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style: format with Ruff #180

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30 changes: 30 additions & 0 deletions .github/workflows/python-package.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
name: Python package

on:
push:
tags:
- '[0-9]+.[0-9]+.[0-9]+'

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Not related to this PR, but wanted to comment that this line is not in bioutils repo

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I may have already said this somewhere else (thought i had) but in general, everything is pretty out of sync w/ the template. Not sure if that's something we want to tackle iteratively or do a single "clean sweep"/reset at some point.

pull_request:

jobs:
cqa:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3

- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.10"
cache: pip
cache-dependency-path: '**/pyproject.yaml'

- name: Install test dependencies
run: |
python -m pip install --upgrade pip
pip install --use-deprecated=legacy-resolver -e .[dev]

- name: Format check with Ruff
run: |
ruff format --check .
6 changes: 6 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.4.4
hooks:
- id: ruff-format
args: [ --check ]
6 changes: 3 additions & 3 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -74,12 +74,12 @@ tox:
#= UTILITY TARGETS

# N.B. Although code is stored in github, I use hg and hg-git on the command line
#=> reformat: reformat code with yapf and commit
#=> reformat: reformat code with Ruff and commit
.PHONY: reformat
reformat:
@if ! git diff --cached --exit-code; then echo "Repository not clean" 1>&2; exit 1; fi
yapf -i -r "${PKGD}" tests
git commit -a -m "reformatted with yapf"
ruff format "${PKGD}"
git commit -a -m "reformatted with ruff"

#=> docs -- make sphinx docs
.PHONY: docs
Expand Down
154 changes: 77 additions & 77 deletions docs/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -22,40 +22,40 @@
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#sys.path.insert(0, os.path.abspath('.'))
# sys.path.insert(0, os.path.abspath('.'))

# -- General configuration ------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0'
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.doctest',
'sphinx.ext.intersphinx',
'sphinx.ext.todo',
'sphinx.ext.coverage',
'sphinx.ext.viewcode',
"sphinx.ext.autodoc",
"sphinx.ext.doctest",
"sphinx.ext.intersphinx",
"sphinx.ext.todo",
"sphinx.ext.coverage",
"sphinx.ext.viewcode",
]

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
templates_path = ["_templates"]

# The suffix of source filenames.
source_suffix = '.rst'
source_suffix = ".rst"

# The encoding of source files.
#source_encoding = 'utf-8-sig'
# source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'
master_doc = "index"

# General information about the project.
project = u'eutils'
copyright = u'2018, eutils Committers'
project = "eutils"
copyright = "2018, eutils Committers"

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
Expand All @@ -68,182 +68,176 @@

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# language = None

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build']
exclude_patterns = ["_build"]

# The reST default role (used for this markup: `text`) to use for all
# documents.
#default_role = None
# default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# show_authors = False

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
pygments_style = "sphinx"

# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = False
# keep_warnings = False


# -- Options for HTML output ----------------------------------------------

# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = 'sphinx_rtd_theme'
html_theme = "sphinx_rtd_theme"

# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#html_theme_options = {}
# html_theme_options = {}

# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
# html_theme_path = []
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# html_title = None

# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# html_short_title = None

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# html_logo = None

# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# html_favicon = None

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
html_static_path = ["_static"]

# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#html_extra_path = []
# html_extra_path = []

# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# html_last_updated_fmt = '%b %d, %Y'

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}
# html_additional_pages = {}

# If false, no module index is generated.
#html_domain_indices = True
# html_domain_indices = True

# If false, no index is generated.
#html_use_index = True
# html_use_index = True

# If true, the index is split into individual pages for each letter.
#html_split_index = False
# html_split_index = False

# If true, links to the reST sources are added to the pages.
html_show_sourcelink = False

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True
# html_show_sphinx = True

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True
# html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# html_use_opensearch = ''

# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None
# html_file_suffix = None

# Output file base name for HTML help builder.
htmlhelp_basename = 'eutilsdoc'
htmlhelp_basename = "eutilsdoc"


# -- Options for LaTeX output ---------------------------------------------

latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',

# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',

# Additional stuff for the LaTeX preamble.
#'preamble': '',
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#'preamble': '',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
('index', 'eutils.tex', u'eutils Documentation',
u'Reece Hart', 'manual'),
("index", "eutils.tex", "eutils Documentation", "Reece Hart", "manual"),
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# latex_logo = None

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# latex_use_parts = False

# If true, show page references after internal links.
#latex_show_pagerefs = False
# latex_show_pagerefs = False

# If true, show URL addresses after external links.
#latex_show_urls = False
# latex_show_urls = False

# Documents to append as an appendix to all manuals.
#latex_appendices = []
# latex_appendices = []

# If false, no module index is generated.
#latex_domain_indices = True
# latex_domain_indices = True


# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'eutils', u'eutils Documentation',
[u'Reece Hart'], 1)
]
man_pages = [("index", "eutils", "eutils Documentation", ["Reece Hart"], 1)]

# If true, show URL addresses after external links.
#man_show_urls = False
# man_show_urls = False


# -- Options for Texinfo output -------------------------------------------
Expand All @@ -252,28 +246,34 @@
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
('index', 'eutils', u'eutils Documentation',
u'Reece Hart', 'eutils', 'One line description of project.',
'Miscellaneous'),
(
"index",
"eutils",
"eutils Documentation",
"Reece Hart",
"eutils",
"One line description of project.",
"Miscellaneous",
),
]

# Documents to append as an appendix to all manuals.
#texinfo_appendices = []
# texinfo_appendices = []

# If false, no module index is generated.
#texinfo_domain_indices = True
# texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'
# texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False
# texinfo_no_detailmenu = False


# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'http://docs.python.org/': None}
intersphinx_mapping = {"http://docs.python.org/": None}

# -- Custom stuff ---

autodoc_default_flags = ['members', 'undoc-members', 'show-inheritance'] #, 'inherited-members']
autoclass_content = 'both'
autodoc_default_flags = ["members", "undoc-members", "show-inheritance"] # , 'inherited-members']
autoclass_content = "both"
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