aiidateam · pre-commit-ci · Dec 1, 2025 · Dec 1, 2025
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,20 +11,20 @@ exclude: &exclude_files >
 repos:
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
     - id: check-json
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
 
   - repo: https://github.com/ikamensh/flynt/
-    rev: '1.0.1'
+    rev: '1.0.6'
     hooks:
     - id: flynt
 
   - repo: https://github.com/executablebooks/mdformat
-    rev: '0.7.17'
+    rev: '1.0.0'
     hooks:
     - id: mdformat
       additional_dependencies:
@@ -34,20 +34,20 @@ repos:
       files: (?x)^(README\.md|CHANGELOG\.md)$
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.14.0
+    rev: v3.21.2
     hooks:
     - id: pyupgrade
       args: [--py37-plus]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.14.7
     hooks:
     - id: ruff-format
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix, --show-fixes]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.19.0
     hooks:
     - id: mypy
       additional_dependencies:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,41 +2,41 @@
 
 ## v1.4.0 (6 October 2025)
 
-- Add `readable`, `writable`, and `closed` properties to stream classes for TextIOWrapper compatibility  [\[1c73d64\]](https://github.com/aiidateam/disk-objectstore/commit/1c73d64137e1b093918337609cb6c8a6dece4a7b)
+- Add `readable`, `writable`, and `closed` properties to stream classes for TextIOWrapper compatibility [[1c73d64]](https://github.com/aiidateam/disk-objectstore/commit/1c73d64137e1b093918337609cb6c8a6dece4a7b)
 
 ## v1.3.0 (17 April 2025)
 
-- Change API of `database.get_session` to always raise an error [\[6686ad0\]](https://github.com/aiidateam/disk-objectstore/commit/6686ad0c3280bf90e1954b3b8052ec999e8532be)
+- Change API of `database.get_session` to always raise an error [[6686ad0]](https://github.com/aiidateam/disk-objectstore/commit/6686ad0c3280bf90e1954b3b8052ec999e8532be)
 
-- Add support for Python 3.13 [\[9b02a50\]](https://github.com/aiidateam/disk-objectstore/commit/9b02a50360749db1ea28ebe20661bf074d6c63a0)
+- Add support for Python 3.13 [[9b02a50]](https://github.com/aiidateam/disk-objectstore/commit/9b02a50360749db1ea28ebe20661bf074d6c63a0)
 
-- Properly close SQL connections that led to open file descriptors in Python3.13 [\[6686ad0\]](https://github.com/aiidateam/disk-objectstore/commit/6686ad0c3280bf90e1954b3b8052ec999e8532be) and [\[f5eed0f\]](https://github.com/aiidateam/disk-objectstore/commit/f5eed0f1afd1576f17e5d71d31df9717041fc9f3)
+- Properly close SQL connections that led to open file descriptors in Python3.13 [[6686ad0]](https://github.com/aiidateam/disk-objectstore/commit/6686ad0c3280bf90e1954b3b8052ec999e8532be) and [[f5eed0f]](https://github.com/aiidateam/disk-objectstore/commit/f5eed0f1afd1576f17e5d71d31df9717041fc9f3)
 
 ## v1.2.0 (26 September 2024)
 
 This only enforces proper semantic versioning as the last release added a new functionality. No changes have been added.
 
 ## 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`
@@ -47,43 +47,43 @@ 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)
 

diff --git a/disk_objectstore/cli.py b/disk_objectstore/cli.py
@@ -167,12 +167,12 @@ def optimize(dostore: ContainerContext, non_interactive: bool, compress: bool, v
     if not non_interactive:
         click.confirm('Is this the only process accessing the container?', abort=True)
     size = sum(f.stat().st_size for f in dostore.path.glob('**/*') if f.is_file())
-    click.echo(f'Initial container size: {round(size/1000, 2)} Mb')
+    click.echo(f'Initial container size: {round(size / 1000, 2)} Mb')
     with dostore.container as container:
         container.pack_all_loose(compress=compress)
         container.clean_storage(vacuum=vacuum)
     size = sum(f.stat().st_size for f in dostore.path.glob('**/*') if f.is_file())
-    click.echo(f'Final container size: {round(size/1000, 2)} Mb')
+    click.echo(f'Final container size: {round(size / 1000, 2)} Mb')
 
 
 @main.command('backup')

diff --git a/disk_objectstore/container.py b/disk_objectstore/container.py
@@ -1548,9 +1548,9 @@ def add_streamed_objects_to_pack(  # pylint: disable=too-many-locals, too-many-b
             operations! (See e.g. the `import_files()` method).
         :return: a list of object hash keys
         """
-        assert isinstance(
-            compress, bool
-        ), 'Only True of False are valid `compress` modes when adding direclty to a pack'
+        assert isinstance(compress, bool), (
+            'Only True of False are valid `compress` modes when adding direclty to a pack'
+        )
         yield_per_size = 1000
         hashkeys: list[str] = []
 
@@ -1875,9 +1875,9 @@ def loosen_object(self, hashkey):
             # This always rewrites it as loose
             written_hashkey = self.add_streamed_object(stream)
 
-        assert (
-            written_hashkey == hashkey
-        ), 'Mismatch in the hashkey when rewriting an existing object as loose! {written_hashkey} vs {hashkey}'
+        assert written_hashkey == hashkey, (
+            'Mismatch in the hashkey when rewriting an existing object as loose! {written_hashkey} vs {hashkey}'
+        )
         return self._get_loose_path_from_hashkey(hashkey)
 
     def _vacuum(self) -> None:
@@ -2546,14 +2546,14 @@ def repack_pack(  # pylint: disable=too-many-branches,too-many-statements,too-ma
             In case of "close", the value is None.
             return value of the callback function is ignored.
         """
-        assert (
-            pack_id != self._REPACK_PACK_ID
-        ), f"The specified pack_id '{pack_id}' is invalid, it is the one used for repacking"
+        assert pack_id != self._REPACK_PACK_ID, (
+            f"The specified pack_id '{pack_id}' is invalid, it is the one used for repacking"
+        )
 
         # Check that it does not exist
-        assert not self._get_pack_path_from_pack_id(
-            self._REPACK_PACK_ID, allow_repack_pack=True
-        ).exists(), f"The repack pack '{self._REPACK_PACK_ID}' already exists, probably a previous repacking aborted?"
+        assert not self._get_pack_path_from_pack_id(self._REPACK_PACK_ID, allow_repack_pack=True).exists(), (
+            f"The repack pack '{self._REPACK_PACK_ID}' already exists, probably a previous repacking aborted?"
+        )
 
         session = self._get_operation_session()
 

diff --git a/disk_objectstore/examples/example_objectstore.py b/disk_objectstore/examples/example_objectstore.py
@@ -71,7 +71,7 @@ def main(
     files = {}
 
     start_counts = container.count_objects()
-    print(f"Currently known objects: {start_counts['packed']} packed, {start_counts['loose']} loose")
+    print(f'Currently known objects: {start_counts["packed"]} packed, {start_counts["loose"]} loose')
     print('Pack objects on disk:', start_counts['pack_files'])
 
     print(f'Generating {num_files} files in memory...')
@@ -95,9 +95,9 @@ def main(
 
         # Check that no loose files were created
         counts = container.count_objects()
-        assert (
-            counts['loose'] == start_counts['loose']
-        ), f"Mismatch (loose in packed case): {start_counts['loose']} != {counts['loose']}"
+        assert counts['loose'] == start_counts['loose'], (
+            f'Mismatch (loose in packed case): {start_counts["loose"]} != {counts["loose"]}'
+        )
         ## Cannot do this with the hash key implenentation - I might have stored the same object twice
         # assert counts['packed'
         #             ] == start_counts['packed'] + num_files, 'Mismatch (packed in packed case): {} + {} != {}'.format(
@@ -156,7 +156,7 @@ def main(
         # Check that all loose files are gone
         counts = container.count_objects()
         loose_folder = container._get_loose_folder()  # pylint: disable=protected-access
-        assert not counts['loose'], 'loose objects left: ' f'{os.listdir(loose_folder)}'
+        assert not counts['loose'], f'loose objects left: {os.listdir(loose_folder)}'
         ## I cannot do this because I could have overlap if the object is identical and has the same hash key
         # assert counts['packed'] == start_counts['packed'] + start_counts[
         #    'loose'] + num_files, 'Mismatch (post-pack): {} + {} + {} != {}'.format(

diff --git a/disk_objectstore/examples/profile_zeros.py b/disk_objectstore/examples/profile_zeros.py
@@ -32,7 +32,7 @@ def main_run(container, size_gb, compress_packs):
     size_bytes = size_gb * 1024 * 1024 * 1024
 
     start_counts = container.count_objects()
-    print(f"Currently known objects: {start_counts['packed']} packed, {start_counts['loose']} loose")
+    print(f'Currently known objects: {start_counts["packed"]} packed, {start_counts["loose"]} loose')
     print('Pack objects on disk:', start_counts['pack_files'])
 
     zero_stream = ZeroStream(length=size_bytes)
@@ -44,12 +44,12 @@ def main_run(container, size_gb, compress_packs):
 
     # Check that no loose files were created
     counts = container.count_objects()
-    assert (
-        counts['loose'] == start_counts['loose']
-    ), f"Mismatch (loose in packed case): {start_counts['loose']} != {counts['loose']}"
-    assert (
-        counts['packed'] == start_counts['packed'] + 1
-    ), f"Mismatch (packed in packed case): {start_counts['packed']} + 1 != {counts['packed']}"
+    assert counts['loose'] == start_counts['loose'], (
+        f'Mismatch (loose in packed case): {start_counts["loose"]} != {counts["loose"]}'
+    )
+    assert counts['packed'] == start_counts['packed'] + 1, (
+        f'Mismatch (packed in packed case): {start_counts["packed"]} + 1 != {counts["packed"]}'
+    )
 
     # print container size info
     size_info = container.get_total_size()
@@ -167,9 +167,9 @@ def main(size_gb, path, clear, check_memory_measurement, with_line_profiler, com
             interval=memory_check_interval,
         )
         # Check that it's not an empty list
-        assert (
-            memory_report
-        ), f'>> Process too fast for checking memory usage with interval {memory_check_interval} s!!!'
+        assert memory_report, (
+            f'>> Process too fast for checking memory usage with interval {memory_check_interval} s!!!'
+        )
         print(
             f'>> Max memory usage (check interval {memory_check_interval} s, '
             f'{len(memory_report)} checks performed): {max(memory_report):.3f} MB'