update URLs and use https where possible

Author: akhmerov

AUTHORS.rst

@@ -8,8 +8,8 @@ The principal developers of Kwant are
 
 * `Christoph Groth <mailto:[email protected]>`_ (CEA Grenoble)
 * `Michael Wimmer <https://michaelwimmer.org>`_ (TU Delft)
-* `Anton Akhmerov <http://antonakhmerov.org>`_ (TU Delft)
-* `Xavier Waintal <http://www.pheliqs.fr/en/Pages/Portrait/Xavier-Waintal.aspx>`_ (CEA Grenoble)
+* `Anton Akhmerov <https://antonakhmerov.org>`_ (TU Delft)
+* `Xavier Waintal <https://www.pheliqs.fr/en/Pages/Portrait/Xavier-Waintal.aspx>`_ (CEA Grenoble)
 * `Joseph Weston <https://joseph.weston.cloud>`_ (TU Delft)
 
 Contributors to Kwant include
@@ -34,7 +34,7 @@ Contributors to Kwant include
 
 We thank Christoph Gohlke for the creation of installers for Microsoft Windows.
 
-`CEA <http://www.cea.fr>`_ is the French Commissariat à l'énergie atomique et aux
+`CEA <https://www.cea.fr>`_ is the French Commissariat à l'énergie atomique et aux
 énergies alternatives.  The CEA is the copyright holder for the contributions of
 C. W. Groth, X. Waintal, and its other employees involved in Kwant.
 

CITING.rst

@@ -15,7 +15,7 @@ cite the main paper that introduces Kwant:
   C. W. Groth, M. Wimmer, A. R. Akhmerov, X. Waintal,
   *Kwant: a software package for quantum transport*,
   `New J. Phys. 16, 063065 (2014)
-  <https://iopscience.iop.org/1367-2630/16/6/063065/article>`_.
+  <https://doi.org/10.1088/1367-2630/16/6/063065>`_.
 
 
 Other references we ask you to consider
@@ -26,7 +26,7 @@ also cite the upcoming paper that describes the relevant algorithms. The
 reference will also be added here once it is available.
 
 Kwant owes much of its current performance to the use of the `MUMPS
-<http://graal.ens-lyon.fr/MUMPS/>`_ library for solving systems of sparse linear
+<https://graal.ens-lyon.fr/MUMPS/>`_ library for solving systems of sparse linear
 equations.  If you have done high-performance calculations, we suggest citing
 
   P. R. Amestoy, I. S. Duff, J. S. Koster, J. Y. L’Excellent, SIAM. J. Matrix

INSTALL.rst

@@ -20,7 +20,7 @@ Obtaining the source code
 
 Source distributions of Kwant (and Tinyarray) are available at the `downloads
 section of the Kwant website <https://downloads.kwant-project.org/kwant/>`_ as well
-as `PyPI <https://pypi.python.org/pypi/kwant>`_.  The sources may be also
+as `PyPI <https://pypi.org/project/kwant>`_.  The sources may be also
 cloned directly from the `official Kwant git repository
 <https://gitlab.kwant-project.org/kwant/kwant>`_.
 
@@ -31,31 +31,31 @@ Prerequisites
 Building Kwant requires
  * `Python <https://www.python.org/>`_ 3.6 or above (Kwant 1.1 is the last
    version to support Python 2),
- * `NumPy <http://numpy.org/>`_ 1.13.3 or newer,
+ * `NumPy <https://numpy.org/>`_ 1.13.3 or newer,
  * `SciPy <https://www.scipy.org/>`_ 0.19.1 or newer,
- * `LAPACK <http://netlib.org/lapack/>`_ and `BLAS <http://netlib.org/blas/>`_,
+ * `LAPACK <https://netlib.org/lapack/>`_ and `BLAS <https://netlib.org/blas/>`_,
    (For best performance we recommend the free `OpenBLAS
-   <http://www.openblas.net/>`_ or the nonfree `MKL
+   <https://www.openblas.net/>`_ or the nonfree `MKL
    <https://software.intel.com/en-us/intel-mkl>`_.)
  * `Tinyarray <https://gitlab.kwant-project.org/kwant/tinyarray>`_ 1.2 or newer,
 a NumPy-like Python package optimized for very small arrays,
  * An environment which allows to compile Python extensions written in C and
    C++.
 
 The following software is highly recommended though not strictly required:
- * `matplotlib <http://matplotlib.org/>`_ 2.1.1 or newer, for the module `kwant.plotter` and the tutorial,
- * `SymPy <http://sympy.org/>`_ 1.1.1 or newer, for the subpackage `kwant.continuum`.
+ * `matplotlib <https://matplotlib.org/>`_ 2.1.1 or newer, for the module `kwant.plotter` and the tutorial,
+ * `SymPy <https://sympy.org/>`_ 1.1.1 or newer, for the subpackage `kwant.continuum`.
  * `Qsymm <https://pypi.org/project/qsymm/>`_ 1.2.6 or newer, for the subpackage `kwant.qsymm`.
- * `MUMPS <http://graal.ens-lyon.fr/MUMPS/>`_, a sparse linear algebra library
+ * `MUMPS <https://graal.ens-lyon.fr/MUMPS/>`_, a sparse linear algebra library
    that will in many cases speed up Kwant several times and reduce the memory
    footprint.  (Kwant uses only the sequential, single core version
    of MUMPS.  The advantages due to MUMPS as used by Kwant are thus independent
    of the number of CPU cores of the machine on which Kwant runs.)
- * The `py.test testing framework <http://pytest.org/>`_ 3.3.2 or newer for running the
+ * The `py.test testing framework <https://docs.pytest.org/>`_ 3.3.2 or newer for running the
    tests included with Kwant.
 
 In addition, to build a copy of Kwant that has been checked-out directly from
-version control, you will also need `Cython <http://cython.org/>`_ 0.26.1 or
+version control, you will also need `Cython <https://cython.org/>`_ 0.26.1 or
 newer.  You do not need Cython to build Kwant that has been unpacked from a
 source .tar.gz-file.
 
@@ -128,7 +128,7 @@ The section ``[kwant.linalg._mumps]`` may be used to adapt the build process.
 
 
 Example ``build.conf`` for linking Kwant against a self-compiled MUMPS, `SCOTCH
-<http://www.labri.fr/perso/pelegrin/scotch/>`_ and `METIS
+<https://www.labri.fr/perso/pelegrin/scotch/>`_ and `METIS
 <http://glaros.dtc.umn.edu/gkhome/metis/metis/overview>`_::
 
     [mumps]
@@ -143,7 +143,7 @@ Building the documentation
 ==========================
 
 To build the documentation, the `Sphinx documentation generator
-<http://www.sphinx-doc.org/en/stable/>`_ is required with ``numpydoc`` extension
+<https://www.sphinx-doc.org/en/stable/>`_ is required with ``numpydoc`` extension
 (version 0.5 or newer), as well as ``jupyter-sphinx`` (version 0.2 or newer).
 If PDF documentation is to be built, the tools
 from the `libRSVG <https://wiki.gnome.org/action/show/Projects/LibRsvg>`_

README.rst

@@ -28,12 +28,12 @@ Kwant can calculate
 Other computations involving tight-binding Hamiltonians can be implemented
 easily.
 
-See the `Kwant web site <http://kwant-project.org/>`_ for the latest stable
+See the `Kwant website <https://kwant-project.org/>`_ for the latest stable
 version.  The current development version is available via the `Kwant gitlab
 instance <https://gitlab.kwant-project.org/kwant/kwant>`_.  Contributions are
 welcome.
 
-A `mailing list <http://kwant-project.org/community>`_ exists for general
+A `mailing list <https://kwant-project.org/community>`_ exists for general
 discussions related to Kwant.  Please report bugs and other issues using the
 `issue tracker <https://gitlab.kwant-project.org/kwant/kwant/issues>`_.
 

RELEASE.rst

@@ -338,7 +338,7 @@ Push the tag to the official Kwant repository::
 PyPI
 ----
 
-Install `twine <https://pypi.python.org/pypi/twine>`_ and run the following
+Install `twine <https://pypi.org/project/twine>`_ and run the following
 (this requires a file ~/.pypirc with a valid username and password: ask
 Christoph Groth to add you as a maintainer on PyPI, if you are not already)::
 
@@ -382,7 +382,7 @@ sure to update the codenames and the versions)::
     Version: 9.0
     Architectures: i386 amd64 source
     Components: main
-    Description: Unofficial Debian package repository of http://kwant-project.org/
+    Description: Unofficial Debian package repository of https://kwant-project.org/
     SignWith: C3F147F5980F3535
 
     Origin: Kwant project
@@ -391,7 +391,7 @@ sure to update the codenames and the versions)::
     Version: 10.0
     Architectures: i386 amd64 source
     Components: main
-    Description: Unofficial Debian package repository of http://kwant-project.org/
+    Description: Unofficial Debian package repository of https://kwant-project.org/
     SignWith: C3F147F5980F3535
 
 If the config had to be updated execute::

conftest.py

@@ -2,9 +2,9 @@
 #
 # This file is part of Kwant.  It is subject to the license terms in the file
 # LICENSE.rst found in the top-level directory of this distribution and at
-# http://kwant-project.org/license.  A list of Kwant authors can be found in
+# https://kwant-project.org/license.  A list of Kwant authors can be found in
 # the file AUTHORS.rst at the top-level directory of this distribution and at
-# http://kwant-project.org/authors.
+# https://kwant-project.org/authors.
 """Pytest plugin to ignore packages that have uninstalled dependencies.
 
 This ignores packages on test collection, which is required when the

doc/source/conf.py

@@ -198,7 +198,6 @@
 
 # -- Options for LaTeX output --------------------------------------------------
 
-# http://thread.gmane.org/gmane.comp.python.sphinx.devel/4220/focus=4238
 latex_elements = {'papersize': 'a4paper',
                   'release': '',
                   'releasename': '',
@@ -271,7 +270,7 @@ class BoundMethodDocumenter(autodoc.FunctionDocumenter):
     @classmethod
     def can_document_member(cls, member, membername, isattr, parent):
         # Return True iff `member` is a bound method.  Taken from
-        # <http://stackoverflow.com/a/1260881>.
+        # <https://stackoverflow.com/a/1260881>.
         return (isinstance(member, types.MethodType) and
                 member.__self__ is not None and
                 not issubclass(member.__self__.__class__, type) and

doc/source/figure/ab_ring_sketch.svg

@@ -21,7 +21,7 @@ New MUMPS-based solver
 ----------------------
 The code for sparse matrix solvers has been reorganized and a new solver has
 been added next to `kwant.solvers.sparse`: `kwant.solvers.mumps`.  The new
-solver uses the `MUMPS <http://graal.ens-lyon.fr/MUMPS/>`_ software package and
+solver uses the `MUMPS <https://graal.ens-lyon.fr/MUMPS/>`_ software package and
 is much (typically several times) faster than the UMFPACK-based old solver.
 In addition, MUMPS uses considerably less memory for a given system while at
 the same time it is able to take advantage of more than 2 GiB of RAM.

doc/source/figure/ab_ring_sketch2.svg

@@ -75,7 +75,7 @@ Improving or adding to Kwant's tutorial is now much simpler. Now
 the text and code for each tutorial is kept in the same file, making
 it easy to see where changes need to be made, and images generated by
 the code are inserted directly into the document thanks to the magic of
-`jupyter-sphinx <https://github.com/jupyter-widgets/jupyter-sphinx/>`_.
+`jupyter-sphinx <https://github.com/jupyter/jupyter-sphinx/>`_.
 It has never been easier to get started contributing to Kwant by
 helping us improve our documentation.
 

doc/source/figure/superconductor_transport_sketch.svg

@@ -3,7 +3,7 @@
 
 .. module:: kwant.solvers.mumps
 
-This solver uses `MUMPS <http://graal.ens-lyon.fr/MUMPS/>`_.  (Only the
+This solver uses `MUMPS <https://graal.ens-lyon.fr/MUMPS/>`_.  (Only the
 sequential, single core version of MUMPS is used.)  MUMPS is a very efficient
 direct sparse solver that can take advantage of memory beyond 3GiB for the
 solution of large problems.  Furthermore, it offers a choice of several

doc/source/pre/whatsnew/0.2.rst

@@ -150,7 +150,7 @@ Printing the Builder produced by ``discretize`` shows the source code of its ons
       When working interactively in `Jupyter notebooks <https://jupyter.org/>`_
       it can be useful to use this to see a symbolic representation of
       the discretized Hamiltonian. This works best when combined with ``sympy``
-      `Pretty Printing <http://docs.sympy.org/latest/tutorial/printing.html#setting-up-pretty-printing>`_.
+      `Pretty Printing <https://docs.sympy.org/latest/tutorial/printing.html#setting-up-pretty-printing>`_.
 
     - The symbolic result of discretization obtained with
       ``discretize_symbolic`` can be converted into a

doc/source/pre/whatsnew/1.5.rst

@@ -750,7 +750,7 @@ Finally, we use the following standard Python construct [#]_ to execute
 .. jupyter-execute::
 
     # Call the main function if the script gets executed (as opposed to imported).
-    # See <http://docs.python.org/library/__main__.html>.
+    # See <https://docs.python.org/library/__main__.html>.
     if __name__ == '__main__':
         main()
 

doc/source/reference/kwant.solvers.mumps.rst

@@ -105,7 +105,7 @@ This gives the result:
     :hide-code:
 
     # Call the main function if the script gets executed (as opposed to imported).
-    # See <http://docs.python.org/library/__main__.html>.
+    # See <https://docs.python.org/library/__main__.html>.
     if __name__ == '__main__':
         main()
 

doc/source/tutorial/discretize.rst

@@ -36,19 +36,19 @@ Here :math:`\sigma_{x,y,z}` denote the Pauli matrices.
 It turns out that this well studied Rashba-Hamiltonian has some peculiar
 properties in (ballistic) nanowires: It was first predicted theoretically
 in `Phys. Rev. Lett. 90, 256601 (2003)
-<http://prl.aps.org/abstract/PRL/v90/i25/e256601>`_ that such a system should
+<https://doi.org/10.1103/PhysRevLett.90.256601>`_ that such a system should
 exhibit non-monotonic conductance steps due to a spin-orbit gap. Only
 very recently, this non-monotonic behavior has been supposedly
 observed in experiment: `Nature Physics 6, 336 (2010)
-<http://www.nature.com/nphys/journal/v6/n5/abs/nphys1626.html>`_. Here
+<https://doi.org/10.1038/nphys1626>`_. Here
 we will show that a very simple extension of our previous examples will
 exactly show this behavior (Note though that no care was taken to choose
 realistic parameters).
 
 The tight-binding model corresponding to the Rashba-Hamiltonian naturally
 exhibits a 2x2-matrix structure of onsite energies and hoppings.  In order to
 use matrices in our program, we import the Tinyarray package.  (`NumPy
-<http://www.numpy.org/>`_ would work as well, but Tinyarray is much faster
+<https://numpy.org/>`_ would work as well, but Tinyarray is much faster
 for small arrays.)
 
 .. jupyter-execute::
@@ -61,9 +61,9 @@ for small arrays.)
     # ------------------
     #  Gaps in quantum wires with spin-orbit coupling and Zeeman splititng,
     #  as theoretically predicted in
-    #   http://prl.aps.org/abstract/PRL/v90/i25/e256601
+    #   https://doi.org/10.1103/PhysRevLett.90.256601
     #  and (supposedly) experimentally oberved in
-    #   http://www.nature.com/nphys/journal/v6/n5/abs/nphys1626.html
+    #   https://doi.org/10.1038/nphys1626
     #
     # Kwant features highlighted
     # --------------------------

doc/source/tutorial/first_steps.rst

@@ -2,9 +2,9 @@
 #
 # This file is part of Kwant.  It is subject to the license terms in the file
 # LICENSE.rst found in the top-level directory of this distribution and at
-# http://kwant-project.org/license.  A list of Kwant authors can be found in
+# https://kwant-project.org/license.  A list of Kwant authors can be found in
 # the file AUTHORS.rst at the top-level directory of this distribution and at
-# http://kwant-project.org/authors.
+# https://kwant-project.org/authors.
 
 """Simple sphinx extension that allows for a section that can be
 hidden/shown on click using javascript"""

doc/source/tutorial/spectrum.rst

@@ -15,7 +15,7 @@
 
 {%- block doctype -%}
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+  "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 {%- endblock %}
 {%- set reldelim1 = reldelim1 is not defined and ' &raquo;' or reldelim1 %}
 {%- set reldelim2 = reldelim2 is not defined and ' |' or reldelim2 %}
@@ -41,7 +41,7 @@ <h3>{{ _('Navigation') }}</h3>
           {%- if not loop.first %}{{ reldelim2 }}{% endif %}</li>
         {%- endfor %}
         {%- block rootrellink %}
-        <li><a href="http://kwant-project.org/">
+        <li><a href="https://kwant-project.org/">
             <img src="{{ pathto('_static/kwant_logo.png', 1) }}"
             style="vertical-align: middle; margin-top: -4px" alt="Kwant logo"/></a>
           {{ reldelim1 }}</li>
@@ -117,7 +117,7 @@ <h3>{{ _('Navigation') }}</h3>
     {%- endfor %}
 {%- endmacro %}
 
-<html xmlns="http://www.w3.org/1999/xhtml" lang="en">
+<html xmlns="https://www.w3.org/1999/xhtml" lang="en">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset={{ encoding }}" />
     {{ metatags }}
@@ -205,7 +205,7 @@ <h3>{{ _('Navigation') }}</h3>
       {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
     {%- endif %}
     {%- if show_sphinx %}
-      {% trans sphinx_version=sphinx_version|e %}Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> {{ sphinx_version }}.{% endtrans %}
+      {% trans sphinx_version=sphinx_version|e %}Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> {{ sphinx_version }}.{% endtrans %}
     {%- endif %}
     </div>
 {%- endblock %}
@@ -226,7 +226,7 @@ <h3>{{ _('Navigation') }}</h3>
       g.defer=true; g.async=true; g.src=u+"piwik.js"; s.parentNode.insertBefore(g,s);
       })();
     </script>
-    <noscript><img src="http://piwik.kwant-project.org/piwik.php?idsite=1&amp;rec=1" style="border:0" alt="" /></noscript>
+    <noscript><img src="https://piwik.kwant-project.org/piwik.php?idsite=1&amp;rec=1" style="border:0" alt="" /></noscript>
     <!-- End Piwik Code: Analytics are used by us to improve the site, and not sent to anyone. -->
 {%- endif %}
   </body>

doc/source/tutorial/spin_potential_shape.rst

@@ -7,7 +7,7 @@ ENV DEBIAN_FRONTEND noninteractive
 RUN apt-get update && apt-get install -y --no-install-recommends \
         gnupg dirmngr apt-transport-https ca-certificates curl software-properties-common
 
-RUN echo "deb http://downloads.kwant-project.org/debian/ stable main" >> /etc/apt/sources.list && \
+RUN echo "deb https://downloads.kwant-project.org/debian/ stable main" >> /etc/apt/sources.list && \
     apt-key adv --no-tty --keyserver pool.sks-keyservers.net --recv-key C3F147F5980F3535 && \
     apt-get update && apt-get install -y --no-install-recommends \
         # all the hard non-Python dependencies

doc/sphinxext/kwantdoc.py

@@ -2,9 +2,9 @@
 #
 # This file is part of Kwant.  It is subject to the license terms in the file
 # LICENSE.rst found in the top-level directory of this distribution and at
-# http://kwant-project.org/license.  A list of Kwant authors can be found in
+# https://kwant-project.org/license.  A list of Kwant authors can be found in
 # the file AUTHORS.rst at the top-level directory of this distribution and at
-# http://kwant-project.org/authors.
+# https://kwant-project.org/authors.
 
 __all__ = []
 

doc/templates/layout.html

@@ -2,9 +2,9 @@
 #
 # This file is part of Kwant.  It is subject to the license terms in the file
 # LICENSE.rst found in the top-level directory of this distribution and at
-# http://kwant-project.org/license.  A list of Kwant authors can be found in
+# https://kwant-project.org/license.  A list of Kwant authors can be found in
 # the file AUTHORS.rst at the top-level directory of this distribution and at
-# http://kwant-project.org/authors.
+# https://kwant-project.org/authors.
 
 import numpy as np
 

docker/Dockerfile.debian

@@ -2,9 +2,9 @@
 #
 # This file is part of Kwant.  It is subject to the license terms in the file
 # LICENSE.rst found in the top-level directory of this distribution and at
-# http://kwant-project.org/license.  A list of Kwant authors can be found in
+# https://kwant-project.org/license.  A list of Kwant authors can be found in
 # the file AUTHORS.rst at the top-level directory of this distribution and at
-# http://kwant-project.org/authors.
+# https://kwant-project.org/authors.
 
 import sys
 import numpy as np