Merge pull request #317 from glotzerlab/ruff

Switch from flake8/yapf to ruff

.pre-commit-config.yaml

@@ -42,21 +42,11 @@ repos:
     - --add=Part of GSD, released under the BSD 2-Clause License.
     - --keep-after=.. include
     - --comment-prefix=..
-- repo: https://github.com/google/yapf
-  rev: 'v0.40.2'
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: 'v0.1.13'
   hooks:
-  - id: yapf
-    additional_dependencies:
-    - toml==0.10.2
-- repo: https://github.com/PyCQA/flake8
-  rev: '6.1.0'
-  hooks:
-  - id: flake8
-    additional_dependencies:
-    - pep8-naming==0.13.3
-    - pydocstyle==6.2.3
-    - flake8-docstrings==1.6.0
-    - flake8-rst-docstrings==0.3.0
+  - id: ruff-format
+  - id: ruff
 - repo: https://github.com/pre-commit/mirrors-clang-format
   rev: v17.0.6
   hooks:

.ruff.toml

@@ -0,0 +1,59 @@
+target-version = "py38"
+
+extend-select = [
+    "A",
+    "B",
+    "D",
+    "E501",
+    "EM",
+    "I",
+    "ICN",
+    "ISC",
+    "N",
+    "NPY",
+    "PL",
+    "PT",
+    "RET",
+    "RUF",
+    "UP",
+    "W",
+]
+
+ignore = [
+  "N806", "N803",  # Allow occasional use of uppercase variable and argument names (e.g. N).
+  "D107", # Do not document __init__ separately from the class.
+  "PLR09", # Allow "too many" statements/arguments/etc...
+  "N816", # Allow mixed case names like kT.
+  "PT011", # PT011 insists that specific pytest.raises checks should impossibly more specific
+  "RUF012", # gsd does not use typing hints
+]
+
+[lint.per-file-ignores]
+
+"__init__.py" = ["F401", # __init__.py import submodules for use by the package importer.
+]
+
+"gsd/test/*.py" = ["PLR2004", # unit test value comparisons are not magic values
+]
+
+"doc/conf.py" = ["A001", # Allow copyright variable name
+                 "D", # conf.py does not need documentation
+    ]
+
+[pydocstyle]
+convention = "google"
+
+[format]
+quote-style = "single"
+
+[lint.flake8-import-conventions]
+# Prefer no import aliases
+aliases = {}
+# Always import hoomd and gsd without 'from'
+banned-from = ["hoomd", "gsd"]
+
+# Ban standard import conventions and force common packages to be imported by their actual name.
+[lint.flake8-import-conventions.banned-aliases]
+"numpy" = ["np"]
+"pandas" = ["pd"]
+"matplotlib" = ["mpl"]

.vscode/settings.json

@@ -13,12 +13,12 @@
     },
     "[python]": {
         "editor.rulers": [
-            80
+            88
         ]
     },
     "[cython]": {
         "editor.rulers": [
-            80
+            88
         ]
     },
     "[markdown]": {

CHANGELOG.rst

@@ -17,6 +17,8 @@ Change Log
 
 * Provide support via GitHub discussions
   (`#308 <https://github.com/glotzerlab/gsd/issues/308>`__).
+* Use ruff
+  (`#317 <https://github.com/glotzerlab/gsd/pull/317>`__).
 
 3.2.0 (2023-09-27)
 ^^^^^^^^^^^^^^^^^^

doc/conf.py

@@ -2,29 +2,31 @@
 # Copyright (c) 2016-2023 The Regents of the University of Michigan
 # Part of GSD, released under the BSD 2-Clause License.
 
+import datetime
 import os
 import subprocess
-import gsd
-import datetime
 import tempfile
 
+import gsd
+
 extensions = [
     'breathe',
     'sphinx.ext.autodoc',
     'sphinx.ext.napoleon',
     'sphinx.ext.intersphinx',
     'sphinx.ext.mathjax',
     'IPython.sphinxext.ipython_console_highlighting',
-    'IPython.sphinxext.ipython_directive'
+    'IPython.sphinxext.ipython_directive',
 ]
 
 napoleon_include_special_with_doc = True
 
-intersphinx_mapping = {'python': ('https://docs.python.org/3', None),
-                       'numpy': ('https://numpy.org/doc/stable', None),
-                       'hoomd': ('https://hoomd-blue.readthedocs.io/en/latest/', None),
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+    'numpy': ('https://numpy.org/doc/stable', None),
+    'hoomd': ('https://hoomd-blue.readthedocs.io/en/latest/', None),
 }
-autodoc_docstring_signature = True;
+autodoc_docstring_signature = True
 
 templates_path = ['_templates']
 
@@ -43,50 +45,53 @@
 
 default_role = 'any'
 
-pygments_style = "friendly"
-pygments_dark_style = "native"
+pygments_style = 'friendly'
+pygments_dark_style = 'native'
 
 html_theme = 'furo'
 html_static_path = ['_static']
 html_theme_options = {
-    "dark_css_variables": {
-        "color-brand-primary": "#5187b2",
-        "color-brand-content": "#5187b2",
+    'dark_css_variables': {
+        'color-brand-primary': '#5187b2',
+        'color-brand-content': '#5187b2',
     },
-    "light_css_variables": {
-        "color-brand-primary": "#406a8c",
-        "color-brand-content": "#406a8c",
+    'light_css_variables': {
+        'color-brand-primary': '#406a8c',
+        'color-brand-content': '#406a8c',
     },
 }
 
+
 ### Add custom directives
 def setup(app):
-    app.add_object_type('chunk', 'chunk',
-                        objname='Data chunk',
-                        indextemplate='single: %s (data chunk)')
+    app.add_object_type(
+        'chunk', 'chunk', objname='Data chunk', indextemplate='single: %s (data chunk)'
+    )
+
 
 tmpdir = tempfile.TemporaryDirectory()
 
 ###### IPython directive settings
 ipython_mplbackend = ''
-ipython_execlines = ['import gsd.fl',
-                     'import gsd.hoomd',
-                     'import gsd.pygsd',
-                     'import numpy',
-                     'import os',
-                     f'os.chdir("{tmpdir.name}")']
+ipython_execlines = [
+    'import gsd.fl',
+    'import gsd.hoomd',
+    'import gsd.pygsd',
+    'import numpy',
+    'import os',
+    f'os.chdir("{tmpdir.name}")',
+]
 
 
 dirname = os.path.abspath(os.path.dirname(__file__))
 breathe_projects = {'gsd': os.path.join(dirname, '..', 'devdoc', 'xml')}
 breathe_default_project = 'gsd'
 
 breathe_domain_by_extension = {
-    "h" : "c",
+    'h': 'c',
 }
 
 read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True'
 
 if read_the_docs_build:
-
-     subprocess.call('cd ..; doxygen', shell=True)
+    subprocess.call('cd ..; doxygen', shell=True)

gsd/__init__.py

@@ -14,7 +14,8 @@
 
 import signal
 import sys
-from . import version  # noqa: F401
+
+from . import version
 
 # Install a SIGTERM handler that gracefully exits, allowing open files to flush
 # buffered writes and close. Catch ValueError and pass as there is no way to