diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
index 795f368d..68239a15 100644
--- a/.github/workflows/gh-ci.yaml
+++ b/.github/workflows/gh-ci.yaml
@@ -72,7 +72,7 @@ jobs:
if: ${{ matrix.os == 'ubuntu-latest' }}
uses: ./.github/actions/run-cookie-ci
with:
- source-directory: ${{ env.OUTPUT_DIRECTORY }}/TestMDAKit_with_condaforge-deps_and_ReadTheDocs/mdakit-cookie
+ source-directory: ${{ env.OUTPUT_DIRECTORY }}/TestMDAKit_with_host_MDAnalysis_condaforge-deps_and_ReadTheDocs/mdakit-cookie
- name: Upload artifact
if: ${{ matrix.os == 'ubuntu-latest' && matrix.last-n-minor-python-release == 0 }}
diff --git a/docs/requirements.yaml b/docs/requirements.yaml
index 5f66ebde..c92a034b 100644
--- a/docs/requirements.yaml
+++ b/docs/requirements.yaml
@@ -6,9 +6,7 @@ dependencies:
- python
- pip
- - sphinx<7.0
- - sphinx_rtd_theme
-
+ - mdanalysis-sphinx-theme >=1.0.1
- tree
# Pip-only installs
diff --git a/docs/source/_static/custom.css b/docs/source/_static/custom.css
deleted file mode 100644
index de8d2e67..00000000
--- a/docs/source/_static/custom.css
+++ /dev/null
@@ -1,225 +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 */
-/* Very light orange: #FFEBD0 */
-/* Code orange: #ca6500 */
-/* 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;
-}
-/* override table width restrictions */
-@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;
- }
- }
-
-dl.footnote p {
- font-weight: lighter;
- font-size: 14px
-}
\ No newline at end of file
diff --git a/docs/source/_static/logos/AUTHOR b/docs/source/_static/logos/AUTHOR
deleted file mode 100644
index 790ced65..00000000
--- a/docs/source/_static/logos/AUTHOR
+++ /dev/null
@@ -1,16 +0,0 @@
-The MDAnalysis 'Atom' logo was created by Christian Beckstein and is
-
-Copyright (c) 2011 Christian Beckstein
-
-MDAnalysis Logo 'Atom' by Christian Beckstein is licensed under a
-Creative Commons Attribution-NoDerivs 3.0 Unported License.
-To view a copy of this license, visit
-http://creativecommons.org/licenses/by-nd/3.0/ or send a letter to Creative
-Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.
-
-The logo is contained in the file 'mdanalysis-logo.png'.
-
-Derivatives in the files 'mdanalysis-logo-127x55.png',
-'mdanalysis-logo-200x150.png', 'mdanalysis-logo.ico' were created for
-inclusion in MDAnalysis and on websites related to MDAnalysis. They
-are distributed under the same license as the 'Atom' logo.
diff --git a/docs/source/_static/logos/mdanalysis-logo-127x55.png b/docs/source/_static/logos/mdanalysis-logo-127x55.png
deleted file mode 100644
index 237f8c61..00000000
Binary files a/docs/source/_static/logos/mdanalysis-logo-127x55.png and /dev/null differ
diff --git a/docs/source/_static/logos/mdanalysis-logo-200x150.png b/docs/source/_static/logos/mdanalysis-logo-200x150.png
deleted file mode 100644
index 4246d67a..00000000
Binary files a/docs/source/_static/logos/mdanalysis-logo-200x150.png and /dev/null differ
diff --git a/docs/source/_static/logos/mdanalysis-logo.ico b/docs/source/_static/logos/mdanalysis-logo.ico
deleted file mode 100644
index 3c102d08..00000000
Binary files a/docs/source/_static/logos/mdanalysis-logo.ico and /dev/null differ
diff --git a/docs/source/_static/logos/mdanalysis-logo.png b/docs/source/_static/logos/mdanalysis-logo.png
deleted file mode 100644
index 774e2ea2..00000000
Binary files a/docs/source/_static/logos/mdanalysis-logo.png and /dev/null differ
diff --git a/docs/source/_static/readable.css b/docs/source/_static/readable.css
deleted file mode 100644
index 1d170214..00000000
--- a/docs/source/_static/readable.css
+++ /dev/null
@@ -1,463 +0,0 @@
-/*
- * Adapted for combining with alabaster for MDAnalysis.
- * To be used as a custom CSS
- *
- * based on:
- *
- * readable.css_t
- * ~~~~~~~~~~~~~~
- *
- * Sphinx stylesheet -- readable theme.
- *
- * :copyright: Copyright 2013 by Ignacy Sokolowski.
- * :license: MIT, see LICENSE for details.
- *
- */
-
-
-/* -- page layout --------------------------------------------------------- */
-
-body {
- font-family: 'Georgia', serif;
- font-size: 17px;
- margin: 0;
- padding: 0;
-}
-
-div.document {
- margin: 10px auto 0 auto;
- /* max-width: {{ page_width }}; */
-}
-
-div.documentwrapper {
- float: left;
- width: 100%;
-}
-
-div.bodywrapper {
- /* margin: 0 0 0 {{ theme_sidebarwidth|toint }}px; */
-}
-
-div.body {
- background-color: #ffffff;
- color: #3e4349;
- padding: 0 30px 30px 30px;
-}
-
-div.footer {
- color: #555;
- font-size: 14px;
- margin: 20px auto 30px auto;
- text-align: right;
- max-width: 880px;
-}
-
-div.footer a {
- color: #444;
- text-decoration: underline;
-}
-
-div.related {
- padding: 10px 10px;
- width: auto;
-}
-
-div.sphinxsidebar {
- float: left;
- font-size: 14px;
- line-height: 1.5em;
- margin-left: -100%;
- /* width: {{ theme_sidebarwidth|toint }}px; */
-}
-
-div.sphinxsidebarwrapper {
- font-size: 14px;
- line-height: 1.5em;
- padding: 10px 0 10px 10px;
-}
-
-div.sphinxsidebar h3,
-div.sphinxsidebar h4 {
- color: #333;
- font-size: 24px;
- font-weight: normal;
- margin: 0 0 5px 0;
- padding: 0;
-}
-
-div.sphinxsidebar h4 {
- font-size: 1.1em;
-}
-
-div.sphinxsidebar h3 a {
- color: #333;
-}
-
-div.sphinxsidebar p {
- color: #888;
-}
-
-div.sphinxsidebar p.searchtip {
- line-height: 1.4em;
-}
-
-div.sphinxsidebar ul {
- color: #000;
- margin: 10px 0 20px;
- padding: 0;
-}
-
-div.sphinxsidebar a {
- color: #444;
-}
-
-div.sphinxsidebar a:hover {
- color: #d00;
-}
-
-div.sphinxsidebar input {
- border: 1px solid #ccc;
- font-family: sans-serif;
- font-size: 1em;
-}
-
-/* -- body styles --------------------------------------------------------- */
-
-a {
- color: #900;
- text-decoration: none;
-}
-
-a:visited {
- color: #700;
-}
-
-a:hover {
- color: #d00;
- text-decoration: underline;
-}
-
-hr {
- border: 1px solid #b1b4b6;
-}
-
-div.body h1,
-div.body h2,
-div.body h3,
-div.body h4,
-div.body h5,
-div.body h6 { font-weight: normal; }
-
-div.body h1,
-div.body h2,
-div.body h3,
-div.body h4 { color: #212224; }
-div.body h5 { color: #000; }
-div.body h6 { color: #777; }
-
-div.body h1 { margin: 0 0 10px 0; }
-div.body h2,
-div.body h3 { margin: 30px 0px 10px 0px; }
-div.body h4,
-div.body h5,
-div.body h6 { margin: 20px 0px 10px 0px; }
-
-div.body h1 { padding: 0 0 10px 0; }
-div.body h2,
-div.body h3 { padding: 10px 0 10px 0; }
-div.body h4 { padding: 10px 0 10px 0; }
-div.body h5,
-div.body h6 { padding: 10px 0 0 0; }
-
-div.body h1,
-div.body h2,
-div.body h3 { border-bottom: 1px solid #ddd; }
-div.body h4 { border-bottom: 1px solid #e5e5e5; }
-
-div.body h1 { font-size: 230%; }
-div.body h2 { font-size: 180%; }
-div.body h3 { font-size: 130%; }
-div.body h4 { font-size: 110%; }
-div.body h5 { font-size: 105%; }
-div.body h6 { font-size: 100%; }
-
-a.headerlink {
- color: #c60f0f;
- font-size: 0.8em;
- padding: 0 4px 0 4px;
- text-decoration: none;
-}
-
-a.headerlink:hover {
- background-color: #c60f0f;
- color: #fff;
-}
-
-div.body ul {
- list-style: disc;
- margin: 1em 0;
- padding-left: 1.3em;
-}
-
-div.body ul ul, div.body ol ul {
- margin: .2em 0;
- padding-left: 1.2em;
-}
-
-div.body ul li {
- padding: 2px 0;
-}
-
-div.body ul.search li {
- padding: 5px 0 5px 20px;
-}
-
-div.body ol {
- counter-reset: li;
- margin-left: 0;
- padding-left: 0;
-}
-
-div.body ol ol {
- margin: .2em 0;
-}
-
-div.body ol > li {
- list-style: none;
- margin: 0 0 0 1.9em;
- padding: 2px 1px;
- position: relative;
-}
-
-div.body ol > li:before {
- content: counter(li) ".";
- counter-increment: li;
- top: -2px;
- left: -1.9em;
- width: 1.9em;
- padding: 4px 0;
- position: absolute;
- text-align: left;
-}
-
-div.body p,
-div.body dd,
-div.body li {
- line-height: 1.4em;
-}
-
-div.admonition p.admonition-title + p {
- display: inline;
-}
-
-div.highlight {
- background-color: #fff;
-}
-
-div.important, div.note {
- background-color: #eee;
- border: 1px solid #ccc;
-}
-
-div.attention, div.caution, div.hint, div.seealso, div.tip {
- background-color: #fef9e9;
- border: 1px solid #fbe091;
-}
-
-div.topic {
- background-color: #eee;
-}
-
-div.danger, div.error, div.warning {
- background-color: #ffe4e4;
- border: 1px solid #f66;
-}
-
-p.admonition-title {
- display: inline;
-}
-
-p.admonition-title:after {
- content: ':';
-}
-
-pre {
- background-color: #f5f5f5;
- border: 1px solid #C6C9CB;
- color: #222;
- font-size: 0.75em;
- line-height: 1.5em;
- margin: 1.5em 0 1.5em 0;
- padding: 10px;
- box-shadow: 1px 1px 1px #d8d8d8;
- -webkit-box-shadow: 1px 1px 1px #d8d8d8;
- -moz-box-shadow: 1px 1px 1px #d8d8d8;
-}
-
-pre, tt, code {
- font-family: 'Consolas', 'Menlo', 'Deja Vu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
-}
-
-tt, code {
- background-color: #ecf0f3;
- font-size: 0.85em;
-}
-
-tt.descname, code.descname {
- font-size: 0.95em;
-}
-
-tt.xref, a tt, code.xref, a code {
- font-weight: normal;
-}
-
-span.pre {
- padding: 0 2px;
-}
-
-dl.class, dl.function {
- margin-bottom: 50px;
-}
-
-dl.function > dt,
-dl.attribute > dt,
-dl.classmethod > dt,
-dl.method > dt,
-dl.class > dt,
-dl.exception > dt {
- background-color: #f5f5f5;
- margin: 25px 0 10px 0;
- padding: 1px 10px;
-}
-
-table.docutils {
- width: 100%;
-}
-
-table.docutils.footnote {
- width: auto;
-}
-
-table.docutils thead,
-table.docutils tfoot {
- background: #f5f5f5;
-}
-
-table.docutils thead tr th {
- color: #000;
- font-weight: normal;
- padding: 7px 5px;
- vertical-align: middle;
-}
-
-table.docutils tbody tr th,
-table.docutils tbody tr td {
- border-bottom: 0;
- border-top: solid 1px #ddd;
- padding: 7px 5px;
- vertical-align: top;
-}
-table.docutils tbody tr:last-child th,
-table.docutils tbody tr:last-child td {
- border-bottom: solid 1px #ddd;
-}
-
-table.docutils thead tr td p,
-table.docutils tfoot tr td p,
-table.docutils tbody tr td p,
-table.docutils thead tr td ul,
-table.docutils tfoot tr td ul,
-table.docutils tbody tr td ul,
-table.docutils thead tr td ol,
-table.docutils tfoot tr td ol,
-table.docutils tbody tr td ol {
- margin: 0 0 .5em;
-}
-table.docutils thead tr td p.last,
-table.docutils tfoot tr td p.last,
-table.docutils tbody tr td p.last,
-table.docutils thead tr td ul.last,
-table.docutils tfoot tr td ul.last,
-table.docutils tbody tr td ul.last,
-table.docutils thead tr td ol.last,
-table.docutils tfoot tr td ol.last,
-table.docutils tbody tr td ol.last {
- margin-bottom: 0;
-}
-
-.viewcode-back {
- font-family: Arial, sans-serif;
-}
-
-div.viewcode-block:target {
- background-color: #fef9e9;
- border-top: 1px solid #fbe091;
- border-bottom: 1px solid #fbe091;
-}
-
-@media screen and (max-width: 870px) {
-
- div.document {
- width: auto;
- margin: 0;
- }
-
- div.documentwrapper {
- float: none;
- }
-
- div.bodywrapper {
- margin: 0;
- }
-
- div.body {
- min-height: 0;
- padding: 0 20px 30px 20px;
- }
-
- div.footer {
- background-color: #333;
- color: #888;
- margin: 0;
- padding: 10px 20px 20px;
- text-align: left;
- width: auto;
- }
-
- div.footer a {
- color: #bbb;
- }
-
- div.footer a:hover {
- color: #fff;
- }
-
- div.sphinxsidebar {
- background-color: #333;
- color: #fff;
- float: none;
- margin: 0;
- padding: 10px 20px;
- width: auto;
- }
-
- div.sphinxsidebar h3,
- div.sphinxsidebar h4,
- div.sphinxsidebar p,
- div.sphinxsidebar h3 a {
- color: #fff;
- }
-
- div.sphinxsidebar ul {
- color: #999;
- }
-
- div.sphinxsidebar a {
- color: #aaa;
- }
-
- div.sphinxsidebar a:hover {
- color: #fff;
- }
-
-}
diff --git a/docs/source/_templates/footer.html b/docs/source/_templates/footer.html
deleted file mode 100644
index 5fd6ad48..00000000
--- a/docs/source/_templates/footer.html
+++ /dev/null
@@ -1,11 +0,0 @@
-{% extends "!footer.html" %}
-
-{% block extrafooter %}
-{{ super() }}
-
-{% endblock %}
diff --git a/docs/source/conf.py b/docs/source/conf.py
index ade20957..75a081f6 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -29,44 +29,45 @@
# -- Project information -----------------------------------------------------
-project = 'MDAKit Cookiecutter'
-# author = 'MDAnalysis'
+project = "MDAKit Cookiecutter"
+# author = "MDAnalysis"
# The short X.Y version
-version = '0.1'
+version = "0.1"
# The full version, including alpha/beta/rc tags
-release = '0.1.0b'
+release = "0.1.0b"
author = ", ".join(parse_authors(sort_alphabetically=True))
now = datetime.datetime.now()
-copyright = f'2022-{now.year}, {author}'
+copyright = f"2022-{now.year}, {author}"
# -- General configuration ---------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
-# needs_sphinx = '1.0'
+needs_sphinx = "6.2.1"
# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# extensions coming with Sphinx (named "sphinx.ext.*") or your custom
# ones.
extensions = [
- 'sphinx.ext.mathjax',
- 'sphinx.ext.autosummary',
+ "sphinx.ext.mathjax",
+ "sphinx.ext.autosummary",
+ "mdanalysis_sphinx_theme",
]
# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+# source_suffix = [".rst", ".md"]
+source_suffix = ".rst"
# The master toctree document.
-master_doc = 'index'
+master_doc = "index"
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
@@ -78,11 +79,11 @@
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path .
-exclude_patterns = ['_build', 'Thumbs.db',
- '.DS_Store', 'generated/example-repository/*']
+exclude_patterns = ["_build", "Thumbs.db",
+ ".DS_Store", "generated/example-repository/*"]
# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
# -- Options for HTML output -------------------------------------------------
@@ -90,72 +91,65 @@
# 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"
# 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.
-color = {'orange': '#FF9200',
- 'gray': '#808080',
- 'white': '#FFFFFF',
- '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', # '#e76900', # dark orange
- # Toc options
- 'collapse_navigation': True,
- 'sticky_navigation': True,
- 'navigation_depth': 4,
- 'includehidden': True,
- 'titles_only': False,
+ "mda_official": True
}
# 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_css_files = ['custom.css']
+html_static_path = []
+html_css_files = []
# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself. Builtin themes are using these templates by
-# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
-# 'searchbox.html']``.
+# default: ``["localtoc.html", "relations.html", "sourcelink.html",
+# "searchbox.html"]``.
#
-# html_sidebars = {'**': ['globaltoc.html', 'localtoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html']}
+# html_sidebars = {
+# "**": [
+# "globaltoc.html",
+# "localtoc.html",
+# "relations.html",
+# "sourcelink.html",
+# "searchbox.html"
+# ]
+# }
# -- Options for HTMLHelp output ---------------------------------------------
# Output file base name for HTML help builder.
-htmlhelp_basename = 'MDAKitCookiecutterdoc'
+htmlhelp_basename = "MDAKitCookiecutterdoc"
# -- Options for LaTeX output ------------------------------------------------
latex_elements = {
- # The paper size ('letterpaper' or 'a4paper').
+ # The paper size ("letterpaper" or "a4paper").
#
- # 'papersize': 'letterpaper',
+ # "papersize": "letterpaper",
- # The font size ('10pt', '11pt' or '12pt').
+ # The font size ("10pt", "11pt" or "12pt").
#
- # 'pointsize': '10pt',
+ # "pointsize": "10pt",
# Additional stuff for the LaTeX preamble.
#
- # 'preamble': '',
+ # "preamble": "",
# Latex figure (float) alignment
#
- # 'figure_align': 'htbp',
+ # "figure_align": "htbp",
}
# Grouping the document tree into LaTeX files. List of tuples
@@ -163,9 +157,9 @@
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc,
- 'MDAKitCookiecutter.tex',
- 'MDAKit Cookiecutter Documentation',
- 'MDAnalysis', 'manual'),
+ "MDAKitCookiecutter.tex",
+ "MDAKit Cookiecutter Documentation",
+ "MDAnalysis", "manual"),
]
@@ -174,8 +168,8 @@
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
- (master_doc, 'mdakitcookiecutter',
- 'MDAKit Cookiecutter Documentation',
+ (master_doc, "mdakitcookiecutter",
+ "MDAKit Cookiecutter Documentation",
[author], 1)
]
@@ -186,11 +180,11 @@
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
- (master_doc, 'MDAKitCookiecutter',
- 'MDAKit Cookiecutter Documentation',
- author, 'MDAKitCookiecutter',
- 'A Cookiecutter which provides a template for packages based on MDAnalysis.',
- 'Miscellaneous'),
+ (master_doc, "MDAKitCookiecutter",
+ "MDAKit Cookiecutter Documentation",
+ author, "MDAKitCookiecutter",
+ "A Cookiecutter which provides a template for packages based on MDAnalysis.",
+ "Miscellaneous"),
]
diff --git a/docs/source/options.rst b/docs/source/options.rst
index 02b48e96..157d4ba3 100644
--- a/docs/source/options.rst
+++ b/docs/source/options.rst
@@ -12,6 +12,7 @@ project_name
This is the name of the project you would
use when writing about it in the documentation.
+This can be anything, e.g. have spaces and hyphens.
repo_name
---------
@@ -58,8 +59,24 @@ account name. This value is used to generate the URL
to the project on GitHub
(i.e. ``github.com//``).
+If you set this to ``MDAnalysis``,
+we will set some options for you.
+For example, the default logo and favicon
+will be the MDAnalysis logo and favicon.
+You will also have a footer detailing our
+privacy policy.
+
+If you set this to another value,
+there will be entries in the documentation
+`conf.py` that use a placeholder logo and favicon.
+
+Please see our `mdanalysis-sphinx-theme`_
+documentation for more information.
+
**Default value:** the ``github_username``.
+.. _`mdanalysis-sphinx-theme`: https://mdanalysis-sphinx-theme.readthedocs.io/en/latest/
+
author_name
-----------
diff --git a/hooks/post_gen_project.py b/hooks/post_gen_project.py
index 4de00c54..8023786b 100644
--- a/hooks/post_gen_project.py
+++ b/hooks/post_gen_project.py
@@ -95,8 +95,17 @@ def remove_analysis():
"{{ cookiecutter.package_name }}/tests/analysis"
)
-remove_rtd()
-remove_analysis()
+def remove_placeholder_icons():
+ """Remove placeholder logos if unnecessary."""
+ host_account = '{{ cookiecutter.github_host_account }}'
+ if host_account.lower() == "mdanalysis":
+ remove_files("docs/source/_static/logo")
-git_init_and_tag()
+
+if __name__ == "__main__":
+ remove_rtd()
+ remove_analysis()
+ remove_placeholder_icons()
+
+ git_init_and_tag()
diff --git a/tests/test_options.py b/tests/test_options.py
index 04f8cbac..047042cd 100644
--- a/tests/test_options.py
+++ b/tests/test_options.py
@@ -26,3 +26,35 @@ def test_analysis(self, tmpdir):
):
assert kit.cookie_package_path_exists(file)
assert clsname in kit.get_classes_from_package_file(file)
+
+
+class TestGitHubHostAccount:
+ def test_official_mda_theme(self, tmpdir):
+ with tmpdir.as_cwd():
+ kit = CookiecutterMDAKit(github_host_account="MDAnalysis")
+ kit.run()
+
+ conf = kit.cookie_directory / "docs/source/conf.py"
+ assert conf.is_file()
+
+ text = conf.read_text()
+ assert '"mda_official": True,' in text
+ assert "html_logo" not in text
+ assert "html_favicon" not in text
+
+ def test_non_official_mda_theme(self, tmpdir):
+ with tmpdir.as_cwd():
+ kit = CookiecutterMDAKit(github_host_account="other")
+ kit.run()
+
+ conf = kit.cookie_directory / "docs/source/conf.py"
+ assert conf.is_file()
+
+ text = conf.read_text()
+ patterns = [
+ '"mda_official": False,',
+ 'html_logo = "_static/logo/placeholder_logo.png"',
+ 'html_favicon = "_static/logo/placeholder_favicon.svg"',
+ ]
+ for pattern in patterns:
+ assert pattern in text, f"{pattern} not found"
diff --git a/tests/test_output.py b/tests/test_output.py
index b530df19..21a57910 100644
--- a/tests/test_output.py
+++ b/tests/test_output.py
@@ -32,10 +32,12 @@ def test_analysis(self, tmpdir):
@pytest.mark.parametrize("dependency_source", DependencyType)
@pytest.mark.parametrize("include_ReadTheDocs", ["y", "n"])
+@pytest.mark.parametrize("github_host_account", ["MDAnalysis", "other"])
def test_write_outputs(
test_output_directory,
dependency_source,
- include_ReadTheDocs
+ include_ReadTheDocs,
+ github_host_account,
):
if include_ReadTheDocs == "y":
rtd_name = "ReadTheDocs"
@@ -43,7 +45,10 @@ def test_write_outputs(
rtd_name = "no-ReadTheDocs"
dep_name = f"{dependency_source.name.lower()}-deps"
- project_name = f"TestMDAKit_with_{dep_name}_and_{rtd_name}"
+ project_name = (
+ "TestMDAKit_with_host_"
+ f"{github_host_account}_{dep_name}_and_{rtd_name}"
+ )
description = (
"Test MDAKit Project with "
f"dependencies using {dependency_source.name.lower()} "
@@ -57,7 +62,7 @@ def test_write_outputs(
repo_name="mdakit-cookie",
package_name="mdakit_cookie",
github_username="test-user-account",
- github_host_account="MDAnalysis",
+ github_host_account=github_host_account,
description=description,
dependency_source=dependency_source,
include_ReadTheDocs=include_ReadTheDocs,
diff --git a/{{cookiecutter.repo_name}}/README.md b/{{cookiecutter.repo_name}}/README.md
index fa798b38..e66821d3 100644
--- a/{{cookiecutter.repo_name}}/README.md
+++ b/{{cookiecutter.repo_name}}/README.md
@@ -19,7 +19,9 @@
[url_docs]: https://{{cookiecutter.repo_name}}.readthedocs.io/en/latest/?badge=latest
[url_latest_release]: https://github.com/{{cookiecutter.github_url}}/releases
[url_license]: https://www.gnu.org/licenses/gpl-2.0
-[url_mda]: https://www.mdanalysis.org{{cookiecutter.description}}
+[url_mda]: https://www.mdanalysis.org
+
+{{cookiecutter.description}}
{{cookiecutter.project_name}} is bound by a [Code of Conduct](https://github.com/{{cookiecutter.github_url}}/blob/{{cookiecutter._central_branch_name}}/CODE_OF_CONDUCT.md).
diff --git a/{{cookiecutter.repo_name}}/docs/requirements.yaml b/{{cookiecutter.repo_name}}/docs/requirements.yaml
index b37826b9..051920e1 100644
--- a/{{cookiecutter.repo_name}}/docs/requirements.yaml
+++ b/{{cookiecutter.repo_name}}/docs/requirements.yaml
@@ -10,14 +10,6 @@ dependencies:
- python
- pip
- - sphinx<7.0
-{% if cookiecutter.dependency_source == 'Prefer default anaconda channel with pip fallback' %}
- # Pip-only installs
- - pip:
- - sphinx_rtd_theme
-{% else %}
- - sphinx_rtd_theme
-
+ - mdanalysis-sphinx-theme >=1.0.1
# Pip-only installs
#- pip:
-{% endif %}
diff --git a/{{cookiecutter.repo_name}}/docs/source/_static/README.md b/{{cookiecutter.repo_name}}/docs/source/_static/README.md
index 2f0cf843..8d30b2b4 100644
--- a/{{cookiecutter.repo_name}}/docs/source/_static/README.md
+++ b/{{cookiecutter.repo_name}}/docs/source/_static/README.md
@@ -7,7 +7,7 @@ so a file named "default.css" will overwrite the builtin "default.css".
The path to this folder is set in the Sphinx `conf.py` file in the line:
```python
-templates_path = ['_static']
+html_static_path = ['_static']
```
## Examples of file to add to this directory
diff --git a/{{cookiecutter.repo_name}}/docs/source/_static/logo/placeholder_favicon.svg b/{{cookiecutter.repo_name}}/docs/source/_static/logo/placeholder_favicon.svg
new file mode 100644
index 00000000..cf62228b
--- /dev/null
+++ b/{{cookiecutter.repo_name}}/docs/source/_static/logo/placeholder_favicon.svg
@@ -0,0 +1,46 @@
+
+
+
+
diff --git a/{{cookiecutter.repo_name}}/docs/source/_static/logo/placeholder_logo.png b/{{cookiecutter.repo_name}}/docs/source/_static/logo/placeholder_logo.png
new file mode 100644
index 00000000..77e9056e
Binary files /dev/null and b/{{cookiecutter.repo_name}}/docs/source/_static/logo/placeholder_logo.png differ
diff --git a/{{cookiecutter.repo_name}}/docs/source/_templates/README.md b/{{cookiecutter.repo_name}}/docs/source/_templates/README.md
index 3f4f8043..e8e210a8 100644
--- a/{{cookiecutter.repo_name}}/docs/source/_templates/README.md
+++ b/{{cookiecutter.repo_name}}/docs/source/_templates/README.md
@@ -7,7 +7,7 @@ so a file named "page.html" will overwrite the builtin "page.html".
The path to this folder is set in the Sphinx `conf.py` file in the line:
```python
-html_static_path = ['_templates']
+templates_path = ['_templates']
```
## Examples of file to add to this directory
diff --git a/{{cookiecutter.repo_name}}/docs/source/conf.py b/{{cookiecutter.repo_name}}/docs/source/conf.py
index 27bee066..7223f5a3 100644
--- a/{{cookiecutter.repo_name}}/docs/source/conf.py
+++ b/{{cookiecutter.repo_name}}/docs/source/conf.py
@@ -12,47 +12,48 @@
# 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.
-# Incase the project was not installed
+# In case the project was not installed
import os
import sys
-sys.path.insert(0, os.path.abspath('../..'))
-import {{cookiecutter.repo_name}} # noqa
+sys.path.insert(0, os.path.abspath("../.."))
+import {{cookiecutter.package_name}} # noqa
# -- Project information -----------------------------------------------------
-project = '{{cookiecutter.project_name}}'
+project = "{{cookiecutter.project_name}}"
copyright = (
- "{% now 'utc', '%Y' %}, {{cookiecutter.author_name}}. "
+ "{% now "utc", "%Y" %}, {{cookiecutter.author_name}}. "
"Project structure based on the "
"MDAnalysis Cookiecutter version {{cookiecutter._mda_cc_version}}"
)
-author = '{{cookiecutter.author_name}}'
+author = "{{cookiecutter.author_name}}"
# The short X.Y version
-version = ''
+version = ""
# The full version, including alpha/beta/rc tags
-release = ''
+release = ""
# -- General configuration ---------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
-# needs_sphinx = '1.0'
+needs_sphinx = "6.2.1"
# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# extensions coming with Sphinx (named "sphinx.ext.*") or your custom
# ones.
extensions = [
- 'sphinx.ext.autosummary',
- 'sphinx.ext.autodoc',
- 'sphinx.ext.mathjax',
- 'sphinx.ext.viewcode',
- 'sphinx.ext.napoleon',
- 'sphinx.ext.intersphinx',
- 'sphinx.ext.extlinks',
+ "sphinx.ext.autosummary",
+ "sphinx.ext.autodoc",
+ "sphinx.ext.mathjax",
+ "sphinx.ext.viewcode",
+ "sphinx.ext.napoleon",
+ "sphinx.ext.intersphinx",
+ "sphinx.ext.extlinks",
+ "mdanalysis_sphinx_theme",
]
autosummary_generate = True
@@ -67,16 +68,16 @@
napoleon_use_ivar = True
# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+# source_suffix = [".rst", ".md"]
+source_suffix = ".rst"
# The master toctree document.
-master_doc = 'index'
+master_doc = "index"
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
@@ -88,10 +89,10 @@
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path .
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'default'
+pygments_style = "default"
# -- Options for HTML output -------------------------------------------------
@@ -99,26 +100,38 @@
# 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"
# 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 = {
+{% if cookiecutter.github_host_account == "MDAnalysis" %}
+ "mda_official": True,
+{% else %}
+ "mda_official": False,
+{% endif %}
+}
+
+{%- if cookiecutter.github_host_account != "MDAnalysis" %}
+# Set your logo and favicon here -- replace the placeholders!
+html_logo = "_static/logo/placeholder_logo.png"
+html_favicon = "_static/logo/placeholder_favicon.svg"
+{% endif %}
# 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"]
# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself. Builtin themes are using these templates by
-# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
-# 'searchbox.html']``.
+# default: ``["localtoc.html", "relations.html", "sourcelink.html",
+# "searchbox.html"]``.
#
# html_sidebars = {}
@@ -126,35 +139,35 @@
# -- Options for HTMLHelp output ---------------------------------------------
# Output file base name for HTML help builder.
-htmlhelp_basename = '{{cookiecutter.repo_name}}doc'
+htmlhelp_basename = "{{cookiecutter.repo_name}}doc"
# -- Options for LaTeX output ------------------------------------------------
latex_elements = {
- # The paper size ('letterpaper' or 'a4paper').
+ # The paper size ("letterpaper" or "a4paper").
#
- # 'papersize': 'letterpaper',
+ # "papersize": "letterpaper",
- # The font size ('10pt', '11pt' or '12pt').
+ # The font size ("10pt", "11pt" or "12pt").
#
- # 'pointsize': '10pt',
+ # "pointsize": "10pt",
# Additional stuff for the LaTeX preamble.
#
- # 'preamble': '',
+ # "preamble": "",
# Latex figure (float) alignment
#
- # 'figure_align': 'htbp',
+ # "figure_align": "htbp",
}
# 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 = [
- (master_doc, '{{cookiecutter.repo_name}}.tex', '{{cookiecutter.project_name}} Documentation',
- '{{cookiecutter.repo_name}}', 'manual'),
+ (master_doc, "{{cookiecutter.repo_name}}.tex", "{{cookiecutter.project_name}} Documentation",
+ "{{cookiecutter.repo_name}}", "manual"),
]
@@ -163,7 +176,7 @@
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
- (master_doc, '{{cookiecutter.repo_name}}', '{{cookiecutter.project_name}} Documentation',
+ (master_doc, "{{cookiecutter.repo_name}}", "{{cookiecutter.project_name}} Documentation",
[author], 1)
]
@@ -174,14 +187,14 @@
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
- (master_doc, '{{cookiecutter.repo_name}}', '{{cookiecutter.project_name}} Documentation',
- author, '{{cookiecutter.repo_name}}', '{{cookiecutter.description}}',
- 'Miscellaneous'),
+ (master_doc, "{{cookiecutter.repo_name}}", "{{cookiecutter.project_name}} Documentation",
+ author, "{{cookiecutter.repo_name}}", "{{cookiecutter.description}}",
+ "Miscellaneous"),
]
# -- Extension configuration -------------------------------------------------
intersphinx_mapping = {
- 'python': ('https://docs.python.org/3/', None),
- 'mdanalysis': ('https://docs.mdanalysis.org/stable/', None),
+ "python": ("https://docs.python.org/3/", None),
+ "mdanalysis": ("https://docs.mdanalysis.org/stable/", None),
}