Commit 9dadd97a authored by Luka Stanisic's avatar Luka Stanisic

doc: changing documentation style and fixing links

parent 3ff881ba
Pipeline #23635 passed with stages
in 8 minutes and 51 seconds
# BioEM: Bayesian inference of Electron Microscopy
# 1.0 VERSION: June, 2016
# 2.0 VERSION: January, 2018
## Build status and test coverage
[![Build status](https://gitlab.mpcdf.mpg.de/MPIBP-Hummer/BioEM/badges/master/build.svg)](https://gitlab.mpcdf.mpg.de/sluka/BioEM/commits/master)
[![Code coverage](https://gitlab.mpcdf.mpg.de/MPIBP-Hummer/BioEM/badges/master/coverage.svg?job=total_coverage)](http://sluka.pages.mpcdf.de/BioEM/)
[![Build status](https://gitlab.mpcdf.mpg.de/MPIBP-Hummer/BioEM/badges/master/build.svg)](https://gitlab.mpcdf.mpg.de/MPIBP-Hummer/BioEM/commits/master)
[![Code coverage](https://gitlab.mpcdf.mpg.de/MPIBP-Hummer/BioEM/badges/master/coverage.svg?job=total_coverage)](http://MPIBP-Hummer.pages.mpcdf.de/BioEM/)
[![Doc](https://readthedocs.org/projects/pip/badge/?version=stable)](http://bioem.readthedocs.io)
[![License: GPL v3][license-badge]](License.txt)
......@@ -28,7 +28,7 @@ The BioEM software computes this integral via numerical grid sampling over a por
By comparing the BioEM posterior probabilities it is possible to discriminate and rank structural models, allowing to characterize
the variability and dynamics of the biological system.
For a detailed description of the BioEM software see the BioEM_Maunal.pdf that is provided in the Manual directory.
For a detailed description of the BioEM software see the [BioEM documentation](http://bioem.readthedocs.io), also provided in the doc/ directory.
### Command line input & help is found by just running the compiled executable ./bioEM
......@@ -47,7 +47,7 @@ For a detailed description of the BioEM software see the BioEM_Maunal.pdf that i
--OutputFile arg (Optional) For changing the outputfile name
--help (Optional) Produce help message
Details for the inputfiles and formats are provided in chapters 1 and 2 of the BioEM_Manual.pdf.
Details for the inputfiles and formats are provided in sections [1](http://bioem.readthedocs.io/en/latest/index.html#the-bioem-software) and [2](http://bioem.readthedocs.io/en/latest/index.html#bioem-input) of the [BioEM documentation](http://bioem.readthedocs.io).
### Output
......@@ -59,12 +59,12 @@ Details for the inputfiles and formats are provided in chapters 1 and 2 of the B
**Important: It is recommended to compare log(P) with respect to other Models or to Noise as in [1].
* (Optional) Write the posterior probabilities as a function of the orientations (key word: WRITE_PROB_ANGLES in InputFile, see BioEM_Manual.pdf).
* (Optional) Write the posterior probabilities as a function of the orientations (key word: WRITE_PROB_ANGLES in InputFile, see [documentation](http://bioem.readthedocs.io/en/latest/index.html#std:inpar-WRITE_PROB_ANGLES)).
### Tutorial
A directory with example EM particles, models, and input files are provided in the Tutorial_BioEM directory.
The tutorial is described in chapter 4 of the BioEM_Manual.pdf
The tutorial is described in [section 4 of the BioEM documentation](http://bioem.readthedocs.io/en/latest/index.html#tutorial).
### Installation
......@@ -106,14 +106,14 @@ Dependencies and software requirements:
for free software see: https://developer.nvidia.com/cuda-downloads
For details on the installation chapter 1 of the BioEM_Manual.pdf.
For details on the installation [section 1 of the BioEM documentation](http://bioem.readthedocs.io/en/latest/index.html#the-bioem-software).
### Performance Variables
The BioEM performance variables enhance or modify the code's computational performance without modifying the numerical results.
They should be tuned for the specific computing node characteristics where bioEM is executed, e.g., select the number of GPUs to use, OpenMP
threads etc. These are passed via environment variables. See chapter 3 of the BioEM_Manual.pdf for a detailed description.
threads etc. These are passed via environment variables. See [section 4 of the BioEM documentation](http://bioem.readthedocs.io/en/latest/index.html#performance) for a detailed description.
### License
......
"""Sphinx ReadTheDocs theme.
From https://github.com/ryan-roemer/sphinx-bootstrap-theme.
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from os import path
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nav.enableSticky = function() {
this.enable(true);
};
nav.init = function ($) {
var doc = $(document),
self = this;
this.navBar = $('div.wy-side-scroll:first');
this.win = $(window);
// Set up javascript UX bits
$(document)
// Shift nav in mobile when clicking the menu.
.on('click', "[data-toggle='wy-nav-top']", function() {
$("[data-toggle='wy-nav-shift']").toggleClass("shift");
$("[data-toggle='rst-versions']").toggleClass("shift");
})
// Nav menu link click operations
.on('click', ".wy-menu-vertical .current ul li a", function() {
var target = $(this);
// Close menu when you click a link.
$("[data-toggle='wy-nav-shift']").removeClass("shift");
$("[data-toggle='rst-versions']").toggleClass("shift");
// Handle dynamic display of l3 and l4 nav lists
self.toggleCurrent(target);
self.hashChange();
})
.on('click', "[data-toggle='rst-current-version']", function() {
$("[data-toggle='rst-versions']").toggleClass("shift-up");
})
// Make tables responsive
$("table.docutils:not(.field-list,.footnote,.citation)")
.wrap("<div class='wy-table-responsive'></div>");
// Add extra class to responsive tables that contain
// footnotes or citations so that we can target them for styling
$("table.docutils.footnote")
.wrap("<div class='wy-table-responsive footnote'></div>");
$("table.docutils.citation")
.wrap("<div class='wy-table-responsive citation'></div>");
// Add expand links to all parents of nested ul
$('.wy-menu-vertical ul').not('.simple').siblings('a').each(function () {
var link = $(this);
expand = $('<span class="toctree-expand"></span>');
expand.on('click', function (ev) {
self.toggleCurrent(link);
ev.stopPropagation();
return false;
});
link.prepend(expand);
});
};
nav.reset = function () {
// Get anchor from URL and open up nested nav
var anchor = encodeURI(window.location.hash);
if (anchor) {
try {
var link = $('.wy-menu-vertical')
.find('[href="' + anchor + '"]');
// If we didn't find a link, it may be because we clicked on
// something that is not in the sidebar (eg: when using
// sphinxcontrib.httpdomain it generates headerlinks but those
// aren't picked up and placed in the toctree). So let's find
// the closest header in the document and try with that one.
if (link.length === 0) {
var doc_link = $('.document a[href="' + anchor + '"]');
var closest_section = doc_link.closest('div.section');
// Try again with the closest section entry.
link = $('.wy-menu-vertical')
.find('[href="#' + closest_section.attr("id") + '"]');
}
// If we found a matching link then reset current and re-apply
// otherwise retain the existing match
if (link.length > 0) {
$('.wy-menu-vertical li.toctree-l1 li.current').removeClass('current');
link.closest('li.toctree-l2').addClass('current');
link.closest('li.toctree-l3').addClass('current');
link.closest('li.toctree-l4').addClass('current');
}
}
catch (err) {
console.log("Error expanding nav for anchor", err);
}
}
};
nav.onScroll = function () {
this.winScroll = false;
var newWinPosition = this.win.scrollTop(),
winBottom = newWinPosition + this.winHeight,
navPosition = this.navBar.scrollTop(),
newNavPosition = navPosition + (newWinPosition - this.winPosition);
if (newWinPosition < 0 || winBottom > this.docHeight) {
return;
}
this.navBar.scrollTop(newNavPosition);
this.winPosition = newWinPosition;
};
nav.onResize = function () {
this.winResize = false;
this.winHeight = this.win.height();
this.docHeight = $(document).height();
};
nav.hashChange = function () {