[pre-commit.ci] pre-commit autoupdate

.github/workflows/check_release_tag.py

@@ -1,4 +1,5 @@
 """Check that the GitHub release tag matches the package version."""
+
 import argparse
 import pathlib
 import re

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ exclude: &exclude_files >
 repos:
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
     - id: check-json
     - id: check-yaml
@@ -24,7 +24,7 @@ repos:
     - id: flynt
 
   - repo: https://github.com/executablebooks/mdformat
-    rev: '0.7.17'
+    rev: '0.7.19'
     hooks:
     - id: mdformat
       additional_dependencies:
@@ -34,23 +34,23 @@ repos:
       files: (?x)^(README\.md|CHANGELOG\.md)$
 
   - repo: https://github.com/pycqa/isort
-    rev: '5.12.0'
+    rev: '5.13.2'
     hooks:
     - id: isort
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.14.0
+    rev: v3.19.0
     hooks:
     - id: pyupgrade
       args: [--py37-plus]
 
   - repo: https://github.com/psf/black
-    rev: '23.9.1'
+    rev: '24.10.0'
     hooks:
     - id: black
 
   - repo: https://github.com/PyCQA/pylint
-    rev: v3.0.0
+    rev: v3.3.2
     hooks:
     - id: pylint
       additional_dependencies:
@@ -64,7 +64,7 @@ repos:
       - h5py
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.13.0
     hooks:
     - id: mypy
       additional_dependencies:

CHANGELOG.md

@@ -6,25 +6,25 @@ This only enforces proper semantic versioning as the last release added a new fu
 
 ## v1.1.1 (19 September 2024)
 
-- Added progress bar functionality for repack and pack_all_loose [\[737f9c7\]](https://github.com/aiidateam/disk-objectstore/commit/737f9c71151bf7ac297c6431688b4a75eac91b7c)
+- Added progress bar functionality for repack and pack_all_loose [[737f9c7]](https://github.com/aiidateam/disk-objectstore/commit/737f9c71151bf7ac297c6431688b4a75eac91b7c)
 
 ## v1.1.0 (7 March 2024)
 
 ### Features
 
-- Add functionality to easily create a container backup [\[23c784a\]](https://github.com/aiidateam/disk-objectstore/commit/23c784a221954a1518a3e35affdec53681f809b7)
+- Add functionality to easily create a container backup [[23c784a]](https://github.com/aiidateam/disk-objectstore/commit/23c784a221954a1518a3e35affdec53681f809b7)
 
 ## v1.0.0 (September 2023)
 
 ### Features
 
-- Add support for `whence=2` in `PackedObjectReader.seek` [\[5515ab6\]](https://github.com/aiidateam/disk-objectstore/commit/5515ab6d75581b36ecb3e0b8ff37407e05abefda)
-- Add support for changing compression when repacking, and add auto compression heuristics [\[599e87c\]](https://github.com/aiidateam/disk-objectstore/commit/599e87c852427e02062f04f5f3d2276013410710)
-- Improve efficiency when accessing packed compressed objects [\[10edd63\]](https://github.com/aiidateam/disk-objectstore/commit/10edd6395455d7c59361e608396b672289d8de58)
+- Add support for `whence=2` in `PackedObjectReader.seek` [[5515ab6]](https://github.com/aiidateam/disk-objectstore/commit/5515ab6d75581b36ecb3e0b8ff37407e05abefda)
+- Add support for changing compression when repacking, and add auto compression heuristics [[599e87c]](https://github.com/aiidateam/disk-objectstore/commit/599e87c852427e02062f04f5f3d2276013410710)
+- Improve efficiency when accessing packed compressed objects [[10edd63]](https://github.com/aiidateam/disk-objectstore/commit/10edd6395455d7c59361e608396b672289d8de58)
 
 ### Changes
 
-- A number of API methods changed the return type from bare dictionaries to dataclass instances [\[7a63462\]](https://github.com/aiidateam/disk-objectstore/commit/7a634626ea3e5f35aa3cdd458daf9d8b825d759a)
+- A number of API methods changed the return type from bare dictionaries to dataclass instances [[7a63462]](https://github.com/aiidateam/disk-objectstore/commit/7a634626ea3e5f35aa3cdd458daf9d8b825d759a)
 
   - `Container.get_object_stream_and_meta -> ObjectMeta`
   - `Container.get_objects_meta -> ObjectMeta`
@@ -35,43 +35,43 @@ This only enforces proper semantic versioning as the last release added a new fu
 
   The dataclasses are importable from `disk_objectstore.dataclasses`.
 
-- A number of API methods replaced using `os.path` with `str` paths, for `pathlib.Path` [\[df96142\]](https://github.com/aiidateam/disk-objectstore/commit/df9614236b7d420fb610313d70ffae51e7aead75)
+- A number of API methods replaced using `os.path` with `str` paths, for `pathlib.Path` [[df96142]](https://github.com/aiidateam/disk-objectstore/commit/df9614236b7d420fb610313d70ffae51e7aead75)
   The following methods now return a `pathlib.Path` instance:
 
   - `Container.get_folder`
   - `LazyOpener.path`
 
-- Various improvements to docs and code [\[5ba9316\]](https://github.com/aiidateam/disk-objectstore/commit/5ba93162cd49d9b1ca7149c502349bfb06833255)
+- Various improvements to docs and code [[5ba9316]](https://github.com/aiidateam/disk-objectstore/commit/5ba93162cd49d9b1ca7149c502349bfb06833255)
 
 ### Devops
 
-- Moving documentation to `sphinx+myst` [\[2002f3c\]](https://github.com/aiidateam/disk-objectstore/commit/2002f3c3ec07f7ff46a04df293c8c9a7dff4db6a)
-- Adopt PEP 621 and move build spec to `pyproject.toml` [\[4bd0c4e\]](https://github.com/aiidateam/disk-objectstore/commit/4bd0c4e01eaf3c149d4e11921b7ff4d42a5d5da5)
-- Make types more permissive [\[c012056\]](https://github.com/aiidateam/disk-objectstore/commit/c0120568a992b41a55b325f3217d4902b5281070)
+- Moving documentation to `sphinx+myst` [[2002f3c]](https://github.com/aiidateam/disk-objectstore/commit/2002f3c3ec07f7ff46a04df293c8c9a7dff4db6a)
+- Adopt PEP 621 and move build spec to `pyproject.toml` [[4bd0c4e]](https://github.com/aiidateam/disk-objectstore/commit/4bd0c4e01eaf3c149d4e11921b7ff4d42a5d5da5)
+- Make types more permissive [[c012056]](https://github.com/aiidateam/disk-objectstore/commit/c0120568a992b41a55b325f3217d4902b5281070)
 
 ### Dependencies
 
-- Add Python 3.11 support [\[afdae26\]](https://github.com/aiidateam/disk-objectstore/commit/afdae261a5849e994b5920ca07665fc6a19f3852)
-- Unpin `sqlalchemy` adding support for `>=1.4.22` [\[a2a987f\]](https://github.com/aiidateam/disk-objectstore/commit/a2a987f02a128b7cc265982e102d210e6e17d6f6)
-- Removed uneeded `ablog` dependencies [\[8165f58\]](https://github.com/aiidateam/disk-objectstore/commit/8165f58fefdd40b55555eef9a2d40ee280593232)
+- Add Python 3.11 support [[afdae26]](https://github.com/aiidateam/disk-objectstore/commit/afdae261a5849e994b5920ca07665fc6a19f3852)
+- Unpin `sqlalchemy` adding support for `>=1.4.22` [[a2a987f]](https://github.com/aiidateam/disk-objectstore/commit/a2a987f02a128b7cc265982e102d210e6e17d6f6)
+- Removed uneeded `ablog` dependencies [[8165f58]](https://github.com/aiidateam/disk-objectstore/commit/8165f58fefdd40b55555eef9a2d40ee280593232)
 
 ## v0.6.0 (September 2021)
 
 - ⬆️ UPGRADE: Remove Python support for 3.5 and 3.6, and add support for 3.9.
-- ⬆️ UPGRADE: SQLAlchemy v1.4 (with v2 API) [\[#114\]](https://github.com/aiidateam/disk-objectstore/pull/114)
-- ✨ NEW: Add basic CLI [\[#117\]](https://github.com/aiidateam/disk-objectstore/pull/117) (see README.md for details)
-- 🔧 MAINTAIN: Add type annotations and mypy type checking [\[#113\]](https://github.com/aiidateam/disk-objectstore/pull/113)
+- ⬆️ UPGRADE: SQLAlchemy v1.4 (with v2 API) [[#114]](https://github.com/aiidateam/disk-objectstore/pull/114)
+- ✨ NEW: Add basic CLI [[#117]](https://github.com/aiidateam/disk-objectstore/pull/117) (see README.md for details)
+- 🔧 MAINTAIN: Add type annotations and mypy type checking [[#113]](https://github.com/aiidateam/disk-objectstore/pull/113)
 
 ## v0.5.0 (November 2020)
 
-- Various general (but very important) speed improvements [\[#96\]](https://github.com/aiidateam/disk-objectstore/pull/96) [\[#102\]](https://github.com/aiidateam/disk-objectstore/pull/102)
-- Add callbacks to a number of functions (e.g. export, add_objects_to_pack, ... to allow showing progress bars or similar indicators [\[#96\]](https://github.com/aiidateam/disk-objectstore/pull/96)
-- Implement repacking (at least when not changing hashing or compression) [\[#96\]](https://github.com/aiidateam/disk-objectstore/pull/96)
-- Remove `export` function, implement `import_objects` function instead, to be called on the other side (it's more efficient) [\[#96\]](https://github.com/aiidateam/disk-objectstore/pull/96)
-- Add support for VACUUMing operations on the SQLite database (very important for efficiency) [\[#96\]](https://github.com/aiidateam/disk-objectstore/pull/96)
-- Add support for multiple hashing algorithms [\[#96\]](https://github.com/aiidateam/disk-objectstore/pull/96)
-- Add concept of (unique) `container_id` [\[#97\]](https://github.com/aiidateam/disk-objectstore/pull/97)
-- Generalize the compression algorithm implementation, and multiple algorithms are supported now [\[#99\]](https://github.com/aiidateam/disk-objectstore/pull/99)
+- Various general (but very important) speed improvements [[#96]](https://github.com/aiidateam/disk-objectstore/pull/96) [[#102]](https://github.com/aiidateam/disk-objectstore/pull/102)
+- Add callbacks to a number of functions (e.g. export, add_objects_to_pack, ... to allow showing progress bars or similar indicators [[#96]](https://github.com/aiidateam/disk-objectstore/pull/96)
+- Implement repacking (at least when not changing hashing or compression) [[#96]](https://github.com/aiidateam/disk-objectstore/pull/96)
+- Remove `export` function, implement `import_objects` function instead, to be called on the other side (it's more efficient) [[#96]](https://github.com/aiidateam/disk-objectstore/pull/96)
+- Add support for VACUUMing operations on the SQLite database (very important for efficiency) [[#96]](https://github.com/aiidateam/disk-objectstore/pull/96)
+- Add support for multiple hashing algorithms [[#96]](https://github.com/aiidateam/disk-objectstore/pull/96)
+- Add concept of (unique) `container_id` [[#97]](https://github.com/aiidateam/disk-objectstore/pull/97)
+- Generalize the compression algorithm implementation, and multiple algorithms are supported now [[#99]](https://github.com/aiidateam/disk-objectstore/pull/99)
 
 ## v0.4.0 (20 July 2020)
 

disk_objectstore/container.py

@@ -183,14 +183,12 @@ def _get_config_file(self) -> Path:
     @overload
     def _get_session(
         self, create: bool = False, raise_if_missing: Literal[True] = True
-    ) -> Session:
-        ...
+    ) -> Session: ...
 
     @overload
     def _get_session(
         self, create: bool = False, raise_if_missing: Literal[False] = False
-    ) -> Session | None:
-        ...
+    ) -> Session | None: ...
 
     def _get_session(
         self, create: bool = False, raise_if_missing: bool = False
@@ -528,17 +526,15 @@ def _get_objects_stream_meta_generator(
         hashkeys: Sequence[str],
         skip_if_missing: bool,
         with_streams: Literal[False],
-    ) -> Iterator[tuple[str, ObjectMeta]]:
-        ...
+    ) -> Iterator[tuple[str, ObjectMeta]]: ...
 
     @overload
     def _get_objects_stream_meta_generator(
         self,
         hashkeys: Sequence[str],
         skip_if_missing: bool,
         with_streams: Literal[True],
-    ) -> Iterator[tuple[str, StreamSeekBytesType | None, ObjectMeta]]:
-        ...
+    ) -> Iterator[tuple[str, StreamSeekBytesType | None, ObjectMeta]]: ...
 
     def _get_objects_stream_meta_generator(  # pylint: disable=too-many-branches,too-many-statements,too-many-locals
         self,
@@ -1323,8 +1319,9 @@ def pack_all_loose(  # pylint: disable=too-many-locals,too-many-branches,too-man
         compress: bool | CompressMode = CompressMode.NO,
         validate_objects: bool = True,
         do_fsync: bool = True,
-        callback: None
-        | (Callable[[Arg(str, "action"), Arg(Any, "value")], None]) = None,
+        callback: None | (
+            Callable[[Arg(str, "action"), Arg(Any, "value")], None]
+        ) = None,
     ) -> None:
         """Pack all loose objects.
 
@@ -2616,8 +2613,9 @@ def delete_objects(self, hashkeys: list[str]) -> list[str | Any]:
     def repack(
         self,
         compress_mode: CompressMode = CompressMode.KEEP,
-        callback: None
-        | (Callable[[Arg(str, "action"), Arg(Any, "value")], None]) = None,
+        callback: None | (
+            Callable[[Arg(str, "action"), Arg(Any, "value")], None]
+        ) = None,
     ) -> None:
         """Perform a repack of all packed objects.
 
@@ -2645,8 +2643,9 @@ def repack_pack(  # pylint: disable=too-many-branches,too-many-statements,too-ma
         self,
         pack_id: str,
         compress_mode: CompressMode = CompressMode.KEEP,
-        callback: None
-        | (Callable[[Arg(str, "action"), Arg(Any, "value")], None]) = None,
+        callback: None | (
+            Callable[[Arg(str, "action"), Arg(Any, "value")], None]
+        ) = None,
     ) -> None:
         """Perform a repack of a given pack object.
 
@@ -2723,9 +2722,9 @@ def repack_pack(  # pylint: disable=too-many-branches,too-many-statements,too-ma
                     source_compressed,
                 ) in session.execute(stmt):
                     # This is the read handle of the bytes in the pack - it might be
-                    read_handle: (
-                        PackedObjectReader | ZlibStreamDecompresser
-                    ) = PackedObjectReader(read_pack, offset, length)
+                    read_handle: PackedObjectReader | ZlibStreamDecompresser = (
+                        PackedObjectReader(read_pack, offset, length)
+                    )
 
                     # Determine if I should compress or not the destination - this function will
                     # try to do it in a cheap way (e.g. if the source is already compressed, will just

disk_objectstore/database.py

@@ -1,4 +1,5 @@
 """Models for the container index file (SQLite DB)."""
+
 from pathlib import Path
 from typing import Optional
 

disk_objectstore/dataclasses.py

@@ -2,6 +2,7 @@
 Definition of the dataclasses used as return values of
 a number of methods.
 """
+
 from dataclasses import asdict, dataclass
 from typing import TYPE_CHECKING, List, Optional, Union
 

disk_objectstore/utils.py

@@ -3,6 +3,7 @@
 Some might be useful also for end users, like the wrappers to get streams,
 like the ``LazyOpener``.
 """
+
 #  pylint: disable= too-many-lines
 from __future__ import annotations
 
@@ -809,9 +810,9 @@ def __init__(
         self._decompressor = self.decompressobj_class()
         self._internal_buffer = b""
         self._pos = 0
-        self._lazy_uncompressed_stream: None | (
-            LazyLooseStream
-        ) = lazy_uncompressed_stream
+        self._lazy_uncompressed_stream: None | (LazyLooseStream) = (
+            lazy_uncompressed_stream
+        )
         # If True, this class just proxies request to the underlying
         # uncompressed stream
         self._use_uncompressed_stream: bool = False
@@ -1326,11 +1327,9 @@ def safe_flush_to_disk(
     fhandle.flush()
 
     # Default fsync function, replaced on Mac OS X
-    _fsync_function: Callable[
-        [Any], Any
-    ] = lambda fileno: os.fsync(  # pylint: disable=unnecessary-lambda
+    _fsync_function: Callable[[Any], Any] = lambda fileno: os.fsync(
         fileno
-    )
+    )  # pylint: disable=unnecessary-lambda
 
     # Flush to disk
     if hasattr(fcntl, "F_FULLFSYNC") is not None and (

tests/conftest.py

@@ -1,4 +1,5 @@
 """Configuration file for pytest tests."""
+
 import hashlib
 import os
 import random

tests/test_basic.py

@@ -2,6 +2,7 @@
 
 This is also a way to verify the behavior of the underlying OS/filesystem.
 """
+
 import os
 import subprocess
 import sys

tests/test_benchmark.py

@@ -1,4 +1,5 @@
 """Test the performance of the container implementation."""
+
 import hashlib
 import random
 

tests/test_cli.py

@@ -1,4 +1,5 @@
 """Test the CLI commands"""
+
 import platform
 from pathlib import Path
 

tests/test_concurrency.py

@@ -1,4 +1,5 @@
 """Test of the object-store container module."""
+
 import os
 import subprocess
 import sys

tests/test_container.py

@@ -1,4 +1,5 @@
 """Test of the object-store container module."""
+
 # pylint: disable=too-many-lines,protected-access
 import dataclasses
 import functools

tests/test_examples.py

@@ -1,4 +1,5 @@
 """Test of the object-store container module."""
+
 import subprocess
 import sys
 import tempfile

tests/test_optional.py

@@ -1,5 +1,6 @@
 """Additional optional tests to check additional functionality, such as
 if the library works also with other external optional modules."""
+
 from pathlib import Path
 
 import numpy as np

tests/test_utils.py

@@ -1,4 +1,5 @@
 """Test of the utils wrappers."""
+
 # pylint: disable=too-many-lines,protected-access
 import functools
 import hashlib