Commit 59edb2f5 authored by Alan O'Cais's avatar Alan O'Cais

Merge branch 'test' into 'master'

Update to RTD theme used and modify it a bit

See merge request e-cam/E-CAM-Library!208
parents 6a513ef5 a3b217b1
......@@ -3,7 +3,6 @@
# sphinx build folder
_build
_templates
# OS generated files #
######################
......
......@@ -22,7 +22,7 @@ pages:
- apt-get -y install dvipng
- pip3 install pygments --upgrade
- pip3 install Sphinx --upgrade
- pip3 install sphinx-bootstrap-theme --upgrade
- pip3 install sphinx-rtd-theme --upgrade
- READTHEDOCS=True sphinx-build -nWT -b html . _build/html
- mv _build/html/ public/
- echo -e "\n\n\e[1mYou can find your build of this documentation at \n\t\e[32m${CI_PAGES_URL}\e[0m\n\n"
......
......@@ -3,6 +3,13 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
.. sidebar:: General Information
.. contents:: :depth: 2
* :ref:`contributing`
* :ref:`search`
.. _readme_classical_md:
********************
......@@ -12,13 +19,6 @@ Classical MD Modules
Introduction
============
.. sidebar:: General Information
.. contents:: :depth: 2
* :ref:`contributing`
* :ref:`search`
.. image:: ./images/lipid.jpg
:width: 15 %
:align: left
......
......@@ -3,6 +3,13 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
.. sidebar:: General Information
.. contents:: :depth: 2
* :ref:`contributing`
* :ref:`search`
.. _readme_electronic_structure:
****************************
......@@ -12,14 +19,7 @@ Electronic Structure Modules
Introduction
============
.. sidebar:: General Information
.. contents:: :depth: 2
* :ref:`contributing`
* :ref:`search`
.. figure:: ./images/wake_nova-rgb.png
.. figure:: ./images/protein-metal-cluster.png
:figwidth: 25 %
:align: left
......
......@@ -3,6 +3,13 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
.. sidebar:: General Information
.. contents:: :depth: 2
* :ref:`contributing`
* :ref:`search`
.. _readme_meso_multi:
*****************************
......@@ -12,13 +19,6 @@ Meso- and Multi-scale Modules
Introduction
============
.. sidebar:: General Information
.. contents:: :depth: 2
* :ref:`contributing`
* :ref:`search`
.. image:: ./images/DPD1.jpg
:width: 10 %
:align: left
......
......@@ -3,23 +3,22 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
.. sidebar:: General Information
.. contents:: :depth: 2
* :ref:`contributing`
* :ref:`search`
.. _readme_quantum_dynamics:
************************
Quantum Dynamics Modules
************************
Introduction
============
.. sidebar:: General Information
.. contents:: :depth: 2
* :ref:`contributing`
* :ref:`search`
.. image:: ./images/AltLogo.png
:width: 30 %
:align: left
......
......@@ -97,7 +97,7 @@ Notice that the quantum momentum tracks the spatial variation of the nuclear den
Applications of the Module
__________________________
The module is designed to apply the CTMQC procedure to one-, two-, and three-dimensional model systems where an arbitrary number of electronic states are coupled via the nuclear dynamics. Tully model systems [Tully]_ are within the class of problems that can be treated by the module, as well as a wide class of multidimensional problems involving, for instance, ultrafast radiationless relaxation of photo-excited molecules [CI]_ through conical intersections.
The module is designed to apply the CTMQC procedure to one-, two-, and three-dimensional model systems where an arbitrary number of electronic states are coupled via the nuclear dynamics. Tully model systems [Tully]_ are within the class of problems that can be treated by the module, as well as a wide class of multidimensional problems involving, for instance, ultrafast radiationless relaxation of photo-excited molecules [CI1]_ through conical intersections.
Installation
......@@ -259,7 +259,7 @@ __________
**93** (1990) 1061 `DOI: 10.1063/1.459170
<https://doi.org/10.1063/1.459170>`_
.. [CI] B. F. E. Curchod, F. Agostini, *J. Phys. Chem. Lett.*
.. [CI1] B. F. E. Curchod, F. Agostini, *J. Phys. Chem. Lett.*
**8** (2017) 831 `DOI: 10.1021/acs.jpclett.7b00043
<https://doi.org/10.1021/acs.jpclett.7b00043>`_
/* main styles */
body {
font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
font-size: 100%;
color: {{ theme_textcolor }};
margin: 0;
padding: 0;
line-height: 135%;
}
a {
color: #3498db;
text-decoration: none;
}
a:visited {
color: #9b59b6;
text-decoration: none;
}
a:hover {
text-decoration: underline;
}
_static/images/ecam_logo.png

2.31 KB | W: | H:

_static/images/ecam_logo.png

65.4 KB | W: | H:

_static/images/ecam_logo.png
_static/images/ecam_logo.png
_static/images/ecam_logo.png
_static/images/ecam_logo.png
  • 2-up
  • Swipe
  • Onion skin
.wy-nav-content {
max-width: none;
}
.wy-side-nav-search, .wy-nav-top {
background: #FCFCFC;
}
.wy-side-nav-search>div.version {
color: #455A64;
}
.wy-nav-side {
background: #FCFCFC;
}
.rst-versions .rst-current-version {
background: #FCFCFC;
}
/* Fix stuff in (right) sidebar */
.rst-content .sidebar p, .rst-content .sidebar ul, .rst-content .sidebar dl {
font-size: 100%;
margin: 6px;
}
.rst-content .sidebar .sidebar-title {
font-family: "Verdana", Verdana, sans-serif;
}
.rst-content .section ol p, .rst-content .section ul p {
margin-bottom: 0px;
}
body {
color: #263238;
}
h1 {
color: #455A64;
}
h2 {
color: #455A64;
}
h3 {
color: #455A64;
}
h4 {
color: #455A64;
}
a:link {
color: #21618C;
}
/* visited link */
a:visited {
color: #633974;
}
/* mouse over link */
a:hover {
text-decoration: underline;
}
/* selected link */
a:active {
color: blue;
}
p {
font-family: "Verdana", Verdana, sans-serif;
}
li a, h1, h2, h3, h4 {
font-family: "Verdana", Verdana, sans-serif;
}
li a:hover {
background-color: #B0BEC5;
color: #263238;
}
li a:hover:not(.active) {
background-color: #B0BEC5;
color: #263238;
}
......@@ -3,12 +3,6 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
.. _best_practices:
==================================
Scientific Software Best Practices
==================================
.. sidebar:: General Information
.. contents:: :local:
......@@ -16,6 +10,12 @@ Scientific Software Best Practices
* :ref:`contributing`
* :ref:`search`
.. _best_practices:
==================================
Scientific Software Best Practices
==================================
.. image:: ./images/512px-Waterfall_model.svg.png
:alt: "By Peter Kemp / Paul Smith [CC BY 3.0], via Wikimedia Commons"
:width: 15%
......
......@@ -15,6 +15,7 @@
import sys
import os
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
......@@ -56,7 +57,7 @@ master_doc = 'index'
# General information about the project.
project = 'E-CAM Software Library'
copyright = '2017, E-CAM Centre of Excellence'
copyright = '2019, E-CAM Centre of Excellence'
author = 'Alan O\'Cais'
# The version info for the project you're documenting, acts as replacement for
......@@ -64,9 +65,9 @@ author = 'Alan O\'Cais'
# built documents.
#
# The short X.Y version.
version = '0.1'
version = 'E-CAM Software Library'
# The full version, including alpha/beta/rc tags.
release = '0.1'
release = '0.2'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
......@@ -122,88 +123,13 @@ numfig = True
# a list of builtin themes.
on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
if on_rtd:
import sphinx_bootstrap_theme
html_theme = 'bootstrap'
# 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 = {
# Navigation bar title. (Default: ``project`` value)
'navbar_title': "Software Library",
# Tab name for entire site. (Default: "Site")
'navbar_site_name': "Site",
# Tab name for the current pages TOC. (Default: "Page")
'navbar_pagenav_name': "Page",
# A list of tuples containing pages or urls to link to.
# Valid tuples should be in the following forms:
# (name, page) # a link to a page
# (name, "/aa/bb", 1) # a link to an arbitrary relative url
# (name, "http://example.com", True) # arbitrary absolute url
# Note the "1" or "True" value above as the third argument to indicate
# an arbitrary url.
# 'navbar_links': [
# ("Examples", "examples"),
# ("Link", "http://example.com", True),
# ],
# Global TOC depth for "site" navbar tab. (Default: 1)
# Switching to -1 shows all levels.
'globaltoc_depth': 2,
# Include hidden TOCs in Site navbar?
#
# Note: If this is "false", you cannot have mixed ``:hidden:`` and
# non-hidden ``toctree`` directives in the same page, or else the build
# will break.
#
# Values: "true" (default) or "false"
'globaltoc_includehidden': "true",
# HTML navbar class (Default: "navbar") to attach to <div> element.
# For black navbar, do "navbar navbar-inverse"
'navbar_class': "navbar",
# Fix navigation bar to top of page?
# Values: "true" (default) or "false"
'navbar_fixed_top': "true",
# Location of link to source.
# Options are "nav" (default), "footer" or anything else to exclude.
'source_link_position': "footer",
# Bootswatch (http://bootswatch.com/) theme.
#
# Options are nothing (default) or the name of a valid theme such
# as "amelia" or "cosmo".
#
# Example themes:
# * flatly
# * sandstone (v3 only)
# * united
# * yeti (v3 only)
'bootswatch_theme': "sandstone",
# Choose Bootstrap version.
# Values: "3" (default) or "2" (in quotes)
'bootstrap_version': "3",
}
# Add any paths that contain custom themes here, relative to this directory.
# ``get_html_theme_path`` returns a list, so you can concatenate with
# any other theme directories you would like.
html_theme_path = sphinx_bootstrap_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
else:
html_theme = 'default'
html_theme_options = {}
html_theme = 'default'
html_theme = 'sphinx_rtd_theme'
html_theme_options = {
'logo_only' : True,
'navigation_depth': 4,
'includehidden': True,
}
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = "Demo"
......@@ -220,7 +146,9 @@ html_favicon = '_static/images/ecam_logo.ico'
# 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']
def setup(app):
app.add_stylesheet("theme_extra.css")
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
......
......@@ -5,10 +5,6 @@
.. _readme:
**************************
The E-CAM Software Library
**************************
.. sidebar:: Scientific Areas
* :ref:`readme_classical_md`
......@@ -26,12 +22,16 @@ The E-CAM Software Library
* :ref:`search`
.. figure:: ./Electronic-Structure-Modules/images/wake_nova-rgb.png
:figwidth: 25 %
**************************
The E-CAM Software Library
**************************
.. figure:: ./Electronic-Structure-Modules/images/protein-metal-cluster.png
:figwidth: 35 %
:align: left
This is a collection of the software modules that have been documented by E-CAM_ (http://www.e-cam2020.eu) community
within the four initial target areas of E-CAM_:
Collected in this website we have a compilation of the *software modules* that have been documented by the E-CAM_ community
within the four initial target areas of E-CAM_. These four areas represent the relative diversity of the broad domain of interest relevant to E-CAM_, and indeed the wider `CECAM <https://www.cecam.org/>`_ community:
.. toctree::
:maxdepth: 1
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment