lamindb 1.1.1__tar.gz → 1.2a2__tar.gz

{lamindb-1.1.1 → lamindb-1.2a2}/.github/workflows/build.yml

@@ -27,7 +27,7 @@ jobs:
       - id: set-matrix
         shell: bash
         run: |
-          BASE_GROUPS=$(jq -n -c '["unit-core", "unit-storage", "tutorial", "guide", "biology", "faq", "storage", "cli"]')
+          BASE_GROUPS=$(jq -n -c '["unit-core", "unit-storage", "tutorial", "guide", "biology", "faq", "storage", "cli", "permissions"]')
 
           if [[ "${{ github.event_name }}" == "push" || "${{ steps.changes.outputs.curator }}" == "true" ]]; then
             # Run everything on push or when curator paths change
@@ -57,6 +57,14 @@ jobs:
           submodules: recursive
           fetch-depth: 0
 
+      - uses: actions/checkout@v4
+        if: ${{ matrix.group == 'permissions' }}
+        with:
+          repository: laminlabs/laminhub
+          token: ${{ secrets.GH_TOKEN_DEPLOY_LAMINAPP }}
+          path: laminhub
+          ref: main
+
       - uses: actions/setup-python@v5
         with:
           python-version: |
@@ -71,7 +79,7 @@ jobs:
           key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
 
       - name: cache postgres
-        if: ${{ matrix.group == 'faq' || matrix.group == 'unit-core' || matrix.group == 'unit-storage' }}
+        if: ${{ matrix.group == 'faq' || matrix.group == 'unit-core' || matrix.group == 'unit-storage' || matrix.group == 'permissions'}}
         id: cache-postgres
         uses: actions/cache@v4
         with:

{lamindb-1.1.1 → lamindb-1.2a2}/.pre-commit-config.yaml

@@ -58,5 +58,6 @@ repos:
               test_notebooks.py|
               script-to-test-versioning.py|
               tests/storage/conftest.py|
-              tests/curators/conftest.py
+              tests/curators/conftest.py|
+              tests/permissions/conftest.py
           )

{lamindb-1.1.1 → lamindb-1.2a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.1.1
+Version: 1.2a2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10,<3.13
@@ -10,7 +10,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: lamin_utils==0.13.10
 Requires-Dist: lamin_cli==1.1.0
-Requires-Dist: lamindb_setup[aws]==1.2.0
+Requires-Dist: lamindb_setup[aws]==1.3.0
 Requires-Dist: pyyaml
 Requires-Dist: pyarrow
 Requires-Dist: pandera
@@ -22,9 +22,9 @@ Requires-Dist: anndata>=0.8.0,<=0.11.3
 Requires-Dist: fsspec
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
-Requires-Dist: bionty==1.1.0 ; extra == "bionty"
+Requires-Dist: bionty ; extra == "bionty"
 Requires-Dist: cellregistry ; extra == "cellregistry"
-Requires-Dist: clinicore==1.1.0 ; extra == "clinicore"
+Requires-Dist: clinicore ; extra == "clinicore"
 Requires-Dist: tomlkit ; extra == "dev"
 Requires-Dist: line_profiler ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
@@ -44,7 +44,7 @@ Requires-Dist: jupytext ; extra == "jupyter"
 Requires-Dist: nbconvert>=7.2.1 ; extra == "jupyter"
 Requires-Dist: mistune!=3.1.0 ; extra == "jupyter"
 Requires-Dist: omop ; extra == "omop"
-Requires-Dist: wetlab==1.1.0 ; extra == "wetlab"
+Requires-Dist: wetlab ; extra == "wetlab"
 Requires-Dist: zarr>=2.16.0,<3.0.0a0 ; extra == "zarr"
 Project-URL: Home, https://github.com/laminlabs/lamindb
 Provides-Extra: bionty

{lamindb-1.1.1 → lamindb-1.2a2}/docs/bio-registries.ipynb

@@ -322,7 +322,7 @@
    "source": [
     "We'd like to load the corresponding records in our in-house registry to annotate a dataset.\n",
     "\n",
-    "To this end, you'll typically use {class}`~lamindb.core.CanCurate.from_values`, which will both validate & retrieve records that match the values."
+    "To this end, you'll typically use {class}`~lamindb.models.CanCurate.from_values`, which will both validate & retrieve records that match the values."
    ]
   },
   {

{lamindb-1.1.1 → lamindb-1.2a2}/docs/curate-any.ipynb

@@ -20,11 +20,11 @@
    "source": [
     ":::{dropdown} How do I validate based on a public ontology?\n",
     "\n",
-    "LaminDB makes it easy to validate categorical variables based on registries that inherit from {class}`~lamindb.core.CanCurate`.\n",
+    "LaminDB makes it easy to validate categorical variables based on registries that inherit from {class}`~lamindb.models.CanCurate`.\n",
     "\n",
-    "{class}`~lamindb.core.CanCurate` methods validate against the registries in your LaminDB instance.\n",
+    "{class}`~lamindb.models.CanCurate` methods validate against the registries in your LaminDB instance.\n",
     "In {doc}`./bio-registries`, you'll see how to extend standard validation to validation against _public references_ using a `ReferenceTable` ontology object: `public = Record.public()`.\n",
-    "By default, {meth}`~lamindb.core.CanCurate.from_values` considers a match in a public reference a validated value for any {mod}`bionty` entity.\n",
+    "By default, {meth}`~lamindb.models.CanCurate.from_values` considers a match in a public reference a validated value for any {mod}`bionty` entity.\n",
     "\n",
     ":::"
    ]
@@ -107,7 +107,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "{meth}`~lamindb.core.CanCurate.validate` validates passed values against reference values in a registry.\n",
+    "{meth}`~lamindb.models.CanCurate.validate` validates passed values against reference values in a registry.\n",
     "It returns a boolean vector indicating whether a value has an exact match in the reference values."
    ]
   },
@@ -124,11 +124,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "When validation fails, you can call {meth}`~lamindb.core.CanCurate.inspect` to figure out what to do.\n",
+    "When validation fails, you can call {meth}`~lamindb.models.CanCurate.inspect` to figure out what to do.\n",
     "\n",
-    "{meth}`~lamindb.core.CanCurate.inspect` applies the same definition of validation as {meth}`~lamindb.core.CanCurate.validate`, but returns a rich return value {class}`~lamindb.core.InspectResult`. Most importantly, it logs recommended curation steps that would render the data validated.\n",
+    "{meth}`~lamindb.models.CanCurate.inspect` applies the same definition of validation as {meth}`~lamindb.models.CanCurate.validate`, but returns a rich return value {class}`~lamindb.core.InspectResult`. Most importantly, it logs recommended curation steps that would render the data validated.\n",
     "\n",
-    "Note: you can use {meth}`~lamindb.core.CanCurate.standardize` to standardize synonyms."
+    "Note: you can use {meth}`~lamindb.models.CanCurate.standardize` to standardize synonyms."
    ]
   },
   {
@@ -146,7 +146,7 @@
    "source": [
     "Following the suggestions to register new labels:\n",
     "\n",
-    "Bulk creating records using {meth}`~lamindb.core.CanCurate.from_values` only returns validated records:\n",
+    "Bulk creating records using {meth}`~lamindb.models.CanCurate.from_values` only returns validated records:\n",
     "\n",
     "Note: Terms validated with public reference are also created with `.from_values`, see {doc}`/bio-registries` for details."
    ]
@@ -295,7 +295,7 @@
    "outputs": [],
    "source": [
     "feature_set = ln.FeatureSet(genes).save()\n",
-    "artifact.features.add_feature_set(feature_set, slot=\"genes\")\n",
+    "artifact.features._add_schema(feature_set, slot=\"genes\")\n",
     "artifact.describe()"
    ]
   },

{lamindb-1.1.1 → lamindb-1.2a2}/docs/curate-df.ipynb

@@ -406,10 +406,28 @@
     ").save()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "28",
+   "metadata": {},
+   "source": [
+    "Check the slots of a schema:"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28",
+   "id": "29",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "anndata_schema.slots"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "30",
    "metadata": {
     "tags": [
      "hide-output"
@@ -426,7 +444,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "29",
+   "id": "31",
    "metadata": {},
    "source": [
     "Subset the `AnnData` to validated genes only:"
@@ -435,7 +453,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30",
+   "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -444,7 +462,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "31",
+   "id": "33",
    "metadata": {},
    "source": [
     "Now let's validate the subsetted object:"
@@ -453,7 +471,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32",
+   "id": "34",
    "metadata": {
     "tags": [
      "hide-output"
@@ -467,7 +485,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "33",
+   "id": "35",
    "metadata": {},
    "source": [
     "The validated `AnnData` can be subsequently saved as an {class}`~lamindb.Artifact`:"
@@ -476,7 +494,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "34",
+   "id": "36",
    "metadata": {
     "tags": [
      "hide-output"
@@ -489,7 +507,25 @@
   },
   {
    "cell_type": "markdown",
-   "id": "35",
+   "id": "37",
+   "metadata": {},
+   "source": [
+    "Access the schema for each slot:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "38",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "artifact.features.slots"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "39",
    "metadata": {},
    "source": [
     "The saved artifact has been annotated with validated features and labels:"
@@ -498,7 +534,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "36",
+   "id": "40",
    "metadata": {
     "tags": [
      "hide-output"
@@ -511,7 +547,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "37",
+   "id": "41",
    "metadata": {},
    "source": [
     "## Standardize an AnnData"
@@ -519,7 +555,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "38",
+   "id": "42",
    "metadata": {},
    "source": [
     "If you need more control, you can access the underlying `\"var\"` and `\"obs\"` `DataFrameCurator` objects directly."
@@ -528,7 +564,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "39",
+   "id": "43",
    "metadata": {
     "tags": [
      "hide-output"
@@ -543,7 +579,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "40",
+   "id": "44",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -559,7 +595,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "41",
+   "id": "45",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -573,7 +609,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "42",
+   "id": "46",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -583,7 +619,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "43",
+   "id": "47",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -592,7 +628,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "44",
+   "id": "48",
    "metadata": {},
    "source": [
     "## Summary"
@@ -600,7 +636,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "45",
+   "id": "49",
    "metadata": {},
    "source": [
     "We've walked through the process of validating, standardizing, and annotating datasets going through these key steps:\n",
@@ -618,7 +654,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "46",
+   "id": "50",
    "metadata": {
     "tags": [
      "hide-cell"