lamindb 0.72.0__tar.gz → 0.72.1__tar.gz

{lamindb-0.72.0 → lamindb-0.72.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.72.0
+Version: 0.72.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -10,7 +10,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: lnschema_core==0.67.1
-Requires-Dist: lamindb_setup==0.72.1
+Requires-Dist: lamindb_setup==0.72.2
 Requires-Dist: lamin_utils==0.13.2
 Requires-Dist: lamin_cli==0.13.2
 Requires-Dist: rapidfuzz
@@ -25,7 +25,7 @@ Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: psutil
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.43.0 ; extra == "bionty"
+Requires-Dist: bionty==0.43.1 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"

{lamindb-0.72.0 → lamindb-0.72.1}/docs/changelog.md

@@ -1,5 +1,6 @@
 # Changelog
 
+
 :::{note}
 
 If using LaminHub, please use the latest version of lamindb.
@@ -14,6 +15,11 @@ LaminDB implements "migration-based versioning". When upgrading your LaminDB ins
 
 ## 0.72
 
+### 0.72.1 {small}`2024-05-19`
+
+- ⬆️ Update bionty [PR](https://github.com/laminlabs/lamindb/pull/1671) [@sunnyosun](https://github.com/sunnyosun)
+- 🐛 Deal with migration errors when keep-artifacts-local is true [PR](https://github.com/laminlabs/lamindb-setup/pull/767) [@falexwolf](https://github.com/falexwolf)
+
 ### 0.72.0 {small}`2024-05-19`
 
 - ✨ Extend managed access for AWS S3 to arbitrary paths [PR](https://github.com/laminlabs/lamindb/pull/1668) [@Koncopd](https://github.com/Koncopd) [@fredericenard](https://github.com/fredericenard)

{lamindb-0.72.0 → lamindb-0.72.1}/docs/introduction.ipynb

@@ -147,12 +147,46 @@
     "artifact.describe()\n",
     "\n",
     "# save data & metadata in one operation\n",
-    "artifact.save()\n",
-    "\n",
-    "# view data lineage\n",
-    "artifact.view_lineage()\n",
-    "\n",
-    "# load an artifact\n",
+    "artifact.save()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "View data lineage:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "artifact.view_lineage()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Load an artifact:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
     "artifact.load()"
    ]
   },

{lamindb-0.72.0 → lamindb-0.72.1}/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__ = "0.72.0"
+__version__ = "0.72.1"
 
 import os as _os
 

{lamindb-0.72.0 → lamindb-0.72.1}/pyproject.toml

@@ -17,7 +17,7 @@ classifiers = [
 dependencies = [
     # Lamin PINNED packages
     "lnschema_core==0.67.1",
-    "lamindb_setup==0.72.1",
+    "lamindb_setup==0.72.2",
     "lamin_utils==0.13.2",
     "lamin_cli==0.13.2",
     # others
@@ -39,7 +39,7 @@ Home = "https://github.com/laminlabs/lamindb"
 
 [project.optional-dependencies]
 bionty = [
-    "bionty==0.43.0",
+    "bionty==0.43.1",
 ]
 aws = [
     "lamindb_setup[aws]",

{lamindb-0.72.0 → lamindb-0.72.1}/sub/bionty/bionty/__init__.py

@@ -122,7 +122,7 @@ Developer API:
    core
 """
 
-__version__ = "0.43.0"
+__version__ = "0.43.1"
 
 from lamindb_setup._check_setup import InstanceNotSetupError, _check_instance_setup
 from lnschema_bionty import ids

{lamindb-0.72.0 → lamindb-0.72.1}/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==0.42.0",
+    "lnschema-bionty==0.42.2",
 ]
 
 [project.urls]

{lamindb-0.72.0 → lamindb-0.72.1}/sub/lamindb-setup/docs/changelog.md

@@ -3,7 +3,9 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🐛 Deal with migration errors when keep-artifacts-local is true | [767](https://github.com/laminlabs/lamindb-setup/pull/767) | [falexwolf](https://github.com/falexwolf) | 2024-05-20 | 0.72.2
 ♻️ Do not error if empty dict in `access_aws` | [764](https://github.com/laminlabs/lamindb-setup/pull/764) | [falexwolf](https://github.com/falexwolf) | 2024-05-19 | 0.72.1
+🐛 Keep training slash in aws cache keys | [766](https://github.com/laminlabs/lamindb-setup/pull/766) | [Koncopd](https://github.com/Koncopd) | 2024-05-19 |
 🐛 Check empty after storage record root init in delete | [763](https://github.com/laminlabs/lamindb-setup/pull/763) | [Koncopd](https://github.com/Koncopd) | 2024-05-18 |
 ✨ Call `access_aws` for all paths and cache | [762](https://github.com/laminlabs/lamindb-setup/pull/762) | [Koncopd](https://github.com/Koncopd) | 2024-05-18 | 0.72.0
 ⚡️ Speed-up file hash | [761](https://github.com/laminlabs/lamindb-setup/pull/761) | [Koncopd](https://github.com/Koncopd) | 2024-05-11 | 0.71.4

{lamindb-0.72.0 → lamindb-0.72.1}/sub/lamindb-setup/lamindb_setup/__init__.py

@@ -34,7 +34,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.72.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.72.2"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import sys
 from os import name as _os_name

{lamindb-0.72.0 → lamindb-0.72.1}/sub/lamindb-setup/lamindb_setup/core/_aws_credentials.py

@@ -22,6 +22,10 @@ else:
     HOSTED_BUCKETS = ("s3://lamin-hosted-test",)  # type: ignore
 
 
+def _keep_trailing_slash(path_str: str):
+    return path_str if path_str[-1] == "/" else path_str + "/"
+
+
 AWS_CREDENTIALS_EXPIRATION = 11 * 60 * 60  # refresh credentials after 11 hours
 
 
@@ -81,7 +85,10 @@ class AWSCredentialsManager:
         return S3Path(path, cache_regions=cache_regions, **connection_options)
 
     def enrich_path(self, path: S3Path, access_token: str | None = None) -> S3Path:
-        path_str = path.as_posix().rstrip("/")
+        # trailing slash is needed to avoid returning incorrect results
+        # with .startswith
+        # for example s3://lamindata-eu should not receive cache for s3://lamindata
+        path_str = _keep_trailing_slash(path.as_posix())
         root = self._find_root(path_str)
 
         if root is not None:
@@ -127,7 +134,7 @@ class AWSCredentialsManager:
                         # write the bucket for everything else
                         root = path._url.netloc
                     root = "s3://" + root
-                self._set_cached_credentials(root, credentials)
+                self._set_cached_credentials(_keep_trailing_slash(root), credentials)
 
         return self._path_inject_options(path, credentials)
 

{lamindb-0.72.0 → lamindb-0.72.1}/sub/lamindb-setup/lamindb_setup/core/_settings_instance.py

@@ -5,6 +5,7 @@ import shutil
 from pathlib import Path
 from typing import TYPE_CHECKING, Literal
 
+from django.db.utils import ProgrammingError
 from lamin_utils import logger
 
 from ._hub_client import call_with_fallback
@@ -106,8 +107,15 @@ class InstanceSettings:
             local_records = Storage.objects.filter(root=local_root)
         else:
             local_records = Storage.objects.filter(type="local")
+        all_local_records = local_records.all()
+        try:
+            # trigger an error in case of a migration issue
+            all_local_records.first()
+        except ProgrammingError:
+            logger.error("not able to load Storage registry: please migrate")
+            return None
         found = False
-        for record in local_records.all():
+        for record in all_local_records:
             root_path = Path(record.root)
             if root_path.exists():
                 marker_path = root_path / ".lamindb/_is_initialized"

{lamindb-0.72.0 → lamindb-0.72.1}/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__ = "0.42.0"  # Denote a release candidate of version 0.1.0 with 0.1rc1
+__version__ = "0.42.2"  # Denote a release candidate of version 0.1.0 with 0.1rc1
 
 from lamindb_setup import _check_instance_setup
 

{lamindb-0.72.0 → lamindb-0.72.1}/sub/lnschema-bionty/pyproject.toml

@@ -15,7 +15,7 @@ classifiers = [
 ]
 dependencies = [
     "lnschema_core",
-    "bionty_base==0.37.2",
+    "bionty_base==0.37.3",
 ]
 
 [project.urls]