From e449a43fa8c4282fb00998fac41d292e43b2f687 Mon Sep 17 00:00:00 2001
From: IAlibay <ialibay@mdanalysis.org>
Date: Sun, 29 Oct 2023 20:46:02 +0000
Subject: [PATCH 1/5] towards the new theme

---
 .github/workflows/docs.yml | 16 ++++++++--------
 .readthedocs.yml           | 26 ++++++++++++++++++++++++++
 2 files changed, 34 insertions(+), 8 deletions(-)
 create mode 100644 .readthedocs.yml

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 0a768f3..0f1d3a1 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -14,27 +14,25 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
     - name: Setup python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
 
     - name: Display Python version
       run: python -c "import sys; print(sys.version)"
 
-    - name: Install sphinx, pytest, pytest plugins
+    - name: Install deps
       run: |
-        python -m pip install wheel
-        python -m pip install pytest pytest-cov pytest-pep8 pytest-mock codecov
-        python -m pip install sphinx sphinx-sitemap sphinx-rtd-theme
+        python -m pip install "mdanalysis-sphinx-theme>=1.0.1" sphinx-sitemap
 
     - name: Install main dependencies
       run: |
-        python -m pip install six setuptools tqdm
+        python -m pip install tqdm
 
     - name: install package
       run: |
@@ -42,10 +40,12 @@ jobs:
 
     - name: build docs
       run: |
-        python setup.py build_sphinx
+        cd docs
+        make html
 
     - name: deploy docs
       uses: peaceiris/actions-gh-pages@v3
+      if: success() && github.event_name == 'push'
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./build/sphinx/html
diff --git a/.readthedocs.yml b/.readthedocs.yml
new file mode 100644
index 0000000..7b8d9a6
--- /dev/null
+++ b/.readthedocs.yml
@@ -0,0 +1,26 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-4.10"
+
+# install the repo
+python:
+  install:
+  - method: setuptools
+    path: .
+
+# Optionally set the version of Python and requirements required to build your docs
+conda:
+  environment: environment.yaml

From e2b28693d675853e0173a803dbc0e7144fd74fa8 Mon Sep 17 00:00:00 2001
From: IAlibay <ialibay@mdanalysis.org>
Date: Sun, 29 Oct 2023 20:54:18 +0000
Subject: [PATCH 2/5] update theme

---
 docs/_static/custom.css                       | 206 ------------------
 .../_static/logos/mdanalysis-logo-200x150.png | Bin 8822 -> 0 bytes
 docs/_static/logos/mdanalysis-logo.ico        | Bin 4542 -> 0 bytes
 docs/conf.py                                  |  37 +---
 environment.yaml                              |  10 +
 5 files changed, 20 insertions(+), 233 deletions(-)
 delete mode 100644 docs/_static/custom.css
 delete mode 100644 docs/_static/logos/mdanalysis-logo-200x150.png
 delete mode 100644 docs/_static/logos/mdanalysis-logo.ico
 create mode 100644 environment.yaml

diff --git a/docs/_static/custom.css b/docs/_static/custom.css
deleted file mode 100644
index c069992..0000000
--- a/docs/_static/custom.css
+++ /dev/null
@@ -1,206 +0,0 @@
-/* custom MDAnalysis styling (User Guide theme) */
-
-/* See https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysis-theme-colours */
-/* 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;
-}
diff --git a/docs/_static/logos/mdanalysis-logo-200x150.png b/docs/_static/logos/mdanalysis-logo-200x150.png
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diff --git a/docs/_static/logos/mdanalysis-logo.ico b/docs/_static/logos/mdanalysis-logo.ico
deleted file mode 100644
index 3c102d087ec61f553bab4b0618843ff735d9e5e1..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/docs/conf.py b/docs/conf.py
index 7bcbed7..4a0c2f1 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -14,8 +14,6 @@
 import sys, os
 import datetime
 
-import sphinx_rtd_theme
-
 # 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.
@@ -39,8 +37,7 @@
               'sphinx.ext.mathjax', 'sphinx.ext.viewcode',
               'sphinx.ext.napoleon', 'sphinx.ext.todo',
               'sphinx.ext.autosummary',
-              'sphinx_sitemap',
-              'sphinx_rtd_theme']
+              'sphinx_sitemap',]
 
 mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
 
@@ -123,11 +120,9 @@
 # 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
@@ -141,20 +136,7 @@
 # /* 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
@@ -164,7 +146,7 @@
 # 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_css_files = []
 
 
 # The name of an image file (relative to this directory) to place at the top
@@ -174,7 +156,7 @@
 # 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,
@@ -305,6 +287,7 @@
 
 # Configuration for intersphinx: refer to the Python standard library
 # and other packages used by MDAnalysis
-intersphinx_mapping = {'https://docs.python.org/': None,
-                       'https://docs.mdanalysis.org/stable': None,
-                       }
+intersphinx_mapping = {
+    "python": ('https://docs.python.org/3/', None),
+    "mdanalysis": ('https://docs.mdanalysis.org/stable', None),
+}
diff --git a/environment.yaml b/environment.yaml
new file mode 100644
index 0000000..38a19b1
--- /dev/null
+++ b/environment.yaml
@@ -0,0 +1,10 @@
+name: mdanalysisdata
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - tqdm
+  - pip
+  - mdanalysis-sphinx-theme >=1.0.1
+  - pip:
+      - sphinx-sitemap

From 97d47b10d6b23db84a10b3fd7d1a7c9ccddaaddc Mon Sep 17 00:00:00 2001
From: IAlibay <ialibay@mdanalysis.org>
Date: Sun, 29 Oct 2023 21:02:42 +0000
Subject: [PATCH 3/5] change docs build dir

---
 .github/workflows/docs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 0f1d3a1..bbf279d 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -48,6 +48,6 @@ jobs:
       if: success() && github.event_name == 'push'
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./build/sphinx/html
+        publish_dir: ./docs/_build/html
         user_name: 'github-actions'
         user_email: 'github-action@users.noreply.github.com'

From 0c755ad7d7c3654e98b46be87921f4b4af0cc523 Mon Sep 17 00:00:00 2001
From: IAlibay <ialibay@mdanalysis.org>
Date: Sun, 29 Oct 2023 21:07:24 +0000
Subject: [PATCH 4/5] no need for push guard on a push action

---
 .github/workflows/docs.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index bbf279d..6315df9 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -45,7 +45,6 @@ jobs:
 
     - name: deploy docs
       uses: peaceiris/actions-gh-pages@v3
-      if: success() && github.event_name == 'push'
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./docs/_build/html

From bd680d783cecbc8fcda5113da4198d324b52b613 Mon Sep 17 00:00:00 2001
From: IAlibay <ialibay@mdanalysis.org>
Date: Sun, 29 Oct 2023 21:08:52 +0000
Subject: [PATCH 5/5] fix pep8

---
 docs/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/conf.py b/docs/conf.py
index 4a0c2f1..5f69231 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -37,7 +37,7 @@
               'sphinx.ext.mathjax', 'sphinx.ext.viewcode',
               'sphinx.ext.napoleon', 'sphinx.ext.todo',
               'sphinx.ext.autosummary',
-              'sphinx_sitemap',]
+              'sphinx_sitemap']
 
 mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML'