Provide strtobool to avoid use of deprecated (removed in 3.12) distut…

…ils (#457)

* Provide strtobool to avoid use of deprecated  (removed in 3.12) distutils

* Add Python 3.12 to supported

* Update docs/developer_guide.rst

---------

Co-authored-by: Cody Baker <[email protected]>

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -40,6 +40,7 @@ body:
         - 3.9
         - "3.10"
         - "3.11"
+        - "3.12"
   - type: dropdown
     id: streaming
     attributes:

.github/workflows/streaming-tests.yml

@@ -9,7 +9,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "windows-latest"]  # TODO: update mac and streaming methods
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: s-weigand/setup-conda@v1
         with:

.github/workflows/testing.yml

@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-13", "windows-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: conda-incubator/setup-miniconda@v3
         with:

CHANGELOG.md

@@ -7,6 +7,7 @@
 ### Improvements
 
 * Exposed progress bar control to `inspect_all` and `run_checks` to allow compatibility with more generic visualizations of inspection progress related to the NWB GUIDED. [#443](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/443)
+* Added Python 3.12 support. [#457](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/457)
 
 ### Testing
 

docs/developer_guide.rst

@@ -48,7 +48,7 @@ Disable Tests That Require Network Connection
 
 Some of the tests in the suite require internet connectivity both to and from the DANDI archive S3 bucket.
 If this is failing for some reason, you can explicitly control all related tests by setting the environment variable
-``NWBI_SKIP_NETWORK_TESTS`` to some value able to be parsed by ``distutils.util.str2tool``. For example, to disable them on
+``NWBI_SKIP_NETWORK_TESTS`` to some value able to be parsed by ``nwbinspector.utils.strtobool``. For example, to disable them on
 a linux system, run
 
 .. code-block::

docs/user_guide/installation.rst

@@ -6,7 +6,7 @@ If you haven't checked it out already, please read the :nwb-overview:`NWB Overvi
 
 The NWBInspector tool offers convenient command-line usage via any standard Conda or Python terminal.
 
-To install the package in any generic Python v3.8-v3.11 environment, simply type
+To install the package in any generic Python v3.8-v3.12 environment, simply type
 
 ::
 

setup.py

@@ -42,5 +42,6 @@
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
 )

src/nwbinspector/nwbinspector.py

@@ -12,7 +12,6 @@
 from concurrent.futures import ProcessPoolExecutor, as_completed
 from types import FunctionType
 from warnings import filterwarnings, warn
-from distutils.util import strtobool
 from collections import defaultdict
 from packaging.version import Version
 
@@ -38,6 +37,7 @@
     robust_s3_read,
     calculate_number_of_cpu,
     get_package_version,
+    strtobool,
 )
 from nwbinspector import __version__
 

src/nwbinspector/testing.py

@@ -3,7 +3,6 @@
 import os
 import json
 from uuid import uuid4
-from distutils.util import strtobool
 from pathlib import Path
 from datetime import datetime
 from typing import Tuple, Optional
@@ -16,7 +15,7 @@
 from pynwb import NWBHDF5IO, NWBFile
 from pynwb.image import ImageSeries
 
-from .utils import is_module_installed, get_package_version
+from .utils import is_module_installed, get_package_version, strtobool
 
 # The tests must be invoked at the outer level of the repository
 TESTING_CONFIG_FILE_PATH = Path.cwd() / "tests" / "testing_config.json"

src/nwbinspector/utils.py

@@ -234,3 +234,22 @@ def __get_shape_helper(local_data):
     if hasattr(data, "__len__") and not isinstance(data, (str, bytes)):
         if not strict_no_data_load or isinstance(data, (list, tuple, set)):
             return __get_shape_helper(data)
+
+
+def strtobool(val: str) -> bool:
+    """
+    Convert a string representation of truth to True or False.
+
+    True values are 'y', 'yes', 't', 'true', 'on', and '1';
+    False values are 'n', 'no', 'f', 'false', 'off', and '0'.
+    Raises ValueError if 'val' is anything else.
+    """
+    if not isinstance(val, str):
+        raise TypeError(f"Invalid type of {val!r} - must be str for `strtobool`")
+    val = val.lower()
+    if val in ("y", "yes", "t", "true", "on", "1"):
+        return True
+    elif val in ("n", "no", "f", "false", "off", "0"):
+        return False
+    else:
+        raise ValueError(f"Invalid truth value {val!r}")

tests/test_utils.py

@@ -11,9 +11,13 @@
     get_package_version,
     calculate_number_of_cpu,
     is_ascending_series,
+    strtobool,
 )
 
 
+import pytest
+
+
 def test_format_byte_size():
     assert format_byte_size(byte_size=12345) == "12.35KB"
 
@@ -142,3 +146,21 @@ def test_is_ascending_series():
     assert is_ascending_series(series=[1, 1, 1])
     assert is_ascending_series(series=[1, 2, 3])
     assert not is_ascending_series(series=[1, 2, 1])
+
+
+@pytest.mark.parametrize(
+    "values,target",
+    [
+        (("y", "yes", "t", "true", "on", "1"), True),
+        (("n", "no", "f", "false", "off", "0"), False),
+    ],
+)
+def test_strtobool(values, target):
+    for v in values:
+        assert strtobool(v) is target
+        assert strtobool(v.upper()) is target
+        with pytest.raises(ValueError):
+            strtobool(v + "1")
+    # it is strtobool, so no bool is allowed
+    with pytest.raises(TypeError):
+        strtobool(target)