lamindb 0.65.1__tar.gz → 0.66.0__tar.gz

{lamindb-0.65.1 → lamindb-0.66.0}/.github/workflows/build.yml

@@ -63,8 +63,6 @@ jobs:
         if: ${{ matrix.group == 'tutorial' }} # choose a fast-running a group
       - run: nox -s "install(group='${{ matrix.group }}')"
       - uses: aws-actions/configure-aws-credentials@v1
-        if: ${{ matrix.group == 'unit' || matrix.group == 'guide' || matrix.group == 'storage' || matrix.group == 'cli' }}
-        # in particular, the tutorial should be run on an anonymous worker *without* AWS credentials
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
           aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}

{lamindb-0.65.1 → lamindb-0.66.0}/.github/workflows/latest-changes.jinja2

@@ -1 +1,2 @@
 - {{pr.title}} [PR{{pr.number}}]({{pr.html_url}}) [@{{pr.user.login}}]({{pr.user.html_url}})
+

{lamindb-0.65.1 → lamindb-0.66.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.65.1
+Version: 0.66.0
 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==0.60.0
-Requires-Dist: lamindb_setup==0.63.1
+Requires-Dist: lnschema_core==0.61.0
+Requires-Dist: lamindb_setup==0.64.0
 Requires-Dist: lamin_utils==0.13.0
-Requires-Dist: lamin_cli==0.5.0
+Requires-Dist: lamin_cli==0.6.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -62,14 +62,14 @@ Provides-Extra: zarr
 
 # LaminDB - A data framework for biology
 
-LaminDB is an open-source Python framework to manage biological data & analyses in generic backends:
+LaminDB is an open-source Python framework to manage biological data & analyses:
 
-- Access data & metadata across storage (files, arrays) & database (SQL) backends.
-- Track data flow across notebooks, pipelines & UI.
-- Manage registries for experimental metadata & in-house ontologies, import public ontologies.
-- Validate, standardize & annotate data using registries.
+- Access data & metadata across storage & databases.
+- Track data lineage across notebooks & pipelines.
+- Manage registries for experimental metadata & in-house ontologies.
+- Validate, standardize & annotate data.
 - Organize and share data across a mesh of LaminDB instances.
-- Manage data access with an auditable system of record.
+- Manage data access, leverage an auditable system of record.
 
 ## Documentation
 

{lamindb-0.65.1 → lamindb-0.66.0}/README.md

@@ -4,14 +4,14 @@
 
 # LaminDB - A data framework for biology
 
-LaminDB is an open-source Python framework to manage biological data & analyses in generic backends:
+LaminDB is an open-source Python framework to manage biological data & analyses:
 
-- Access data & metadata across storage (files, arrays) & database (SQL) backends.
-- Track data flow across notebooks, pipelines & UI.
-- Manage registries for experimental metadata & in-house ontologies, import public ontologies.
-- Validate, standardize & annotate data using registries.
+- Access data & metadata across storage & databases.
+- Track data lineage across notebooks & pipelines.
+- Manage registries for experimental metadata & in-house ontologies.
+- Validate, standardize & annotate data.
 - Organize and share data across a mesh of LaminDB instances.
-- Manage data access with an auditable system of record.
+- Manage data access, leverage an auditable system of record.
 
 ## Documentation
 

{lamindb-0.65.1 → lamindb-0.66.0}/docs/annotate.ipynb

@@ -58,7 +58,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lb.settings.organism = \"human\"  # globally set organism\n",
     "lb.settings.auto_save_parents = False  # ignores ontological hierarchy\n",
     "ln.settings.verbosity = \"info\""
    ]
@@ -212,7 +211,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data_features = lb.Gene.from_values(adata.var_names)\n",
+    "data_features = lb.Gene.from_values(\n",
+    "    adata.var_names, \n",
+    "    organism=\"human\", # or set globally: lb.settings.organism = \"human\"\n",
+    "    )\n",
     "ln.save(data_features)\n",
     "data_features"
    ]
@@ -372,6 +374,7 @@
     "    adata,\n",
     "    name=\"my RNA-seq\",\n",
     "    field=lb.Gene.symbol,  # the registry field to use for the data features\n",
+    "    organism=\"human\", # or set globally: lb.settings.organism = \"human\"\n",
     ")\n",
     "collection.save()"
    ]

{lamindb-0.65.1 → lamindb-0.66.0}/docs/changelog.md

@@ -4,6 +4,14 @@
 .. role:: small
 ```
 
+## 0.66
+
+### 0.66.0 {small}`2024-01-07`
+
+- 🚸 Add anonymous access (now works without login) [PR1386](https://github.com/laminlabs/lamindb/pull/1386) [@falexwolf](https://github.com/falexwolf)
+- 🎨 Introduce ordered collections and simplify `.mapped()` [PR1390](https://github.com/laminlabs/lamindb/pull/1390) [@falexwolf](https://github.com/falexwolf)
+- 📝 Re-write quickstart [PR1387](https://github.com/laminlabs/lamindb/pull/1387) [@falexwolf](https://github.com/falexwolf)
+
 ## 0.65
 
 ### 0.65.1 {small}`2024-01-05`

{lamindb-0.65.1 → lamindb-0.66.0}/docs/installation.md

@@ -1,7 +1,7 @@
 ![pyversions](https://img.shields.io/pypi/pyversions/lamindb)
 
 ```shell
-pip install lamindb  # basic data management
+pip install lamindb
 ```
 
 You can configure the installation using `extras`, e.g.,