Merge pull request #247 from Becksteinlab/blacken

Blacken

.git-blame-ignore-revs

@@ -0,0 +1 @@
+0de56b004dac74ae0221592293823b83c82a3c9a

.github/workflows/black.yaml

@@ -0,0 +1,10 @@
+name: Lint (black)
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable

CHANGES

@@ -2,6 +2,13 @@
  CHANGELOG for GromacsWrapper
 ==============================
 
+2023-??-??      0.8.5
+orbeckst
+
+* use black for uniformly formatted code (#246)
+* minor doc/installation updates
+
+
 2023-03-13      0.8.4
 orbeckst
 

README.rst

@@ -7,7 +7,7 @@
  README: GromacsWrapper
 ========================
 
-|build| |cov| |docs| |zenodo| |PRsWelcome| |anaconda|
+|build| |cov| |docs| |zenodo| |black| |PRsWelcome| |anaconda|
 
 A primitive Python wrapper around the Gromacs_ tools. The library is
 tested with GROMACS 4.6.5, 2018.x, 2019.x, 2020.x, 2021.x, 2022.x (and 5.x
@@ -50,6 +50,9 @@ running simulations with sensible parameters.
 .. |anaconda| image:: https://anaconda.org/conda-forge/gromacswrapper/badges/version.svg
    :target: https://anaconda.org/conda-forge/gromacswrapper
    :alt: Anaconda.org package
+.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
+   :target: https://github.com/psf/black	 
+   :alt: black   
 
 
 
@@ -136,15 +139,16 @@ wonderful ways. Please report issues through the `Issue Tracker`_.
 
 To use the *development code base*:  checkout the ``main`` branch::
 
-   git clone https://github.com/Becksteinlab/GromacsWrapper.git
-   cd GromacsWrapper
+   git clone https://github.com/Becksteinlab/GromacsWrapper.git   
 
 and install ::
 
-   python setup.py install
-
+   pip install GromacsWrapper/
 
+Code contributions are welcome. We use `black`_ for uniform code
+formatting so please install black_ and run it on your code.
 
+.. _`black`: https://github.com/psf/black
 
 Download and Availability
 =========================

doc/sphinx/source/conf.py

@@ -14,6 +14,7 @@
 import sys
 import os
 import datetime
+
 # https://sphinx-rtd-theme.readthedocs.io/en/stable/
 import sphinx_rtd_theme
 
@@ -22,110 +23,112 @@
 # is relative to the documentation root, use os.path.abspath to make it
 # absolute, like shown here.
 # make sure sphinx always uses the current branch
-sys.path.insert(0, os.path.abspath('../../..'))
+sys.path.insert(0, os.path.abspath("../../.."))
 
 # General configuration
 # ---------------------
 
 # 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.intersphinx',
-              'sphinx.ext.mathjax', 'sphinx.ext.viewcode',
-              'sphinx_rtd_theme']
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx_rtd_theme",
+]
 
-mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
+mathjax_path = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = '.txt'
+source_suffix = ".txt"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General substitutions.
-project = u'GromacsWrapper'
+project = "GromacsWrapper"
 now = datetime.datetime.now()
-copyright = u'2009-{}, The Authors of GromacsWrapper (see AUTHORS)'.format(now.year)
+copyright = "2009-{}, The Authors of GromacsWrapper (see AUTHORS)".format(now.year)
 
 # The default replacements for |version| and |release|, also used in various
 # other places throughout the built documents.
 #
 # Dynamically calculate the version (uses versioneer)
-packageversion = __import__('gromacs').__version__
+packageversion = __import__("gromacs").__version__
 
 # The short X.Y version.
-version = '.'.join(packageversion.split('.')[:2])
+version = ".".join(packageversion.split(".")[:2])
 # The full version, including alpha/beta/rc tags.
 release = packageversion
 
 # 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 documents that shouldn't be included in the build.
-#unused_docs = []
+# unused_docs = []
 
 # List of directories, relative to source directories, that shouldn't be searched
 # for source files.
 exclude_trees = []
 
 # 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"
 
 
 # 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"
 
 html_theme_options = {
-    'canonical_url': '',
-    'logo_only': True,
-    'display_version': True,
-    'prev_next_buttons_location': 'bottom',
-    'style_external_links': False,
-    'style_nav_header_background': 'white',
+    "canonical_url": "",
+    "logo_only": True,
+    "display_version": True,
+    "prev_next_buttons_location": "bottom",
+    "style_external_links": False,
+    "style_nav_header_background": "white",
     # Toc options
-    'collapse_navigation': True,
-    'sticky_navigation': True,
-    'navigation_depth': 4,
-    'includehidden': True,
-    'titles_only': False,
+    "collapse_navigation": True,
+    "sticky_navigation": True,
+    "navigation_depth": 4,
+    "includehidden": True,
+    "titles_only": False,
 }
 
 
 # Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = [
-    sphinx_rtd_theme.get_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.
@@ -139,88 +142,94 @@
 # 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"]
 
 # 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_use_modindex = True
+# html_use_modindex = 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, the reST sources are included in the HTML build as _sources/<name>.
-#html_copy_source = True
+# html_copy_source = 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 = ''
 
 # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = ''
+# html_file_suffix = ''
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'GromacsWrapperdoc'
+htmlhelp_basename = "GromacsWrapperdoc"
 
 
 # Options for LaTeX output
 # ------------------------
 
 # The paper size ('letter' or 'a4').
-#latex_paper_size = 'letter'
+# latex_paper_size = 'letter'
 
 # The font size ('10pt', '11pt' or '12pt').
-#latex_font_size = '10pt'
+# latex_font_size = '10pt'
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, document class [howto/manual]).
 latex_documents = [
-  ('index', 'GromacsWrapper.tex', u'GromacsWrapper Documentation',
-   u'Oliver Beckstein', 'manual'),
+    (
+        "index",
+        "GromacsWrapper.tex",
+        "GromacsWrapper Documentation",
+        "Oliver Beckstein",
+        "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
 
 # Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
+# latex_preamble = ''
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_use_modindex = True
+# latex_use_modindex = True
 
 
 # Options for ext.intersphinx
 # ---------------------------
 # intersphinx: reference standard lib and RecSQL
 # http://sphinx.pocoo.org/latest/ext/intersphinx.html
-intersphinx_mapping = {'https://docs.python.org/': None,
-                       'https://numpy.org/doc/stable/': None,
-                       'https://docs.scipy.org/doc/scipy/reference/': None,
+intersphinx_mapping = {
+    "https://docs.python.org/": None,
+    "https://numpy.org/doc/stable/": None,
+    "https://docs.scipy.org/doc/scipy/reference/": None,
 }
 
 
@@ -231,5 +240,3 @@
 # This value selects what content will be inserted into the main body of an autoclass directive.
 # "class", "init", "both"
 autoclass_content = "both"
-
-

doc/sphinx/source/installation.txt

@@ -77,7 +77,7 @@ or install from the unpacked source::
 
   tar -zxvf GromacsWrapper-0.8.3.tar.gz
   cd GromacsWrapper-0.8.3
-  python setup.py install
+  pip install .
 
 
 
@@ -94,6 +94,11 @@ and checkout the *main* branch::
    git clone https://github.com/Becksteinlab/GromacsWrapper.git
    cd GromacsWrapper
 
+Code contributions are welcome. We use `black`_ for uniform code
+formatting so please install black_ and run it on your code.
+
+.. _`black`: https://github.com/psf/black
+
 
 Requirements
 ============