diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e4a64c0a..5fb5eccc 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
               docs/notes/
           )
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.5
+    rev: v0.8.6
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
diff --git a/docs/hub-cloud/01-init-local-instance.ipynb b/docs/hub-cloud/01-init-local-instance.ipynb
index d06e4ccc..c023f2c2 100644
--- a/docs/hub-cloud/01-init-local-instance.ipynb
+++ b/docs/hub-cloud/01-init-local-instance.ipynb
@@ -50,7 +50,7 @@
     "from pathlib import Path\n",
     "from lamindb.models import Storage\n",
     "\n",
-    "assert ln_setup.settings.instance.storage.type_is_cloud == False\n",
+    "assert ln_setup.settings.instance.storage.type_is_cloud is False\n",
     "assert ln_setup.settings.instance.owner == ln_setup.settings.user.handle\n",
     "assert ln_setup.settings.instance.name == \"mydata\"\n",
     "assert ln_setup.settings.storage.root.as_posix() == Path(\"mydata\").resolve().as_posix()\n",
@@ -62,7 +62,10 @@
     "    == f\"sqlite:///{Path('./mydata').resolve().as_posix()}/{ln_setup.settings.instance._id.hex}.lndb\"\n",
     ")\n",
     "assert ln_setup.settings.storage._instance_id == ln_setup.settings.instance._id\n",
-    "assert Storage.objects.get(instance_uid=ln_setup.settings.instance.uid).root == ln_setup.settings.storage.root_as_str\n"
+    "assert (\n",
+    "    Storage.objects.get(instance_uid=ln_setup.settings.instance.uid).root\n",
+    "    == ln_setup.settings.storage.root_as_str\n",
+    ")"
    ]
   },
   {
@@ -84,7 +87,7 @@
     "\n",
     "settings_file = instance_settings_file(\"mydata\", \"testuser1\")\n",
     "assert not storage_root.exists()\n",
-    "assert settings_file.exists() == False"
+    "assert settings_file.exists() is False"
    ]
   }
  ],
diff --git a/docs/hub-cloud/02-connect-local-instance.ipynb b/docs/hub-cloud/02-connect-local-instance.ipynb
index a1b89586..5c2abb09 100644
--- a/docs/hub-cloud/02-connect-local-instance.ipynb
+++ b/docs/hub-cloud/02-connect-local-instance.ipynb
@@ -74,7 +74,7 @@
    "source": [
     "from pathlib import Path\n",
     "\n",
-    "assert ln_setup.settings.instance.storage.type_is_cloud == False\n",
+    "assert ln_setup.settings.instance.storage.type_is_cloud is False\n",
     "assert ln_setup.settings.instance.name == \"mydata\"\n",
     "\n",
     "root_path = Path(\"./mydata\").resolve()\n",
diff --git a/docs/hub-cloud/03-add-managed-storage.ipynb b/docs/hub-cloud/03-add-managed-storage.ipynb
index 4d10929e..343494f5 100644
--- a/docs/hub-cloud/03-add-managed-storage.ipynb
+++ b/docs/hub-cloud/03-add-managed-storage.ipynb
@@ -85,7 +85,10 @@
    "source": [
     "with pytest.raises(ValueError) as error:\n",
     "    set_managed_storage(\"./storage2\")\n",
-    "assert error.exconly() == \"ValueError: Can't add additional managed storage locations for instances that aren't managed through the hub.\""
+    "assert (\n",
+    "    error.exconly()\n",
+    "    == \"ValueError: Can't add additional managed storage locations for instances that aren't managed through the hub.\"\n",
+    ")"
    ]
   },
   {
@@ -129,7 +132,9 @@
    "source": [
     "storage2_uid = ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage2\"\n",
-    "assert (ln_setup.settings.storage.root / \".lamindb/_is_initialized\").read_text() == ln_setup.settings.storage.uid\n",
+    "assert (\n",
+    "    ln_setup.settings.storage.root / \".lamindb/_is_initialized\"\n",
+    ").read_text() == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub"
    ]
   },
@@ -159,7 +164,9 @@
    "outputs": [],
    "source": [
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage1\"\n",
-    "assert (ln_setup.settings.storage.root / \".lamindb/_is_initialized\").read_text() == ln_setup.settings.storage.uid\n",
+    "assert (\n",
+    "    ln_setup.settings.storage.root / \".lamindb/_is_initialized\"\n",
+    ").read_text() == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub\n",
     "assert ln_setup.settings.storage.uid == storage1_uid"
    ]
@@ -190,7 +197,9 @@
    "outputs": [],
    "source": [
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage1\"\n",
-    "assert (ln_setup.settings.storage.root / \".lamindb/_is_initialized\").read_text() == ln_setup.settings.storage.uid\n",
+    "assert (\n",
+    "    ln_setup.settings.storage.root / \".lamindb/_is_initialized\"\n",
+    ").read_text() == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub\n",
     "assert ln_setup.settings.storage.uid == storage1_uid"
    ]
@@ -214,7 +223,9 @@
    "source": [
     "storage2_uid = ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.root_as_str == f\"{Path.cwd()}/storage2\"\n",
-    "assert (ln_setup.settings.storage.root / \".lamindb/_is_initialized\").read_text() == ln_setup.settings.storage.uid\n",
+    "assert (\n",
+    "    ln_setup.settings.storage.root / \".lamindb/_is_initialized\"\n",
+    ").read_text() == ln_setup.settings.storage.uid\n",
     "assert ln_setup.settings.storage.is_on_hub\n",
     "assert ln_setup.settings.storage.uid == storage2_uid"
    ]
@@ -251,7 +262,9 @@
     "assert ln_setup.settings.storage.type_is_cloud\n",
     "assert ln_setup.settings.storage.root_as_str == \"s3://lamindb-ci/storage3\"\n",
     "assert ln_setup.settings.storage.region == \"us-west-1\"\n",
-    "assert (ln_setup.settings.storage.root / \".lamindb/_is_initialized\").read_text() == ln_setup.settings.storage.uid\n",
+    "assert (\n",
+    "    ln_setup.settings.storage.root / \".lamindb/_is_initialized\"\n",
+    ").read_text() == 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",
@@ -305,7 +318,9 @@
    "source": [
     "with pytest.raises(ValueError) as error:\n",
     "    set_managed_storage(\"gs://rxrx1-europe-west4/images/test/HEPG2-08\")\n",
-    "assert error.exconly().startswith(\"ValueError: Cannot manage storage without write access\")"
+    "assert error.exconly().startswith(\n",
+    "    \"ValueError: Cannot manage storage without write access\"\n",
+    ")"
    ]
   },
   {
@@ -335,7 +350,7 @@
     "    account_id=testuser2.id,\n",
     "    role=\"write\",\n",
     "    schema_id=None,\n",
-    "    skip_insert_user_table=True\n",
+    "    skip_insert_user_table=True,\n",
     ")\n",
     "User.objects.create(uid=testuser2.lnid, handle=testuser2.handle, name=testuser2.name)\n",
     "admin_hub.auth.close()"
@@ -418,7 +433,10 @@
     "from lamindb_setup.core._hub_client import call_with_fallback_auth\n",
     "from lamindb_setup.core._hub_crud import select_instance_by_id\n",
     "from lamindb_setup.core._hub_core import get_storage_records_for_instance\n",
-    "assert call_with_fallback_auth(select_instance_by_id, instance_id=instance_id.hex) is None\n",
+    "\n",
+    "assert (\n",
+    "    call_with_fallback_auth(select_instance_by_id, instance_id=instance_id.hex) is None\n",
+    ")\n",
     "assert not get_storage_records_for_instance(instance_id)"
    ]
   }
diff --git a/docs/hub-cloud/05-init-hosted-instance.ipynb b/docs/hub-cloud/05-init-hosted-instance.ipynb
index 9060d0f7..5841c999 100644
--- a/docs/hub-cloud/05-init-hosted-instance.ipynb
+++ b/docs/hub-cloud/05-init-hosted-instance.ipynb
@@ -91,7 +91,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert ln_setup.settings.instance.storage.type_is_cloud == True\n",
+    "assert ln_setup.settings.instance.storage.type_is_cloud is True\n",
     "assert ln_setup.settings.instance.owner == ln_setup.settings.user.handle\n",
     "assert ln_setup.settings.instance.name == \"my-hosted\"\n",
     "assert ln_setup.settings.storage.root.as_posix().startswith(HOSTED_BUCKETS)\n",
@@ -114,7 +114,13 @@
    "outputs": [],
    "source": [
     "hub = connect_hub_with_auth()\n",
-    "response = hub.table(\"storage\").select(\"*\").eq(\"root\", ln_setup.settings.storage.root.as_posix()).execute().data\n",
+    "response = (\n",
+    "    hub.table(\"storage\")\n",
+    "    .select(\"*\")\n",
+    "    .eq(\"root\", ln_setup.settings.storage.root.as_posix())\n",
+    "    .execute()\n",
+    "    .data\n",
+    ")\n",
     "assert len(response) == 1\n",
     "assert response[0][\"is_default\"]"
    ]
diff --git a/docs/hub-cloud/06-connect-hosted-instance.ipynb b/docs/hub-cloud/06-connect-hosted-instance.ipynb
index 08679367..ab0f6cc5 100644
--- a/docs/hub-cloud/06-connect-hosted-instance.ipynb
+++ b/docs/hub-cloud/06-connect-hosted-instance.ipynb
@@ -87,7 +87,7 @@
    "outputs": [],
    "source": [
     "target_dir = root / \"test-dir-upload\"\n",
-    "target_dir.upload_from(test_dir, create_folder=True) # default\n",
+    "target_dir.upload_from(test_dir, create_folder=True)  # default\n",
     "\n",
     "assert target_dir.is_dir()\n",
     "assert (target_dir / \"test-dir-upload\").exists()\n",
diff --git a/docs/hub-cloud/07-keep-artifacts-local.ipynb b/docs/hub-cloud/07-keep-artifacts-local.ipynb
index 161ed145..fe3ceeb2 100644
--- a/docs/hub-cloud/07-keep-artifacts-local.ipynb
+++ b/docs/hub-cloud/07-keep-artifacts-local.ipynb
@@ -29,13 +29,10 @@
     "\n",
     "assert ln_setup.settings.instance.name == name\n",
     "assert ln_setup.settings.instance.storage.type_is_cloud\n",
-    "assert (\n",
-    "    ln_setup.settings.instance.storage.root_as_str\n",
-    "    == storage\n",
-    ")\n",
+    "assert ln_setup.settings.instance.storage.root_as_str == storage\n",
     "assert (\n",
     "    ln_setup.settings.instance._sqlite_file.as_posix()\n",
-    "    == f\"{storage}/{ln_setup.settings.instance._id.hex}.lndb\"  # noqa\n",
+    "    == f\"{storage}/{ln_setup.settings.instance._id.hex}.lndb\"\n",
     ")"
    ]
   },
@@ -47,7 +44,10 @@
    "source": [
     "with pytest.raises(ValueError) as error:\n",
     "    ln_setup.settings.instance.storage_local\n",
-    "assert error.exconly() == \"ValueError: `keep_artifacts_local` is not enabled for this instance.\""
+    "assert (\n",
+    "    error.exconly()\n",
+    "    == \"ValueError: `keep_artifacts_local` is not enabled for this instance.\"\n",
+    ")"
    ]
   },
   {
@@ -74,7 +74,9 @@
     "    ln_setup.settings.instance.storage_local.root.as_posix()\n",
     "    == UPath(\"./my_storage_local\").resolve().as_posix()\n",
     ")\n",
-    "assert (ln_setup.settings.instance.storage_local.root / \".lamindb/_is_initialized\").read_text() == ln_setup.settings.instance.storage_local.uid\n",
+    "assert (\n",
+    "    ln_setup.settings.instance.storage_local.root / \".lamindb/_is_initialized\"\n",
+    ").read_text() == 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"
@@ -106,7 +108,9 @@
     "    ln_setup.settings.instance.storage_local.root.as_posix()\n",
     "    == UPath(\"./my_storage_local2\").resolve().as_posix()\n",
     ")\n",
-    "assert (ln_setup.settings.instance.storage_local.root / \".lamindb/_is_initialized\").read_text() == ln_setup.settings.instance.storage_local.uid"
+    "assert (\n",
+    "    ln_setup.settings.instance.storage_local.root / \".lamindb/_is_initialized\"\n",
+    ").read_text() == ln_setup.settings.instance.storage_local.uid"
    ]
   },
   {
@@ -154,7 +158,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "test_file = (ln_setup.settings.instance.storage_local.root / \".lamindb/test_file.txt\")\n",
+    "test_file = ln_setup.settings.instance.storage_local.root / \".lamindb/test_file.txt\"\n",
     "test_file.write_text(\"test\")"
    ]
   },
diff --git a/docs/hub-prod/test-cloud-sync.ipynb b/docs/hub-prod/test-cloud-sync.ipynb
index 39f72705..b06d6b09 100644
--- a/docs/hub-prod/test-cloud-sync.ipynb
+++ b/docs/hub-prod/test-cloud-sync.ipynb
@@ -17,7 +17,7 @@
    "source": [
     "import os\n",
     "\n",
-    "instance_name = f\"test-sqlite-sync\"\n",
+    "instance_name = \"test-sqlite-sync\"\n",
     "!lamin connect {instance_name}\n",
     "!yes | lamin delete {instance_name}"
    ]
@@ -33,7 +33,6 @@
     "from lamindb_setup.core.upath import UPath, LocalPathClasses\n",
     "import shutil\n",
     "import time\n",
-    "import os\n",
     "import pytest"
    ]
   },
@@ -131,8 +130,14 @@
    "source": [
     "test_local_path = UPath(\"./some/local/path\")\n",
     "assert settings.paths.cloud_to_local_no_update(test_local_path) == test_local_path\n",
-    "assert settings.paths.cloud_to_local_no_update(test_local_path.as_posix()) == test_local_path\n",
-    "assert settings.paths.cloud_to_local_no_update(test_local_path, cache_key=\"some/cache/key\") == test_local_path"
+    "assert (\n",
+    "    settings.paths.cloud_to_local_no_update(test_local_path.as_posix())\n",
+    "    == test_local_path\n",
+    ")\n",
+    "assert (\n",
+    "    settings.paths.cloud_to_local_no_update(test_local_path, cache_key=\"some/cache/key\")\n",
+    "    == test_local_path\n",
+    ")"
    ]
   },
   {
@@ -142,11 +147,25 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert settings.paths.cloud_to_local_no_update(dir_sync) == settings.cache_dir / f\"lamindb-ci/{instance_name}/dir_sync\"\n",
-    "assert settings.paths.cloud_to_local_no_update(dir_sync.as_posix()) == settings.cache_dir / f\"lamindb-ci/{instance_name}/dir_sync\"\n",
+    "assert (\n",
+    "    settings.paths.cloud_to_local_no_update(dir_sync)\n",
+    "    == settings.cache_dir / f\"lamindb-ci/{instance_name}/dir_sync\"\n",
+    ")\n",
+    "assert (\n",
+    "    settings.paths.cloud_to_local_no_update(dir_sync.as_posix())\n",
+    "    == settings.cache_dir / f\"lamindb-ci/{instance_name}/dir_sync\"\n",
+    ")\n",
     "\n",
-    "assert settings.paths.cloud_to_local_no_update(dir_sync, cache_key=\"dir_cache/key\") == settings.cache_dir / \"dir_cache/key\"\n",
-    "assert settings.paths.cloud_to_local_no_update(dir_sync.as_posix(), cache_key=\"dir_cache/key\") == settings.cache_dir / \"dir_cache/key\""
+    "assert (\n",
+    "    settings.paths.cloud_to_local_no_update(dir_sync, cache_key=\"dir_cache/key\")\n",
+    "    == settings.cache_dir / \"dir_cache/key\"\n",
+    ")\n",
+    "assert (\n",
+    "    settings.paths.cloud_to_local_no_update(\n",
+    "        dir_sync.as_posix(), cache_key=\"dir_cache/key\"\n",
+    "    )\n",
+    "    == settings.cache_dir / \"dir_cache/key\"\n",
+    ")"
    ]
   },
   {
@@ -157,7 +176,9 @@
    "outputs": [],
    "source": [
     "# for http urls\n",
-    "http_path = UPath(\"https://raw.githubusercontent.com/laminlabs/lamindb-setup/refs/heads/main/README.md\")\n",
+    "http_path = UPath(\n",
+    "    \"https://raw.githubusercontent.com/laminlabs/lamindb-setup/refs/heads/main/README.md\"\n",
+    ")\n",
     "assert http_path.protocol == \"https\"\n",
     "\n",
     "http_stat = http_path.stat()\n",
@@ -175,9 +196,17 @@
    "source": [
     "http_key = \"raw.githubusercontent.com/laminlabs/lamindb-setup/refs/heads/main/README.md\"\n",
     "\n",
-    "assert settings.paths.cloud_to_local_no_update(http_path) == settings.cache_dir / http_key\n",
-    "assert settings.paths.cloud_to_local_no_update(str(http_path)) == settings.cache_dir / http_key\n",
-    "assert settings.paths.cloud_to_local_no_update(http_path, cache_key=\"check/README.md\") == settings.cache_dir / \"check/README.md\""
+    "assert (\n",
+    "    settings.paths.cloud_to_local_no_update(http_path) == settings.cache_dir / http_key\n",
+    ")\n",
+    "assert (\n",
+    "    settings.paths.cloud_to_local_no_update(str(http_path))\n",
+    "    == settings.cache_dir / http_key\n",
+    ")\n",
+    "assert (\n",
+    "    settings.paths.cloud_to_local_no_update(http_path, cache_key=\"check/README.md\")\n",
+    "    == settings.cache_dir / \"check/README.md\"\n",
+    ")"
    ]
   },
   {
@@ -195,7 +224,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dir_sync_local = settings.paths.cloud_to_local(dir_sync.as_posix(), cache_key=\"dir_cache/key\")"
+    "dir_sync_local = settings.paths.cloud_to_local(\n",
+    "    dir_sync.as_posix(), cache_key=\"dir_cache/key\"\n",
+    ")"
    ]
   },
   {
@@ -410,7 +441,7 @@
     "time.sleep(1)\n",
     "cloud_file = dir_sync / \"file1\"\n",
     "# update cloud timestamp\n",
-    "cloud_file.fs.touch(cloud_file.as_posix(), truncate=True)  \n",
+    "cloud_file.fs.touch(cloud_file.as_posix(), truncate=True)\n",
     "\n",
     "assert cloud_file.modified.timestamp() > local_file_new.stat().st_mtime"
    ]
diff --git a/docs/hub-prod/test-sqlite-lock.ipynb b/docs/hub-prod/test-sqlite-lock.ipynb
index 8c3bdc3b..032cc991 100644
--- a/docs/hub-prod/test-sqlite-lock.ipynb
+++ b/docs/hub-prod/test-sqlite-lock.ipynb
@@ -76,7 +76,10 @@
     "ln_setup.init(storage=\"s3://lamindb-ci/test-load-lock\", name=\"test-load-lock\")\n",
     "instance_id = ln_setup.settings.instance._id\n",
     "\n",
-    "assert ln_setup.settings.instance._cloud_sqlite_locker is ln_setup.settings.instance._cloud_sqlite_locker\n",
+    "assert (\n",
+    "    ln_setup.settings.instance._cloud_sqlite_locker\n",
+    "    is ln_setup.settings.instance._cloud_sqlite_locker\n",
+    ")\n",
     "\n",
     "ln_setup.close()"
    ]
diff --git a/lamindb_setup/core/upath.py b/lamindb_setup/core/upath.py
index 0110e471..092d7371 100644
--- a/lamindb_setup/core/upath.py
+++ b/lamindb_setup/core/upath.py
@@ -865,7 +865,7 @@ def check_storage_is_empty(
     )
     if n_diff > 0:
         if raise_error:
-            raise InstanceNotEmpty(message)
+            raise InstanceNotEmpty(message) from None
         else:
             logger.warning(message)
     return n_diff
diff --git a/pyproject.toml b/pyproject.toml
index 485e14aa..028c47e3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -54,7 +54,7 @@ dev = [
 [tool.ruff]
 src = ["src"]
 line-length = 88
-select = [
+lint.select = [
     "F",  # Errors detected by Pyflakes
     "E",  # Error detected by Pycodestyle
     "W",  # Warning detected by Pycodestyle
@@ -70,7 +70,7 @@ select = [
     "NPY",  # Numpy specific rules
     "PTH"  # Use pathlib
 ]
-ignore = [
+lint.ignore = [
     # Do not catch blind exception: `Exception`
     "BLE001",
     # Errors from function calls in argument defaults. These are fine when the result is immutable.
@@ -139,10 +139,10 @@ ignore = [
     "PTH123",
 ]
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "google"
 
-[tool.ruff.per-file-ignores]
-"docs/*" = ["I"]
+[tool.ruff.lint.per-file-ignores]
+"docs/*" = ["I", "B018", "B017"]
 "tests/*" = ["D"]
 "*/__init__.py" = ["F401"]