lamindb 0.69.3__tar.gz → 0.69.4__tar.gz

{lamindb-0.69.3 → lamindb-0.69.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.69.3
+Version: 0.69.4
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -10,7 +10,7 @@ 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: lamindb_setup==0.68.2
 Requires-Dist: lamin_utils==0.13.1
 Requires-Dist: lamin_cli==0.10.2
 Requires-Dist: rapidfuzz

{lamindb-0.69.3 → lamindb-0.69.4}/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()"
    ]
   },
   {

{lamindb-0.69.3 → lamindb-0.69.4}/docs/annotate.ipynb

@@ -448,7 +448,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifact = annotate.register_artifact(description=\"test AnnData\")"
+    "artifact = annotate.save_artifact(description=\"test AnnData\")"
    ]
   },
   {
@@ -493,7 +493,7 @@
    "outputs": [],
    "source": [
     "# register a new collection\n",
-    "collection = annotate.register_collection(\n",
+    "collection = annotate.save_collection(\n",
     "    artifact,  # registered artifact above, can also pass a list of artifacts\n",
     "    name=\"Experiment X in brain\",  # title of the publication\n",
     "    description=\"10.1126/science.xxxxx\",  # DOI of the publication\n",
@@ -508,17 +508,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.artifact"
+    "collection.artifacts"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6e963036",
+   "id": "2a46e57a",
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifact.collection"
+    "artifact.collections"
    ]
   }
  ],

{lamindb-0.69.3 → lamindb-0.69.4}/docs/changelog.md

@@ -6,6 +6,11 @@
 
 ## 0.69
 
+### 0.69.4 {small}`2024-03-30`
+
+- ♻️ Add Vitessce integration [PR](https://github.com/laminlabs/lamindb/pull/1532) [@falexwolf](https://github.com/falexwolf)
+- ♻️ Refactor collections [PR](https://github.com/laminlabs/lamindb/pull/1531) [@falexwolf](https://github.com/falexwolf)
+
 ### 0.69.3 {small}`2024-03-28`
 
 - ✨ Introduce annotation flow via `Annotate.from_df` and `Annotate.from_anndata` [PR 1](https://github.com/laminlabs/lamindb/pull/1524) [2](https://github.com/laminlabs/lamindb/pull/1526) [3](https://github.com/laminlabs/lamindb/pull/1528) [@sunnyosun](https://github.com/sunnyosun)

{lamindb-0.69.3 → lamindb-0.69.4}/docs/introduction.ipynb

@@ -341,7 +341,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "annotate.register_features(validated_only=False)\n",
+    "annotate.save_features(validated_only=False)\n",
     "annotate.update_registry(\"perturbation\")"
    ]
   },
@@ -387,7 +387,7 @@
    "outputs": [],
    "source": [
     "# create, annotate and save an artifact\n",
-    "artifact = annotate.register_artifact(description=\"my RNA-seq\", version=\"1\")\n",
+    "artifact = annotate.save_artifact(description=\"my RNA-seq\", version=\"1\")\n",
     "artifact.describe()"
    ]
   },
@@ -471,7 +471,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifact = annotate.register_artifact(description=\"my RNA-seq\", version=\"1\")\n",
+    "artifact = annotate.save_artifact(description=\"my RNA-seq\", version=\"1\")\n",
     "artifact.describe()"
    ]
   },
@@ -565,7 +565,7 @@
     "                      var_field=bt.Gene.symbol, \n",
     "                      organism=\"human\")\n",
     "annotate.validate()\n",
-    "artifact2 = annotate.register_artifact(description=\"my RNA-seq batch 2\")"
+    "artifact2 = annotate.save_artifact(description=\"my RNA-seq batch 2\")"
    ]
   },
   {

{lamindb-0.69.3 → lamindb-0.69.4}/docs/tutorial2.ipynb

@@ -419,7 +419,7 @@
     "    ln.track(transform=transform)\n",
     "    input_data = ln.Collection.filter(name__startswith=\"Iris collection\", version=\"1\").one()\n",
     "    input_paths = [\n",
-    "        path.download_to(path.name) for path in input_data.artifact.path.glob(\"*\")\n",
+    "        path.download_to(path.name) for path in input_data.artifacts[0].path.glob(\"*\")\n",
     "    ]\n",
     "    # apply ML model\n",
     "    output_data = ln.core.datasets.df_iris_in_meter_study1()\n",
@@ -507,7 +507,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can now validate & register the dataframe in one line by creating a {class}`~lamindb.Collection` record:"
+    "We can now validate & register the dataframe in one line:"
    ]
   },
   {
@@ -516,13 +516,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection = ln.Collection.from_df(\n",
+    "artifact = ln.Artifact.from_df(\n",
     "    df,\n",
-    "    name=\"Iris study 1 - transformed\",\n",
-    "    description=\"Iris collection after measuring sepal & petal metrics\",\n",
+    "    description=\"Iris study 1 - after measuring sepal & petal metrics\",\n",
     ")\n",
-    "\n",
-    "collection.save()"
+    "artifact.save()"
    ]
   },
   {
@@ -531,7 +529,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.features.add(new_features)"
+    "artifact.features.add(new_features)"
    ]
   },
   {
@@ -554,7 +552,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.features"
+    "artifact.features"
    ]
   },
   {
@@ -584,7 +582,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.features[\"columns\"].df()"
+    "artifact.features[\"columns\"].df()"
    ]
   },
   {
@@ -601,7 +599,7 @@
    "outputs": [],
    "source": [
     "organism_labels = ln.ULabel.filter(parents__name=\"is_organism\").all()\n",
-    "collection.labels.add(organism_labels, feature=features.iris_organism_name)"
+    "artifact.labels.add(organism_labels, feature=features.iris_organism_name)"
    ]
   },
   {
@@ -617,7 +615,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.labels.add(ulabels.study0, feature=features.study_name)"
+    "artifact.labels.add(ulabels.study0, feature=features.study_name)"
    ]
   },
   {
@@ -633,7 +631,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.features"
+    "artifact.features"
    ]
   },
   {
@@ -649,7 +647,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.describe()"
+    "artifact.describe()"
    ]
   },
   {
@@ -658,7 +656,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.artifact.view_lineage()"
+    "artifact.view_lineage()"
    ]
   },
   {
@@ -743,7 +741,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Let's load both data batches as artifacts:"
+    "Let's load it:"
    ]
   },
   {
@@ -752,8 +750,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection1 = ln.Collection.filter(name=\"Iris study 1 - transformed\").one()\n",
-    "artifact1 = collection1.artifact\n",
     "artifact2 = ln.Artifact.filter(description=\"Iris study 2 - transformed\").one()"
    ]
   },
@@ -771,7 +767,7 @@
    "outputs": [],
    "source": [
     "collection = ln.Collection(\n",
-    "    [artifact1, artifact2], name=\"Iris flower study 1 & 2 - transformed\"\n",
+    "    [artifact, artifact2], name=\"Iris flower study 1 & 2 - transformed\"\n",
     ")\n",
     "collection.save()"
    ]

{lamindb-0.69.3 → lamindb-0.69.4}/lamindb/__init__.py

@@ -15,7 +15,7 @@ Registries:
    Feature
    FeatureSet
 
-Functions:
+Key functionality:
 
 .. autosummary::
    :toctree: .
@@ -23,6 +23,7 @@ Functions:
    connect
    track
    finish
+   Annotate
    view
    save
 
@@ -31,7 +32,7 @@ Modules & settings:
 .. autosummary::
    :toctree: .
 
-   Annotate
+   integrations
    settings
    setup
    UPath
@@ -39,7 +40,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.69.3"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.69.4"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 
@@ -88,6 +89,7 @@ if _check_instance_setup(from_lamindb=True):
     )
 
     dev = core  # backward compat
+    from . import integrations
     from ._annotate import Annotate
     from ._finish import finish
     from ._save import save