Merge pull request usnistgov#1525 from usnistgov/security

Security updates

Author: wd15

ABOUT.md

@@ -21,11 +21,11 @@ comment:
 <h4> Details and Mentions </h4>
 
 - Olle Heinonen wrote a philosophical introduction to the {{ site.title }}
-  benchmarking effort, available as an [extended essay]({{ site.baseurl }}/benchmarks){:target="_blank"}.
+  benchmarking effort, available as an [extended essay]({{ site.baseurl }}/benchmarks){:}.
 - [Andrea Jokisaari][aj], [Peter Voorhees][pv], [Jon Guyer][jg], [Jim Warren][jw] and [Olle Heinonen][oh]
   published a peer-reviewed journal article in
   *Computational Materials Science* entitled ["Benchmark problems for numerical
-  implementations of phase field models"](http://dx.doi.org/10.1016/j.commatsci.2016.09.022){:target="_blank"}.
+  implementations of phase field models"](http://dx.doi.org/10.1016/j.commatsci.2016.09.022){:}.
   - CHiMaD News posted an overview of the article entitled
     ["Benchmark Problems for Phase Field Methods"](
     http://chimad.northwestern.edu/news-events/articles/2016/PhaseField_BenchMark.html).

DEVELOPMENT.md

@@ -5,7 +5,7 @@ comment: How to modify this site (beyond adding new simulations)
 ---
 
 <p align="center">
-<a href="https://travis-ci.org/{{ site.links.repo }}" target="_blank">
+<a href="https://travis-ci.org/{{ site.links.repo }}" >
 <img src="https://api.travis-ci.org/{{ site.links.repo }}.svg"
      alt="Travis CI badge">
 </a>

README.md

@@ -15,7 +15,7 @@ See the live website at <a href="https://pages.nist.gov/pfhub">pages.nist.gov/pf
 </strong></sup></p>
 
 <p align="center">
-<a href="https://travis-ci.org/usnistgov/pfhub" target="_blank">
+<a href="https://travis-ci.org/usnistgov/pfhub" >
   <img src="https://api.travis-ci.org/usnistgov/pfhub.svg"
        alt="Travis CI badge">
 </a>
@@ -24,7 +24,7 @@ See the live website at <a href="https://pages.nist.gov/pfhub">pages.nist.gov/pf
        alt="Zenodo DOI badge">
 </a>
 <a href="https://www.openhub.net/p/pfhub"
-   target="_blank">
+   >
   <img src="https://www.openhub.net/p/pfhub/widgets/project_thin_badge.gif"
        class="badge"
        alt="OpenHub badge">

_includes/coffee/test.coffee

@@ -235,7 +235,7 @@ describe('test benchmark_id', ->
       }
     assert.deepEqual(
       benchmark_id({}, {}, data())
-      '<a href="http://wow.com" target="_blank">\n1a.0\n</a>'
+      '<a href="http://wow.com">\n1a.0\n</a>'
     )
   )
 )
@@ -257,7 +257,7 @@ describe('test commit', ->
       {revisions:{commit:{sha:'abcd', url:'a/b'}}}
     data_out = ->
       '<a href="{{ site.links.github }}/\
-      blob/abcd/a/b" target="_blank">\nabcd\n</a>'
+      blob/abcd/a/b">\nabcd\n</a>'
     assert.deepEqual(commit({}, {}, data_in()), data_out())
   )
 )

_includes/footer.html

@@ -4,12 +4,12 @@
       <div class="container">
         <ul class="footer-nav">
           <li><a class="grey-text text-lighten-4"
-             target="_blank"
+            
              href="{{ site.links.contributors }}">
             PFHub Developers
           </a></li>
           <li><a class="grey-text text-lighten-4 right"
-                 target="_blank"
+                
                  href="{{ site.links.license }}"
                  id="license">
               NIST License

_includes/navbar.html

@@ -47,8 +47,8 @@
       <li><a href="{{ site.baseurl }}/community" class="navbar-text">Community</a></li>
       <li><a href="{{ site.baseurl }}/CODE_OF_CONDUCT" class="navbar-text">Code of Conduct</a></li>
       <li><a href="{{ site.baseurl }}/codes">Suggested Codes</a></li>
-      <li><a href="{{ site.links.github }}" title="GitHub" class="navbar-text" target="_blank">GitHub</a></li>
-      <li><a href="{{ site.baseurl }}/slack" title="Slack" class="navbar-text" target="_blank">Slack</a></li>
+      <li><a href="{{ site.links.github }}" title="GitHub" class="navbar-text">GitHub</a></li>
+      <li><a href="{{ site.baseurl }}/slack" title="Slack" class="navbar-text">Slack</a></li>
 
     </ul>
 
@@ -57,12 +57,12 @@
              title="Mailing List">
           <i class="medium material-icons">email</i>
       </a></li>
-      <li><a target="_blank"
+      <li><a
              href="{{ site.links.chat }}"
              title="Chat">
           <i class="medium material-icons">chat</i>
       </a></li>
-      <li><a target="_blank"
+      <li><a
              href="{{ site.links.github }}"
              title="GitHub">
           <i class="medium material-icons">
@@ -72,7 +72,7 @@
           </i>
       </a></li>
 
-      <li><a target="_blank"
+      <li><a
              href="{{ site.baseurl }}/slack"
              title="Slack">
           <i class="medium material-icons">

_includes/simulation.html

@@ -114,15 +114,15 @@ <h5 class="sideheader">Results</h5>
   </div>
 </div>
 
-<script>
-  var SIM_NAME = new URL(window.location.href).searchParams.get("sim");
-  var CHART_DATA={{ site.data.charts.plot1d | jsonify }};
-  var ALL_DATA={{ site.data.simulations | jsonify }};
-  var CODES_DATA={{ site.data.codes | jsonify }};
-  var AXES_NAMES={{ site.data.axes_names | jsonify }};
-  var REPO={{ site.links.repo | jsonify }};
-  var BENCHMARK_DATA={{ site.data.benchmarks | jsonify }};
-</script>
+<!-- <script> -->
+<!--   var SIM_NAME = new URL(window.location.href).searchParams.get("sim"); -->
+<!--   var CHART_DATA={{ site.data.charts.plot1d | jsonify }}; -->
+<!--   var ALL_DATA={{ site.data.simulations | jsonify }}; -->
+<!--   var CODES_DATA={{ site.data.codes | jsonify }}; -->
+<!--   var AXES_NAMES={{ site.data.axes_names | jsonify }}; -->
+<!--   var REPO={{ site.links.repo | jsonify }}; -->
+<!--   var BENCHMARK_DATA={{ site.data.benchmarks | jsonify }}; -->
+<!-- </script> -->
 
 <script src="{{ site.baseurl }}/js/simulation.js"></script>
 

_includes/title.html

@@ -13,7 +13,7 @@ <h5>
         {% if page.author %}
           by
           <a href="{{ page.author_url }}"
-             target="_blank">
+            >
             {{ page.author }}
           </a>
         {% endif %}

benchmarks/benchmark1.ipynb.raw.html

@@ -698,7 +698,7 @@ <h4 id="Figure-2:-initial-$c$-for-(a),-(b)-and-(c)">Figure 2: initial $c$ for (a
 
 <div class="output_html rendered_html output_subarea ">
 <div class="bk-root">
-        <a href="https://bokeh.org" target="_blank" class="bk-logo bk-logo-small bk-logo-notebook"></a>
+        <a href="https://bokeh.org" class="bk-logo bk-logo-small bk-logo-notebook"></a>
         <span id="1002">Loading BokehJS ...</span>
     </div>
 

benchmarks/benchmark2.ipynb.raw.html

@@ -3170,7 +3170,7 @@ <h4 id="Figure-2:-initial-$c$-for-(a),-(b)-and-(c)">Figure 2: initial $c$ for (a
 <div class="output_html rendered_html output_subarea ">
 
     <div class="bk-root">
-        <a href="http://bokeh.pydata.org" target="_blank" class="bk-logo bk-logo-small bk-logo-notebook"></a>
+        <a href="http://bokeh.pydata.org" class="bk-logo bk-logo-small bk-logo-notebook"></a>
         <span id="7e84b706-d181-4438-ad99-c354b49e1cb9">Loading BokehJS ...</span>
     </div>
 </div>

benchmarks/index.md

@@ -84,7 +84,7 @@ codes, but were still designed to be not too computationally
 demanding. The National Institute of Standards and Technology has
 played a coordinating role in the development and management of these
 problems, and also hosts a [website for the Micromagnetic Standard
-Problems](http://www.ctcms.nist.gov/~rdm/mumag.org){:target="_blank"},
+Problems](http://www.ctcms.nist.gov/~rdm/mumag.org),
 as well as solutions submitted by the community. The Micromagnetic
 Standard Problems were extremely useful to the community in the
 development of codes such as OOMMF, Mumax, and Magpar. It should be
@@ -108,36 +108,36 @@ to test a simple, targeted aspect of either the numerical implementation
 or the physics.
 
 The first set of benchmark problems, [BM1]({{ site.baseurl
-}}/benchmarks/benchmark1.ipynb/){:target="_blank"} and [BM2]({{
-site.baseurl }}/benchmarks/benchmark2.ipynb/){:target="_blank"},
+}}/benchmarks/benchmark1.ipynb/) and [BM2]({{
+site.baseurl }}/benchmarks/benchmark2.ipynb/),
 involve diffusion of a solute and grain growth. Technically, they use
 the Cahn-Hilliard equation for a conserved order parameter, and
 coupled Cahn-Hilliard and Allen-Cahn equations for conserved and
 non-conserved order parameters. Successfully solving the models
 demonstrates that the fundamentals of a modeling framework are sound.
 
 The second set of benchmark problems, [BM3]({{ site.baseurl
-}}/benchmarks/benchmark3.ipynb/){:target="_blank"} and [BM4]({{
-site.baseurl }}/benchmarks/benchmark4.ipynb/){:target="_blank"},
+}}/benchmarks/benchmark3.ipynb/) and [BM4]({{
+site.baseurl }}/benchmarks/benchmark4.ipynb/),
 involve coupling phase transformations with additional physics,
 namely, Fourier's heat equation and Hooke's Law. BM3, which is
 dendritic growth in solidification from an undercooled liquid, also
 focuses on how a solver can address the very different length scales
 that arise in the problem. 
 
 The third set of benchmark problems, [BM5]({{ site.baseurl
-}}/benchmarks/benchmark5-hackathon.ipynb/){:target="_blank"} and
+}}/benchmarks/benchmark5-hackathon.ipynb/) and
 [BM6]({{ site.baseurl
-}}/benchmarks/benchmark6-hackathon.ipynb/){:target="_blank"}, extend to
+}}/benchmarks/benchmark6-hackathon.ipynb/), extend to
 additional physics less commonly seen in phase field problems.
 Specifically, BM5 involves modeling Stokes' flow equations and BM6
 couples diffusion to the Poisson equation for electrostatic charge.
 
 The fourth set of benchmark problems, [BM7]({{ site.baseurl
-}}/benchmarks/benchmark7.ipynb/){:target="_blank"}, directly tests the
+}}/benchmarks/benchmark7.ipynb/), directly tests the
 implemented discretizations of space and time using the Method of
 Manufactured Solutions applied to the Allen-Cahn equation.
 
 For details of any or all of these benchmark problems, please refer to
 the [list of benchmarks 
-problems]({{ site.baseurl }}/#benchmarks){:target="_blank"}.
+problems]({{ site.baseurl }}/#benchmarks).

community.html

@@ -25,7 +25,7 @@ <h5 class="sideheader">
 
               <span class="card-title">
                 <a href="{% if item.home %}{{ item.home }}{% else %}{{ github_url }}{% endif %}"
-                   target="_blank"
+                  
                    title="home page"
                    data-proofer-ignore>
                   {{ item.name }}

hackathons/hackathon2/index.ipynb.raw.html

@@ -102,9 +102,9 @@ <h3 id="Solutions">Solutions<a class="anchor-link" href="#Solutions">&#182;</a><
 <div class="text_cell_render border-box-sizing rendered_html">
 <h4 id="University-of-Connecticut:-Moose">University of Connecticut: Moose<a class="anchor-link" href="#University-of-Connecticut:-Moose">&#182;</a></h4><p><a href="https://github.com/kcpitike/Hackathon-2">GitHub Repo</a></p>
 <iframe src="//www.slideshare.net/slideshow/embed_code/key/1qcfv6PO3oSgS" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe><p><strong>
-<a href="//www.slideshare.net/DanielWheeler18/chimad-phase-field-hackathon-2-university-of-connecticut" title="CHiMaD Hackathon 2: University of Connecticut" target="_blank">CHiMaD Phase Field Hackathon 2: University of Connecticut</a> </strong> by <strong>
-<a target="_blank" href="https://github.com/kcpitike">Krishina Pitike</a> </strong> and
-<strong><a target="_blank" href="https://github.com/mangerij">John Mangeri</a>
+<a href="//www.slideshare.net/DanielWheeler18/chimad-phase-field-hackathon-2-university-of-connecticut" title="CHiMaD Hackathon 2: University of Connecticut">CHiMaD Phase Field Hackathon 2: University of Connecticut</a> </strong> by <strong>
+<a href="https://github.com/kcpitike">Krishina Pitike</a> </strong> and
+<strong><a href="https://github.com/mangerij">John Mangeri</a>
 </strong>
 <br>
 <br></p>
@@ -117,11 +117,11 @@ <h4 id="University-of-Connecticut:-Moose">University of Connecticut: Moose<a cla
 <div class="inner_cell">
 <div class="text_cell_render border-box-sizing rendered_html">
 <h4 id="Pennsylvania-State-University:-Moose">Pennsylvania State University: Moose<a class="anchor-link" href="#Pennsylvania-State-University:-Moose">&#182;</a></h4><p><a href="https://github.com/wd15/penn-hackathon2/tree/master">GitHub Repo</a></p>
-<iframe src="//www.slideshare.net/slideshow/embed_code/key/Dbgdhk1Zs5JWtC" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe><p><strong> <a href="//www.slideshare.net/DanielWheeler18/chimad-hackathon-2-pennsylvania-state-university" title="CHiMaD Hackathon 2: Pennsylvania State University" target="_blank">CHiMaD Hackathon 2: Pennsylvania State University</a> 
+<iframe src="//www.slideshare.net/slideshow/embed_code/key/Dbgdhk1Zs5JWtC" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe><p><strong> <a href="//www.slideshare.net/DanielWheeler18/chimad-hackathon-2-pennsylvania-state-university" title="CHiMaD Hackathon 2: Pennsylvania State University">CHiMaD Hackathon 2: Pennsylvania State University</a> 
 </strong> by
-<strong><a target="_blank" href="https://github.com/tonkmr">Mike Tonks</a></strong>,
-<strong><a target="_blank" href="https://github.com/itgreenquist">I. Greenquist</a></strong> and
-<strong><a target="_blank" href="https://github.com/kasra83">Kasra Momeni</a></strong></p>
+<strong><a href="https://github.com/tonkmr">Mike Tonks</a></strong>,
+<strong><a href="https://github.com/itgreenquist">I. Greenquist</a></strong> and
+<strong><a href="https://github.com/kasra83">Kasra Momeni</a></strong></p>
 <p><br>
 <br></p>
 
@@ -133,9 +133,9 @@ <h4 id="Pennsylvania-State-University:-Moose">Pennsylvania State University: Moo
 <div class="inner_cell">
 <div class="text_cell_render border-box-sizing rendered_html">
 <h4 id="McGill-University:-Unknown-FE-Code-and-Julia">McGill University: Unknown FE Code and Julia<a class="anchor-link" href="#McGill-University:-Unknown-FE-Code-and-Julia">&#182;</a></h4><p><a href="https://github.com/nsmith5/chimadQ2">GitHub Repo</a></p>
-<iframe src="//www.slideshare.net/slideshow/embed_code/key/4QZp8GXqomEC0B" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe><p><strong> <a href="//www.slideshare.net/DanielWheeler18/chimad-hackathon-2-team-mcgill" title="CHiMaD Hackathon 2: Team mcgill" target="_blank">CHiMaD Hackathon 2: McGill University</a>
+<iframe src="//www.slideshare.net/slideshow/embed_code/key/4QZp8GXqomEC0B" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe><p><strong> <a href="//www.slideshare.net/DanielWheeler18/chimad-hackathon-2-team-mcgill" title="CHiMaD Hackathon 2: Team mcgill">CHiMaD Hackathon 2: McGill University</a>
 </strong> by
-<strong><a target="_blank" href="https://github.com/nsmith5">Nathan Smith</a></strong>,
+<strong><a href="https://github.com/nsmith5">Nathan Smith</a></strong>,
 <strong>T Pinomma</strong> and
 <strong>K. N. Shampur</strong></p>
 <p><br>
@@ -159,7 +159,7 @@ <h4 id="NIST:-FiPy">NIST: FiPy<a class="anchor-link" href="#NIST:-FiPy">&#182;</
 </div>
 <div class="inner_cell">
 <div class="text_cell_render border-box-sizing rendered_html">
-<h4 id="INL:-Moose">INL: Moose<a class="anchor-link" href="#INL:-Moose">&#182;</a></h4><p><iframe src="//www.slideshare.net/slideshow/embed_code/key/E1OGX4YyH0HtzK" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe> <strong> <a href="//www.slideshare.net/DanielWheeler18/chimad-hackathon-2" title="CHiMaD Hackathon 2" target="_blank">CHiMaD Hackathon 2: INL</a> </strong> by 
+<h4 id="INL:-Moose">INL: Moose<a class="anchor-link" href="#INL:-Moose">&#182;</a></h4><p><iframe src="//www.slideshare.net/slideshow/embed_code/key/E1OGX4YyH0HtzK" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe> <strong> <a href="//www.slideshare.net/DanielWheeler18/chimad-hackathon-2" title="CHiMaD Hackathon 2">CHiMaD Hackathon 2: INL</a> </strong> by 
 <strong>Karim Ahmed</strong> and
 <strong>Sudipta Biwas</strong></p>
 <p><br>
@@ -172,7 +172,7 @@ <h4 id="INL:-Moose">INL: Moose<a class="anchor-link" href="#INL:-Moose">&#182;</
 </div>
 <div class="inner_cell">
 <div class="text_cell_render border-box-sizing rendered_html">
-<h4 id="University-of-Michigan:-PRISMS">University of Michigan: PRISMS<a class="anchor-link" href="#University-of-Michigan:-PRISMS">&#182;</a></h4><p><iframe src="//www.slideshare.net/slideshow/embed_code/key/3ERQSQGzAh1dZq" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe> <strong> <a href="//www.slideshare.net/DanielWheeler18/chimad-hackathon-2-university-of-michigan" title="CHiMaD Hackathon 2: University of Michigan" target="_blank">CHiMaD Hackathon 2: University of Michigan</a> </strong> by
+<h4 id="University-of-Michigan:-PRISMS">University of Michigan: PRISMS<a class="anchor-link" href="#University-of-Michigan:-PRISMS">&#182;</a></h4><p><iframe src="//www.slideshare.net/slideshow/embed_code/key/3ERQSQGzAh1dZq" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe> <strong> <a href="//www.slideshare.net/DanielWheeler18/chimad-hackathon-2-university-of-michigan" title="CHiMaD Hackathon 2: University of Michigan">CHiMaD Hackathon 2: University of Michigan</a> </strong> by
 <strong>Jason Luce</strong> and
 <strong>Beck Andrews</strong></p>
 

js/data_table.coffee

@@ -15,7 +15,7 @@ fauthor = (data, type, row) ->
 
 fcode = (data, type, row) ->
   if data.url
-    '<a href="' + data.url + '" target="_blank">' + data.name + '</a>'
+    '<a href="' + data.url + '">' + data.name + '</a>'
   else
     data.name
 

js/moment.min.js

@@ -18,7 +18,7 @@
   </div>
 </div>
 
-<script>
-  var SIM_NAME = new URL(window.location.href).searchParams.get("sim");
-  $('#sim_name').html(SIM_NAME);
-</script>
+<!-- <script> -->
+<!--   var SIM_NAME = new URL(window.location.href).searchParams.get("sim"); -->
+<!--   $('#sim_name').html(SIM_NAME); -->
+<!-- </script> -->

results/benchmark1a.1.ipynb.raw.html

@@ -10,7 +10,7 @@ <h2 class="header">
       </h2>
       <h4>
         This upload form no longer works.
-        <a target="_blank"
+        <a
            href="{{ site.baseurl }}/simulations/upload/">
           Please use the manual upload procedure.
         </a>
@@ -20,12 +20,12 @@ <h4>
           Fill out this form to submit a new benchmark result to the
           website. The data will be submitted via a pull-request on
           GitHub. Please go to
-          <a target="_blank" href="{{ site.links.github }}/pulls">
+          <a href="{{ site.links.github }}/pulls">
              {{ site.links.repo }}
           </a>
           to view the pull-request. To upload a new benchmark result
           with a manual pull request, please follow the
-          <a target="_blank"
+          <a
              href="{{ site.baseurl }}/simulations/upload">
             manual upload instructions
           </a>. This form can be populated from an existing result by