lamindb 0.73.1__tar.gz → 0.73.2__tar.gz

{lamindb-0.73.1 → lamindb-0.73.2}/.github/workflows/build.yml

@@ -119,6 +119,12 @@ jobs:
         env:
           NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
           NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+      - uses: peter-evans/repository-dispatch@v2
+        if: ${{ github.event_name == 'push' }}
+        with:
+          token: ${{ secrets.LAMIN_BUILD_DOCS }}
+          repository: "laminlabs/lamin-docs"
+          event-type: build
 
   coverage:
     needs: test

{lamindb-0.73.1 → lamindb-0.73.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.73.1
+Version: 0.73.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,7 +9,7 @@ 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==0.68.1
+Requires-Dist: lnschema_core==0.69.0
 Requires-Dist: lamindb_setup==0.73.1
 Requires-Dist: lamin_utils==0.13.2
 Requires-Dist: lamin_cli==0.14.0
@@ -25,7 +25,7 @@ Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: psutil
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.43.1 ; extra == "bionty"
+Requires-Dist: bionty==0.44.0 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"

{lamindb-0.73.1 → lamindb-0.73.2}/docs/changelog.md

@@ -14,6 +14,11 @@ LaminDB implements "migration-based versioning". When upgrading your LaminDB ins
 
 ## 0.73
 
+### 0.73.2 {small}`2024-06-13`
+
+- 🐛 Fix clashing reverse accessors for `.previous_runs` and `.run` [PR](https://github.com/laminlabs/lamindb/pull/1698) [@falexwolf](https://github.com/falexwolf)
+- 🐛 Import IPython inside view [PR](https://github.com/laminlabs/lamindb/pull/1696) [@Koncopd](https://github.com/Koncopd)
+
 ### 0.73.1 {small}`2024-06-05`
 
 - 🏗️ Instantly synchronize instance schema with the hub [PR](https://github.com/laminlabs/lamindb/pull/1689) [@fredericenard](https://github.com/fredericenard)

{lamindb-0.73.1 → lamindb-0.73.2}/docs/introduction.ipynb

@@ -77,6 +77,26 @@
     "!lamin init --storage ./lamin-intro --schema bionty"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now you're ready to import lamindb in a Python session."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "import lamindb as ln"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -98,8 +118,6 @@
    },
    "outputs": [],
    "source": [
-    "import lamindb as ln\n",
-    "\n",
     "# copy-pasted identifiers for your notebook or script\n",
     "ln.settings.transform.stem_uid = \"FPnfDtJz8qbE\"  # <-- auto-generated by running ln.track()\n",
     "ln.settings.transform.version = \"1\"  # <-- auto-generated by running ln.track()\n",
@@ -107,7 +125,7 @@
     "# track the execution of your notebook or script\n",
     "run = ln.track()\n",
     "\n",
-    "# get your currently running transform\n",
+    "# see your currently running transform\n",
     "run.transform"
    ]
   },
@@ -115,7 +133,31 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "`ln.track()` added a record to the {class}`~lamindb.Transform` registry to query & search your notebook and a {class}`~lamindb.Run` registry to store the specific notebook run."
+    "Calling `ln.track()` created a run and a transform and stored them in {class}`~lamindb.Run` and {class}`~lamindb.Transform`, respectively. The transform registry allows to find your notebook, scripts and pipelines. The {class}`~lamindb.Run` registry allows to find their runs.\n",
+    "\n",
+    ":::{dropdown} Is this compliant with OpenLineage?\n",
+    "\n",
+    "Yes. What OpenLineage calls a \"job\", LaminDB calls a \"transform\". What OpenLineage calls a \"run\", LaminDB calls a \"run\".\n",
+    "\n",
+    ":::\n",
+    "\n",
+    ":::{dropdown} Are the global identifiers `stem_uid` and `version` really necessary?\n",
+    "\n",
+    "Yes, if you want to track data lineage outside of workflow managers.\n",
+    "\n",
+    "To tie a piece of code to a record in a database in a way that survives name changes (notebook file name, script name, pipeline name) and content changes, you need to attach the code to an immutable identifier.\n",
+    "\n",
+    "Content changes need to correlate with the identifier, but shouldn't give rise to an entirely new identifier. To implement this behavior we code hashes with user input for `version` and create a universal identifier as follows:\n",
+    "\n",
+    "```python\n",
+    "stem_uid = random_base62(n_char)  # a random base62 sequence of length n_char\n",
+    "version_uid = encode_base62(md5_hash(version))[:4]  # version is, e.g., \"1\" or \"2.1.0\" or \"2022-03-01\"\n",
+    "uid = f\"{stem_uid}{version_uid}\"  # concatenate the stem_uid & version_uid\n",
+    "```\n",
+    "\n",
+    "git, by comparison, identifies code by its content hash alone. Notebook platforms like Google Colab and DeepNote [do not encode versions into their notebook ids](https://lamin.ai/blog/nbproject#metadata-tracking). \n",
+    "\n",
+    ":::"
    ]
   },
   {

{lamindb-0.73.1 → lamindb-0.73.2}/lamindb/__init__.py

@@ -41,7 +41,7 @@ Modules & settings:
 """
 
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "0.73.1"
+__version__ = "0.73.2"
 
 import os as _os
 

{lamindb-0.73.1 → lamindb-0.73.2}/lamindb/_registry.py

@@ -54,7 +54,7 @@ def suggest_records_with_similar_names(record: Registry, kwargs) -> bool:
     """
     if kwargs.get("name") is None:
         return False
-    queryset = _search(record.__class__, kwargs["name"], truncate_words=True, limit=5)
+    queryset = _search(record.__class__, kwargs["name"], truncate_words=True, limit=20)
     if not queryset.exists():  # empty queryset
         return False
     for alternative_record in queryset:

{lamindb-0.73.1 → lamindb-0.73.2}/lamindb/_view.py

@@ -1,14 +1,16 @@
 from __future__ import annotations
 
+import builtins
 import importlib
 import inspect
 
-from IPython.display import display
 from lamin_utils import colors, logger
 from lamindb_setup import settings
 from lamindb_setup._init_instance import get_schema_module_name
 from lnschema_core import Registry
 
+is_run_from_ipython = getattr(builtins, "__IPYTHON__", False)
+
 
 def view(
     n: int = 7, schema: str | None = None, registries: list[str] | None = None
@@ -25,6 +27,11 @@ def view(
     Examples:
         >>> ln.view()
     """
+    if is_run_from_ipython:
+        from IPython.display import display as show
+    else:
+        show = logger.print
+
     if schema is not None:
         schema_names = [schema]
     else:
@@ -60,4 +67,4 @@ def view(
                 df = orm.df().iloc[-n:]
             if df.shape[0] > 0:
                 logger.print(colors.blue(colors.bold(orm.__name__)))
-                display(df)
+                show(df)

{lamindb-0.73.1 → lamindb-0.73.2}/pyproject.toml

@@ -16,7 +16,7 @@ classifiers = [
 ]
 dependencies = [
     # Lamin PINNED packages
-    "lnschema_core==0.68.1",
+    "lnschema_core==0.69.0",
     "lamindb_setup==0.73.1",
     "lamin_utils==0.13.2",
     "lamin_cli==0.14.0",
@@ -39,7 +39,7 @@ Home = "https://github.com/laminlabs/lamindb"
 
 [project.optional-dependencies]
 bionty = [
-    "bionty==0.43.1",
+    "bionty==0.44.0",
 ]
 aws = [
     "lamindb_setup[aws]",

{lamindb-0.73.1 → lamindb-0.73.2}/sub/bionty/bionty/__init__.py

@@ -122,7 +122,7 @@ Developer API:
    core
 """
 
-__version__ = "0.43.1"
+__version__ = "0.44.0"
 
 from lamindb_setup._check_setup import InstanceNotSetupError, _check_instance_setup
 from lnschema_bionty import ids

{lamindb-0.73.1 → lamindb-0.73.2}/sub/bionty/pyproject.toml

@@ -8,7 +8,7 @@ authors = [{name = "Lamin Labs", email = "open-source@lamin.ai"}]
 readme = "README.md"
 dynamic = ["version", "description"]
 dependencies = [
-    "lnschema-bionty==0.42.2",
+    "lnschema-bionty==0.43.0",
 ]
 
 [project.urls]

{lamindb-0.73.1 → lamindb-0.73.2}/sub/lnschema-bionty/docs/changelog.md

@@ -3,6 +3,7 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🐛 Fix clashing reverse accessors between `.previous_runs` and `.run` | [249](https://github.com/laminlabs/lnschema-bionty/pull/249) | [falexwolf](https://github.com/falexwolf) | 2024-06-13 | 0.43.0
 ♻️ Reformulate data lineage, remove json field from run | [247](https://github.com/laminlabs/lnschema-bionty/pull/247) | [falexwolf](https://github.com/falexwolf) | 2024-05-19 | 0.42.0
 ♻️ Protect gene, protein, cell_marker & pathway in their FeatureSet relationships | [246](https://github.com/laminlabs/lnschema-bionty/pull/246) | [falexwolf](https://github.com/falexwolf) | 2024-05-18 |
 🏗️ Naming conventions for link tables, protecting deletion in link tables, maintaining integrity upon label & feature renames | [245](https://github.com/laminlabs/lnschema-bionty/pull/245) | [falexwolf](https://github.com/falexwolf) | 2024-05-18 |

{lamindb-0.73.1 → lamindb-0.73.2}/sub/lnschema-bionty/lnschema_bionty/__init__.py

@@ -4,7 +4,7 @@ Since version 0.40.0, `bionty` replaces `lnschema-bionty` as the user-facing pac
 
 """
 
-__version__ = "0.42.2"  # Denote a release candidate of version 0.1.0 with 0.1rc1
+__version__ = "0.43.0"  # Denote a release candidate of version 0.1.0 with 0.1rc1
 
 from lamindb_setup import _check_instance_setup
 

lamindb-0.73.2/sub/lnschema-bionty/lnschema_bionty/migrations/0029_alter_cellline_previous_runs_and_more.py

@@ -0,0 +1,83 @@
+# Generated by Django 5.1 on 2024-06-13 10:31
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("lnschema_bionty", "0028_squashed"),
+        ("lnschema_core", "0054_alter_feature_previous_runs_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="cellline",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="cellmarker",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="celltype",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="developmentalstage",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="disease",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="ethnicity",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="experimentalfactor",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="gene",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="organism",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="pathway",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="phenotype",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="protein",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="publicsource",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="tissue",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+    ]

{lamindb-0.73.1 → lamindb-0.73.2}/sub/lnschema-bionty/pyproject.toml

@@ -14,7 +14,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
 ]
 dependencies = [
-    "lnschema_core",
+    "lnschema_core>=0.69.0",
     "bionty_base==0.37.3",
 ]
 

{lamindb-0.73.1 → lamindb-0.73.2}/sub/lnschema-bionty/tests/test_integrity.py

@@ -2,7 +2,7 @@ import lamindb_setup as ln_setup
 import pytest
 
 
-@pytest.fixture
+@pytest.fixture(scope="module")
 def setup_instance():
     ln_setup.init(storage="./testdb", schema="bionty")
     yield
@@ -11,3 +11,7 @@ def setup_instance():
 
 def test_migrate_check(setup_instance):
     assert ln_setup.migrate.check()
+
+
+def test_system_check(setup_instance):
+    ln_setup.django("check")

{lamindb-0.73.1 → lamindb-0.73.2}/sub/lnschema-core/CHANGELOG.md

@@ -3,6 +3,7 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🐛 Fix clashing reverse accessors between `.previous_runs` and `.run` | [391](https://github.com/laminlabs/lnschema-core/pull/391) | [falexwolf](https://github.com/falexwolf) | 2024-06-13 | 0.69.0
 ♻️ Add constraints & simple schema fixes | [388](https://github.com/laminlabs/lnschema-core/pull/388) | [falexwolf](https://github.com/falexwolf) | 2024-05-29 | 0.68.0
 ♻️ Migrate featuremanager to being available on the class level | [387](https://github.com/laminlabs/lnschema-core/pull/387) | [falexwolf](https://github.com/falexwolf) | 2024-05-29 |
 ♻️ Better representation | [386](https://github.com/laminlabs/lnschema-core/pull/386) | [falexwolf](https://github.com/falexwolf) | 2024-05-25 |

{lamindb-0.73.1 → lamindb-0.73.2}/sub/lnschema-core/lnschema_core/__init__.py

@@ -1,6 +1,6 @@
 """LaminDB's core registries."""
 
-__version__ = "0.68.1"
+__version__ = "0.69.0"
 
 
 from lamindb_setup import _check_instance_setup

lamindb-0.73.2/sub/lnschema-core/lnschema_core/migrations/0054_alter_feature_previous_runs_and_more.py

@@ -0,0 +1,35 @@
+# Generated by Django 5.1 on 2024-06-13 10:31
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        (
+            "lnschema_core",
+            "0053_alter_featureset_hash_alter_paramvalue_created_by_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="feature",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="param",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="storage",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+        migrations.AlterField(
+            model_name="ulabel",
+            name="previous_runs",
+            field=models.ManyToManyField(related_name="+", to="lnschema_core.run"),
+        ),
+    ]

{lamindb-0.73.1 → lamindb-0.73.2}/sub/lnschema-core/lnschema_core/models.py

@@ -171,7 +171,9 @@ class TracksUpdates(models.Model):
 
     updated_at = models.DateTimeField(auto_now=True, db_index=True)
     """Time of last update to record."""
-    previous_runs = models.ManyToManyField("lnschema_core.Run")
+    # no default related_name below because it'd clash with the reverse accessor
+    # of the .run field
+    previous_runs = models.ManyToManyField("lnschema_core.Run", related_name="+")
     """Sequence of runs that created or updated the record."""
 
     @overload

{lamindb-0.73.1 → lamindb-0.73.2}/sub/lnschema-core/tests/test_integrity.py

@@ -2,7 +2,7 @@ import lamindb_setup as ln_setup
 import pytest
 
 
-@pytest.fixture
+@pytest.fixture(scope="module")
 def setup_instance():
     ln_setup.init(storage="./testdb")
     yield
@@ -11,3 +11,7 @@ def setup_instance():
 
 def test_migrate_check(setup_instance):
     assert ln_setup.migrate.check()
+
+
+def test_system_check(setup_instance):
+    ln_setup.django("check")