Apply repo-review suggestions (#559)

* Apply repo-review rule PP304

PP304: Sets the log level in pytest
log_cli_level should be set. This will allow logs to be displayed on failures.

* Apply repo-review rule PP305

PP305: Specifies xfail_strict
xfail_strict should be set. You can manually specify if a check should be strict when setting each xfail.

* Apply repo-review rules PP306, PP307, PP308

PP306: Specifies strict config
--strict-config should be in addopts = [...]. This forces an error if a config setting is misspelled.

PP307: Specifies strict markers
--strict-markers should be in addopts = [...]. This forces all markers to be specified in config, avoiding misspellings.

PP308: Specifies useful pytest summary
An explicit summary flag like -ra should be in addopts = [...] (print summary of all fails/errors).

* Apply ruff/pygrep-hooks rule PGH004

PGH004 Use specific rule codes when using `noqa`
PGH004 Use specific rule codes when using `ruff: noqa`

* Apply and enforce ruff rules (RUF)

Apply ruff rule RUF012:
RUF012 Mutable class attributes should be annotated with `typing.ClassVar`

Disable ruff rule RUF001

* Apply and enforce ruff/flake8-bugbear rules (B)

B007 Loop control variable not used within loop body

B028 No explicit `stacklevel` keyword argument found

B904 Within an `except` clause, raise exceptions with `raise ... from err` or
     `raise ... from None` to distinguish them from errors in exception handling

B905 `zip()` without an explicit `strict=` parameter

Co-authored-by: David Stansby <[email protected]>

* Apply and enforce ruff/isort rules (I)

* Apply repo-review rule PC100

PC100: Has pre-commit-hooks
Must have https://github.com/pre-commit/pre-commit-hooks repo in .pre-commit-config.yaml

* Enforce repo-review rules

* Apply ruff/flake8-implicit-str-concat rules (ISC)

ISC001 Implicitly concatenated string literals on one line

ISC003 Explicitly concatenated string should be implicitly concatenated

* Apply ruff/refurb rules (FURB)

FURB163 Prefer `math.log10`/`math.log2` over `math.log` with a redundant base

* Fix DeprecationWarning

	'pkgutil.find_loader' is deprecated and slated for removal
	in Python 3.14; use importlib.util.find_spec() instead

---------

Co-authored-by: David Stansby <[email protected]>

Author: DimitriPapadopoulos

.pre-commit-config.yaml

@@ -1,3 +1,4 @@
+exclude: ^fixture/  # files with trailing whitespaces on purpose
 ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autofix_commit_msg: "style: pre-commit fixes"
@@ -6,9 +7,21 @@ default_stages: [commit, push]
 default_language_version:
   python: python3
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    - id: trailing-whitespace
+    - id: check-yaml
+    - id: debug-statements
+
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.6.9'
+    rev: v0.6.9
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
     - id: ruff-format
+
+  - repo: https://github.com/scientific-python/cookie
+    rev: 2024.04.23
+    hooks:
+    - id: sp-repo-review

.pyup.yml

@@ -1,4 +1,4 @@
-# autogenerated pyup.io config file 
+# autogenerated pyup.io config file
 # see https://pyup.io/docs/configuration/ for all available options
 
 schedule: every month

README.rst

@@ -1,7 +1,7 @@
 Numcodecs
 =========
 
-Numcodecs is a Python package providing buffer compression and transformation 
+Numcodecs is a Python package providing buffer compression and transformation
 codecs for use in data storage and communication applications.
 
 .. image:: https://readthedocs.org/projects/numcodecs/badge/?version=latest

adhoc/blosc_memleak_check.py

@@ -1,13 +1,13 @@
 import sys
 
-import numcodecs
 import numpy as np
 from numpy.testing import assert_array_equal
 
+import numcodecs
 
 codec = numcodecs.Blosc()
 data = np.arange(int(sys.argv[1]))
-for i in range(int(sys.argv[2])):
+for _ in range(int(sys.argv[2])):
     enc = codec.encode(data)
     dec = codec.decode(enc)
     arr = np.frombuffer(dec, dtype=data.dtype)

docs/conf.py

@@ -13,9 +13,10 @@
 # serve to show the default.
 
 
-import sys
 import os
+import sys
 from unittest.mock import Mock as MagicMock
+
 import numcodecs
 
 

notebooks/benchmark_vlen.ipynb

@@ -25,6 +25,7 @@
    ],
    "source": [
     "import numpy as np\n",
+    "\n",
     "import numcodecs\n",
     "\n",
     "numcodecs.__version__"

numcodecs/__init__.py

@@ -1,4 +1,4 @@
-# flake8: noqa
+# ruff: noqa: E402,F401
 """Numcodecs is a Python package providing buffer compression and
 transformation codecs for use in data storage and communication
 applications. These include:
@@ -17,14 +17,12 @@
 
 """
 
-import multiprocessing
 import atexit
+import multiprocessing
 from contextlib import suppress
 
-
-from numcodecs.version import version as __version__
 from numcodecs.registry import get_codec, register_codec
-
+from numcodecs.version import version as __version__
 from numcodecs.zlib import Zlib
 
 register_codec(Zlib)
@@ -130,7 +128,7 @@
 
 with suppress(ImportError):
     from numcodecs import vlen
-    from numcodecs.vlen import VLenUTF8, VLenBytes, VLenArray
+    from numcodecs.vlen import VLenArray, VLenBytes, VLenUTF8
 
     register_codec(VLenUTF8)
     register_codec(VLenBytes)

numcodecs/astype.py

@@ -1,7 +1,7 @@
 import numpy as np
 
 from .abc import Codec
-from .compat import ndarray_copy, ensure_ndarray
+from .compat import ensure_ndarray, ndarray_copy
 
 
 class AsType(Codec):

numcodecs/bitround.py

@@ -1,6 +1,5 @@
 import numpy as np
 
-
 from .abc import Codec
 from .compat import ensure_ndarray_like, ndarray_copy
 

numcodecs/blosc.pyx

@@ -468,7 +468,7 @@ def decompress_partial(source, start, nitems, dest=None):
         raise RuntimeError('error during blosc partial decompression: %d', ret)
 
     return dest
-        
+
 
 # set the value of this variable to True or False to override the
 # default adaptive behaviour