diff --git a/CHANGELOG b/CHANGELOG
index 7a03d90..3e0a7c1 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -13,20 +13,20 @@ The rules for this file:
* accompany each entry with github issue/PR number (Issue #xyz)
------------------------------------------------------------------------------
-10/21/2023 IAlibay, orbeckst
+10/21/2023 IAlibay, orbeckst, lilyminium
* 1.0.2
Changes
- * Python 3.12 is now supported
-
+ * Python 3.12 is now supported (PR #128)
+ * Use new MDAnalysis docs theme (PR #127)
Fixes
* updated versioneer to be able to run under Python 3.12 (#124, PR #128)
* replaced deprecated pkg_resources in tests with importlib (#130)
-
+
05/24/2022 IAlibay
diff --git a/ci/environment.yaml b/ci/environment.yaml
index b002ee0..9a3355f 100644
--- a/ci/environment.yaml
+++ b/ci/environment.yaml
@@ -6,7 +6,8 @@ dependencies:
- numpy>=1.21
- scipy
- mrcfile
- - sphinx<7.0
+
+ # documentation
+ - mdanalysis-sphinx-theme >=1.0.1
- pip:
- - sphinx-sitemap
- - sphinx-rtd-theme
+ - sphinx_sitemap
\ No newline at end of file
diff --git a/doc/source/_static/custom.css b/doc/source/_static/custom.css
deleted file mode 100644
index 480aa32..0000000
--- a/doc/source/_static/custom.css
+++ /dev/null
@@ -1,206 +0,0 @@
-/* override css for readable.css */
-
-/* styles/fonts to match http://mdanalysis.org (see public/css) */
-/* MDAnalysis orange: #FF9200 */
-/* MDAnalysis gray: #808080 */
-/* MDAnalysis white: #FFFFFF */
-/* MDAnalysis black: #000000 */
-/* Darker orange: e76900 */
-/* Even darker orange: #a24900 */
-/* RTD dark grey: #343131 */
-/* RTD light grey: #e6e6e6 */
-
-/* -- page layout --------------------------------------------------------- */
-
-body {
- font-family: 'PT Sans', Helvetica, Arial, 'sans-serif';
- font-size: 17px;
-}
-
-div.body {
- color: #000000;
-}
-
-div.sphinxsidebar a:hover {
- text-decoration: none !important;
-}
-
-div.sphinxsidebar p {
- color: #808080;
-}
-
-/* Home MDAnalysis colour */
-.wy-side-nav-search > a {
- color: #343131;
-}
-
-/* Side MDAnalysis version colour */
-.wy-side-nav-search > div.version {
- color: #808080;
-}
-
-/* Menubar caption colour */
-div.wy-menu-vertical span.caption-text {
- color: #FF9200;
-}
-
-/* Mobile layout menubar option */
-nav.wy-nav-top {
- background: #343131;
-}
-
-/* Menu search bar outline (default blue) */
-.wy-side-nav-search input[type="text"] {
- border-color: #808080;
-}
-
-
-/* -- body styles --------------------------------------------------------- */
-
-/* Different coloured links for sidebar vs body) */
-div.rst-content a {
- color: #FF9200;
- text-decoration: none;
-}
-
-div.rst-content a:visited {
- color: #FF9200;
-}
-
-a:hover {
- color: #FF9200 !important;
- text-decoration: underline;
-}
-
-
-pre, tt, code {
- font-family: Menlo, Monaco, 'Courier New', monospace
-}
-
-
-div.body h1 {
- font-weight: bolder;
-}
-
-a.headerlink {
- color: #808080;
- font-size: 0.8em;
- padding: 0 4px 0 4px;
- text-decoration: none;
-}
-
-a.headerlink:hover {
- background-color: #808080;
- color: #fff;
-}
-
-/* ------- admonition boxes ------- */
-
-div.admonition {
- margin: 10px 0px;
- padding: 10px 10px;
-}
-
-div.admonition p.admonition-title {
- font-size: 100%;
- font-weight: bolder;
-}
-
-/* ----- Tables ----- */
-
-/* override table width restrictions */
-/* wrap tables instead of scrolling */
-@media screen and (min-width: 767px) {
-
- .wy-table-responsive table td, .wy-table-responsive table th {
- /* !important prevents the common CSS stylesheets from overriding
- this as on RTD they are loaded after this stylesheet */
- white-space: normal !important;
- }
-
- .wy-table-responsive {
- overflow: visible !important;
- max-width: 100% !important;
- }
- }
-
-/* ----- Field lists ------ */
-
-.section > dl.field-list {
- display: flex;
- flex-wrap: wrap;
- margin: 0;
- padding: 0;
-}
-
-dl.field-list > dt::after {
- content: ":";
-}
-
-.rst-content dl:not(.docutils) dt {
- background: none;
- color: #000000;
- border-top: none;
-}
-
-.section > dl.field-list dt {
- margin: 0;
- padding: 0;
- flex-basis: 20%;
- display: block;
-}
-
-.section > dl.field-list > dd {
- flex-basis: 70%;
- margin: 0;
-}
-
-.section > dl.field-list > dd p {
- margin: 0;
-}
-
-/* ----- MDAnalysis coloured elements ------ */
-
-.rst-content dl.class dt, .rst-content dl.function dt {
- color: #ca6500;
- background: #FFEBD0;
- border-top: solid 3px #FF9200;
-}
-
-.rst-content .viewcode-link, .rst-content .viewcode-back {
- color: #808080;
-}
-
-.rst-content .guilabel {
- background: #efefef;
- border: 1px solid #808080;
-}
-
-
-.rst-content .seealso p.admonition-title {
- background: #808080;
-}
-
-.rst-content .seealso {
- background: #e3e3e3;
-}
-
-.rst-content .error p.admonition-title, .rst-content .warning p.admonition-title {
- background: #F45F4B;
-}
-
-.rst-content .error, .rst-content .warning {
- background: #FFEEED;
-}
-
-.rst-content .caution p.admonition-title, .rst-content .note p.admonition-title, .rst-content .important p.admonition-title {
- background: #FF9200;
-}
-
-.rst-content .caution, .rst-content .note, .rst-content .important {
- background: #FFEBD0;
-}
-
-.rst-content code:not(.xref).literal {
- color: #ca6500;
-}
\ No newline at end of file
diff --git a/doc/source/_static/logos/mdanalysis-logo-200x150.png b/doc/source/_static/logos/mdanalysis-logo-200x150.png
deleted file mode 100644
index 4246d67..0000000
Binary files a/doc/source/_static/logos/mdanalysis-logo-200x150.png and /dev/null differ
diff --git a/doc/source/_static/logos/mdanalysis-logo.ico b/doc/source/_static/logos/mdanalysis-logo.ico
deleted file mode 100644
index 3c102d0..0000000
Binary files a/doc/source/_static/logos/mdanalysis-logo.ico and /dev/null differ
diff --git a/doc/source/_templates/footer.html b/doc/source/_templates/footer.html
deleted file mode 100644
index 5fd6ad4..0000000
--- a/doc/source/_templates/footer.html
+++ /dev/null
@@ -1,11 +0,0 @@
-{% extends "!footer.html" %}
-
-{% block extrafooter %}
-{{ super() }}
-
-{% endblock %}
diff --git a/doc/source/conf.py b/doc/source/conf.py
index f282183..e4261dd 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -16,12 +16,11 @@
# 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('.'))
# make sure sphinx always uses the current branch
-sys.path.insert(0, os.path.abspath('../..'))
+sys.path.insert(0, os.path.abspath("../.."))
-import sphinx_rtd_theme
# -- General configuration -----------------------------------------------------
@@ -32,82 +31,88 @@
# 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.ext.napoleon', 'sphinx.ext.todo',
- 'sphinx_sitemap',
- ]
+extensions = [
+ "sphinx.ext.autodoc",
+ "sphinx.ext.intersphinx",
+ "sphinx.ext.mathjax",
+ "sphinx.ext.viewcode",
+ "sphinx.ext.napoleon",
+ "sphinx.ext.todo",
+ "sphinx_sitemap",
+]
-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"
# for sitemap with https://github.com/jdillard/sphinx-sitemap
site_url = "https://www.mdanalysis.org/GridDataFormats/"
sitemap_url_scheme = "{link}"
# https://stackoverflow.com/questions/5599254/how-to-use-sphinxs-autodoc-to-document-a-classs-init-self-method
-autoclass_content = 'both'
+autoclass_content = "both"
# 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'GridDataFormats'
-authors = (u'Oliver Beckstein, Jan Domanski, Jesse Johnson, Max Linke, Tyler Luchko, '
- u'Dominik Mierzejewski, Giacomo Fiorin, Lily Wang, Josh Vermaas, '
- u'Irfan Alibay，Zhiyi Wu')
-copyright = u'2007-2021, ' + authors
+project = "GridDataFormats"
+authors = (
+ "Oliver Beckstein, Jan Domanski, Jesse Johnson, Max Linke, Tyler Luchko, "
+ "Dominik Mierzejewski, Giacomo Fiorin, Lily Wang, Josh Vermaas, "
+ "Irfan Alibay，Zhiyi Wu"
+)
+copyright = "2007-2023, " + authors
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The full version, including alpha/beta/rc tags.
-release = __import__('gridData').__version__
+release = __import__("gridData").__version__
# The short X.Y version.
-version = ".".join(release.split('.')[:2])
+version = ".".join(release.split(".")[:2])
# 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 = []
# 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 = 'default'
+pygments_style = "default"
# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
# -- Options for HTML output ---------------------------------------------------
@@ -115,37 +120,17 @@
# 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 = "mdanalysis_sphinx_theme"
-html_theme_path = [
- sphinx_rtd_theme.get_html_theme_path()
-]
+# html_theme_path = []
# 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.
#
-# styles/fonts to match https://userguide.mdanalysis.org
-#
-# /* MDAnalysis orange: #FF9200 */
-# /* MDAnalysis gray: #808080 */
-# /* MDAnalysis white: #FFFFFF */
-# /* MDAnalysis black: #000000 */
-
-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',
- # Toc options
- 'collapse_navigation': True,
- 'sticky_navigation': True,
- 'navigation_depth': 4,
- 'includehidden': True,
- 'titles_only': False,
-}
+
+
+html_theme_options = {"mda_official": True}
# options common to RTD and MDAnalysis theme
@@ -154,8 +139,8 @@
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
# For RTD theme: custom.css to override theme defaults.
-html_static_path = ['_static']
-html_css_files = ['custom.css']
+html_static_path = ["_static"]
+# html_css_files = []
# The name of an image file (relative to this directory) to place at the top
@@ -165,91 +150,94 @@
# 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 = "_static/logos/mdanalysis-logo.ico"
+# html_favicon = "_static/logos/mdanalysis-logo.ico"
# 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
# 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 = True
+# html_show_sourcelink = True
# 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 tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
-html_use_opensearch = 'https://www.mdanalysis.org/GridDataFormats'
+html_use_opensearch = "https://www.mdanalysis.org/GridDataFormats"
# 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 = 'GridDataFormatsDoc'
+htmlhelp_basename = "GridDataFormatsDoc"
# -- 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]).
latex_documents = [
- ('index', 'gridDataFormats.tex', u'gridDataFormats Documentation',
- authors, 'manual'),
+ (
+ "index",
+ "gridDataFormats.tex",
+ "gridDataFormats Documentation",
+ authors,
+ "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 --------------------------------------------
@@ -257,12 +245,11 @@
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
- ('index', 'griddataformats', u'gridDataFormats Documentation',
- authors.split(), 1)
+ ("index", "griddataformats", "gridDataFormats Documentation", authors.split(), 1)
]
# If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
# -- Options for Texinfo output ------------------------------------------------
@@ -271,23 +258,30 @@
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
- ('index', 'gridDataFormats', u'gridDataFormats Documentation',
- authors, 'gridDataFormats', 'Grid structure for regular data together with common format readers.',
- 'Miscellaneous'),
+ (
+ "index",
+ "gridDataFormats",
+ "gridDataFormats Documentation",
+ authors,
+ "gridDataFormats",
+ "Grid structure for regular data together with common format readers.",
+ "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'
# Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None,
- 'https://docs.scipy.org/doc/numpy/': None,
- 'https://docs.scipy.org/doc/scipy/reference/': None,
- }
+intersphinx_mapping = {
+ "python": ("https://docs.python.org/3/", None),
+ "numpy": ("https://numpy.org/doc/stable/", None),
+ "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+}