lamindb 0.76.0__tar.gz → 0.76.2__tar.gz

{lamindb-0.76.0 → lamindb-0.76.2}/.github/workflows/build.yml

@@ -21,7 +21,7 @@ jobs:
           - "faq"
           - "storage"
           - "cli"
-    timeout-minutes: 7
+    timeout-minutes: 11
 
     steps:
       - uses: actions/checkout@v4
@@ -37,14 +37,14 @@ jobs:
         with:
           python-version: "3.11"
       - name: cache pre-commit
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pre-commit
           key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
       - name: cache postgres
         if: ${{ matrix.group == 'faq' || matrix.group == 'unit' }}
         id: cache-postgres
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/postgres.tar
           key: cache-postgres-0
@@ -64,7 +64,7 @@ jobs:
       - run: nox -s lint
         if: ${{ matrix.group == 'tutorial' }} # choose a fast-running a group
       - run: nox -s "install_ci(group='${{ matrix.group }}')"
-      - uses: aws-actions/configure-aws-credentials@v1
+      - uses: aws-actions/configure-aws-credentials@v4
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
           aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
@@ -97,7 +97,7 @@ jobs:
           ssh-key: ${{ secrets.READ_LNDOCS }}
           path: lndocs
           ref: main
-      - uses: aws-actions/configure-aws-credentials@v1
+      - uses: aws-actions/configure-aws-credentials@v4
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
           aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}

{lamindb-0.76.0 → lamindb-0.76.2}/.gitignore

@@ -62,6 +62,7 @@ test-search4
 test-search5
 default_storage
 test.ipynb
+run-tests
 
 # General
 .DS_Store

{lamindb-0.76.0 → lamindb-0.76.2}/.pre-commit-config.yaml

@@ -51,5 +51,5 @@ repos:
         additional_dependencies: ["types-requests", "types-attrs"]
         exclude: |
           (?x)(
-              test_notebooks.py
+              test_notebooks.py|script-to-test-versioning.py
           )

{lamindb-0.76.0 → lamindb-0.76.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.76.0
+Version: 0.76.2
 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==0.73.0
-Requires-Dist: lamindb_setup==0.76.4
-Requires-Dist: lamin_utils==0.13.2
-Requires-Dist: lamin_cli==0.16.1
+Requires-Dist: lnschema_core==0.73.2
+Requires-Dist: lamindb_setup==0.76.6
+Requires-Dist: lamin_utils==0.13.4
+Requires-Dist: lamin_cli==0.16.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -24,7 +24,7 @@ Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.48.1 ; extra == "bionty"
+Requires-Dist: bionty==0.48.3 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"
@@ -57,13 +57,5 @@ Provides-Extra: zarr
 
 # LaminDB - A data framework for biology
 
-- Manage data & metadata with a unified Python API ("lakehouse").
-- Track data lineage across notebooks & pipelines.
-- Integrate registries for experimental metadata & in-house ontologies.
-- Validate, standardize & annotate.
-- Collaborate across distributed databases.
-
-## Documentation
-
-Read the [docs](https://lamin.ai/docs).
+Read the [docs](https://docs.lamin.ai).
 

{lamindb-0.76.0 → lamindb-0.76.2}/README.md

@@ -4,12 +4,4 @@
 
 # LaminDB - A data framework for biology
 
-- Manage data & metadata with a unified Python API ("lakehouse").
-- Track data lineage across notebooks & pipelines.
-- Integrate registries for experimental metadata & in-house ontologies.
-- Validate, standardize & annotate.
-- Collaborate across distributed databases.
-
-## Documentation
-
-Read the [docs](https://lamin.ai/docs).
+Read the [docs](https://docs.lamin.ai).

{lamindb-0.76.0 → lamindb-0.76.2}/docs/faq/idempotency.ipynb

@@ -71,9 +71,8 @@
     "import pytest\n",
     "\n",
     "ln.settings.verbosity = \"hint\"\n",
-    "ln.settings.transform.stem_uid = \"ANW20Fr4eZgM\"\n",
-    "ln.settings.transform.version = \"1\"\n",
-    "ln.track()"
+    "ln.context.uid = \"ANW20Fr4eZgM0000\"\n",
+    "ln.context.track()"
    ]
   },
   {
@@ -398,7 +397,7 @@
    },
    "outputs": [],
    "source": [
-    "ln.track(new_run=True)\n",
+    "ln.context.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",

{lamindb-0.76.0 → lamindb-0.76.2}/docs/faq/keep-artifacts-local.ipynb

@@ -37,9 +37,8 @@
     "# !pip install 'lamindb[jupyter,aws]'\n",
     "import lamindb as ln\n",
     "\n",
-    "ln.settings.transform.stem_uid = \"l9lFf83aPwRc\"\n",
-    "ln.settings.transform.version = \"1\"\n",
-    "ln.track()"
+    "ln.context.uid = \"l9lFf83aPwRc0000\"\n",
+    "ln.context.track()"
    ]
   },
   {

{lamindb-0.76.0 → lamindb-0.76.2}/docs/faq/key.ipynb

@@ -119,9 +119,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.settings.transform.stem_uid = \"WIwaNDvlEkwS\"\n",
-    "ln.settings.transform.version = \"1\"\n",
-    "ln.track()"
+    "ln.context.uid = \"WIwaNDvlEkwS0000\"\n",
+    "ln.context.track()"
    ]
   },
   {

{lamindb-0.76.0 → lamindb-0.76.2}/docs/faq/setup.ipynb

@@ -56,7 +56,7 @@
    "outputs": [],
    "source": [
     "with pytest.raises(ln._InstanceNotSetupError):\n",
-    "    ln.track()"
+    "    ln.context.track()"
    ]
   },
   {
@@ -85,9 +85,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.settings.transform.stem_uid = \"2lhqA4uTKSFP\"\n",
-    "ln.settings.transform.version = \"0\"\n",
-    "ln.track()"
+    "ln.context.uid = \"2lhqA4uTKSFP0000\"\n",
+    "ln.context.track()"
    ]
   },
   {

{lamindb-0.76.0 → lamindb-0.76.2}/docs/faq/track-run-inputs.ipynb

@@ -53,7 +53,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.track(transform=ln.Transform(name=\"Dummpy pipeline\"))\n",
+    "ln.context.track(transform=ln.Transform(name=\"Dummpy pipeline\"))\n",
     "ln.Artifact(ln.core.datasets.file_jpg_paradisi05(), description=\"My image\").save()\n",
     "ln.Artifact(ln.core.datasets.file_mini_csv(), description=\"My csv\").save()"
    ]
@@ -63,7 +63,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Call `ln.track()`:"
+    "Call `ln.context.track()`:"
    ]
   },
   {
@@ -72,9 +72,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.settings.transform.stem_uid = \"Rx2s9aPTMQLY\"\n",
-    "ln.settings.transform.version = \"1\"\n",
-    "ln.track()"
+    "ln.context.uid = \"Rx2s9aPTMQLY0000\"\n",
+    "ln.context.track()"
    ]
   },
   {
@@ -126,7 +125,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.Run.filter(id=ln.core.run_context.run.id).one().input_artifacts.all()"
+    "ln.Run.filter(id=ln.context.run.id).one().input_artifacts.all()"
    ]
   },
   {
@@ -139,7 +138,7 @@
    },
    "outputs": [],
    "source": [
-    "assert len(ln.Run.filter(id=ln.core.run_context.run.id).one().input_artifacts.all()) == 0"
+    "assert len(ln.Run.filter(id=ln.context.run.id).one().input_artifacts.all()) == 0"
    ]
   },
   {
@@ -181,7 +180,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "for input in ln.Run.filter(id=ln.core.run_context.run.id).one().input_artifacts.all():\n",
+    "for input in ln.Run.filter(id=ln.context.run.id).one().input_artifacts.all():\n",
     "    print(input)"
    ]
   },
@@ -195,7 +194,7 @@
    },
    "outputs": [],
    "source": [
-    "assert len(ln.Run.filter(id=ln.core.run_context.run.id).one().input_artifacts.all()) == 1"
+    "assert len(ln.Run.filter(id=ln.context.run.id).one().input_artifacts.all()) == 1"
    ]
   },
   {
@@ -247,7 +246,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "for input in ln.Run.filter(id=ln.core.run_context.run.id).one().input_artifacts.all():\n",
+    "for input in ln.Run.filter(id=ln.context.run.id).one().input_artifacts.all():\n",
     "    print(input)"
    ]
   },
@@ -261,7 +260,7 @@
    },
    "outputs": [],
    "source": [
-    "assert len(ln.Run.filter(id=ln.core.run_context.run.id).one().input_artifacts.all()) == 2"
+    "assert len(ln.Run.filter(id=ln.context.run.id).one().input_artifacts.all()) == 2"
    ]
   },
   {