Apply black code formatting (#247)

* Update CHANGELOG.md

* Update requirements files

* Update test for updated hdf5plugin

* Fix test

* Update release instructions

* Update Sphinx workflow

* Update workflows to remove cancel action and align with hdmf

* Update HDMF_dev.yaml

* Fix dateutil requirement

* Update CHANGELOG.md

* Remove requirements files, update tox and workflows

* Fix rtd

* Update per-PR workflows

* Update docs, change optional deps group

* Configure dependabot

* Fix workflow

* Update changelog

* Update changelog

* Apply black to src directory

* Add ruff exception

* Fix spelling

* Run black on tests

* Update changelog

---------

Co-authored-by: Matthew Avaylon <[email protected]>

.pre-commit-config.yaml

@@ -1,12 +1,18 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v5.0.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
+    -   id: check-added-large-files
+    -   id: check-json
+    -   id: check-toml
+    -   id: name-tests-test
+        args: [--pytest-test-first]
+    -   id: check-docstring-first
 -   repo: https://github.com/psf/black
-    rev: 22.6.0
+    rev: 24.10.0
     hooks:
     -   id: black
         exclude: ^docs/

CHANGELOG.md

@@ -11,6 +11,7 @@
 * Remove support for python 3.8 and added testing for Python 3.13. @mavaylon1 [#240](https://github.com/hdmf-dev/hdmf-zarr/pull/240)
 * Added `NWBZarrIO.read_nwb` convenience method to simplify reading an NWB file. @oruebel [#226](https://github.com/hdmf-dev/hdmf-zarr/pull/226)
 * Updated optional dependency groups in `pyproject.toml` and GitHub Actions workflows. @rly, @mavaylon1 [#239](https://github.com/hdmf-dev/hdmf-zarr/pull/239)
+* Applied black code formatter. @rly [#247](https://github.com/hdmf-dev/hdmf-zarr/pull/247)
 
 ### Bug Fixes
 * Fix reading of cached specs and caching of specs during export. @rly [#232](https://github.com/hdmf-dev/hdmf-zarr/pull/232)

pyproject.toml

@@ -109,31 +109,9 @@ omit = [
 
 [tool.black]
 line-length = 120
-target-version = ['py38']
+target-version = ['py313']
 include = '\.pyi?$'
-extend-exclude = '''
-/(
-  \.toml
-  |\.yml
-  |\.txt
-  |\.sh
-  |\.git
-  |\.ini
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | build
-  | dist
-)/
-'''
-force-exclude = '''
-/(
-   /*.txt
-   /docs
-   /docs/*
-)\
-'''
+force-exclude = 'docs/*'
 
 [tool.ruff]
 lint.select = ["E", "F", "T100", "T201", "T203"]

src/hdmf_zarr/__init__.py

@@ -12,9 +12,14 @@
     __version__ = version("hdmf")
     del version
 
+__all__ = ["ZarrIO", "ZarrDataIO", "NWBZarrIO"]
+
 # Duecredit definitions
 from ._due import due, BibTeX  # noqa: E402
-due.cite(BibTeX("""
+
+due.cite(
+    BibTeX(
+        """
 @INPROCEEDINGS{9005648,
   author={A. J. {Tritt} and O. {Rübel} and B. {Dichter} and R. {Ly} and D. {Kang} and E. F. {Chang} and L. M. {Frank} and K. {Bouchard}},
   booktitle={2019 IEEE International Conference on Big Data (Big Data)},
@@ -24,6 +29,11 @@
   number={},
   pages={165-179},
   doi={10.1109/BigData47090.2019.9005648}}
-"""), description="HDMF: Hierarchical Data Modeling Framework for Modern Science Data Standards",  # noqa: E501
-         path="hdmf/", version=__version__, cite_module=True)
+"""  # noqa: E501
+    ),
+    description="HDMF: Hierarchical Data Modeling Framework for Modern Science Data Standards",
+    path="hdmf/",
+    version=__version__,
+    cite_module=True,
+)
 del due, BibTeX

src/hdmf_zarr/_due.py

@@ -1,6 +1,10 @@
 # emacs: at the end of the file
 # ex: set sts=4 ts=4 sw=4 et:
 # ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
+from __future__ import annotations
+
+from typing import Any
+
 """
 
 Stub file for a guaranteed safe import of duecredit constructs:  if duecredit
@@ -24,46 +28,49 @@
 License:    BSD-2
 """
 
-__version__ = '0.0.9'
+__version__ = "0.0.9"
 
 
-class InactiveDueCreditCollector(object):
+class InactiveDueCreditCollector:
     """Just a stub at the Collector which would not do anything"""
-    def _donothing(self, *args, **kwargs):
+
+    def _donothing(self, *_args: Any, **_kwargs: Any) -> None:
         """Perform no good and no bad"""
         pass
 
-    def dcite(self, *args, **kwargs):
+    def dcite(self, *_args: Any, **_kwargs: Any):
         """If I could cite I would"""
+
         def nondecorating_decorator(func):
             return func
+
         return nondecorating_decorator
 
     active = False
     activate = add = cite = dump = load = _donothing
 
-    def __repr__(self):
-        return self.__class__.__name__ + '()'
+    def __repr__(self) -> str:
+        return self.__class__.__name__ + "()"
 
 
-def _donothing_func(*args, **kwargs):
+def _donothing_func(*args: Any, **kwargs: Any) -> None:
     """Perform no good and no bad"""
     pass
 
 
 try:
-    from duecredit import due, BibTeX, Doi, Url, Text  # lgtm [py/unused-import]
-    if 'due' in locals() and not hasattr(due, 'cite'):
-        raise RuntimeError(
-            "Imported due lacks .cite. DueCredit is now disabled")
+    from duecredit import BibTeX, Doi, Text, Url, due  # lgtm [py/unused-import]
+
+    if "due" in locals() and not hasattr(due, "cite"):
+        raise RuntimeError("Imported due lacks .cite. DueCredit is now disabled")
 except Exception as e:
     if not isinstance(e, ImportError):
         import logging
-        logging.getLogger("duecredit").error(
-            "Failed to import duecredit due to %s" % str(e))
+
+        logging.getLogger("duecredit").error("Failed to import duecredit due to %s" % str(e))
     # Initiate due stub
-    due = InactiveDueCreditCollector()
-    BibTeX = Doi = Url = Text = _donothing_func
+    due = InactiveDueCreditCollector()  # type: ignore
+    BibTeX = Doi = Url = Text = _donothing_func  # type: ignore
 
 # Emacs mode definitions
 # Local Variables: