lamindb 1.1.0__tar.gz → 1.2.0__tar.gz

{lamindb-1.1.0 → lamindb-1.2.0}/.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-1.1.0 → lamindb-1.2.0}/.gitignore

@@ -59,6 +59,7 @@ default_storage
 default_storage_unit_core
 default_storage_unit_storage
 test.ipynb
+test2.ipynb
 run-tests
 test-django-validation/
 

{lamindb-1.1.0 → lamindb-1.2.0}/.pre-commit-config.yaml

@@ -6,8 +6,8 @@ default_stages:
   - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.5.1
     hooks:
       - id: prettier
         exclude: |
@@ -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-1.1.0 → lamindb-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.1.0
+Version: 1.2.0
 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]==1.1.0
+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"
@@ -39,12 +39,12 @@ Requires-Dist: faker-biology ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=2.0.1 ; extra == "fcs"
 Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
-Requires-Dist: nbproject==0.10.5 ; extra == "jupyter"
+Requires-Dist: nbproject==0.10.6 ; extra == "jupyter"
 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-1.1.0 → lamindb-1.2.0}/docs/arrays.ipynb

@@ -125,7 +125,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "artifact_shard1 = ln.Artifact(\n",
@@ -472,7 +476,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "backed.to_table().to_pandas()"

{lamindb-1.1.0 → lamindb-1.2.0}/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-1.1.0 → lamindb-1.2.0}/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()"
    ]
   },