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Commit 00e5fd40 authored by Studer Gabriel's avatar Studer Gabriel
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Merge branch 'release-3.2.1'

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CHANGELOG
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......@@ -5,6 +5,11 @@
Changelog
================================================================================
Release 3.2.1
--------------------------------------------------------------------------------
* Bugfix release: Updates OpenStructure dependency to 2.3.0
Release 3.2.0
--------------------------------------------------------------------------------
......
CMakeLists.txt
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......@@ -25,7 +25,7 @@ include(PROMOD3)
# versioning info
set(PROMOD3_VERSION_MAJOR 3)
set(PROMOD3_VERSION_MINOR 2)
set(PROMOD3_VERSION_PATCH 0)
set(PROMOD3_VERSION_PATCH 1)
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
......@@ -103,7 +103,7 @@ if(NOT DISABLE_DOCUMENTATION)
# this URL should always point to the latest version of OST
set(OST_DOC_URL "https://www.openstructure.org/docs")
endif()
find_package(OPENSTRUCTURE 2.2.0 REQUIRED
find_package(OPENSTRUCTURE 2.3.0 REQUIRED
COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm)
if(CMAKE_COMPILER_IS_GNUCXX)
......
NOTICE
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......@@ -7,5 +7,8 @@ The main authors are: Gabriel Studer, Gerardo Tauriello, Stefan Bienert,
Marco Biasini, Niklaus Johner
If you find this software useful, please cite:
TO BE PUBLISHED
Studer, Gabriel; Tauriello, Gerardo; Bienert, Stefan; Biasini, Marco; Johner,
Niklaus; Schwede, Torsten (2021). ProMod3 - A versatile homology modelling
toolbox. PLoS computational biology, 17 (1), e1008667.
container/Dockerfile
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ARG OPENSTRUCTURE_IMAGE_TAG="2.2.0-focal"
ARG OPENSTRUCTURE_IMAGE_TAG="2.3.0-focal"
FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_IMAGE_TAG}
# ARGUMENTS
###########
ARG PROMOD_VERSION="3.2.0"
ARG PROMOD_VERSION="3.2.1"
ARG SRC_FOLDER="/usr/local/src"
......@@ -17,7 +17,7 @@ ENV PROMOD_ROOT="/usr/local"
#################
RUN cd ${SRC_FOLDER} && \
# copy promod release
wget -O promod-${PROMOD_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/ProMod3/repository/${PROMOD_VERSION}/archive.tar.gz && \
wget -O promod-${PROMOD_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/ProMod3/-/archive/${PROMOD_VERSION}/promod-${PROMOD_VERSION}.tar.gz && \
mkdir promod-${PROMOD_VERSION} && \
tar xf promod-${PROMOD_VERSION}.tar.gz -C ${SRC_FOLDER}/promod-${PROMOD_VERSION} --strip-components=1 && \
mkdir -p ${SRC_FOLDER}/promod-${PROMOD_VERSION}/build && \
......
container/Singularity
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BootStrap: docker
From: registry.scicore.unibas.ch/schwede/promod3:3.2.0-OST2.2.0-focal
From: registry.scicore.unibas.ch/schwede/promod3:3.2.1-OST2.3.0-focal
%post
##############################################################################
# POST
......
doc/conf.py.in
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......@@ -58,7 +58,7 @@ master_doc = 'index'
# General information about the project.
project = u'ProMod3'
copyright = u'2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel'# pylint: disable=redefined-builtin
copyright = u'2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel'# pylint: disable=redefined-builtin
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
......@@ -286,7 +286,7 @@ rst_epilog = """
.. |cmake| replace:: CMake
.. |ost_l| replace:: OpenStructure
.. |ost_s| replace:: OST
.. |ost_version| replace:: 2.2.0
.. |ost_version| replace:: 2.3.0
.. |python| replace:: Python
.. |sphinx| replace:: Sphinx
.. _sphinx: http://sphinx-doc.org/
......
doc/html/_sources/changelog.rst.txt
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......@@ -5,6 +5,11 @@
Changelog
================================================================================
Release 3.2.1
--------------------------------------------------------------------------------
* Bugfix release: Updates OpenStructure dependency to 2.3.0
Release 3.2.0
--------------------------------------------------------------------------------
......
doc/html/_static/ajax-loader.gif 0 → 100644
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doc/html/_static/ajax-loader.gif

673 B

doc/html/_static/alabaster.css
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@import url("basic.css");
/* -- page layout ----------------------------------------------------------- */
body {
font-family: Georgia, serif;
font-family: 'goudy old style', 'minion pro', 'bell mt', Georgia, 'Hiragino Mincho Pro', serif;
font-size: 17px;
background-color: #fff;
background-color: white;
color: #000;
margin: 0;
padding: 0;
......@@ -37,7 +54,7 @@ hr {
}
div.body {
background-color: #fff;
background-color: #ffffff;
color: #3E4349;
padding: 0 30px 0 30px;
}
......@@ -59,7 +76,7 @@ div.footer a {
}
p.caption {
font-family: inherit;
font-family: ;
font-size: inherit;
}
......@@ -107,7 +124,7 @@ div.sphinxsidebarwrapper p.blurb {
div.sphinxsidebar h3,
div.sphinxsidebar h4 {
font-family: Georgia, serif;
font-family: 'Garamond', 'Georgia', serif;
color: #444;
font-size: 24px;
font-weight: normal;
......@@ -151,7 +168,7 @@ div.sphinxsidebar ul li.toctree-l2 > a {
div.sphinxsidebar input {
border: 1px solid #CCC;
font-family: Georgia, serif;
font-family: 'goudy old style', 'minion pro', 'bell mt', Georgia, 'Hiragino Mincho Pro', serif;
font-size: 1em;
}
......@@ -166,19 +183,6 @@ div.sphinxsidebar hr {
width: 50%;
}
div.sphinxsidebar .badge {
border-bottom: none;
}
div.sphinxsidebar .badge:hover {
border-bottom: none;
}
/* To address an issue with donation coming after search */
div.sphinxsidebar h3.donation {
margin-top: 10px;
}
/* -- body styles ----------------------------------------------------------- */
a {
......@@ -197,7 +201,7 @@ div.body h3,
div.body h4,
div.body h5,
div.body h6 {
font-family: Georgia, serif;
font-family: 'Garamond', 'Georgia', serif;
font-weight: normal;
margin: 30px 0px 10px 0px;
padding: 0;
......@@ -228,17 +232,21 @@ div.body p, div.body dd, div.body li {
div.admonition {
margin: 20px 0px;
padding: 10px 30px;
background-color: #EEE;
border: 1px solid #CCC;
background-color: #FCC;
border: 1px solid #FAA;
}
div.admonition tt.xref, div.admonition code.xref, div.admonition a tt {
background-color: #FBFBFB;
div.admonition tt.xref, div.admonition a tt {
border-bottom: 1px solid #fafafa;
}
dd div.admonition {
margin-left: -60px;
padding-left: 60px;
}
div.admonition p.admonition-title {
font-family: Georgia, serif;
font-family: 'Garamond', 'Georgia', serif;
font-weight: normal;
font-size: 24px;
margin: 0 0 10px 0;
......@@ -251,71 +259,25 @@ div.admonition p.last {
}
div.highlight {
background-color: #fff;
background-color: white;
}
dt:target, .highlight {
background: #FAF3E8;
}
div.warning {
background-color: #FCC;
border: 1px solid #FAA;
}
div.danger {
background-color: #FCC;
border: 1px solid #FAA;
-moz-box-shadow: 2px 2px 4px #D52C2C;
-webkit-box-shadow: 2px 2px 4px #D52C2C;
box-shadow: 2px 2px 4px #D52C2C;
}
div.error {
background-color: #FCC;
border: 1px solid #FAA;
-moz-box-shadow: 2px 2px 4px #D52C2C;
-webkit-box-shadow: 2px 2px 4px #D52C2C;
box-shadow: 2px 2px 4px #D52C2C;
}
div.caution {
background-color: #FCC;
border: 1px solid #FAA;
}
div.attention {
background-color: #FCC;
border: 1px solid #FAA;
}
div.important {
background-color: #EEE;
border: 1px solid #CCC;
}
div.note {
background-color: #EEE;
border: 1px solid #CCC;
}
div.tip {
background-color: #EEE;
border: 1px solid #CCC;
}
div.hint {
background-color: #EEE;
border: 1px solid #CCC;
}
div.seealso {
background-color: #EEE;
border: 1px solid #CCC;
}
div.topic {
background-color: #EEE;
background-color: #eee;
}
p.admonition-title {
......@@ -327,7 +289,7 @@ p.admonition-title:after {
}
pre, tt, code {
font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
font-family: 'Consolas', 'Menlo', 'Deja Vu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
font-size: 0.9em;
}
......@@ -350,16 +312,16 @@ tt.descname, code.descname {
}
img.screenshot {
-moz-box-shadow: 2px 2px 4px #EEE;
-webkit-box-shadow: 2px 2px 4px #EEE;
box-shadow: 2px 2px 4px #EEE;
-moz-box-shadow: 2px 2px 4px #eee;
-webkit-box-shadow: 2px 2px 4px #eee;
box-shadow: 2px 2px 4px #eee;
}
table.docutils {
border: 1px solid #888;
-moz-box-shadow: 2px 2px 4px #EEE;
-webkit-box-shadow: 2px 2px 4px #EEE;
box-shadow: 2px 2px 4px #EEE;
-moz-box-shadow: 2px 2px 4px #eee;
-webkit-box-shadow: 2px 2px 4px #eee;
box-shadow: 2px 2px 4px #eee;
}
table.docutils td, table.docutils th {
......@@ -399,16 +361,6 @@ table.field-list p {
margin-bottom: 0.8em;
}
/* Cloned from
* https://github.com/sphinx-doc/sphinx/commit/ef60dbfce09286b20b7385333d63a60321784e68
*/
.field-name {
-moz-hyphens: manual;
-ms-hyphens: manual;
-webkit-hyphens: manual;
hyphens: manual;
}
table.footnote td.label {
width: .1px;
padding: 0.3em 0 0.3em 0.5em;
......@@ -445,15 +397,16 @@ pre {
line-height: 1.3em;
}
div.viewcode-block:target {
background: #ffd;
}
dl pre, blockquote pre, li pre {
margin-left: 0;
padding-left: 30px;
}
dl dl pre {
margin-left: -90px;
padding-left: 90px;
}
tt, code {
background-color: #ecf0f3;
color: #222;
......@@ -462,7 +415,7 @@ tt, code {
tt.xref, code.xref, a tt {
background-color: #FBFBFB;
border-bottom: 1px solid #fff;
border-bottom: 1px solid white;
}
a.reference {
......@@ -564,7 +517,7 @@ a:hover tt, a:hover code {
div.documentwrapper {
float: none;
background: #fff;
background: white;
}
div.sphinxsidebar {
......@@ -579,7 +532,7 @@ a:hover tt, a:hover code {
div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p,
div.sphinxsidebar h3 a {
color: #fff;
color: white;
}
div.sphinxsidebar a {
......@@ -651,51 +604,4 @@ table.docutils.citation, table.docutils.citation td, table.docutils.citation th
-moz-box-shadow: none;
-webkit-box-shadow: none;
box-shadow: none;
}
/* relbar */
.related {
line-height: 30px;
width: 100%;
font-size: 0.9rem;
}
.related.top {
border-bottom: 1px solid #EEE;
margin-bottom: 20px;
}
.related.bottom {
border-top: 1px solid #EEE;
}
.related ul {
padding: 0;
margin: 0;
list-style: none;
}
.related li {
display: inline;
}
nav#rellinks {
float: right;
}
nav#rellinks li+li:before {
content: "|";
}
nav#breadcrumbs li+li:before {
content: "\00BB";
}
/* Hide certain items when printing */
@media print {
div.related {
display: none;
}
}
\ No newline at end of file
doc/html/_static/basic.css
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......@@ -231,16 +231,6 @@ a.headerlink {
visibility: hidden;
}
a.brackets:before,
span.brackets > a:before{
content: "[";
}
a.brackets:after,
span.brackets > a:after {
content: "]";
}
h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
......@@ -289,12 +279,6 @@ img.align-center, .figure.align-center, object.align-center {
margin-right: auto;
}
img.align-default, .figure.align-default {
display: block;
margin-left: auto;
margin-right: auto;
}
.align-left {
text-align: left;
}
......@@ -303,10 +287,6 @@ img.align-default, .figure.align-default {
text-align: center;
}
.align-default {
text-align: center;
}
.align-right {
text-align: right;
}
......@@ -378,11 +358,6 @@ table.align-center {
margin-right: auto;
}
table.align-default {
margin-left: auto;
margin-right: auto;
}
table caption span.caption-number {
font-style: italic;
}
......@@ -416,16 +391,6 @@ table.citation td {
border-bottom: none;
}
th > p:first-child,
td > p:first-child {
margin-top: 0px;
}
th > p:last-child,
td > p:last-child {
margin-bottom: 0px;
}
/* -- figures --------------------------------------------------------------- */
div.figure {
......@@ -495,57 +460,11 @@ ol.upperroman {
list-style: upper-roman;
}
li > p:first-child {
margin-top: 0px;
}
li > p:last-child {
margin-bottom: 0px;
}
dl.footnote > dt,
dl.citation > dt {
float: left;
}
dl.footnote > dd,
dl.citation > dd {
margin-bottom: 0em;
}
dl.footnote > dd:after,
dl.citation > dd:after {
content: "";
clear: both;
}
dl.field-list {
display: flex;
flex-wrap: wrap;
}
dl.field-list > dt {
flex-basis: 20%;
font-weight: bold;
word-break: break-word;
}
dl.field-list > dt:after {
content: ":";
}
dl.field-list > dd {
flex-basis: 70%;
padding-left: 1em;
margin-left: 0em;
margin-bottom: 0em;
}
dl {
margin-bottom: 15px;
}
dd > p:first-child {
dd p {
margin-top: 0px;
}
......@@ -618,12 +537,6 @@ dl.glossary dt {
font-style: oblique;
}
.classifier:before {
font-style: normal;
margin: 0.5em;
content: ":";
}
abbr, acronym {
border-bottom: dotted 1px;
cursor: help;
......
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756 B

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doc/html/_static/comment-close.png

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doc/html/_static/doctools.js
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......@@ -87,13 +87,14 @@ jQuery.fn.highlightText = function(text, className) {
node.nextSibling));
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
var bbox = span.getBBox();
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
var bbox = node.parentElement.getBBox();
rect.x.baseVal.value = bbox.x;
rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute('class', className);
var parentOfText = node.parentNode.parentNode;
addItems.push({
"parent": node.parentNode,
"target": rect});
......
doc/html/_static/documentation_options.js
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− 2
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var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '3.2.0',
VERSION: '3.2.1',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
NAVIGATION_WITH_KEYS: false
NAVIGATION_WITH_KEYS: false,
};
\ No newline at end of file
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doc/html/_static/down-pressed.png

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doc/html/_static/down.png 0 → 100644
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doc/html/_static/down.png

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doc/html/_static/jquery.js
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doc/html/_static/searchtools.js
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− 38
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......@@ -36,10 +36,8 @@ if (!Scorer) {
// query found in title
title: 15,
partialTitle: 7,
// query found in terms
term: 5,
partialTerm: 2
term: 5
};
}
......@@ -58,14 +56,6 @@ var Search = {
_queued_query : null,
_pulse_status : -1,
htmlToText : function(htmlString) {
var htmlElement = document.createElement('span');
htmlElement.innerHTML = htmlString;
$(htmlElement).find('.headerlink').remove();
docContent = $(htmlElement).find('[role=main]')[0];
return docContent.textContent || docContent.innerText;
},
init : function() {
var params = $.getQueryParameters();
if (params.q) {
......@@ -130,7 +120,7 @@ var Search = {
this.out = $('#search-results');
this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
this.dots = $('<span></span>').appendTo(this.title);
this.status = $('<p class="search-summary">&nbsp;</p>').appendTo(this.out);
this.status = $('<p style="display: none"></p>').appendTo(this.out);
this.output = $('<ul class="search"/>').appendTo(this.out);
$('#search-progress').text(_('Preparing search...'));
......@@ -269,7 +259,11 @@ var Search = {
displayNextItem();
});
} else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
$.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX,
var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
if (suffix === undefined) {
suffix = '.txt';
}
$.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
dataType: "text",
complete: function(jqxhr, textstatus) {
var data = jqxhr.responseText;
......@@ -319,13 +313,12 @@ var Search = {
for (var prefix in objects) {
for (var name in objects[prefix]) {
var fullname = (prefix ? prefix + '.' : '') + name;
var fullnameLower = fullname.toLowerCase()
if (fullnameLower.indexOf(object) > -1) {
if (fullname.toLowerCase().indexOf(object) > -1) {
var score = 0;
var parts = fullnameLower.split('.');
var parts = fullname.split('.');
// check for different match types: exact matches of full name or
// "last name" (i.e. last dotted part)
if (fullnameLower == object || parts[parts.length - 1] == object) {
if (fullname == object || parts[parts.length - 1] == object) {
score += Scorer.objNameMatch;
// matches in last name
} else if (parts[parts.length - 1].indexOf(object) > -1) {
......@@ -392,19 +385,6 @@ var Search = {
{files: terms[word], score: Scorer.term},
{files: titleterms[word], score: Scorer.title}
];
// add support for partial matches
if (word.length > 2) {
for (var w in terms) {
if (w.match(word) && !terms[word]) {
_o.push({files: terms[w], score: Scorer.partialTerm})
}
}
for (var w in titleterms) {
if (w.match(word) && !titleterms[word]) {
_o.push({files: titleterms[w], score: Scorer.partialTitle})
}
}
}
// no match but word was a required one
if ($u.every(_o, function(o){return o.files === undefined;})) {
......@@ -444,12 +424,8 @@ var Search = {
var valid = true;
// check if all requirements are matched
var filteredTermCount = // as search terms with length < 3 are discarded: ignore
searchterms.filter(function(term){return term.length > 2}).length
if (
fileMap[file].length != searchterms.length &&
fileMap[file].length != filteredTermCount
) continue;
if (fileMap[file].length != searchterms.length)
continue;
// ensure that none of the excluded terms is in the search result
for (i = 0; i < excluded.length; i++) {
......@@ -480,8 +456,7 @@ var Search = {
* words. the first one is used to find the occurrence, the
* latter for highlighting it.
*/
makeSearchSummary : function(htmlText, keywords, hlwords) {
var text = Search.htmlToText(htmlText);
makeSearchSummary : function(text, keywords, hlwords) {
var textLower = text.toLowerCase();
var start = 0;
$.each(keywords, function() {
......
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