamindb-0.65.1}/docs/faq/reference-field.ipynb

@@ -11,9 +11,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "When registering data in LaminDB, you might want to store a reference link or ID to indicate the source of the dataset.\n",
+    "When registering data in LaminDB, you might want to store a reference link or ID to indicate the source of the collection.\n",
     "\n",
-    "We have `reference` and `reference_type` fields for this purpose, they are available for {class}`~lamindb.Dataset`, {class}`~lamindb.Transform`, {class}`~lamindb.Run` and {class}`~lamindb.ULabel`."
+    "We have `reference` and `reference_type` fields for this purpose, they are available for {class}`~lamindb.Collection`, {class}`~lamindb.Transform`, {class}`~lamindb.Run` and {class}`~lamindb.ULabel`."
    ]
   },
   {

{lamindb-0.64.2 → lamindb-0.65.1}/docs/faq/validator.ipynb

@@ -57,7 +57,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Let's use an AnnData as the dataset to validate:"
+    "Let's use an AnnData as the collection to validate:"
    ]
   },
   {

{lamindb-0.64.2 → lamindb-0.65.1}/docs/faq/visibility.ipynb

@@ -4,9 +4,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# When do visibility of artifacts and datasets change?\n",
+    "# When do visibility of artifacts and collections change?\n",
     "\n",
-    "Files and datasets in LaminDB have the following 3 levels if visibility:\n",
+    "Files and collections in LaminDB have the following 3 levels if visibility:\n",
     "- 1: \"default\", visible in the UI by default, returned from the query results\n",
     "- 0: \"hidden\", excluded from the query results, notebook artifacts (generated by `lamin save`) are default to be hidden\n",
     "- -1: \"trash\", excluded from the query results, set with `.delete()`"

{lamindb-0.64.2 → lamindb-0.65.1}/docs/features-lamindb.md

@@ -5,10 +5,10 @@
 - Model data using {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.Dataset`
-- Version artifacts, datasets & transforms
+- Bridge artifacts and warehousing: {class}`~lamindb.Artifact`, {class}`~lamindb.Collection`
+- Version artifacts, collections & transforms
 
-**Track data flow across notebooks, pipelines & UI: {meth}`~lamindb.track`, {class}`~lamindb.Transform` & {class}`~lamindb.Run`.**
+**Track data lineage across notebooks, pipelines & UI: {meth}`~lamindb.track`, {class}`~lamindb.Transform` & {class}`~lamindb.Run`.**
 
 - Execution reports & source code for [notebooks & scripts](/track)
 - Integrate with workflow managers: [redun](docs:redun), [nextflow](docs:nextflow), [snakemake](docs:snakemake)

{lamindb-0.64.2 → lamindb-0.65.1}/docs/guide.md

@@ -17,7 +17,6 @@ setup
 query-search
 track
 validate
-public-ontologies
 bio-registries
 annotate
 schemas