lamindb_setup 1.6.0__tar.gz → 1.7.0__tar.gz

{lamindb_setup-1.6.0 → lamindb_setup-1.7.0}/.github/workflows/build.yml

@@ -14,10 +14,10 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 12
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: "3.10" # run one job on 3.9
+          python-version: "3.10"
           cache: "pip"
       - uses: aws-actions/configure-aws-credentials@v4
         with:
@@ -35,7 +35,7 @@ jobs:
 
   # tests both on production and staging hub
   hub-cloud:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
@@ -43,7 +43,7 @@ jobs:
           - lamin_env: "prod"
             python-version: "3.11"
           - lamin_env: "staging"
-            python-version: "3.10" # test on 3.9
+            python-version: "3.10"
     timeout-minutes: 12
     steps:
       - uses: aws-actions/configure-aws-credentials@v4
@@ -97,7 +97,7 @@ jobs:
     timeout-minutes: 12
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
           cache: "pip"
@@ -205,7 +205,7 @@ jobs:
           ssh-key: ${{ secrets.READ_LNDOCS }}
           path: lndocs
           ref: main
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
           cache: "pip"

{lamindb_setup-1.6.0 → lamindb_setup-1.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.6.0
+Version: 1.7.0
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10
@@ -9,7 +9,7 @@ Requires-Dist: lamin_utils>=0.3.3
 Requires-Dist: django>=5.1,<5.2
 Requires-Dist: dj_database_url>=1.3.0,<3.0.0
 Requires-Dist: pydantic-settings
-Requires-Dist: appdirs<2.0.0
+Requires-Dist: platformdirs<5.0.0
 Requires-Dist: requests
 Requires-Dist: universal_pathlib==0.2.6
 Requires-Dist: botocore<2.0.0

{lamindb_setup-1.6.0 → lamindb_setup-1.7.0}/docs/hub-cloud/01-init-local-instance.ipynb

@@ -27,6 +27,15 @@
     "import lamindb_setup as ln_setup"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "assert not ln_setup.settings.is_connected"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -36,6 +45,15 @@
     "ln_setup.init(storage=\"./mydata\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "assert ln_setup.settings.is_connected"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -107,11 +125,6 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.10.16"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "40d3a090f54c6569ab1632332b64b2c03c39dcf918b08424e98f38b5ae0af88f"
-   }
   }
  },
  "nbformat": 4,

{lamindb_setup-1.6.0 → lamindb_setup-1.7.0}/docs/hub-cloud/02-connect-local-instance.ipynb

@@ -147,9 +147,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert ln_setup.settings._instance_settings_path.exists()\n",
-    "ln_setup.delete(\"mydata\", force=True)\n",
-    "assert not ln_setup.settings._instance_settings_path.exists()"
+    "ln_setup.delete(\"mydata\", force=True)"
    ]
   }
  ],

{lamindb_setup-1.6.0 → lamindb_setup-1.7.0}/docs/hub-cloud/03-add-managed-storage.ipynb

@@ -7,7 +7,7 @@
     "tags": []
    },
    "source": [
-    "# Add managed storage"
+    "# Add managed and referenced storage locations"
    ]
   },
   {
@@ -27,6 +27,24 @@
     "!docker stop pgtest && docker rm pgtest"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "6dcaa297",
+   "metadata": {},
+   "source": [
+    "Create a local instance that's not registered on the hub, so that we can test interplay."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "599eae6a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!lamin init --storage \"./storage-of-another-instance\""
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -65,6 +83,35 @@
     "ln_setup.init(storage=\"./storage1\", name=\"test-add-managed-storage\", db=pgurl)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "b62e84cb",
+   "metadata": {},
+   "source": [
+    "Test adding referenced storage location."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dbf195e3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import lamindb as ln\n",
+    "\n",
+    "storage = ln.Storage(root=\"./storage-of-another-instance\").save()\n",
+    "assert storage.instance_uid == \"__unknown__\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "93234f70",
+   "metadata": {},
+   "source": [
+    "Now continue with managed storage locations."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -134,7 +181,7 @@
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage2\"\n",
     "assert (\n",
     "    ln_setup.settings.storage.root / \".lamindb/storage_uid.txt\"\n",
-    ").read_text() == ln_setup.settings.storage.uid\n",
+    ").read_text().splitlines()[0] == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub"
    ]
   },
@@ -166,7 +213,7 @@
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage1\"\n",
     "assert (\n",
     "    ln_setup.settings.storage.root / \".lamindb/storage_uid.txt\"\n",
-    ").read_text() == ln_setup.settings.storage.uid\n",
+    ").read_text().splitlines()[0] == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub\n",
     "assert ln_setup.settings.storage.uid == storage1_uid"
    ]
@@ -199,7 +246,7 @@
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage1\"\n",
     "assert (\n",
     "    ln_setup.settings.storage.root / \".lamindb/storage_uid.txt\"\n",
-    ").read_text() == ln_setup.settings.storage.uid\n",
+    ").read_text().splitlines()[0] == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub\n",
     "assert ln_setup.settings.storage.uid == storage1_uid"
    ]
@@ -225,7 +272,7 @@
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage2\"\n",
     "assert (\n",
     "    ln_setup.settings.storage.root / \".lamindb/storage_uid.txt\"\n",
-    ").read_text() == ln_setup.settings.storage.uid\n",
+    ").read_text().splitlines()[0] == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub\n",
     "assert ln_setup.settings.storage.uid == storage2_uid"
    ]
@@ -264,7 +311,7 @@
     "assert ln_setup.settings.storage.region == \"us-west-1\"\n",
     "assert (\n",
     "    ln_setup.settings.storage.root / \".lamindb/storage_uid.txt\"\n",
-    ").read_text() == ln_setup.settings.storage.uid\n",
+    ").read_text().splitlines()[0] == ln_setup.settings.storage.uid\n",
     "# root.fs contains the underlying fsspec filesystem\n",
     "assert (\n",
     "    ln_setup.settings.storage.root.fs.cache_regions  # set by lamindb to True for s3 by default\n",
@@ -443,7 +490,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "py312",
    "language": "python",
    "name": "python3"
   },
@@ -457,12 +504,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.16"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "61b4062b24dfb1010f420dad5aa3bd73a4d2af47d0ec44eafec465a35a9d7239"
-   }
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

{lamindb_setup-1.6.0 → lamindb_setup-1.7.0}/docs/hub-cloud/05-init-hosted-instance.ipynb

@@ -23,7 +23,7 @@
    "outputs": [],
    "source": [
     "import lamindb_setup as ln_setup\n",
-    "from lamindb_setup.core.upath import create_path, UPath, InstanceNotEmpty\n",
+    "from lamindb_setup.core.upath import create_path, UPath, StorageNotEmpty\n",
     "from lamindb_setup.core._hub_core import (\n",
     "    delete_instance,\n",
     "    call_with_fallback_auth,\n",
@@ -44,7 +44,7 @@
    "source": [
     "try:\n",
     "    delete_instance(f\"testuser1/{instance_name}\")\n",
-    "except InstanceNotEmpty:\n",
+    "except StorageNotEmpty:\n",
     "    instance_with_storage = call_with_fallback_auth(\n",
     "        select_instance_by_owner_name,\n",
     "        owner=\"testuser1\",\n",
@@ -137,7 +137,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "py312",
    "language": "python",
    "name": "python3"
   },
@@ -151,7 +151,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

{lamindb_setup-1.6.0 → lamindb_setup-1.7.0}/docs/hub-cloud/06-connect-hosted-instance.ipynb

@@ -19,7 +19,7 @@
     "from lamindb_setup.core.upath import UPath\n",
     "from lamindb_setup.core._hub_core import delete_instance\n",
     "from lamindb_setup.core._hub_client import connect_hub_with_auth\n",
-    "from lamindb_setup.core.upath import InstanceNotEmpty\n",
+    "from lamindb_setup.core.upath import StorageNotEmpty\n",
     "\n",
     "instance_name = \"my-hosted\"\n",
     "assert ln_setup.settings.user.handle == \"testuser1\""
@@ -123,7 +123,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with pytest.raises(InstanceNotEmpty):\n",
+    "with pytest.raises(StorageNotEmpty):\n",
     "    delete_instance(f\"testuser1/{instance_name}\")"
    ]
   },

{lamindb_setup-1.6.0 → lamindb_setup-1.7.0}/docs/hub-cloud/07-keep-artifacts-local.ipynb

@@ -20,9 +20,10 @@
     "import pytest\n",
     "import lamindb_setup as ln_setup\n",
     "from upath import UPath\n",
+    "from pathlib import Path\n",
     "\n",
     "name = f\"keep-artifacts-local-setup-{os.environ['LAMIN_ENV']}\"\n",
-    "storage = (UPath(\"s3://lamindb-ci\") / name).as_posix()\n",
+    "storage = UPath(f\"s3://lamindb-ci/{name}\").as_posix()\n",
     "\n",
     "ln_setup.login(\"testuser1\")\n",
     "ln_setup.init(storage=storage)\n",
@@ -75,7 +76,7 @@
     ")\n",
     "assert (\n",
     "    ln_setup.settings.instance.storage_local.root / \".lamindb/storage_uid.txt\"\n",
-    ").read_text() == ln_setup.settings.instance.storage_local.uid\n",
+    ").read_text().splitlines()[0] == ln_setup.settings.instance.storage_local.uid\n",
     "assert ln_setup.settings.instance.storage_local is not None\n",
     "# the remote storage location is still in the regular slot\n",
     "assert ln_setup.settings.instance.storage.root.as_posix() == storage"
@@ -109,7 +110,7 @@
     ")\n",
     "assert (\n",
     "    ln_setup.settings.instance.storage_local.root / \".lamindb/storage_uid.txt\"\n",
-    ").read_text() == ln_setup.settings.instance.storage_local.uid"
+    ").read_text().splitlines()[0] == ln_setup.settings.instance.storage_local.uid"
    ]
   },
   {
@@ -176,7 +177,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with pytest.raises(ln_setup.core.upath.InstanceNotEmpty):\n",
+    "with pytest.raises(ln_setup.errors.StorageNotEmpty):\n",
     "    ln_setup.delete(name, force=True)"
    ]
   },
@@ -189,6 +190,31 @@
     "test_file.unlink()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Expand user directory:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Test expanduser works\n",
+    "test_path = \"~/test/file.txt\"\n",
+    "result = ln_setup.core.upath.create_path(test_path)\n",
+    "expected = UPath(Path(test_path).expanduser())\n",
+    "assert result.as_posix() == expected.as_posix()\n",
+    "\n",
+    "# Test it doesn't affect absolute paths\n",
+    "test_path = \"/absolute/path/file.txt\"\n",
+    "result = ln_setup.core.upath.create_path(test_path)\n",
+    "assert str(result) == test_path"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -215,7 +241,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
+   "version": "3.10.16"
   }
  },
  "nbformat": 4,

{lamindb_setup-1.6.0 → lamindb_setup-1.7.0}/docs/hub-cloud/08-test-multi-session.ipynb

@@ -54,6 +54,15 @@
     "ln_setup.init(storage=\"./testsetup\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "assert ln_setup.settings.instance.slug == \"testuser1/testsetup\""
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -111,43 +120,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Let us try to init another instance in the same Python session:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from lamindb_setup._init_instance import CannotSwitchDefaultInstance\n",
-    "\n",
-    "with pytest.raises(CannotSwitchDefaultInstance):\n",
-    "    ln_setup.init(storage=\"./testsetup2\")\n",
-    "with pytest.raises(CannotSwitchDefaultInstance):\n",
-    "    ln_setup.connect(\"testsetup\")\n",
-    "with pytest.raises(RuntimeError):\n",
-    "    ln_setup.migrate.create()\n",
-    "with pytest.raises(RuntimeError):\n",
-    "    ln_setup.migrate.deploy()\n",
-    "\n",
-    "assert ln_setup.settings.instance.slug == \"testuser1/testsetup\""
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Reset `django` and connect to another instance:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "ln_setup.core.django.reset_django()"
+    "Connect to another instance in the same process:"
    ]
   },
   {