lamindb 0.69.8__tar.gz → 0.69.10__tar.gz

{lamindb-0.69.8 → lamindb-0.69.10}/.github/workflows/build.yml

@@ -30,6 +30,11 @@ jobs:
           submodules: recursive
           fetch-depth: 0
       - uses: actions/setup-python@v5
+        if: ${{ matrix.group == 'storage' }}
+        with:
+          python-version: "3.9" # run just one job with a different python version
+      - uses: actions/setup-python@v5
+        if: ${{ matrix.group != 'storage' }}
         with:
           python-version: "3.11"
       - name: cache pre-commit
@@ -100,7 +105,7 @@ jobs:
           aws-region: us-east-1
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.10" # use 3.10, 3.8 and 3.11 give issues
       - run: pip install -U laminci
       - run: nox -s "install(group='docs')"
       - uses: actions/download-artifact@v2

{lamindb-0.69.8 → lamindb-0.69.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.69.8
+Version: 0.69.10
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,15 +9,15 @@ 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==0.64.5
-Requires-Dist: lamindb_setup==0.68.5
+Requires-Dist: lnschema_core==0.64.11
+Requires-Dist: lamindb_setup==0.69.0
 Requires-Dist: lamin_utils==0.13.1
-Requires-Dist: lamin_cli==0.12.0
+Requires-Dist: lamin_cli==0.12.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
 Requires-Dist: python-dateutil
-Requires-Dist: anndata>=0.8.0,<0.10.6
+Requires-Dist: anndata>=0.8.0,<0.10.8
 Requires-Dist: scipy<1.13.0rc1
 Requires-Dist: fsspec
 Requires-Dist: pandas
@@ -27,7 +27,7 @@ Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: aiobotocore[boto3]>=2.5.4,<3.0.0 ; extra == "aws"
 Requires-Dist: s3fs==2023.12.2 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.12.2 ; extra == "aws"
-Requires-Dist: bionty==0.42.5 ; extra == "bionty"
+Requires-Dist: bionty==0.42.8 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
@@ -37,7 +37,6 @@ Requires-Dist: coverage ; extra == "dev"
 Requires-Dist: pytest-cov ; extra == "dev"
 Requires-Dist: nbproject_test>=0.5.1 ; extra == "dev"
 Requires-Dist: faker-biology ; extra == "dev"
-Requires-Dist: lamin_vault ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=1.1.7 ; extra == "fcs"
 Requires-Dist: fsspec[gs]==2023.12.2 ; extra == "gcp"
@@ -65,7 +64,7 @@ Provides-Extra: zarr
 - Track data lineage across notebooks & pipelines.
 - Integrate registries for experimental metadata & in-house ontologies.
 - Validate, standardize & annotate.
-- Collaborate across distributed LaminDB instances.
+- Collaborate across distributed databases.
 
 ## Documentation
 

{lamindb-0.69.8 → lamindb-0.69.10}/README.md

@@ -8,7 +8,7 @@
 - Track data lineage across notebooks & pipelines.
 - Integrate registries for experimental metadata & in-house ontologies.
 - Validate, standardize & annotate.
-- Collaborate across distributed LaminDB instances.
+- Collaborate across distributed databases.
 
 ## Documentation
 

{lamindb-0.69.8 → lamindb-0.69.10}/docs/bio-registries.ipynb

@@ -375,7 +375,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We'd like to load the corresponding records in our in-house ontology to annotate the batch of data.\n",
+    "We'd like to load the corresponding records in our in-house ontology to annotate a dataset.\n",
     "\n",
     "To this end, you'll typically use {class}`~lamindb.core.Registry.from_values`, which will both validate & load records that match the values."
    ]
@@ -387,7 +387,6 @@
    "outputs": [],
    "source": [
     "cell_types = bt.CellType.from_values(adata.obs.cell_type)\n",
-    "\n",
     "cell_types"
    ]
   },
@@ -396,7 +395,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Logging informed us that 3 cell types were validated. Since we loaded these records at the same time, we could readily use them to annotate a batch of data.\n",
+    "Logging informed us that 3 cell types were validated. Since we loaded these records at the same time, we could readily use them to annotate a dataset.\n",
     "\n",
     ":::{dropdown} What happened under-the-hood?\n",
     "\n",

{lamindb-0.69.8 → lamindb-0.69.10}/docs/changelog.md

@@ -6,9 +6,18 @@
 
 ## 0.69
 
+### 0.69.10 {small}`2024-04-12`
+
+- ✨ Add `.obsm` and  `.layers` to `MappedCollection` [PR](https://github.com/laminlabs/lamindb/pull/1562) [@Koncopd](https://github.com/Koncopd)
+- 🚸 Eliminate kwargs [PR](https://github.com/laminlabs/lamindb/pull/1561) [@sunnyosun](https://github.com/sunnyosun)
+- ✨ Introduce `Annotate.from_mudata` [PR](https://github.com/laminlabs/lamindb/pull/1554) [@sunnyosun](https://github.com/sunnyosun)
+
+### 0.69.9 {small}`2024-04-08`
+
+- 🐛 Fix clashes for multiple processes [PR](https://github.com/laminlabs/lamindb/pull/1553) [@falexwolf](https://github.com/falexwolf)
+
 ### 0.69.8 {small}`2024-04-04`
 
-- 🐛 Avoid an error due to deleting the same file by multiple processes [PR](https://github.com/laminlabs/lamindb-setup/pull/703) [@Koncopd](https://github.com/Koncopd)
 - ♻️ Use future annotations [PR](https://github.com/laminlabs/lamindb/pull/1549) [@Zethson](https://github.com/Zethson)
 
 ### 0.69.7 {small}`2024-04-03`

{lamindb-0.69.8 → lamindb-0.69.10}/docs/faq/key.ipynb

@@ -144,8 +144,8 @@
     "Lamin has three storage classes that manage different types of in-memory and on-disk objects:\n",
     "\n",
     "1. {class}`~lamindb.Storage`: Manages the default storage root that can be either local or in the cloud. For more details we refer to {doc}`docs:faq/storage`.\n",
-    "2. {class}`~lamindb.Artifact`: Manages data batches with an optional `key` that acts as a relative path within the current default storage root (see {class}`~lamindb.Storage`). An example is a single h5 artifact.\n",
-    "3. {class}`~lamindb.Collection`: Manages a collection of data batches with an optional `key` that acts as a relative path within the current default storage root (see {class}`~lamindb.Storage`). An example is a collection of h5 artifacts.\n",
+    "2. {class}`~lamindb.Artifact`: Manages datasets with an optional `key` that acts as a relative path within the current default storage root (see {class}`~lamindb.Storage`). An example is a single h5 artifact.\n",
+    "3. {class}`~lamindb.Collection`: Manages a collection of datasets with an optional `key` that acts as a relative path within the current default storage root (see {class}`~lamindb.Storage`). An example is a collection of h5 artifacts.\n",
     "\n",
     "For more details we refer to {doc}`docs:tutorial`."
    ]
@@ -265,8 +265,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds_1 = ln.Collection(data=[artifact_no_key_1, artifact_no_key_2], name=\"no key collection\")\n",
-    "ds_2 = ln.Collection(data=[artifact_key_3, artifact_key_4], name=\"sample collection\")\n",
+    "ds_1 = ln.Collection([artifact_no_key_1, artifact_no_key_2], name=\"no key collection\")\n",
+    "ds_2 = ln.Collection([artifact_key_3, artifact_key_4], name=\"sample collection\")\n",
     "ds_1"
    ]
   },

lamindb-0.69.10/docs/features-lamindb.md

@@ -0,0 +1 @@
+Actual content in lamin-docs.

lamindb-0.69.10/docs/features-laminhub.md

@@ -0,0 +1 @@
+Actual content in lamin-docs.