Add and update links.

mutalyzer/__init__.py

@@ -21,7 +21,7 @@
 # [1] http://peak.telecommunity.com/DevCenter/setuptools#specifying-your-project-s-version
 # [2] http://semver.org/
 
-__version_info__ = ('2', '0', '33')
+__version_info__ = ('2', '0', '34' 'dev')
 __date__ = '24 November 2020'
 
 

mutalyzer/website/templates/about.html

@@ -98,13 +98,12 @@ <h2>Development</h2>
 </p>
 
 <p>
-Since references to WWW-sites are not yet acknowledged as citations,
-please mention
-<a href="http://www.ncbi.nlm.nih.gov/pubmed/18000842">
-  &quot;Wildeman M et al. (2008). Improving sequence variant
-  descriptions in mutation databases and literature using the
-  Mutalyzer sequence variation nomenclature checker. Hum Mutat 29,
-  6-13&quot;</a> (<a href="http://dx.doi.org/10.1002/humu.20654">direct
+Please mention
+
+<a href="https://pubmed.ncbi.nlm.nih.gov/33538839/">
+  &quot;Lefter M et al. (2021). Mutalyzer 2: Next Generation HGVS
+  Nomenclature Checker. Bioinformatics, btab051&quot;</a>
+  (<a href="https://doi.org/10.1093/bioinformatics/btab051">direct
   link</a>) when referring to these pages.
 </p>
 

mutalyzer/website/templates/base.html

@@ -93,11 +93,13 @@
             <li class="dropdown {% if id == active_page %} active{% endif %}">
               <a href="#" class="dropdown-toggle" data-toggle="dropdown">External links <span class="caret"></span></a>
               <ul class="dropdown-menu">
-                <li class="menu{% if id == active_page %} active{% endif %}"><a href="http://www.genenames.org/guidelines.html">Human Gene Nomenclature</a></li>
+                <li class="menu{% if id == active_page %} active{% endif %}">
+                    <a href="http://www.genenames.org/guidelines.html" target="_blank">Human Gene Nomenclature</a></li>
                 <li class="menu{% if id == active_page %} active{% endif
-                %}"><a href="https://varnomen.hgvs.org/">HGVS Sequence
+                %}"><a href="https://varnomen.hgvs.org/" target="_blank">HGVS Sequence
                 Variant Nomenclature</a></li>
-                <li class="menu{% if id == active_page %} active{% endif %}"><a href="http://www.lovd.nl/">LOVD</a></li>
+                <li class="menu{% if id == active_page %} active{% endif %}">
+                    <a href="http://www.lovd.nl/" target="_blank">LOVD</a></li>
               </ul>
             </li>
 
@@ -106,16 +108,16 @@
                 <ul class="dropdown-menu">
 
                     <li>
-                        <a href="https://github.com/mutalyzer/mutalyzer/wiki/Documentation">Documentation</a>
+                        <a href="https://github.com/mutalyzer/mutalyzer/wiki/Documentation" target="_blank">Documentation</a>
                     </li>
                     <li>
-                        <a href="https://github.com/mutalyzer/mutalyzer/wiki/Mutalyzer-FAQ">FAQ</a>
+                        <a href="https://github.com/mutalyzer/mutalyzer/wiki/Mutalyzer-FAQ" target="_blank">FAQ</a>
                     </li>
                     <li>
-                        <a href="https://github.com/mutalyzer/mutalyzer/wiki/Mutalyzer-Exercise">Exercise</a>
+                        <a href="https://github.com/mutalyzer/mutalyzer/wiki/Mutalyzer-Exercise" target="_blank">Exercise</a>
                     </li>
                     <li>
-                        <a href="https://groups.google.com/forum/#!forum/mutalyzer">Mailing list</a>
+                        <a href="https://groups.google.com/forum/#!forum/mutalyzer" target="_blank">Mailing list</a>
                     </li>
                 </ul>
             </li>
@@ -127,7 +129,7 @@
         </ul>
         <ul class="nav navbar-nav navbar-right">
             <li>
-                <a class="navbar-brand" href="https://github.com/mutalyzer/mutalyzer"><img
+                <a class="navbar-brand" href="https://github.com/mutalyzer/mutalyzer" target="_blank"><img
                   src="{{ url_for('static', filename='images/github_logo.png') }}" title="Mutalyzer on GitHub"></a>
             </li>
         </ul>
@@ -150,6 +152,16 @@
                 </div>
                 {% endif %}
 
+                <div id="new-version"
+                     class="alert alert-info block"
+                     style="background-color: #d9edf7; padding-top:20px; padding-bottom:20px;">
+                    <p>
+                        <strong>Check out the</strong>
+                        <a href="https://v3.mutalyzer.nl/">Mutalyzer 3 Alpha</a>
+                        <strong>release!</strong>
+                    </p>
+                </div>
+
                 <!-- Main content -->
                 <div class="block block-shadow">
                 {% if page_title %}<h1>{{ page_title }}</h1>{% endif %}

requirements.txt

@@ -1,30 +1,30 @@
 -e git+https://github.com/mutalyzer/magic-python.git@centos6-fix#egg=Magic_file_extensions
-Flask==1.1.1
-Jinja2==2.10.1
+Flask==1.1.2
+Jinja2==2.11.3
 MySQL-python==1.2.5
-PyYAML==5.2
-SQLAlchemy==1.3.11
+PyYAML==5.4.1
+SQLAlchemy==1.3.23
 Sphinx==1.8.5
-Werkzeug==0.16.0
-alembic==1.3.1
+Werkzeug==1.0.1
+alembic==1.5.7
 backtranslate==0.0.5
 biopython==1.75
-chardet==3.0.4
+chardet==4.0.0
 cssselect==1.1.0
 -e git+https://github.com/mutalyzer/crossmapper-legacy.git#egg=crossmapper
 description-extractor==2.3.5
 interval-binning==1.0.0
-lxml==4.4.2
+lxml==4.6.2
 mock==3.0.5
 mockredispy==2.9.3
 pyparsing==2.0.5
-pytest==4.6.7
-pytz==2019.3
-redis==3.3.11
-requests==2.22.0
-simplejson==3.17.0
-sphinx-rtd-theme==0.4.3
-spyne==2.12.16
+pytest==4.6.11
+pytz==2021.1
+redis==3.5.3
+requests==2.25.1
+simplejson==3.17.2
+sphinx-rtd-theme==0.5.1
+spyne==2.13.16
 suds==0.4
 wsgiref==0.1.2
 xlrd==1.2.0