lamindb 0.69.3__tar.gz → 0.69.5__tar.gz

{lamindb-0.69.3 → lamindb-0.69.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.69.3
+Version: 0.69.5
 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==0.64.1
-Requires-Dist: lamindb_setup==0.68.1
+Requires-Dist: lnschema_core==0.64.4
+Requires-Dist: lamindb_setup==0.68.3
 Requires-Dist: lamin_utils==0.13.1
-Requires-Dist: lamin_cli==0.10.2
+Requires-Dist: lamin_cli==0.11.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0

{lamindb-0.69.3 → lamindb-0.69.5}/docs/annotate-for-developers.ipynb

@@ -68,7 +68,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Register a collection"
+    "## Register a artifact"
    ]
   },
   {
@@ -112,7 +112,7 @@
     "    index=[\"sample1\", \"sample2\", \"sample3\"],\n",
     ")\n",
     "\n",
-    "# external metadata (describes the entire collection)\n",
+    "# external metadata (describes the entire artifact)\n",
     "external_meta = {\n",
     "    \"organism\": \"human\",\n",
     "    \"assay\": \"scRNA-seq\",\n",
@@ -158,15 +158,15 @@
    "source": [
     "ln.track()\n",
     "\n",
-    "collection = ln.Collection.from_anndata(adata, name=\"my RNA-seq\")\n",
-    "collection.save()"
+    "artifact = ln.Artifact.from_anndata(adata, description=\"my RNA-seq\")\n",
+    "artifact.save()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We don't see any metadata in the registered collection yet:"
+    "We don't see any metadata in the registered artifact yet:"
    ]
   },
   {
@@ -175,7 +175,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.describe()"
+    "artifact.describe()"
    ]
   },
   {
@@ -234,7 +234,7 @@
    "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 collection.\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 artifact.\n",
     "\n",
     "Here we define them using the {class}`~lamindb.Feature` registry:"
    ]
@@ -357,7 +357,7 @@
    "source": [
     "## Annotate with features\n",
     "\n",
-    "Non-external features are annotated when registering collections using `.from_df` or `.from_anndata` methods:\n",
+    "Non-external features are annotated when registering artifacts using `.from_df` or `.from_anndata` methods:\n",
     "\n",
     "(See the below \"Annotate with labels stratified by metadata features\" session for adding external features.)"
    ]
@@ -372,8 +372,8 @@
    },
    "outputs": [],
    "source": [
-    "collection = ln.Collection.from_anndata(adata, name=\"my RNA-seq\")\n",
-    "collection.save()"
+    "artifact = ln.Artifact.from_anndata(adata, description=\"my RNA-seq\")\n",
+    "artifact.save()"
    ]
   },
   {
@@ -382,14 +382,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.features.add_from_anndata(var_field=bt.Gene.symbol, organism=\"human\")"
+    "artifact.features.add_from_anndata(var_field=bt.Gene.symbol, organism=\"human\")"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This collection is now annotated with features:"
+    "This artifact is now annotated with features:"
    ]
   },
   {
@@ -398,7 +398,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.describe()"
+    "artifact.describe()"
    ]
   },
   {
@@ -416,7 +416,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.features"
+    "artifact.features"
    ]
   },
   {
@@ -432,7 +432,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.features[\"var\"].df()"
+    "artifact.features[\"var\"].df()"
    ]
   },
   {
@@ -441,7 +441,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.features[\"obs\"].df()"
+    "artifact.features[\"obs\"].df()"
    ]
   },
   {
@@ -450,7 +450,7 @@
    "source": [
     "## Annotate with labels\n",
     "\n",
-    "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:"
+    "If you simply want to tag a artifact 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 artifact:"
    ]
   },
   {
@@ -459,15 +459,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.labels.add(experiment)\n",
-    "collection.labels.add(project)"
+    "artifact.labels.add(experiment)\n",
+    "artifact.labels.add(project)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now you see the collection is annotated with 'EXP0001', 'PRJ0001' labels:"
+    "Now you see the artifact is annotated with 'EXP0001', 'PRJ0001' labels:"
    ]
   },
   {
@@ -476,7 +476,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.describe()"
+    "artifact.describe()"
    ]
   },
   {
@@ -492,7 +492,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.labels"
+    "artifact.labels"
    ]
   },
   {
@@ -510,7 +510,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.ulabels.df()"
+    "artifact.ulabels.df()"
    ]
   },
   {
@@ -521,7 +521,7 @@
     "\n",
     "For labels associated with metadata features, you can pass \"feature\" to `.labels.add` to stratify 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 collection again, this time specifying their features:"
+    "Let's add the experiment label \"EXP0001\" and project label \"PRJ0001\" to the artifact again, this time specifying their features:"
    ]
   },
   {
@@ -537,15 +537,15 @@
     "# an auto-complete object of registered features\n",
     "features = ln.Feature.lookup()\n",
     "\n",
-    "collection.labels.add(experiment, feature=features.experiment)\n",
-    "collection.labels.add(project, feature=features.project)"
+    "artifact.labels.add(experiment, feature=features.experiment)\n",
+    "artifact.labels.add(project, feature=features.project)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "You now see a 3rd featureset is added to the collection at slot \"external\", and the labels are stratified by two features:"
+    "You now see a 3rd featureset is added to the artifact at slot \"external\", and the labels are stratified by two features:"
    ]
   },
   {
@@ -554,7 +554,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.describe()"
+    "artifact.describe()"
    ]
   },
   {
@@ -570,7 +570,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.labels.get(features.experiment).df()"
+    "artifact.labels.get(features.experiment).df()"
    ]
   },
   {
@@ -590,7 +590,7 @@
    },
    "outputs": [],
    "source": [
-    "collection.labels.add(assay, feature=features.assay)"
+    "artifact.labels.add(assay, feature=features.assay)"
    ]
   },
   {
@@ -600,7 +600,7 @@
    "outputs": [],
    "source": [
     "# access labels directly via default accessor \"experimental_factors\"\n",
-    "collection.experimental_factors.df()"
+    "artifact.experimental_factors.df()"
    ]
   },
   {
@@ -610,7 +610,7 @@
    "outputs": [],
    "source": [
     "# access labels via feature\n",
-    "collection.labels.get(features.assay).df()"
+    "artifact.labels.get(features.assay).df()"
    ]
   },
   {
@@ -631,18 +631,18 @@
    "outputs": [],
    "source": [
     "# labels of obs metadata features\n",
-    "collection.labels.add(cell_types, feature=features.cell_type)\n",
-    "collection.labels.add(tissues, feature=features.tissue)\n",
+    "artifact.labels.add(cell_types, feature=features.cell_type)\n",
+    "artifact.labels.add(tissues, feature=features.tissue)\n",
     "\n",
     "# labels of external metadata features\n",
-    "collection.labels.add(organism, feature=features.organism)"
+    "artifact.labels.add(organism, feature=features.organism)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now you've annotated your collection with all features and labels:"
+    "Now you've annotated your artifact with all features and labels:"
    ]
   },
   {
@@ -651,7 +651,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.describe()"
+    "artifact.describe()"
    ]
   },
   {