Update URLs per suggestions from make linkcheck

Author: pavoljuhas

Diff for: NSFnugget.rst

@@ -36,6 +36,6 @@ the beamtime is over. PDFgui has numerous extensions
 that are described in more detail in [#]_. 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 http://www.diffpy.org.
+found at https://www.diffpy.org.
 
 .. [#] |citeFarrowJpcm07|

Diff for: abbreviations.txt

@@ -2,8 +2,8 @@
 
 .. Named web links -----------------------------------------------------
 
-.. |anaconda-download| replace:: https://www.anaconda.com/download
-.. _anaconda-download: https://www.anaconda.com/download
+.. |anaconda-download| replace:: https://www.anaconda.com/distribution
+.. _anaconda-download: https://www.anaconda.com/distribution
 .. _diffpy-users: https://groups.google.com/d/forum/diffpy-users
 .. _ctv-xpdfsuite: https://columbia.resoluteinnovation.com/technologies/M11-120
 
@@ -46,7 +46,7 @@
    C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch,
    Th. Proffen and S. J. L. Billinge, `PDFfit2 and PDFgui: computer
    programs for studying nanostructure in crystals
-   <http://iopscience.iop.org/0953-8984/19/33/335219/>`__,
+   <https://doi.org/10.1088/0953-8984/19/33/335219>`__,
    *J. Phys.: Condens.  Mat.* **19**, 335219 (2007)
    |downloadFarrowJpcm07|
 

Diff for: index.rst

@@ -47,11 +47,11 @@ centered at Columbia University and, before that, Michigan State University.
 
 .. _danse: http://danse.us/
 
-.. _national science foundation: http://www.nsf.gov/
+.. _national science foundation: https://www.nsf.gov/
 
 .. _department of energy, office of basic energy sciences: https://science.energy.gov/bes/
 
-.. _brookhaven national laboratory: http://www.bnl.gov/
+.. _brookhaven national laboratory: https://www.bnl.gov/
 
 .. image:: images/blank1x1.png
    :align: left

Diff for: products/SrMise.rst

@@ -65,8 +65,8 @@ executables, installation instructions, and licensing information
 for some popular options are listed below.
 
 * `Anaconda`_
-* `Enthought Canopy <https://www.enthought.com/products/canopy/>`_
-* `Python(x,y) <https://code.google.com/p/pythonxy/>`_
+* `Enthought Canopy <https://www.enthought.com/product/canopy/>`_
+* `Python(x,y) <https://python-xy.github.io>`_
 * `WinPython <http://winpython.github.io>`_
 
 .. _Anaconda: anaconda-download_
@@ -77,14 +77,14 @@ Numpy and SciPy do not currently support 64-bit Python installations, so be
 sure to download the 32-bit versions of these packages.
 
 * `Python 2.6/2.7 <https://www.python.org/downloads/windows/>`_
-* `NumPy <http://sourceforge.net/projects/numpy/files/NumPy/>`_
-* `SciPy <http://sourceforge.net/projects/scipy/files/scipy/>`_
-* `matplotlib <http://matplotlib.org/downloads.html>`_
+* `NumPy <https://sourceforge.net/projects/numpy/files/NumPy/>`_
+* `SciPy <https://sourceforge.net/projects/scipy/files/scipy/>`_
+* `matplotlib <https://matplotlib.org/downloads.html>`_
 
 After installing Python and the required packages, we can install SrMise.
 The simplest way to obtain diffpy.srmise on Windows systems
 is using ``pip`` to download and install the latest release from the
-`Python Package Index <https://pypi.python.org>`_ (PyPI).  To do so, open a
+`Python Package Index <https://pypi.org>`_ (PyPI).  To do so, open a
 command window by running ``cmd`` from the Start Menu's application search box
 (Windows 7/8/10) or Run command (Windows Vista and earlier).  Verify that the
 ``pip`` program is installed by running ::
@@ -124,13 +124,13 @@ in MacPorts::
 
 The simplest way to obtain diffpy.srmise on Mac OS X systems
 is using ``pip`` to download and install the latest release from
-`PyPI <https://pypi.python.org>`_. ::
+`PyPI <https://pypi.org>`_. ::
 
    sudo pip install diffpy.srmise
 
 If you prefer to install from sources, download them from the
 `GitHub <https://github.com/diffpy/diffpy.srmise/releases>`__ or
-`PyPI <https://pypi.python.org/pypi/diffpy.srmise>`__ pages for SrMise.
+`PyPI <https://pypi.org/project/diffpy.srmise>`__ pages for SrMise.
 Uncompress them to a directory, and from that directory run ::
 
    sudo python setup.py install
@@ -159,13 +159,13 @@ For other Linux distributions consult the appropriate package manager.
 
 The simplest way to obtain diffpy.srmise on Linux systems
 is using ``pip`` to download and install the latest release from
-`PyPI <https://pypi.python.org>`_. ::
+`PyPI <https://pypi.org>`_. ::
 
    sudo pip install diffpy.srmise
 
 If you prefer to install from sources, download them from the
 `GitHub <https://github.com/diffpy/diffpy.srmise/releases>`__ or
-`PyPI <https://pypi.python.org/pypi/diffpy.srmise>`__ pages for SrMise.
+`PyPI <https://pypi.org/project/diffpy.srmise>`__ pages for SrMise.
 Uncompress them to a directory, and from that directory run ::
 
    sudo python setup.py install

Diff for: products/diffpycmi/install.rst

@@ -41,8 +41,8 @@ Mac OS X
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 For Mac OS X the system dependencies can be installed using the
-`MacPorts <http://www.macports.org>`_ software manager.  A similar
-package system `Homebrew <http://brew.sh>`_ works as well, but has
+`MacPorts <https://www.macports.org>`_ software manager.  A similar
+package system `Homebrew <https://brew.sh>`_ works as well, but has
 been considerably less tested with DiffPy-CMI.
 
 For best results with MacPorts follow these tips:

Diff for: products/mPDF.rst

@@ -79,7 +79,7 @@ prerequisite software and then use the command ::
 *Alternative option: Download and install from source.*
 
 If you prefer to install from source, you can also zip and download the entire package
-from `PyPI <https://pypi.python.org/pypi/diffpy.mpdf>`__ or
+from `PyPI <https://pypi.org/project/diffpy.mpdf>`__ or
 `GitHub <https://github.com/benfrandsen/diffpy.magpdf>`__, then unzip the file and
 execute the following command from inside the unzipped directory ::
 
@@ -89,7 +89,7 @@ Note that this will only work if all the dependencies are already properly insta
 
 Documentation
 -------------
-Please see `http://pythonhosted.org/diffpy.mpdf/ <http://pythonhosted.org/diffpy.mpdf/>`__
+Please see https://pythonhosted.org/diffpy.mpdf
 for the documentation.
 
 What next?

Diff for: products/pdfgui.rst

@@ -34,7 +34,7 @@ By downloading and using this software you are agreeing to the
 conditions specified in the :doc:`software license <pdfguilicense>`.
 
 PDFgui is distributed as a software package for
-`Anaconda Python <https://www.continuum.io>`__.  PDFgui is available
+`Anaconda Python <https://www.anaconda.com>`__.  PDFgui is available
 for all operating systems supported by Anaconda, namely for
 Linux, Mac OS X, and Windows.
 
@@ -110,7 +110,7 @@ Other versions
 
 When Anaconda Python is not available, PDFgui can be installed from
 sources.  The latest source package is at the `Python Package
-Index <https://pypi.python.org/pypi/diffpy.pdfgui>`__ and the
+Index <https://pypi.org/project/diffpy.pdfgui>`__ and the
 prior versions are at
 https://github.com/diffpy/diffpy.pdfgui/releases.  See the `README
 <https://github.com/diffpy/diffpy.pdfgui#pdfgui>`__ document