lamindb 1.3.1__tar.gz → 1.4.0__tar.gz

{lamindb-1.3.1 → lamindb-1.4.0}/.github/workflows/build.yml

@@ -103,7 +103,7 @@ jobs:
         run: sudo apt-get install libpq-dev
 
       - name: install graphviz
-        if: ${{ matrix.group == 'tutorial' || matrix.group == 'guide' || matrix.group == 'biology' }}
+        if: ${{ matrix.group == 'tutorial' || matrix.group == 'guide' || matrix.group == 'biology' || matrix.group == 'faq'}}
         run: sudo apt-get -y install graphviz
 
       - run: nox -s lint

{lamindb-1.3.1 → lamindb-1.4.0}/CONTRIBUTING.md

@@ -48,11 +48,12 @@ Please add a test for every function added to the package.
 Running tests requires the [Docker daemon][] up, then run at the root of the repository:
 
 ```bash
-pytest
+pytest --ignore=tests/storage --ignore=tests/permission
 ```
 
 in the root of the repository.
-Continuous integration will automatically run the tests on all pull requests.
+We exclude specific directories in local `pytest` runs because they directly access external resources such as AWS, which require specific access keys.
+Continuous integration will automatically run **all** tests on pull requests.
 
 ## Code-style
 

{lamindb-1.3.1 → lamindb-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.3.1
+Version: 1.4.0
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10,<3.14
@@ -10,8 +10,8 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: lamin_utils==0.13.11
-Requires-Dist: lamin_cli==1.2.0
-Requires-Dist: lamindb_setup[aws]==1.4.0
+Requires-Dist: lamin_cli==1.3.0
+Requires-Dist: lamindb_setup[aws]==1.5.1
 Requires-Dist: pyyaml
 Requires-Dist: pyarrow
 Requires-Dist: pandera
@@ -19,11 +19,11 @@ Requires-Dist: typing_extensions!=4.6.0
 Requires-Dist: python-dateutil
 Requires-Dist: scipy<1.15.0
 Requires-Dist: pandas>=2.0.0
-Requires-Dist: anndata>=0.8.0,<=0.11.3
+Requires-Dist: anndata>=0.8.0,<=0.11.4
 Requires-Dist: fsspec
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
-Requires-Dist: bionty>=1.2a1 ; extra == "bionty"
+Requires-Dist: bionty>=1.3.0 ; extra == "bionty"
 Requires-Dist: cellregistry ; extra == "cellregistry"
 Requires-Dist: clinicore ; extra == "clinicore"
 Requires-Dist: tomlkit ; extra == "dev"
@@ -46,6 +46,7 @@ Requires-Dist: nbconvert>=7.2.1 ; extra == "jupyter"
 Requires-Dist: mistune!=3.1.0 ; extra == "jupyter"
 Requires-Dist: omop ; extra == "omop"
 Requires-Dist: wetlab ; extra == "wetlab"
+Requires-Dist: numcodecs<0.16.0 ; extra == "zarr"
 Requires-Dist: zarr>=2.16.0,<3.0.0a0 ; extra == "zarr"
 Project-URL: Home, https://github.com/laminlabs/lamindb
 Provides-Extra: bionty

{lamindb-1.3.1 → lamindb-1.4.0}/docs/bio-registries.ipynb

@@ -493,7 +493,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can also add new synonyms to a record like so:"
+    "We can also add new synonyms to a record:"
    ]
   },
   {
@@ -559,8 +559,7 @@
    "outputs": [],
    "source": [
     "cell_types = bt.CellType.lookup(\"abbr\")\n",
-    "hsc = cell_types.hsc\n",
-    "hsc"
+    "cell_types.hsc"
    ]
   },
   {
@@ -756,17 +755,43 @@
    },
    "outputs": [],
    "source": [
-    "records = bt.Organism.from_values(\n",
-    "    [\"iris setosa\", \"iris versicolor\", \"iris virginica\"], source=source\n",
-    ")\n",
-    "\n",
     "# since we didn't seed the Organism registry with the NCBITaxon public ontology\n",
     "# we need to save the records to the database\n",
-    "ln.save(records)\n",
+    "records = bt.Organism.from_values(\n",
+    "    [\"iris setosa\", \"iris versicolor\", \"iris virginica\"], source=source\n",
+    ").save()\n",
     "\n",
     "# now we can query a iris organism and view its parents and children\n",
-    "iris = bt.Organism.get(name=\"iris\")\n",
-    "iris.view_parents(with_children=True)"
+    "bt.Organism.get(name=\"iris\").view_parents(with_children=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Access any Ensembl genes\n",
+    "\n",
+    "Genes from all Ensembl versions and organisms can be accessed, even though they are not yet present in the `bt.Source` registry.\n",
+    "\n",
+    "For instance, if you want to use `rabbit` genes from Ensembl version `release-103`:\n",
+    "\n",
+    "```python\n",
+    "\n",
+    "# pip install pymysql\n",
+    "import bionty as bt\n",
+    "\n",
+    "# automatically download genes for a new organism\n",
+    "gene_ontology = bt.base.Gene(source=\"ensembl\", organism=\"rabbit\", version='release-103')\n",
+    "\n",
+    "# register the new source in lamindb\n",
+    "gene_ontology.register_source_in_lamindb()\n",
+    "\n",
+    "# now you can start using this source\n",
+    "\n",
+    "# import all genes from this source to your Gene registry\n",
+    "source = bt.Source.get(entity=\"bionty.Gene\", name=\"ensembl\", organism=\"rabbit\", \n",
+    "bt.Gene.import_source(source=source)\n",
+    "```"
    ]
   },
   {

{lamindb-1.3.1 → lamindb-1.4.0}/docs/curate.ipynb

@@ -210,7 +210,7 @@
    "id": "15",
    "metadata": {},
    "source": [
-    "For \"cerebral pyramidal neuron\", let's understand which cell type in the public ontology might be the actual match."
+    "For \"CD8-pos alpha-beta T cell\", let's understand which cell type in the public ontology might be the actual match."
    ]
   },
   {
@@ -367,7 +367,7 @@
     "        \"ENSG00000198851\": [7, 8, 9],\n",
     "        \"ENSG00000010610\": [10, 11, 12],\n",
     "        \"ENSG00000153563\": [13, 14, 15],\n",
-    "        \"ENSGcorrupted\": [16, 17, 18],\n",
+    "        \"ENSG00corrupted\": [16, 17, 18],\n",
     "    },\n",
     "    index=df.index,  # because we already curated the dataframe above, it will validate\n",
     ")\n",
@@ -452,7 +452,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata_validated = adata[:, ~adata.var.index.isin([\"ENSGcorrupted\"])].copy()"
+    "adata_validated = adata[:, ~adata.var.index.isin([\"ENSG00corrupted\"])].copy()"
    ]
   },
   {
@@ -683,7 +683,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "py312",
+   "display_name": "py311",
    "language": "python",
    "name": "python3"
   },
@@ -697,7 +697,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.11.11"
   },
   "nbproject": {
    "id": "WOK3vP0bNGLx",