lamindb 0.69.9__tar.gz → 0.70.0__tar.gz

{lamindb-0.69.9 → lamindb-0.70.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.69.9
+Version: 0.70.0
 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==0.64.6
-Requires-Dist: lamindb_setup==0.69.0
+Requires-Dist: lnschema_core==0.65.0
+Requires-Dist: lamindb_setup==0.69.2
 Requires-Dist: lamin_utils==0.13.1
-Requires-Dist: lamin_cli==0.12.1
+Requires-Dist: lamin_cli==0.12.3
 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-0.69.9 → lamindb-0.70.0}/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-0.69.9 → lamindb-0.70.0}/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-0.69.9 → lamindb-0.70.0}/docs/changelog.md

@@ -1,12 +1,34 @@
 # Changelog
 
+:::{note}
+
+LaminDB implements "migration-based versioning".
+
+When upgrading your LaminDB installation to a new `minor` version in `major.minor.patch`, you also migrate your database by calling `lamin migrate deploy`.
+
+:::
+
 ```{eval-rst}
 .. role:: small
 ```
 
+## 0.70
+
+### 0.70.0 {small}`2024-04-17`
+
+- 🚸 Update data source in case transform is re-run [PR](https://github.com/laminlabs/lamindb/pull/1571) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Enable to label transforms via `transform.ulabels` [PR](https://github.com/laminlabs/lnschema-core/pull/370) [@falexwolf](https://github.com/falexwolf)
+- 🚚 Deprecate `stage()` in favor of `cache()` [PR](https://github.com/laminlabs/lamindb/pull/1572) [@falexwolf](https://github.com/falexwolf)
+
 ## 0.69
 
-### 0.69.9 {small}`2024-04-04`
+### 0.69.10 {small}`2024-04-12`
+
+- ✨ Add `.obsm` and  `.layers` to `MappedCollection` and rename `label_keys` to `obs_keys` [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)
 

{lamindb-0.69.9 → lamindb-0.70.0}/docs/faq/idempotency.ipynb

@@ -31,7 +31,7 @@
     "\n",
     "If you set {attr}`~lamindb.core.Settings.upon_create_search_names` to `False`, you'll directly populate the DB.\n",
     "\n",
-    "### Files\n",
+    "### Data: artifacts & collections\n",
     "\n",
     "If you try to create a {class}`~lamindb.Artifact` object from the same content, depending on {attr}`~lamindb.core.Settings.upon_artifact_create_if_hash_exists`, \n",
     "\n",
@@ -69,7 +69,10 @@
     "import lamindb as ln\n",
     "import pytest\n",
     "\n",
-    "ln.settings.verbosity = \"hint\""
+    "ln.settings.verbosity = \"hint\"\n",
+    "ln.settings.transform.stem_uid = \"ANW20Fr4eZgM\"\n",
+    "ln.settings.transform.version = \"1\"\n",
+    "ln.track()"
    ]
   },
   {
@@ -251,7 +254,7 @@
    "id": "01bfec00",
    "metadata": {},
    "source": [
-    "### Files"
+    "### Data: artifacts and collections"
    ]
   },
   {
@@ -289,7 +292,7 @@
    "id": "a2e9114a",
    "metadata": {},
    "source": [
-    "Create a `File` object."
+    "Create an `Artifact`:"
    ]
   },
   {
@@ -323,7 +326,7 @@
    "id": "153caaea",
    "metadata": {},
    "source": [
-    "Create a `File` object from the same path:"
+    "Create an `Artifact` from the same path:"
    ]
   },
   {
@@ -333,7 +336,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifact2 = ln.Artifact(filepath)"
+    "artifact2 = ln.Artifact(filepath, description=\"My fcs artifact\")"
    ]
   },
   {
@@ -352,7 +355,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert artifact.id == artifact2.id"
+    "assert artifact.id == artifact2.id\n",
+    "assert artifact.run == artifact2.run"
    ]
   },
   {
@@ -374,6 +378,32 @@
     "artifact2.save()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "ae33a6a1",
+   "metadata": {},
+   "source": [
+    "In the hidden cell below, you'll see how this interplays with data lineage."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "470d155a",
+   "metadata": {
+    "tags": [
+     "hide-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "ln.track(new_run=True)\n",
+    "artifact3 = ln.Artifact(filepath, description=\"My fcs artifact\")\n",
+    "assert artifact3.id == artifact2.id\n",
+    "assert artifact3.run != artifact2.run\n",
+    "assert artifact3.replicating_runs.first() == artifact2.run"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -409,7 +439,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with pytest.raises(RuntimeError):\n",
+    "with pytest.raises(FileExistsError):\n",
     "    artifact3 = ln.Artifact(filepath, description=\"My new fcs artifact\")"
    ]
   },
@@ -522,26 +552,16 @@
    "name": "python3"
   },
   "language_info": {
-   "artifact_extension": ".py",
    "codemirror_mode": {
     "name": "ipython",
     "version": 3
    },
+   "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
-  },
-  "nbproject": {
-   "id": "ANW20Fr4eZgM",
-   "parent": null,
-   "pypackage": null,
-   "time_init": "2022-10-12T22:55:00.562920+00:00",
-   "user_handle": "testuser1",
-   "user_id": "DzTjkKse",
-   "user_name": "Test User1",
-   "version": "0"
+   "version": "3.10.13"
   },
   "vscode": {
    "interpreter": {

{lamindb-0.69.9 → lamindb-0.70.0}/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-0.69.9 → lamindb-0.70.0}/docs/faq/track-run-inputs.ipynb

@@ -115,7 +115,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifact.stage()"
+    "artifact.cache()"
    ]
   },
   {
@@ -161,7 +161,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Let us manually track an artifact by passing `is_run_input` to either `.stage()`, `.load()` or `.backed()`:"
+    "Let us manually track an artifact by passing `is_run_input` to either `.cache()`, `.load()` or `.backed()`:"
    ]
   },
   {
@@ -170,7 +170,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "artifact.stage(is_run_input=True)"
+    "artifact.cache(is_run_input=True)"
    ]
   },
   {
@@ -217,7 +217,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "If you switch the following setting, and call to `.load()`, `.stage()` and `.backed()` will track the artifact as run input."
+    "If you switch the following setting, and call to `.load()`, `.cache()` and `.backed()` will track the artifact as run input."
    ]
   },
   {

lamindb-0.70.0/docs/features-lamindb.md

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

lamindb-0.70.0/docs/features-laminhub.md

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