Use and apply black formatting

.pre-commit-config.yaml

@@ -13,10 +13,10 @@ repos:
         args: [--pytest-test-first]
         exclude: ^tests/unit/helpers/
     -   id: check-docstring-first
-# -   repo: https://github.com/psf/black
-#     rev: 23.3.0
-#     hooks:
-#     -   id: black
+-   repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+    -   id: black
 -   repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: v0.0.272
     hooks:

CHANGELOG.md

@@ -1,5 +1,10 @@
 # HDMF Changelog
 
+## HDMF 3.7.0 (Upcoming)
+
+## Minor improvements
+- Set code style guide to `black`. @rly [#860](https://github.com/hdmf-dev/hdmf/pull/860)
+
 ## HMDF 3.6.1 (May 18, 2023)
 
 ### Bug fixes

docs/CONTRIBUTING.rst

@@ -90,21 +90,25 @@ Style Guides
 Python Code Style Guide
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-Before you create a Pull Request, make sure you are following the PEP8_ style guide. .
-To check whether your code conforms to the HDMF style guide, simply run the ruff_ tool in the project's root
-directory. ``ruff`` will also sort imports automatically and check against additional code style rules.
+Before you create a Pull Request, make sure you are following the Black_ preview style guide, which follows PEP8.
+We also break from the Black format by configuring it with a max line length of 120.
+To check whether your code conforms to the Black_ preview style guide, simply run the ``black`` tool in the
+project's root directory with the ``--check`` argument. You can also run the ``black`` tool without
+the ``--check`` argument to have black automatically format the codebase to comply with the style guide.
 
-We also use ``ruff`` to sort python imports automatically and double-check that the codebase
+We also use the ruff_ tool to sort python imports automatically and double-check that the codebase
 conforms to PEP8 standards, while using the codespell_ tool to check spelling.
 
-``ruff`` and ``codespell`` are installed when you follow the developer installation instructions. See
+The ``black``, ``ruff``, and ``codespell`` tools are installed when you follow the developer installation instructions. See
 :ref:`install_developers`.
 
+.. _Black: https://black.readthedocs.io/en/stable/
 .. _ruff: https://beta.ruff.rs/docs/
 .. _codespell: https://github.com/codespell-project/codespell
 
 .. code::
 
+   $ black .
    $ ruff check .
    $ codespell
 

pyproject.toml

@@ -85,11 +85,11 @@ exclude_lines = [
 
 [tool.setuptools_scm]
 
-# [tool.black]
-# line-length = 120
-# preview = true
-# exclude = ".git|.mypy_cache|.tox|.venv|venv|.ipynb_checkpoints|_build/|dist/|__pypackages__|.ipynb"
-# force-exclude = "src/hdmf/common/hdmf-common-schema|docs/gallery"
+[tool.black]
+line-length = 120
+preview = true
+exclude = ".git|.mypy_cache|.tox|.venv|venv|.ipynb_checkpoints|_build/|dist/|__pypackages__|.ipynb"
+force-exclude = "src/hdmf/common/hdmf-common-schema|docs/gallery"
 
 [tool.ruff]
 select = ["E", "F", "T100", "T201", "T203"]

src/hdmf/array.py

@@ -1,13 +1,12 @@
-from abc import abstractmethod, ABCMeta
+from abc import ABCMeta, abstractmethod
 
 import numpy as np
 
 
 class Array:
-
     def __init__(self, data):
         self.__data = data
-        if hasattr(data, 'dtype'):
+        if hasattr(data, "dtype"):
             self.dtype = data.dtype
         else:
             tmp = data
@@ -41,17 +40,20 @@ def __getitem__(self, arg):
                     idx.append(i)
             return np.fromiter((self.__getidx__(x) for x in idx), dtype=self.dtype)
         elif isinstance(arg, slice):
-            return np.fromiter((self.__getidx__(x) for x in self.__sliceiter(arg)), dtype=self.dtype)
+            return np.fromiter(
+                (self.__getidx__(x) for x in self.__sliceiter(arg)),
+                dtype=self.dtype,
+            )
         elif isinstance(arg, tuple):
             return (self.__getidx__(arg[0]), self.__getidx__(arg[1]))
         else:
             return self.__getidx__(arg)
 
 
 class AbstractSortedArray(Array, metaclass=ABCMeta):
-    '''
+    """
     An abstract class for representing sorted array
-    '''
+    """
 
     @abstractmethod
     def find_point(self, val):
@@ -160,11 +162,11 @@ def __ne__(self, other):
 
 
 class SortedArray(AbstractSortedArray):
-    '''
+    """
     A class for wrapping sorted arrays. This class overrides
     <,>,<=,>=,==, and != to leverage the sorted content for
     efficiency.
-    '''
+    """
 
     def __init__(self, array):
         super().__init__(array)
@@ -174,7 +176,6 @@ def find_point(self, val):
 
 
 class LinSpace(SortedArray):
-
     def __init__(self, start, stop, step):
         self.start = start
         self.stop = stop

src/hdmf/backends/hdf5/__init__.py

@@ -1,3 +1,3 @@
 from . import h5_utils, h5tools
-from .h5_utils import H5RegionSlicer, H5DataIO
-from .h5tools import HDF5IO, H5SpecWriter, H5SpecReader
+from .h5_utils import H5DataIO, H5RegionSlicer
+from .h5tools import HDF5IO, H5SpecReader, H5SpecWriter