Sync with the source at 5c272af

Author: pavoljuhas

NSFnugget.html

@@ -120,11 +120,11 @@ <h1>Enabling new science in nanoscale structure characterization of complex mate
 that are described in more detail in <a class="footnote-reference brackets" href="#id2" id="id1">1</a>. The beta version of PDFgui
 is now in public release, available for Windows, Linux and Mac OSX platforms,
 and in the first month has been downloaded 220 times. More information can be
-found at <a class="reference external" href="http://www.diffpy.org">http://www.diffpy.org</a>.</p>
+found at <a class="reference external" href="https://www.diffpy.org">https://www.diffpy.org</a>.</p>
 <dl class="footnote brackets">
 <dt class="label" id="id2"><span class="brackets"><a class="fn-backref" href="#id1">1</a></span></dt>
 <dd><p>C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch,
-Th. Proffen and S. J. L. Billinge, <a class="reference external" href="http://iopscience.iop.org/0953-8984/19/33/335219/">PDFfit2 and PDFgui: computer
+Th. Proffen and S. J. L. Billinge, <a class="reference external" href="https://doi.org/10.1088/0953-8984/19/33/335219">PDFfit2 and PDFgui: computer
 programs for studying nanostructure in crystals</a>,
 <em>J. Phys.: Condens.  Mat.</em> <strong>19</strong>, 335219 (2007)
 <a class="reference external" href="doc/pdfgui/Farrow-jpcm-2007.pdf"><img alt="downloadFarrowJpcm07" src="_images/pdficon_small.png" /></a></p>

index.html

@@ -109,15 +109,15 @@ <h1>DiffPy - Atomic Structure Analysis in Python<a class="headerlink" href="#dif
 Complex Modeling framework, a modular software framework for robust and extensible
 modeling of diffraction data.  We welcome contributions to this project from the
 community.</p>
-<p>The project is currently centered at <a class="reference external" href="http://www.bnl.gov/">Brookhaven National Laboratory</a>, a US <a class="reference external" href="https://science.energy.gov/bes/">Department of
+<p>The project is currently centered at <a class="reference external" href="https://www.bnl.gov/">Brookhaven National Laboratory</a>, a US <a class="reference external" href="https://science.energy.gov/bes/">Department of
 Energy, Office of Basic Energy Sciences</a> funded laboratory.
 Many parts of the code were developed under the diffraction part of the <a class="reference external" href="http://danse.us/">DANSE</a> project,
-a software construction project funded by the <a class="reference external" href="http://www.nsf.gov/">National Science Foundation</a> to provide
+a software construction project funded by the <a class="reference external" href="https://www.nsf.gov/">National Science Foundation</a> to provide
 data analysis software tools for neutron scattering experiments.  This project was previously
 centered at Columbia University and, before that, Michigan State University.</p>
 <a class="reference internal image-reference" href="_images/blank1x1.png"><img alt="_images/blank1x1.png" class="align-left" src="_images/blank1x1.png" style="height: 10px;" /></a>
 <div class="figure align-left">
-<a class="reference external image-reference" href="http://www.bnl.gov/"><img alt="_images/BNL_logo.jpg" src="_images/BNL_logo.jpg" /></a>
+<a class="reference external image-reference" href="https://www.bnl.gov/"><img alt="_images/BNL_logo.jpg" src="_images/BNL_logo.jpg" /></a>
 </div>
 <div class="figure align-right">
 <a class="reference external image-reference" href="https://science.energy.gov/bes/"><img alt="_images/DOE_logo.png" src="_images/DOE_logo.png" /></a>

products/SrMise.html

@@ -144,9 +144,9 @@ <h2>Getting Started<a class="headerlink" href="#getting-started" title="Permalin
 executables, installation instructions, and licensing information
 for some popular options are listed below.</p>
 <ul class="simple">
-<li><p><a class="reference external" href="https://www.anaconda.com/download">Anaconda</a></p></li>
-<li><p><a class="reference external" href="https://www.enthought.com/products/canopy/">Enthought Canopy</a></p></li>
-<li><p><a class="reference external" href="https://code.google.com/p/pythonxy/">Python(x,y)</a></p></li>
+<li><p><a class="reference external" href="https://www.anaconda.com/distribution">Anaconda</a></p></li>
+<li><p><a class="reference external" href="https://www.enthought.com/product/canopy/">Enthought Canopy</a></p></li>
+<li><p><a class="reference external" href="https://python-xy.github.io">Python(x,y)</a></p></li>
 <li><p><a class="reference external" href="http://winpython.github.io">WinPython</a></p></li>
 </ul>
 <p>Alternately, individual Windows executables for Python and the required
@@ -155,14 +155,14 @@ <h2>Getting Started<a class="headerlink" href="#getting-started" title="Permalin
 sure to download the 32-bit versions of these packages.</p>
 <ul class="simple">
 <li><p><a class="reference external" href="https://www.python.org/downloads/windows/">Python 2.6/2.7</a></p></li>
-<li><p><a class="reference external" href="http://sourceforge.net/projects/numpy/files/NumPy/">NumPy</a></p></li>
-<li><p><a class="reference external" href="http://sourceforge.net/projects/scipy/files/scipy/">SciPy</a></p></li>
-<li><p><a class="reference external" href="http://matplotlib.org/downloads.html">matplotlib</a></p></li>
+<li><p><a class="reference external" href="https://sourceforge.net/projects/numpy/files/NumPy/">NumPy</a></p></li>
+<li><p><a class="reference external" href="https://sourceforge.net/projects/scipy/files/scipy/">SciPy</a></p></li>
+<li><p><a class="reference external" href="https://matplotlib.org/downloads.html">matplotlib</a></p></li>
 </ul>
 <p>After installing Python and the required packages, we can install SrMise.
 The simplest way to obtain diffpy.srmise on Windows systems
 is using <code class="docutils literal notranslate"><span class="pre">pip</span></code> to download and install the latest release from the
-<a class="reference external" href="https://pypi.python.org">Python Package Index</a> (PyPI).  To do so, open a
+<a class="reference external" href="https://pypi.org">Python Package Index</a> (PyPI).  To do so, open a
 command window by running <code class="docutils literal notranslate"><span class="pre">cmd</span></code> from the Start Menu’s application search box
 (Windows 7/8/10) or Run command (Windows Vista and earlier).  Verify that the
 <code class="docutils literal notranslate"><span class="pre">pip</span></code> program is installed by running</p>
@@ -199,13 +199,13 @@ <h2>Getting Started<a class="headerlink" href="#getting-started" title="Permalin
 </div>
 <p>The simplest way to obtain diffpy.srmise on Mac OS X systems
 is using <code class="docutils literal notranslate"><span class="pre">pip</span></code> to download and install the latest release from
-<a class="reference external" href="https://pypi.python.org">PyPI</a>.</p>
+<a class="reference external" href="https://pypi.org">PyPI</a>.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">pip</span> <span class="n">install</span> <span class="n">diffpy</span><span class="o">.</span><span class="n">srmise</span>
 </pre></div>
 </div>
 <p>If you prefer to install from sources, download them from the
 <a class="reference external" href="https://github.com/diffpy/diffpy.srmise/releases">GitHub</a> or
-<a class="reference external" href="https://pypi.python.org/pypi/diffpy.srmise">PyPI</a> pages for SrMise.
+<a class="reference external" href="https://pypi.org/project/diffpy.srmise">PyPI</a> pages for SrMise.
 Uncompress them to a directory, and from that directory run</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span>
 </pre></div>
@@ -230,13 +230,13 @@ <h2>Getting Started<a class="headerlink" href="#getting-started" title="Permalin
 <p>For other Linux distributions consult the appropriate package manager.</p>
 <p>The simplest way to obtain diffpy.srmise on Linux systems
 is using <code class="docutils literal notranslate"><span class="pre">pip</span></code> to download and install the latest release from
-<a class="reference external" href="https://pypi.python.org">PyPI</a>.</p>
+<a class="reference external" href="https://pypi.org">PyPI</a>.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">pip</span> <span class="n">install</span> <span class="n">diffpy</span><span class="o">.</span><span class="n">srmise</span>
 </pre></div>
 </div>
 <p>If you prefer to install from sources, download them from the
 <a class="reference external" href="https://github.com/diffpy/diffpy.srmise/releases">GitHub</a> or
-<a class="reference external" href="https://pypi.python.org/pypi/diffpy.srmise">PyPI</a> pages for SrMise.
+<a class="reference external" href="https://pypi.org/project/diffpy.srmise">PyPI</a> pages for SrMise.
 Uncompress them to a directory, and from that directory run</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span>
 </pre></div>

products/diffpycmi/index.html

@@ -120,7 +120,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <p>As of version 2.0 DiffPy-CMI is available for Linux and
 Mac as a collection of packages for Anaconda Python.  As
 a first step download and install <strong>Anaconda for Python 2.7</strong>
-from <a class="reference external" href="https://www.anaconda.com/download">https://www.anaconda.com/download</a>.</p>
+from <a class="reference external" href="https://www.anaconda.com/distribution">https://www.anaconda.com/distribution</a>.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
 <p>If you already have Anaconda for Python 3.5, create a separate

products/diffpycmi/install.html

@@ -127,8 +127,8 @@ <h3>Fedora<a class="headerlink" href="#fedora" title="Permalink to this headline
 <div class="section" id="mac-os-x">
 <h3>Mac OS X<a class="headerlink" href="#mac-os-x" title="Permalink to this headline">¶</a></h3>
 <p>For Mac OS X the system dependencies can be installed using the
-<a class="reference external" href="http://www.macports.org">MacPorts</a> software manager.  A similar
-package system <a class="reference external" href="http://brew.sh">Homebrew</a> works as well, but has
+<a class="reference external" href="https://www.macports.org">MacPorts</a> software manager.  A similar
+package system <a class="reference external" href="https://brew.sh">Homebrew</a> works as well, but has
 been considerably less tested with DiffPy-CMI.</p>
 <p>For best results with MacPorts follow these tips:</p>
 <ul class="simple">

products/mPDF.html

@@ -124,7 +124,7 @@ <h2>Getting Started<a class="headerlink" href="#getting-started" title="Permalin
 <div class="section" id="installation">
 <h3>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h3>
 <p>The recommended way to install this package is through conda. For help installing conda,
-please visit <a class="reference external" href="https://www.anaconda.com/download">https://www.anaconda.com/download</a>.
+please visit <a class="reference external" href="https://www.anaconda.com/distribution">https://www.anaconda.com/distribution</a>.
 Once conda is installed, you can follow the simple steps below to install diffpy.mpdf.
 You will also install the full diffpy-cmi suite along the way.</p>
 <p><em>Step 1: Add the appropriate conda channels to your conda configuration.</em></p>
@@ -155,7 +155,7 @@ <h3>Installation<a class="headerlink" href="#installation" title="Permalink to t
 </div>
 <p><em>Alternative option: Download and install from source.</em></p>
 <p>If you prefer to install from source, you can also zip and download the entire package
-from <a class="reference external" href="https://pypi.python.org/pypi/diffpy.mpdf">PyPI</a> or
+from <a class="reference external" href="https://pypi.org/project/diffpy.mpdf">PyPI</a> or
 <a class="reference external" href="https://github.com/benfrandsen/diffpy.magpdf">GitHub</a>, then unzip the file and
 execute the following command from inside the unzipped directory</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span>
@@ -165,7 +165,7 @@ <h3>Installation<a class="headerlink" href="#installation" title="Permalink to t
 </div>
 <div class="section" id="documentation">
 <h3>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h3>
-<p>Please see <a class="reference external" href="http://pythonhosted.org/diffpy.mpdf/">http://pythonhosted.org/diffpy.mpdf/</a>
+<p>Please see <a class="reference external" href="https://pythonhosted.org/diffpy.mpdf">https://pythonhosted.org/diffpy.mpdf</a>
 for the documentation.</p>
 </div>
 </div>

products/pdfgui.html

@@ -116,49 +116,57 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <p>By downloading and using this software you are agreeing to the
 conditions specified in the <a class="reference internal" href="pdfguilicense.html"><span class="doc">software license</span></a>.</p>
 <p>PDFgui is distributed as a software package for
-<a class="reference external" href="https://www.continuum.io">Anaconda Python</a>.  PDFgui is available
-for all operating systems supported by Anaconda, namely for 32 and
-64-bit Linux, Mac OS X, and 32 and 64-bit Windows.</p>
+<a class="reference external" href="https://www.anaconda.com">Anaconda Python</a>.  PDFgui is available
+for all operating systems supported by Anaconda, namely for
+Linux, Mac OS X, and Windows.</p>
 <p>As a prerequisite for PDFgui installation, download and
-install <strong>Anaconda for Python 2.7</strong> from
-<a class="reference external" href="https://www.anaconda.com/download">https://www.anaconda.com/download</a>.</p>
+install <strong>Anaconda Python</strong> from
+<a class="reference external" href="https://www.anaconda.com/distribution">https://www.anaconda.com/distribution</a>.</p>
 <div class="admonition important">
 <p class="admonition-title">Important</p>
 <p>As of July 2019 Anaconda stopped providing older versions
 of several packages that are required by PDFgui
 (details <a class="reference external" href="https://www.anaconda.com/why-we-removed-the-free-channel-in-conda-4-7">here</a>).
 We are working on making PDFgui compatible with the current
 set of Anaconda packages.
-In the meantime to install PDFgui you must
-re-activate the old Anaconda packages as follows</p>
+In the meantime you must re-activate the old packages
+as follows</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda update -n base conda
 conda config --set restore_free_channel <span class="nb">true</span>
 </pre></div>
 </div>
 </div>
-<div class="admonition note">
-<p class="admonition-title">Note</p>
-<p>If you already use Anaconda for Python 3.7, create a separate
-Anaconda environment <em>py27</em> which will provide Python 2.7
-instead of 3.7.</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda create --name<span class="o">=</span>py27 <span class="nv">python</span><span class="o">=</span><span class="m">2</span>.7
-<span class="nb">source</span> activate py27
-</pre></div>
-</div>
-<p>On Windows use just <code class="docutils literal notranslate"><span class="pre">activate</span> <span class="pre">py27</span></code>.  Make sure that <em>py27</em>
-environment is activated in your shell prior to running
-the “install” or “update” commands below.</p>
-</div>
 <p>PDFgui is available from the “diffpy” channel of Anaconda packages.
-Open a <em>Terminal</em> window or <em>Anaconda Command Prompt</em> on Windows
-and install PDFgui using the <strong class="program">conda</strong> command</p>
+Because PDFgui requires Python 2.7 and wxpython 3,
+it is strongly recommended to install it in a dedicated
+Anaconda environment <em>py27</em>.
+To do so open a <em>Terminal</em> window or <em>Anaconda Command Prompt</em> on Windows
+and use the <strong class="program">conda</strong> command as follows</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda config --add channels diffpy
+conda create --name<span class="o">=</span>py27 <span class="nv">python</span><span class="o">=</span><span class="m">2</span>.7
+conda activate py27
 conda install <span class="s2">&quot;diffpy.pdfgui&gt;=1.1.2&quot;</span>
 </pre></div>
 </div>
 <p>All done.  To start PDFgui enter <strong class="program">pdfgui</strong> command in a
 Terminal or use the <em>DiffPy</em> start menu on Windows.  PDFgui can be
 also started from the <em>Launcher</em> application included with Anaconda.</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>To start PDFgui from a Terminal make sure <em>py27</em> is
+the active Anaconda environment:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda activate py27
+</pre></div>
+</div>
+<p>Alternatively you can add the following line to your shell startup
+file <code class="file docutils literal notranslate"><span class="pre">.bashrc</span></code> to define an alias which will work in
+any Anaconda environment</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">alias</span> <span class="nv">pdfgui</span><span class="o">=</span><span class="s2">&quot;/path/to/py27/bin/pdfgui&quot;</span>
+</pre></div>
+</div>
+<p>where <code class="docutils literal notranslate"><span class="pre">/path/to</span></code> needs to be adjusted according to the output of
+<code class="docutils literal notranslate"><span class="pre">which</span> <span class="pre">pdfgui</span></code> command.</p>
+</div>
 </div>
 <div class="section" id="pdfgui-updates">
 <h2>PDFgui updates<a class="headerlink" href="#pdfgui-updates" title="Permalink to this headline">¶</a></h2>
@@ -175,7 +183,7 @@ <h2>PDFgui updates<a class="headerlink" href="#pdfgui-updates" title="Permalink
 <div class="section" id="other-versions">
 <h2>Other versions<a class="headerlink" href="#other-versions" title="Permalink to this headline">¶</a></h2>
 <p>When Anaconda Python is not available, PDFgui can be installed from
-sources.  The latest source package is at the <a class="reference external" href="https://pypi.python.org/pypi/diffpy.pdfgui">Python Package
+sources.  The latest source package is at the <a class="reference external" href="https://pypi.org/project/diffpy.pdfgui">Python Package
 Index</a> and the
 prior versions are at
 <a class="reference external" href="https://github.com/diffpy/diffpy.pdfgui/releases">https://github.com/diffpy/diffpy.pdfgui/releases</a>.  See the <a class="reference external" href="https://github.com/diffpy/diffpy.pdfgui#pdfgui">README</a> document

products/xinterpdf.html

@@ -134,7 +134,7 @@ <h2>Getting Started<a class="headerlink" href="#getting-started" title="Permalin
 <h3>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h3>
 <p>xINTERPDF can be installed on Linux and Mac OS machines. The recommended
 way to install this package is through conda. Please visit
-<a class="reference external" href="https://www.anaconda.com/download">https://www.anaconda.com/download</a>, and select Python 2.7 version
+<a class="reference external" href="https://www.anaconda.com/distribution">https://www.anaconda.com/distribution</a>, and select Python 2.7 version
 to download and install. Once conda is installed, you can follow the
 steps below to install xINTERPDF.</p>
 <p><em>Step 1: Add the diffpy conda channel to your conda configuration.</em></p>