diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index 56f6f984..393a9449 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -7,12 +7,6 @@ updates:
       interval: "weekly"
     labels:
       - "maintenance"
-    # Update via cruft
-    ignore:
-      - dependency-name: "mkdocs*"
-      - dependency-name: "pytest*"
-      - dependency-name: "pylint"
-      - dependency-name: "mypy"
 
   - directory: "/"
     package-ecosystem: "github-actions"
@@ -20,10 +14,3 @@ updates:
       interval: "weekly"
     labels:
       - "maintenance"
-    # Update via cruft
-    ignore:
-      - dependency-name: "actions/checkout"
-      - dependency-name: "actions/setup-python"
-      - dependency-name: "pypa/gh-action-pypi-publish"
-      - dependency-name: "codecov/codecov-action"
-      - dependency-name: "peter-evans/create-pull-request"
diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
index dc0d9e81..118b5d65 100644
--- a/.github/workflows/benchmark.yml
+++ b/.github/workflows/benchmark.yml
@@ -21,18 +21,18 @@ jobs:
     env:
       PYTEST_BENCHMARK_STORAGE: file://${{ github.workspace }}/.benchmarks
     steps:
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         ref: ${{ github.event.pull_request.base.sha }}
         fetch-depth: 0
         path: base
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
         path: pr
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 20e499d8..85a370f7 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -21,10 +21,10 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
 
     - name: Upgrade pip and nox
       run: |
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index b4d9ecca..98026353 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -32,7 +32,7 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python ${{ matrix.pyv }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.pyv }}
 
@@ -49,7 +49,7 @@ jobs:
       run: nox -s tests-${{ matrix.nox_pyv || matrix.pyv }} -- --cov-report=xml
 
     - name: Upload coverage report
-      uses: codecov/codecov-action@v3.1.4
+      uses: codecov/codecov-action@v3
 
     - name: Build package
       run: nox -s build
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3c44cc02..468bcd88 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -20,18 +20,18 @@ repos:
       - id: sort-simple-yaml
       - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.1.5'
+    rev: 'v0.1.7'
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         additional_dependencies: ["tomli"]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+    rev: v3.15.0
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
diff --git a/pyproject.toml b/pyproject.toml
index 86ca5b12..fc6da9ae 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dvc-data"
-description = "dvc data"
+description = "DVC's data management subsystem"
 readme = "README.rst"
 license = {text = "Apache-2.0"}
 authors = [{ name = "Iterative", email = "support@dvc.org" }]
@@ -44,12 +44,12 @@ all = [
     "dvc-data[cli]",
 ]
 tests = [
-    "pytest==7.2.0",
-    "pytest-sugar==0.9.6",
-    "pytest-cov==4.0.0",
-    "pytest-mock==3.10.0",
-    "pytest-benchmark==4.0.0",
-    "mypy==1.5.1",
+    "pytest<8,>=7",
+    "pytest-sugar",
+    "pytest-cov>=4.1.0",
+    "pytest-mock",
+    "pytest-benchmark",
+    "mypy==1.7.1",
     "pytest-servers[s3]==0.1.3",
 ]
 dev = [
@@ -62,7 +62,7 @@ dev = [
 dvc-data = "dvc_data.__main__:main"
 
 [tool.setuptools.package-data]
-dvc_objects = ["py.typed"]
+dvc_data = ["py.typed"]
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -121,3 +121,81 @@ module = [
 
 [tool.codespell]
 ignore-words-list = "fo"
+
+[tool.ruff]
+ignore = [
+    "ISC001", # single-line-implicit-string-concatenation
+    "PLR2004", # magic-value-comparison
+    "PLW2901", # redefined-loop-name
+    "RET501", # unnecessary-return-none
+    "RET502", # implicit-return-value
+    "RET503", # implicit-return
+    "S101", # assert
+    "SIM105", # suppressible-exception
+    "SIM108", # if-else-block-instead-of-if-exp
+    "SIM117", # multiple-with-statements
+]
+select = [
+    "A", # flake8-buitlins
+    "ASYNC", # flake8-async
+    "B", # flake8-bugbear
+    "BLE", # flake8-blind-except
+    "C4", # flake8-comprehensions
+    "C90", # mccabe
+    "DTZ", # flake8-datetimez
+    "E", # pycodestyle - Error
+    "EXE", # flake8-executable
+    "F", # pyflakes
+    "FLY", # flynt-rules
+    "G", # flake8-logging-format
+    "I", # isort
+    "ICN", # flake8-import-conventions
+    "INP", # flake8-no-pep420
+    "ISC", # flake8-implicit-str-concat
+    "N", # pep8-naming
+    "PERF101", # perflint
+    "PGH", # pygrep-hooks
+    "PIE", # flake8-pie
+    "PL", # pylint
+    "PT", # flake8-pytest-style
+    "PYI", # flake8-pyi
+    "Q", # flae8-quotes
+    "RET", # flake8-return
+    "RSE", # flake8-raise
+    "RUF", # ruff
+    "S", # flake8-bandit
+    "SIM", # flake8-simplify
+    "SLOT", # flake8-slots
+    "T10", # flake8-debugger
+    "T20", # flake8-print
+    "TCH", # flake8-type-checking
+    "TCH", # flake8-type-checking
+    "TID", # flake8-tidy-imports
+    "UP", # pyupgrade
+    "W", # pycodestyle - Warning
+    "YTT", # flake8-2020
+]
+show-source = true
+show-fixes = true
+
+[tool.ruff.lint.flake8-pytest-style]
+fixture-parentheses = false
+mark-parentheses = false
+parametrize-names-type = "csv"
+
+[tool.ruff.lint.flake8-tidy-imports]
+[tool.ruff.lint.flake8-tidy-imports.banned-api]
+"funcy.cached_property" = {msg = "use `from dvc_data.utils import cached_property` instead."}
+"functools.cached_property" = {msg = "use `from dvc_data.utils import cached_property` instead."}
+
+[tool.ruff.lint.flake8-type-checking]
+strict = true
+
+[tool.ruff.lint.isort]
+known-first-party = ["dvc_data"]
+
+[tool.ruff.lint.pylint]
+max-args = 10
+
+[tool.ruff.per-file-ignores]
+"src/dvc_data/cli.py" = ["T201", "B008"]
diff --git a/src/dvc_data/__main__.py b/src/dvc_data/__main__.py
index cc8cc558..ae21793b 100644
--- a/src/dvc_data/__main__.py
+++ b/src/dvc_data/__main__.py
@@ -5,7 +5,7 @@
     def main():  # type: ignore[misc]
         import sys
 
-        print(
+        print(  # noqa: T201
             "dvc-data could not run because the required "
             "dependencies are not installed.\n"
             "Please install it with: pip install 'dvc-data[cli]'"
diff --git a/src/dvc_data/cli.py b/src/dvc_data/cli.py
index b53ea72d..b0bb8add 100644
--- a/src/dvc_data/cli.py
+++ b/src/dvc_data/cli.py
@@ -13,7 +13,7 @@
 from typing import List, cast
 
 import click
-import typer  # pylint: disable=import-error
+import typer
 from attrs import asdict
 from dvc_objects._tqdm import Tqdm
 from dvc_objects.errors import ObjectFormatError
@@ -34,10 +34,9 @@
 from dvc_data.hashfile.obj import HashFile
 from dvc_data.hashfile.state import State
 from dvc_data.hashfile.transfer import transfer as _transfer
-from dvc_data.hashfile.tree import Tree
+from dvc_data.hashfile.tree import Tree, merge
 from dvc_data.hashfile.tree import du as _du
-from dvc_data.hashfile.tree import merge
-from dvc_data.repo import NotARepo, Repo
+from dvc_data.repo import NotARepoError, Repo
 
 install(show_locals=True, suppress=[typer, click])
 
@@ -224,9 +223,9 @@ def from_shortoid(odb: HashFileDB, oid: str) -> str:
 def get_odb(**config):
     try:
         repo = Repo.discover()
-    except NotARepo as exc:
+    except NotARepoError as exc:
         typer.echo(exc, err=True)
-        raise typer.Abort(1)
+        raise typer.Abort(1)  # noqa: B904
 
     if "state" not in config:
         config.setdefault("state", State(root_dir=repo.root, tmp_dir=repo.tmp_dir))
@@ -324,7 +323,7 @@ def show(oid: str = typer.Argument(..., allow_dash=True)):
     obj = load(odb, odb.get(oid).hash_info)
     if isinstance(obj, Tree):
         return _ls_tree(obj)
-    elif isinstance(obj, HashFile):
+    if isinstance(obj, HashFile):
         return _cat_object(odb, obj.oid)
     raise AssertionError(f"unknown object of type {type(obj)}")
 
@@ -429,14 +428,15 @@ def merge_tree(oid1: str, oid2: str, force: bool = False):
     oid2 = from_shortoid(odb, oid2)
     obj1 = load(odb, odb.get(oid1).hash_info)
     obj2 = load(odb, odb.get(oid2).hash_info)
-    assert isinstance(obj1, Tree) and isinstance(obj2, Tree), "not a tree obj"
+    assert isinstance(obj1, Tree)
+    assert isinstance(obj2, Tree), "not a tree obj"
 
     if not force:
         # detect conflicts
         d = _diff(obj1, obj2, odb)
         modified = [
             posixpath.join(*change.old.key)
-            for change in d.modified  # pylint: disable=not-an-iterable
+            for change in d.modified
             if change.old.key != ROOT
         ]
         if modified:
@@ -478,7 +478,6 @@ def apply_op(odb, obj, application):
     op = application["op"]
     path = application["path"]
     keys = tuple(path.split("/"))
-    # pylint: disable=protected-access
     if op in ("add", "modify"):
         new = tuple(application["to"].split("/"))
         if op == "add" and new in obj._dict:
@@ -594,7 +593,7 @@ def checkout(
     path: Path = typer.Argument(..., resolve_path=True),
     relink: bool = False,
     force: bool = False,
-    type: List[LinkEnum] = typer.Option(["copy"]),  # pylint: disable=redefined-builtin
+    type: List[LinkEnum] = typer.Option(["copy"]),  # noqa: A002
 ):
     odb = get_odb(type=[t.value for t in type])
     oid = from_shortoid(odb, oid)
diff --git a/src/dvc_data/fs.py b/src/dvc_data/fs.py
index da7634a1..aec677c8 100644
--- a/src/dvc_data/fs.py
+++ b/src/dvc_data/fs.py
@@ -9,8 +9,6 @@
 from dvc_objects.fs.callbacks import DEFAULT_CALLBACK
 from fsspec import AbstractFileSystem
 
-from dvc_data.hashfile.db import HashFileDB
-
 from .utils import cached_property
 
 if typing.TYPE_CHECKING:
@@ -18,6 +16,8 @@
     from dvc_objects.fs.callbacks import Callback
     from dvc_objects.fs.path import Path
 
+    from dvc_data.hashfile.db import HashFileDB
+
     from .hashfile.hash_info import HashInfo
     from .index import DataIndex, DataIndexEntry, ObjectStorage
 
@@ -33,7 +33,7 @@ class FileInfo(NamedTuple):
     fs_path: "AnyFSPath"
 
 
-class DataFileSystem(AbstractFileSystem):  # pylint:disable=abstract-method
+class DataFileSystem(AbstractFileSystem):
     root_marker = "/"
 
     def __init__(self, index: "DataIndex", **kwargs: Any):
@@ -55,7 +55,7 @@ def _get_key(self, path: str) -> Tuple[str, ...]:
             return ()
 
         key = self.path.relparts(path, self.root_marker)
-        if key == (".",) or key == ("",):
+        if key in ((".",), ("",)):
             key = ()
 
         return key
@@ -108,9 +108,7 @@ def _cache_remote_file(
         odb.add(path, fs, oid)
         return odb.fs, odb.oid_to_path(oid)
 
-    def _open(  # pylint: disable=arguments-differ
-        self, path: "AnyFSPath", **kwargs: Any
-    ) -> "BinaryIO":
+    def _open(self, path: "AnyFSPath", **kwargs: Any) -> "BinaryIO":
         typ, _, cache_storage, hi, fs, fspath = self._get_fs_path(path)
 
         if kwargs.get("cache", False) and typ == "remote" and cache_storage:
@@ -156,7 +154,7 @@ def info(self, path: "AnyFSPath", **kwargs: Any):
         info["name"] = path
         return info
 
-    def get_file(  # pylint: disable=arguments-differ
+    def get_file(
         self,
         rpath: "AnyFSPath",
         lpath: "AnyFSPath",
diff --git a/src/dvc_data/hashfile/_ignore.py b/src/dvc_data/hashfile/_ignore.py
index b0f7f32b..3ea4cee5 100644
--- a/src/dvc_data/hashfile/_ignore.py
+++ b/src/dvc_data/hashfile/_ignore.py
@@ -5,8 +5,6 @@
 if TYPE_CHECKING:
     from dvc_objects.fs.base import AnyFSPath, FileSystem
 
-# pylint: disable=unused-argument
-
 
 class Ignore(Protocol):
     def find(self, fs: "FileSystem", path: "AnyFSPath") -> Iterator["AnyFSPath"]:
diff --git a/src/dvc_data/hashfile/build.py b/src/dvc_data/hashfile/build.py
index 908a711f..d1bd6bcb 100644
--- a/src/dvc_data/hashfile/build.py
+++ b/src/dvc_data/hashfile/build.py
@@ -72,7 +72,8 @@ def _build_file(path, fs, name, odb=None, upload_odb=None, dry_run=False):
     state = odb.state if odb else None
     meta, hash_info = hash_file(path, fs, name, state=state)
     if upload_odb and not dry_run:
-        assert odb and name == "md5"
+        assert odb
+        assert name == "md5"
         return _upload_file(path, fs, odb, upload_odb)
 
     oid = hash_info.value
@@ -197,7 +198,8 @@ def _build_external_tree_info(odb: "HashFileDB", tree: "Tree", name: str) -> "Tr
     # able to validate .dir files right in the workspace (e.g. check s3
     # etag), but could be dropped for manual validation with regular md5,
     # that would be universal for all clouds.
-    assert odb and name != "md5"
+    assert odb
+    assert name != "md5"
 
     assert tree.fs
     assert tree.path
diff --git a/src/dvc_data/hashfile/cache.py b/src/dvc_data/hashfile/cache.py
index 9ac92423..dca5fe43 100644
--- a/src/dvc_data/hashfile/cache.py
+++ b/src/dvc_data/hashfile/cache.py
@@ -1,18 +1,18 @@
 import os
-import pickle  # nosec B403
+import pickle
 from functools import wraps
 from typing import Any, Optional
 
 import diskcache
-from diskcache import Disk as disk
-from diskcache import Index  # noqa: F401, pylint: disable=unused-import
-from diskcache import Timeout  # noqa: F401, pylint: disable=unused-import
-
-# pylint: disable=redefined-builtin
+from diskcache import Disk as _Disk
+from diskcache import (
+    Index,  # noqa: F401
+    Timeout,  # noqa: F401
+)
 
 
 class DiskError(Exception):
-    def __init__(self, directory: str, type: str) -> None:
+    def __init__(self, directory: str, type: str) -> None:  # noqa: A002
         self.directory = directory
         self.type = type
         super().__init__(f"Could not open disk '{type}' in {directory}")
@@ -26,22 +26,22 @@ def wrapped(self, *args, **kwargs):
         except (pickle.PickleError, ValueError) as e:
             if isinstance(e, ValueError) and "pickle protocol" not in str(e):
                 raise
-            # pylint: disable=protected-access
+
             raise DiskError(self._directory, type=self._type) from e
 
     return wrapped
 
 
-class Disk(disk):
+class Disk(_Disk):
     """Reraise pickle-related errors as DiskError."""
 
     # we need type to differentiate cache for better error messages
     _type: str
 
-    put = translate_pickle_error(disk.put)
-    get = translate_pickle_error(disk.get)
-    store = translate_pickle_error(disk.store)
-    fetch = translate_pickle_error(disk.fetch)
+    put = translate_pickle_error(_Disk.put)
+    get = translate_pickle_error(_Disk.get)
+    store = translate_pickle_error(_Disk.store)
+    fetch = translate_pickle_error(_Disk.fetch)
 
 
 class Cache(diskcache.Cache):
@@ -51,8 +51,8 @@ def __init__(
         self,
         directory: Optional[str] = None,
         timeout: int = 60,
-        disk: disk = Disk,  # pylint: disable=redefined-outer-name
-        type: Optional[str] = None,
+        disk: _Disk = Disk,
+        type: Optional[str] = None,  # noqa: A002
         **settings: Any,
     ) -> None:
         settings.setdefault("disk_pickle_protocol", 4)
diff --git a/src/dvc_data/hashfile/checkout.py b/src/dvc_data/hashfile/checkout.py
index 7452a8b5..dcdcd8f4 100644
--- a/src/dvc_data/hashfile/checkout.py
+++ b/src/dvc_data/hashfile/checkout.py
@@ -143,7 +143,7 @@ def _diff(
     if relink:
         diff.modified.extend(diff.unchanged)
     else:
-        for change in diff.unchanged:  # pylint: disable=not-an-iterable
+        for change in diff.unchanged:
             if not change.new.in_cache and not (
                 change.new.oid and change.new.oid.isdir
             ):
@@ -232,7 +232,7 @@ def _checkout(
         raise CheckoutError(failed)
 
 
-def checkout(
+def checkout(  # noqa: PLR0913
     path,
     fs,
     obj,
diff --git a/src/dvc_data/hashfile/db/__init__.py b/src/dvc_data/hashfile/db/__init__.py
index b936447b..6f7aebe3 100644
--- a/src/dvc_data/hashfile/db/__init__.py
+++ b/src/dvc_data/hashfile/db/__init__.py
@@ -3,20 +3,21 @@
 import os
 from contextlib import suppress
 from copy import copy
-from typing import TYPE_CHECKING, Callable, List, Optional, Union
+from typing import TYPE_CHECKING, Callable, ClassVar, List, Optional, Union
 
 from dvc_objects.db import ObjectDB
 from dvc_objects.errors import ObjectFormatError
 from dvc_objects.fs.callbacks import DEFAULT_CALLBACK
 
-from ..hash_info import HashInfo
-from ..obj import HashFile
+from dvc_data.hashfile.hash_info import HashInfo
+from dvc_data.hashfile.obj import HashFile
 
 if TYPE_CHECKING:
     from dvc_objects.fs.base import AnyFSPath, FileSystem
     from dvc_objects.fs.callbacks import Callback
 
-    from ..tree import Tree
+    from dvc_data.hashfile.tree import Tree
+
     from .index import ObjectDBIndexBase
 
 
@@ -48,11 +49,11 @@ def get_index(odb) -> "ObjectDBIndexBase":
 
 class HashFileDB(ObjectDB):
     DEFAULT_VERIFY = False
-    DEFAULT_CACHE_TYPES = ["copy"]
+    DEFAULT_CACHE_TYPES: ClassVar[List[str]] = ["copy"]
     CACHE_MODE: Optional[int] = None
 
     def __init__(self, fs: "FileSystem", path: str, **config):
-        from ..state import StateNoop
+        from dvc_data.hashfile.state import StateNoop
 
         super().__init__(fs, path)
         self.state = config.get("state", StateNoop())
@@ -133,16 +134,16 @@ def add(
                 pass
         return transferred
 
-    def protect(self, path):  # pylint: disable=unused-argument
+    def protect(self, path):
         pass
 
-    def is_protected(self, path):  # pylint: disable=unused-argument
+    def is_protected(self, path):
         return False
 
-    def unprotect(self, path):  # pylint: disable=unused-argument
+    def unprotect(self, path):
         pass
 
-    def set_exec(self, path):  # pylint: disable=unused-argument
+    def set_exec(self, path):
         pass
 
     def check(
@@ -163,7 +164,7 @@ def check(
 
         - Remove the file from cache if it doesn't match the actual hash
         """
-        from ..hash import hash_file
+        from dvc_data.hashfile.hash import hash_file
 
         obj = self.get(oid)
         if self.is_protected(obj.path):
diff --git a/src/dvc_data/hashfile/db/index.py b/src/dvc_data/hashfile/db/index.py
index abcb26fe..6b5d9f64 100644
--- a/src/dvc_data/hashfile/db/index.py
+++ b/src/dvc_data/hashfile/db/index.py
@@ -55,7 +55,7 @@ def __init__(
         self,
         tmp_dir: "AnyFSPath",
         name: str,
-    ) -> None:  # pylint: disable=super-init-not-called
+    ) -> None:
         pass
 
     def __iter__(self) -> Iterator[str]:
@@ -87,10 +87,10 @@ def __init__(
         self,
         tmp_dir: "AnyFSPath",
         name: str,
-    ) -> None:  # pylint: disable=super-init-not-called
+    ) -> None:
         from dvc_objects.fs import LocalFileSystem
 
-        from ..cache import Cache, Index
+        from dvc_data.hashfile.cache import Cache, Index
 
         self.index_dir = os.path.join(tmp_dir, self.INDEX_DIR, name)
         self.fs = LocalFileSystem()
@@ -110,7 +110,7 @@ def dir_hashes(self) -> Iterator[str]:
 
     def clear(self) -> None:
         """Clear this index (to force re-indexing later)."""
-        from ..cache import Timeout
+        from dvc_data.hashfile.cache import Timeout
 
         try:
             self.index.clear()
@@ -119,7 +119,7 @@ def clear(self) -> None:
 
     def update(self, dir_hashes: Iterable[str], file_hashes: Iterable[str]) -> None:
         """Update this index, adding the specified hashes."""
-        from ..cache import Timeout
+        from dvc_data.hashfile.cache import Timeout
 
         try:
             with self.index.transact():
diff --git a/src/dvc_data/hashfile/db/local.py b/src/dvc_data/hashfile/db/local.py
index 1aaf6049..0338f18e 100644
--- a/src/dvc_data/hashfile/db/local.py
+++ b/src/dvc_data/hashfile/db/local.py
@@ -2,6 +2,7 @@
 import os
 import stat
 from functools import partial
+from typing import ClassVar, List
 
 from dvc_objects.db import noop, wrap_iter
 from dvc_objects.errors import ObjectDBError, ObjectFormatError
@@ -17,7 +18,7 @@
 
 
 class LocalHashFileDB(HashFileDB):
-    DEFAULT_CACHE_TYPES = ["reflink", "copy"]
+    DEFAULT_CACHE_TYPES: ClassVar[List[str]] = ["reflink", "copy"]
     CACHE_MODE = 0o444
     UNPACKED_DIR_SUFFIX = ".unpacked"
 
@@ -47,7 +48,7 @@ def oid_to_path(self, oid):
         # being ~5.5 times faster.
         return f"{self.path}{os.sep}{oid[0:2]}{os.sep}{oid[2:]}"
 
-    def oids_exist(self, oids, jobs=None, progress=noop):  # pylint: disable=unused-argument
+    def oids_exist(self, oids, jobs=None, progress=noop):
         ret = []
         progress = partial(progress, "querying", len(oids))
 
diff --git a/src/dvc_data/hashfile/db/migrate.py b/src/dvc_data/hashfile/db/migrate.py
index 50aa1a41..d7c1b07d 100644
--- a/src/dvc_data/hashfile/db/migrate.py
+++ b/src/dvc_data/hashfile/db/migrate.py
@@ -39,7 +39,6 @@ def prepare(
 
     Objects from src will be rehashed for addition to dest.
     """
-    # pylint: disable-next=protected-access
     src_paths = [src.oid_to_path(oid) for oid in src._list_oids()]
     callback.set_size(len(src_paths))
     with ThreadPoolExecutor(
diff --git a/src/dvc_data/hashfile/db/reference.py b/src/dvc_data/hashfile/db/reference.py
index 7d3ff89e..4d6181e5 100644
--- a/src/dvc_data/hashfile/db/reference.py
+++ b/src/dvc_data/hashfile/db/reference.py
@@ -1,7 +1,8 @@
 import logging
 from typing import TYPE_CHECKING, Callable, Dict, List, Optional, Union
 
-from ..obj import HashFile
+from dvc_data.hashfile.obj import HashFile
+
 from . import HashFileDB, HashInfo
 
 if TYPE_CHECKING:
diff --git a/src/dvc_data/hashfile/gc.py b/src/dvc_data/hashfile/gc.py
index 2f0ca02c..293b5a6a 100644
--- a/src/dvc_data/hashfile/gc.py
+++ b/src/dvc_data/hashfile/gc.py
@@ -5,7 +5,7 @@
     from .hash_info import HashInfo
 
 
-def gc(
+def gc(  # noqa: C901
     odb: "HashFileDB",
     used: Iterable["HashInfo"],
     jobs: Optional[int] = None,
@@ -46,7 +46,6 @@ def _is_dir_hash(_hash):
         path = odb.oid_to_path(hash_)
         if _is_dir_hash(hash_):
             # backward compatibility
-            # pylint: disable=protected-access
             odb._remove_unpacked_dir(hash_)
             dir_paths.append(path)
         else:
diff --git a/src/dvc_data/hashfile/hash.py b/src/dvc_data/hashfile/hash.py
index 97bffd83..4f369980 100644
--- a/src/dvc_data/hashfile/hash.py
+++ b/src/dvc_data/hashfile/hash.py
@@ -170,8 +170,8 @@ def call(self, hook_name=None, **kwargs):
         if self.size and self.size > self.LARGE_FILE_SIZE:
             if not self._logged:
                 logger.info(
-                    f"Computing md5 for a large file '{self.fname}'. "
-                    "This is only done once."
+                    "Computing md5 for a large file %r. This is only done once.",
+                    self.fname,
                 )
                 self._logged = True
             super().call()
diff --git a/src/dvc_data/hashfile/state.py b/src/dvc_data/hashfile/state.py
index 13b1aaf6..557680ea 100644
--- a/src/dvc_data/hashfile/state.py
+++ b/src/dvc_data/hashfile/state.py
@@ -52,7 +52,7 @@ def close(self):
     def save(self, path, fs, hash_info, info=None):
         pass
 
-    def get(self, path, fs, info=None):  # pylint: disable=unused-argument
+    def get(self, path, fs, info=None):
         return None, None
 
     def save_link(self, path, fs):
@@ -71,7 +71,7 @@ def _checksum(info):
     return str(int(tokenize([info["ino"], info["mtime"], info["size"]]), 16))
 
 
-class State(StateBase):  # pylint: disable=too-many-instance-attributes
+class State(StateBase):
     HASH_VERSION = 1
 
     def __init__(self, root_dir=None, tmp_dir=None, ignore: Optional["Ignore"] = None):
@@ -116,7 +116,7 @@ def save(self, path, fs, hash_info, info=None):
 
         self.hashes[path] = json.dumps(entry)
 
-    def get(self, path, fs, info=None):
+    def get(self, path, fs, info=None):  # noqa: PLR0911
         """Gets the hash for the specified path info. Hash will be
         retrieved from the state database if available.
 
diff --git a/src/dvc_data/hashfile/status.py b/src/dvc_data/hashfile/status.py
index ed835185..59492170 100644
--- a/src/dvc_data/hashfile/status.py
+++ b/src/dvc_data/hashfile/status.py
@@ -1,13 +1,14 @@
 import logging
 from typing import TYPE_CHECKING, Dict, Iterable, NamedTuple, Optional, Set
 
-from dvc_objects.db import ObjectDB
 from dvc_objects.fs import Schemes
 
 from .hash_info import HashInfo
 from .tree import Tree
 
 if TYPE_CHECKING:
+    from dvc_objects.db import ObjectDB
+
     from .db import HashFileDB
     from .db.index import ObjectDBIndexBase
     from .obj import HashFile
@@ -82,7 +83,7 @@ def _indexed_dir_hashes(
         yield tree.hash_info.value
 
 
-def status(
+def status(  # noqa: C901, PLR0912
     odb: "HashFileDB",
     obj_ids: Iterable["HashInfo"],
     name: Optional[str] = None,
@@ -117,7 +118,8 @@ def status(
             else:
                 tree = Tree.load(cache_odb, hash_info)
                 for _, _, oid in tree:
-                    assert oid and oid.value
+                    assert oid
+                    assert oid.value
                     hash_infos[oid.value] = oid
             if index:
                 dir_objs[hash_info.value] = tree
diff --git a/src/dvc_data/hashfile/transfer.py b/src/dvc_data/hashfile/transfer.py
index 567ada5b..31ed5cc3 100644
--- a/src/dvc_data/hashfile/transfer.py
+++ b/src/dvc_data/hashfile/transfer.py
@@ -39,7 +39,6 @@ class TransferResult(NamedTuple):
 def _log_exception(oid: str, exc: BaseException):
     # NOTE: this means we ran out of file descriptors and there is no
     # reason to try to proceed, as we will hit this error anyways.
-    # pylint: disable=no-member
     if isinstance(exc, OSError) and exc.errno == errno.EMFILE:
         raise exc
     logger.error("failed to transfer '%s'", oid, exc_info=exc)
@@ -113,11 +112,10 @@ def _do_transfer(
                 "directory '%s' contains missing files, skipping .dir file upload",
                 dir_hash,
             )
+        elif _add(src, dest, [dir_obj.hash_info], **kwargs):
+            failed_ids.add(dir_obj.hash_info)
         else:
-            if _add(src, dest, [dir_obj.hash_info], **kwargs):
-                failed_ids.add(dir_obj.hash_info)
-            else:
-                succeeded_dir_objs.append(dir_obj)
+            succeeded_dir_objs.append(dir_obj)
 
     # insert the rest
     failed_ids.update(_add(src, dest, all_file_ids, **kwargs))
@@ -135,7 +133,8 @@ def _do_transfer(
                 dir_obj.hash_info,
                 len(file_hashes),
             )
-            assert dir_obj.hash_info and dir_obj.hash_info.value
+            assert dir_obj.hash_info
+            assert dir_obj.hash_info.value
             dest_index.update([dir_obj.hash_info.value], file_hashes)
 
     return set()
@@ -173,7 +172,7 @@ def _error(oid: str, exc: BaseException):
     return failed
 
 
-def transfer(
+def transfer(  # noqa: PLR0913
     src: "HashFileDB",
     dest: "HashFileDB",
     obj_ids: Iterable["HashInfo"],
diff --git a/src/dvc_data/hashfile/tree.py b/src/dvc_data/hashfile/tree.py
index e868dd3f..53ad7acc 100644
--- a/src/dvc_data/hashfile/tree.py
+++ b/src/dvc_data/hashfile/tree.py
@@ -5,17 +5,16 @@
 
 from dvc_objects.errors import ObjectFormatError
 
+from dvc_data.hashfile.hash import DEFAULT_ALGORITHM, hash_file
+from dvc_data.hashfile.meta import Meta
+from dvc_data.hashfile.obj import HashFile
 from dvc_data.utils import cached_property
 
-from ..hashfile.hash import DEFAULT_ALGORITHM, hash_file
-from ..hashfile.meta import Meta
-from ..hashfile.obj import HashFile
-
 if TYPE_CHECKING:
     from pygtrie import Trie
 
-    from ..hashfile.db import HashFileDB
-    from ..hashfile.hash_info import HashInfo
+    from dvc_data.hashfile.db import HashFileDB
+    from dvc_data.hashfile.hash_info import HashInfo
 
 logger = logging.getLogger(__name__)
 
@@ -47,7 +46,7 @@ def _try_load(
 class Tree(HashFile):
     PARAM_RELPATH: Final = "relpath"
 
-    def __init__(self):  # pylint: disable=super-init-not-called
+    def __init__(self):
         # this should really be part of a TreeBuilder.
         # HashFile does not support these properties as none values, so we may be losing
         # type-safety with this.
@@ -148,7 +147,7 @@ def _hi_to_dict(hi: Optional["HashInfo"]) -> Dict[str, Any]:
                     **_hi_to_dict(hi),
                     self.PARAM_RELPATH: posixpath.sep.join(parts),
                 }
-                for parts, meta, hi in self  # noqa: B301
+                for parts, meta, hi in self
             ),
             key=itemgetter(self.PARAM_RELPATH),
         )
@@ -163,7 +162,7 @@ def as_bytes(self, with_meta: bool = False):
 
     @classmethod
     def from_list(cls, lst, hash_name: Optional[str] = None):
-        from ..hashfile.hash_info import HashInfo
+        from dvc_data.hashfile.hash_info import HashInfo
 
         tree = cls()
         for _entry in lst:
@@ -212,7 +211,7 @@ def load(cls, odb, hash_info, hash_name: Optional[str] = None) -> "Tree":
 
         return tree
 
-    def filter(self, prefix: Tuple[str]) -> Optional["Tree"]:
+    def filter(self, prefix: Tuple[str]) -> Optional["Tree"]:  # noqa: A003
         """Return a filtered copy of this tree that only contains entries
         inside prefix.
 
@@ -316,7 +315,7 @@ def _merge(ancestor, our, their, allowed=None):
         patch_theirs_first = patch(their_diff + our_diff, ancestor)
     except KeyError as e:
         # todo: fails if both diffs delete the same object
-        raise MergeError(
+        raise MergeError(  # noqa: B904
             f"unable to auto-merge the following paths:\nboth deleted: {e}"
         )
     unmergeable = list(diff(patch_ours_first, patch_theirs_first))
diff --git a/src/dvc_data/hashfile/utils.py b/src/dvc_data/hashfile/utils.py
index a2974c10..670c46cf 100644
--- a/src/dvc_data/hashfile/utils.py
+++ b/src/dvc_data/hashfile/utils.py
@@ -41,7 +41,7 @@ def get_mtime_and_size(
 
     # We track file changes and moves, which cannot be detected with simply
     # max(mtime(f) for f in non_ignored_files)
-    hasher = hashlib.md5()  # nosec B303, B324
+    hasher = hashlib.md5()  # noqa: S324
     hasher.update(json.dumps(files_mtimes, sort_keys=True).encode("utf-8"))
     mtime = hasher.hexdigest()
     return mtime, size
diff --git a/src/dvc_data/index/__init__.py b/src/dvc_data/index/__init__.py
index 0799c099..d7279671 100644
--- a/src/dvc_data/index/__init__.py
+++ b/src/dvc_data/index/__init__.py
@@ -1,13 +1,13 @@
-from .add import add  # noqa: F401, pylint: disable=unused-import
-from .build import build  # noqa: F401, pylint: disable=unused-import
-from .diff import diff  # noqa: F401, pylint: disable=unused-import
-from .index import *  # noqa: F401,F403, pylint: disable=unused-import
-from .save import md5, save  # noqa: F401, pylint: disable=unused-import
-from .serialize import (  # noqa: F401, pylint: disable=unused-import
-    read_db,
-    read_json,
-    write_db,
-    write_json,
+from .add import add  # noqa: F401
+from .build import build  # noqa: F401
+from .diff import diff  # noqa: F401
+from .index import *  # noqa: F403
+from .save import md5, save  # noqa: F401
+from .serialize import (
+    read_db,  # noqa: F401
+    read_json,  # noqa: F401
+    write_db,  # noqa: F401
+    write_json,  # noqa: F401
 )
-from .update import update  # noqa: F401, pylint: disable=unused-import
-from .view import DataIndexView, view  # noqa: F401, pylint: disable=unused-import
+from .update import update  # noqa: F401
+from .view import DataIndexView, view  # noqa: F401
diff --git a/src/dvc_data/index/add.py b/src/dvc_data/index/add.py
index 4065a681..82b295b2 100644
--- a/src/dvc_data/index/add.py
+++ b/src/dvc_data/index/add.py
@@ -6,7 +6,8 @@
 if TYPE_CHECKING:
     from dvc_objects.fs import FileSystem
 
-    from ..hashfile._ignore import Ignore
+    from dvc_data.hashfile._ignore import Ignore
+
     from .index import DataIndex, DataIndexKey
 
 
diff --git a/src/dvc_data/index/build.py b/src/dvc_data/index/build.py
index e9e16064..1e46cb8a 100644
--- a/src/dvc_data/index/build.py
+++ b/src/dvc_data/index/build.py
@@ -1,17 +1,17 @@
 from itertools import chain
 from typing import TYPE_CHECKING, Any, Dict, Iterable, Optional, Tuple
 
-from ..hashfile.hash import DEFAULT_ALGORITHM, hash_file
-from ..hashfile.meta import Meta
+from dvc_data.hashfile.hash import DEFAULT_ALGORITHM, hash_file
+from dvc_data.hashfile.meta import Meta
+
 from .index import DataIndex, DataIndexEntry, FileStorage
 
 if TYPE_CHECKING:
     from dvc_objects.fs.base import FileSystem
 
+    from dvc_data.hashfile._ignore import Ignore
     from dvc_data.hashfile.state import StateBase
 
-    from ..hashfile._ignore import Ignore
-
 
 def build_entry(
     path: str,
diff --git a/src/dvc_data/index/checkout.py b/src/dvc_data/index/checkout.py
index 33e4fc64..c3da00d2 100644
--- a/src/dvc_data/index/checkout.py
+++ b/src/dvc_data/index/checkout.py
@@ -20,7 +20,8 @@
 from dvc_objects.fs.local import LocalFileSystem
 from dvc_objects.fs.utils import exists as batch_exists
 
-from ..hashfile.meta import Meta
+from dvc_data.hashfile.meta import Meta
+
 from .diff import ADD, DELETE, MODIFY, UNCHANGED
 from .diff import diff as idiff
 from .index import FileStorage, ObjectStorage
@@ -28,14 +29,15 @@
 if TYPE_CHECKING:
     from dvc_objects.fs.base import AnyFSPath, FileSystem
 
-    from ..hashfile.state import StateBase
+    from dvc_data.hashfile.state import StateBase
+
     from .diff import Change
     from .index import BaseDataIndex, DataIndexEntry, DataIndexKey, Storage
 
 logger = logging.getLogger(__name__)
 
 
-class VersioningNotSupported(Exception):
+class VersioningNotSupported(Exception):  # noqa: N818
     pass
 
 
@@ -67,7 +69,7 @@ def _delete_files(
     fs.remove([fs.path.join(path, *(entry.key or ())) for entry in entries])
 
 
-def _create_files(  # noqa: C901
+def _create_files(  # noqa: C901, PLR0912, PLR0913
     entries,
     index: Optional["BaseDataIndex"],
     path: str,
@@ -204,7 +206,7 @@ class Diff:
     dirs_failed: list = field(default=Factory(list))
 
 
-def _compare(  # noqa: C901
+def _compare(  # noqa: C901, PLR0912
     old,
     new,
     relink: bool = False,
@@ -288,14 +290,14 @@ def meta_cmp_key(meta):
             else:
                 continue
         else:
-            raise AssertionError()
+            raise AssertionError
 
         ret.changes[change.key] = change
 
     return ret
 
 
-def compare(  # noqa: C901
+def compare(
     old,
     new,
     relink: bool = False,
@@ -335,7 +337,7 @@ def _onerror_noop(*args, **kwargs):
     pass
 
 
-def apply(
+def apply(  # noqa: PLR0913
     diff: "Diff",
     path: str,
     fs: "FileSystem",
diff --git a/src/dvc_data/index/collect.py b/src/dvc_data/index/collect.py
index 8fa59c8c..14e44ef4 100644
--- a/src/dvc_data/index/collect.py
+++ b/src/dvc_data/index/collect.py
@@ -71,7 +71,7 @@ def _collect_from_index(
         cache[(*cache_prefix, *key)] = entry
 
 
-def collect(  # noqa: C901
+def collect(  # noqa: C901, PLR0912
     idxs,
     storage,
     callback: "Callback" = DEFAULT_CALLBACK,
@@ -104,9 +104,8 @@ def collect(  # noqa: C901
 
             key = (fsid, tokenize(data.path))
 
-            if key not in storage_by_fs:
-                if cache_index.has_node((*cache_key, *key)):
-                    skip.add(key)
+            if key not in storage_by_fs and cache_index.has_node((*cache_key, *key)):
+                skip.add(key)
 
             if key not in skip:
                 _collect_from_index(
diff --git a/src/dvc_data/index/diff.py b/src/dvc_data/index/diff.py
index 411f69cb..ff98ab4c 100644
--- a/src/dvc_data/index/diff.py
+++ b/src/dvc_data/index/diff.py
@@ -5,8 +5,9 @@
 from dvc_objects.fs.callbacks import DEFAULT_CALLBACK, Callback
 
 if TYPE_CHECKING:
-    from dvc_data.hashfile.meta import Meta
     from dvc_data.hashfile.hash_info import HashInfo
+    from dvc_data.hashfile.meta import Meta
+
     from .index import BaseDataIndex, DataIndexKey
 
 from .index import DataIndexDirError, DataIndexEntry
@@ -82,7 +83,7 @@ def _diff_hash_info(
     return UNCHANGED
 
 
-def _diff_entry(
+def _diff_entry(  # noqa: PLR0911
     old: Optional["DataIndexEntry"],
     new: Optional["DataIndexEntry"],
     *,
@@ -156,7 +157,7 @@ def _get_items(
     return items, unknown
 
 
-def _diff(
+def _diff(  # noqa: C901, PLR0912
     old: Optional["BaseDataIndex"],
     new: Optional["BaseDataIndex"],
     *,
@@ -284,7 +285,7 @@ def _get_key(change):
     yield from deleted
 
 
-def diff(
+def diff(  # noqa: PLR0913
     old: Optional["BaseDataIndex"],
     new: Optional["BaseDataIndex"],
     *,
diff --git a/src/dvc_data/index/fetch.py b/src/dvc_data/index/fetch.py
index 4e8c61c6..bffb65a2 100644
--- a/src/dvc_data/index/fetch.py
+++ b/src/dvc_data/index/fetch.py
@@ -8,7 +8,7 @@
 
 from .build import build
 from .checkout import apply, compare
-from .collect import collect  # noqa: F401, pylint: disable=unused-import
+from .collect import collect  # noqa: F401
 from .index import ObjectStorage
 from .save import md5, save
 
@@ -52,9 +52,11 @@ def fetch(
         try:
             # NOTE: make sure there are no auth errors
             data.fs.exists(data.path)
-        except Exception:  # pylint: disable=W0703
+        except Exception:
             failed += len(fs_index)
-            logger.exception(f"failed to connect to {data.fs.protocol} ({data.path})")
+            logger.exception(
+                "failed to connect to %s (%s)", data.fs.protocol, data.path
+            )
             continue
 
         with cb:
diff --git a/src/dvc_data/index/index.py b/src/dvc_data/index/index.py
index c4ae9ab4..d17ade31 100644
--- a/src/dvc_data/index/index.py
+++ b/src/dvc_data/index/index.py
@@ -15,19 +15,22 @@
 )
 
 import attrs
-from sqltrie import ShortKeyError  # noqa: F401, pylint: disable=unused-import
-from sqltrie import JSONTrie, PyGTrie, SQLiteTrie
+from sqltrie import (
+    JSONTrie,
+    PyGTrie,
+    ShortKeyError,
+    SQLiteTrie,
+)
 
+from dvc_data.hashfile.hash_info import HashInfo
+from dvc_data.hashfile.meta import Meta
+from dvc_data.hashfile.tree import Tree
 from dvc_data.utils import cached_property
 
-from ..hashfile.hash_info import HashInfo
-from ..hashfile.meta import Meta
-from ..hashfile.tree import Tree
-
 if TYPE_CHECKING:
     from dvc_objects.fs.base import FileSystem
 
-    from ..hashfile.db import HashFileDB
+    from dvc_data.hashfile.db import HashFileDB
 
 
 logger = logging.getLogger(__name__)
@@ -97,7 +100,7 @@ def _trie(self):
         return SQLiteTrie()
 
     @classmethod
-    def open(cls, path):
+    def open(cls, path):  # noqa: A003
         ret = cls()
         ret._trie = SQLiteTrie.open(path)
         return ret
@@ -186,9 +189,7 @@ def get_key(self, entry: "DataIndexEntry") -> "DataIndexKey":
         if not entry.hash_info or not entry.hash_info.value:
             raise ValueError
 
-        return self.odb._oid_parts(  # pylint: disable=protected-access
-            entry.hash_info.value
-        )
+        return self.odb._oid_parts(entry.hash_info.value)
 
     def get(self, entry: "DataIndexEntry") -> Tuple["FileSystem", str]:
         if not entry.hash_info:
@@ -205,7 +206,7 @@ def exists(self, entry: "DataIndexEntry", refresh: bool = False) -> bool:
         if self.index is None:
             return self.odb.exists(value)
 
-        key = self.odb._oid_parts(value)  # pylint: disable=protected-access
+        key = self.odb._oid_parts(value)
         if not refresh:
             return key in self.index
 
@@ -583,7 +584,7 @@ def _load_from_storage(trie, entry, storage_info):
             else:
                 _load_from_file_storage(trie, entry, storage)
             return True
-        except Exception as exc:  # pylint: disable=W0703
+        except Exception as exc:  # noqa: BLE001
             # NOTE: this might be some random fs exception, e.g. auth error
             last_exc = exc
             logger.debug(
@@ -613,7 +614,7 @@ def _onerror(_, exc):
         self.update(*args, **kwargs)
 
     @classmethod
-    def open(cls, path):
+    def open(cls, path):  # noqa: A003
         ret = cls()
         ret._trie = DataIndexTrie.open(path)
         return ret
@@ -622,7 +623,7 @@ def view(self, key):
         import copy
 
         ret = DataIndex()
-        ret._trie = self._trie.view(key)  # pylint: disable=protected-access
+        ret._trie = self._trie.view(key)
         ret.storage_map = copy.deepcopy(self.storage_map)
         return ret
 
diff --git a/src/dvc_data/index/save.py b/src/dvc_data/index/save.py
index 416f9339..26706d24 100644
--- a/src/dvc_data/index/save.py
+++ b/src/dvc_data/index/save.py
@@ -4,16 +4,17 @@
 
 from dvc_objects.fs.callbacks import DEFAULT_CALLBACK
 
-from ..hashfile.hash import DEFAULT_ALGORITHM, hash_file
-from ..hashfile.meta import Meta
-from ..hashfile.tree import Tree
+from dvc_data.hashfile.hash import DEFAULT_ALGORITHM, hash_file
+from dvc_data.hashfile.meta import Meta
+from dvc_data.hashfile.tree import Tree
 
 if TYPE_CHECKING:
     from dvc_objects.fs.base import FileSystem
     from dvc_objects.fs.callbacks import Callback
 
-    from ..hashfile.db import HashFileDB
-    from ..hashfile.state import StateBase
+    from dvc_data.hashfile.db import HashFileDB
+    from dvc_data.hashfile.state import StateBase
+
     from .index import BaseDataIndex, DataIndexKey
 
 
@@ -65,7 +66,8 @@ def build_tree(
     name: str = DEFAULT_ALGORITHM,
 ) -> Tuple["Meta", Tree]:
     tree_meta = Meta(size=0, nfiles=0, isdir=True)
-    assert tree_meta.size is not None and tree_meta.nfiles is not None
+    assert tree_meta.size is not None
+    assert tree_meta.nfiles is not None
     tree = Tree()
     for key, entry in index.iteritems(prefix=prefix):
         if key == prefix or entry.meta and entry.meta.isdir:
@@ -83,7 +85,8 @@ def _save_dir_entry(
     key: "DataIndexKey",
     odb: Optional["HashFileDB"] = None,
 ) -> None:
-    from ..hashfile.db import add_update_tree
+    from dvc_data.hashfile.db import add_update_tree
+
     from .index import StorageKeyError
 
     entry = index[key]
@@ -98,7 +101,8 @@ def _save_dir_entry(
     tree = add_update_tree(cache, tree)
     entry.meta = meta
     entry.hash_info = tree.hash_info
-    assert tree.hash_info.name and tree.hash_info.value
+    assert tree.hash_info.name
+    assert tree.hash_info.value
     setattr(entry.meta, tree.hash_info.name, tree.hash_info.value)
 
 
diff --git a/src/dvc_data/index/serialize.py b/src/dvc_data/index/serialize.py
index e6b361ce..5cb0267b 100644
--- a/src/dvc_data/index/serialize.py
+++ b/src/dvc_data/index/serialize.py
@@ -1,6 +1,7 @@
 import json
 
-from ..hashfile.cache import Cache
+from dvc_data.hashfile.cache import Cache
+
 from .index import DataIndex, DataIndexEntry
 
 
diff --git a/src/dvc_data/index/view.py b/src/dvc_data/index/view.py
index e171031c..7c870f41 100644
--- a/src/dvc_data/index/view.py
+++ b/src/dvc_data/index/view.py
@@ -102,7 +102,7 @@ def _load_dir_keys(
             and entry.hash_info.isdir
             and not entry.loaded
         ):
-            self._index._load(prefix, entry)  # pylint: disable=protected-access
+            self._index._load(prefix, entry)
             if not shallow:
                 yield from (
                     (key, val)
@@ -126,7 +126,7 @@ def _node_factory(path_conv, key, children, *args):
         return self._index.traverse(_node_factory, **kwargs)
 
     def ls(self, root_key: DataIndexKey, detail=True):
-        self._index._ensure_loaded(root_key)  # pylint: disable=protected-access
+        self._index._ensure_loaded(root_key)
 
         def _filter_fn(entry):
             key = entry[0] if detail else entry
diff --git a/src/dvc_data/repo.py b/src/dvc_data/repo.py
index 407dada5..a4097988 100644
--- a/src/dvc_data/repo.py
+++ b/src/dvc_data/repo.py
@@ -7,7 +7,7 @@
 from .index import DataIndex
 
 
-class NotARepo(Exception):
+class NotARepoError(Exception):
     pass
 
 
@@ -18,7 +18,7 @@ def __init__(self, root: str = "", fs: Optional[FileSystem] = None) -> None:
         control_dir: str = os.getenv("DVC_DIR") or fs.path.join(root, ".dvc")
 
         if not fs.isdir(control_dir):
-            raise NotARepo(f"{root} is not a data repo.")
+            raise NotARepoError(f"{root} is not a data repo.")
 
         self.fs = fs or localfs
         self.root = root
@@ -40,9 +40,9 @@ def discover(
         while remaining:
             try:
                 return cls(path, fs)
-            except NotARepo:
+            except NotARepoError:
                 path, remaining = fs.path.split(path)
-        raise NotARepo(f"No data repository was found at {start}")
+        raise NotARepoError(f"No data repository was found at {start}")
 
     @property
     def control_dir(self):
diff --git a/src/dvc_data/utils.py b/src/dvc_data/utils.py
index bfe703c9..6ef6405d 100644
--- a/src/dvc_data/utils.py
+++ b/src/dvc_data/utils.py
@@ -1,7 +1,7 @@
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
-    from functools import cached_property
+    from functools import cached_property  # noqa: TID251
 else:
     from funcy import cached_property  # noqa: TID251
 
diff --git a/tests/benchmarks/test_checkout.py b/tests/benchmarks/test_checkout.py
index 438c724d..0dee511c 100644
--- a/tests/benchmarks/test_checkout.py
+++ b/tests/benchmarks/test_checkout.py
@@ -1,11 +1,11 @@
 import shutil
 from os import fspath
+from pathlib import Path
+from tempfile import TemporaryDirectory
 
 import pytest
 from dvc_objects.fs import localfs
 from dvc_objects.fs.generic import test_links as _test_links
-from pathlib import Path
-from tempfile import TemporaryDirectory
 
 from dvc_data.cli import build, gentree, get_odb
 from dvc_data.hashfile.checkout import checkout
diff --git a/tests/hashfile/test_cache.py b/tests/hashfile/test_cache.py
index d3082d2a..1064fdf8 100644
--- a/tests/hashfile/test_cache.py
+++ b/tests/hashfile/test_cache.py
@@ -44,6 +44,6 @@ def test_pickle_backwards_compat(tmp_path, proto_a, proto_b):
         directory=fspath(tmp_path / "test"),
         disk_pickle_protocol=proto_b,
     ) as cache:
-        assert ("value1", "value2") == cache["key"]
+        assert cache["key"] == ("value1", "value2")
         set_value(cache, "key", ("value3", "value4"))
-        assert ("value3", "value4") == cache["key"]
+        assert cache["key"] == ("value3", "value4")
diff --git a/tests/hashfile/test_db_index.py b/tests/hashfile/test_db_index.py
index f7cb38ae..00e0f016 100644
--- a/tests/hashfile/test_db_index.py
+++ b/tests/hashfile/test_db_index.py
@@ -6,8 +6,7 @@
 
 @pytest.fixture
 def index(tmp_upath):
-    index_ = ObjectDBIndex(tmp_upath, "foo")
-    yield index_
+    return ObjectDBIndex(tmp_upath, "foo")
 
 
 def test_roundtrip(tmp_upath, index):
diff --git a/tests/hashfile/test_diff.py b/tests/hashfile/test_diff.py
index be7a9f29..00550597 100644
--- a/tests/hashfile/test_diff.py
+++ b/tests/hashfile/test_diff.py
@@ -14,7 +14,7 @@ def tree():
         ]
     )
     tree.digest()
-    yield tree
+    return tree
 
 
 @pytest.fixture
diff --git a/tests/hashfile/test_tree.py b/tests/hashfile/test_tree.py
index f5cff11e..0f97ac40 100644
--- a/tests/hashfile/test_tree.py
+++ b/tests/hashfile/test_tree.py
@@ -127,7 +127,7 @@ def test_list_dos2unix(lst, trie_dict):
 )
 def test_nfiles(trie_dict, nfiles):
     tree = Tree()
-    tree._dict = trie_dict  # pylint:disable=protected-access
+    tree._dict = trie_dict
     assert len(tree) == nfiles
 
 
@@ -150,7 +150,7 @@ def test_nfiles(trie_dict, nfiles):
 )
 def test_items(trie_dict):
     tree = Tree()
-    tree._dict = trie_dict  # pylint:disable=protected-access
+    tree._dict = trie_dict
     assert list(tree) == [(key, value[0], value[1]) for key, value in trie_dict.items()]
 
 
diff --git a/tests/index/test_index.py b/tests/index/test_index.py
index ac40639d..115c44d8 100644
--- a/tests/index/test_index.py
+++ b/tests/index/test_index.py
@@ -1,6 +1,5 @@
 import pytest
 
-import dvc_data.index.checkout as checkout
 from dvc_data.hashfile.hash_info import HashInfo
 from dvc_data.hashfile.meta import Meta
 from dvc_data.index import (
@@ -9,6 +8,7 @@
     ObjectStorage,
     add,
     build,
+    checkout,
     md5,
     read_db,
     read_json,