.gitignore

 *~
 *.pyc
-/catalog.yaml
+.doit.db
+cache/
+output/

.gitlab-ci.yml

+image: kwant/website-deploy
+
+before_script:
+  - nikola build
+  - mkdir -p ~/.ssh
+  - chmod 700 ~/.ssh
+  - eval $(ssh-agent -s)
+
+test_deploy:
+  script:
+    - echo "$TEST_WEBSITE_KEY" | tr -d '\r' | ssh-add -
+    - nikola deploy
+  except:
+    - master
+
+master_deploy:
+  script:
+    - echo "$MASTER_WEBSITE_KEY" | tr -d '\r' | ssh-add -
+    - nikola deploy master
+  only:
+    - master

content/.gitignore

-*.html

content/2015-survey.rst

+Kwant user survey
+=================
+
+The kwant user survey is finished, please use the `mailing list
+</community.html>`_ if you would like to leave feedback.

content/about.rst

+Quantum transport simulations made easy
+=======================================
+
+Kwant is a `free (open source) <https://gitlab.kwant-project.org/kwant/kwant>`_ Python
+package for numerical calculations on tight-binding models with a strong focus
+on quantum transport.  It is designed to be flexible and easy to use.  Thanks to
+the use of innovative algorithms, Kwant is often faster than other available
+codes, even those entirely written in the low level FORTRAN and C/C++ languages.
+
+Tight-binding models can describe a vast variety of systems and phenomena in
+quantum physics.  Therefore, Kwant can be used to simulate metals, graphene,
+topological insulators, quantum Hall effect, superconductivity, spintronics,
+molecular electronics, any combination of the above, and many other things.
+
+Kwant does not use the traditional input files often found in scientific
+software packages. Instead, one writes short programs in the powerful yet
+easy-to-learn Python language.  These programs define a system and calculate its
+quantum properties (conductance, density of states, etc).  This workflow can be
+summarized as follows:
+
+.. raw:: html
+
+    <object type="image/svg+xml" data="kwant-workflow.svgz" class="img-responsive">kwant-workflow.svgz</object>
+
+Kwant was designed to be easy to use: Section 2 of the `Kwant paper
+<http://downloads.kwant-project.org/doc/kwant-paper.pdf>`_ contains a
+line-by-line walkthrough of a program very similar to the one used to generate
+the above image.  That complete Python script is 26 lines long (including
+comments).
+
+
+Examples of Kwant usage
+-----------------------
+
+The following examples are meant to give an overview of what is possible with
+Kwant.  The tutorial section of `Kwant documentation <doc/1/>`_ and the
+`Kwant paper`_ each contain several pedagogical examples with line-by-line
+explanations (`zipfile of all examples
+<http://downloads.kwant-project.org/examples/kwant-examples-1.0.0.zip>`_).
+
+Graphene flake
+..............
+
+.. raw:: html
+
+       <object type="image/svg+xml" class="col-md-4 pull-left img-responsive" data="graphene-edgestate.svgz">graphene-edgestate.svgz</object>
+
+The complete code that constructs the graphene flake shown on the right side is
+
+.. code:: python
+
+          def disk(pos):
+              x, y = pos
+              return x**2 + y**2 < 8**2
+
+          lat = kwant.lattice.honeycomb()
+          syst = kwant.Builder()
+          syst[lat.shape(disk, (0, 0))] = 0
+          syst[lat.neighbors()] = -1
+
+In addition to the flake itself, the image also shows the wave function of a
+low energy eigenstate. The size of each circle is proportional to the wave
+function probability amplitude on that site.  It can be clearly seen that the
+wave function is peaked near the zigzag segments of the boundary, as `expected
+<http://arxiv.org/abs/1003.4602>`_ for graphene quantum dots.
+
+Taken from the Kwant `plotting tutorial <doc/1/tutorial/tutorial6.html>`_.
+
+.. class:: row nomargin
+
+Quantum Hall effect
+...................
+
+.. raw:: html
+
+       <object type="image/svg+xml" class="col-md-4 img-responsive pull-left" data="qhe-edgestate.svgz">qhe-edgestate.svgz</object>
+
+       <object type="image/svg+xml" class="col-md-4 img-responsive pull-right" data="qhe-plateaus.svgz">qhe-plateaus.svgz</object>
+
+
+One of the most common applications of Kwant is to calculate the conductance of
+a nanoelectronic system.  The plot on the left shows the conductance through a
+2-d electron gas as a function of magnetic flux.  The quantization of
+conductance that is visible (plateaus) is the hallmark of the quantum Hall
+effect.  The third plateau does not develop due to a constriction in the system
+that leads to backscattering.  The scattering wave function from the left lead
+at magnetic field strength corresponding to the middle of the third QHE plateau
+is shown on the right.
+
+Taken from example 6 of the `Kwant paper
+<http://downloads.kwant-project.org/doc/kwant-paper.pdf>`_.
+
+.. class:: row
+
+3-d system: Majorana states
+...........................
+
+.. class:: col-md-4 img-responsive pull-left
+
+.. image:: quantum-wire.png
+
+Kwant allows systems of any dimensionality, for example three-dimensional ones.
+This image shows a 3-d model of a semiconducting quantum wire (gray cylinder).
+The red region is a tunnel barrier, used to measure tunneling conductance, the
+blue region is a superconducting electrode.  In this simulated device, a
+Majorana bound state appears close to the superconducting-normal interface.
+
+Taken from an unpublished work by S. Mi, A. R. Akhmerov, and M. Wimmer.
+
+.. class:: row
+
+Numerical experiment: flying qubit
+..................................
+
+.. class:: col-md-4 col-sm-12 img-responsive pull-right
+
+.. image:: flying-qubit.png
+
+Numerical simulations and experimental results for a flying qubit sample made in
+a GaAs/GaAlAs heterostrucutre. The Kwant simulations were performed with
+particular attention to a realistic model of the confining potential seen by the
+electrons.  This allows for rather subtle aspects of the experiment could be
+reproduced.  Such "numerical experiments" can not only be used to interpret the
+experimental data but also can help to design the sample geometry and in to
+choose the right materials.
+
+Taken from an unpublished work by T. Bautze et al.  See Yamamoto et al., `Nature
+Nanotechnology 7, 247 (2012) <http://dx.doi.org/doi:10.1038/nnano.2012.28>`_ for
+details about the experiment.
+
+.. class:: row
+
+Conductance of a Corbino disk in a quantum Hall regime
+......................................................
+
+.. raw:: html
+
+   <object type="image/svg+xml" class="col-md-4 col-sm-6 img-responsive pull-left" data="corbino-layout.svgz">corbino-layout.svgz</object>
+
+.. class:: col-md-4 col-sm-6 img-responsive pull-right
+
+.. image:: corbino-conductance.png
+
+Transport properties of a Corbino disk across a quantum Hall transition. Left:
+geometry of the sample consisting of a ring-shaped two-dimensional electron gas
+(grey) in a perpendicular magnetic field.  Right: conductance across the
+transition, showing quantized conductance peaks.
+
+Taken from I. C. Fulga, F. Hassler, A. R. Akhmerov, C. W. J. Beenakker,
+`Phys. Rev. B 84, 245447 (2011)
+<http://link.aps.org/doi/10.1103/PhysRevB.84.245447>`_; `arXiv:1110.4280
+<http://arxiv.org/abs/1110.4280>`_.

content/authors.txt → content/authors.rst

@@ -6,9 +6,8 @@ The principal developers of kwant are:
 
 * `Christoph W. Groth <mailto:christoph.groth@cea.fr>`_ (SPSMS-INAC-CEA
   Grenoble)
-* `Michael Wimmer <http://www.lorentz.leidenuniv.nl/~wimmer/>`_ (Leiden
-  University)
-* `Anton R. Akhmerov <http://antonakhmerov.org>`_ (Delft University)
+* `Michael Wimmer <http://www.lorentz.leidenuniv.nl/~wimmer/>`_ (TU Delft)
+* `Anton R. Akhmerov <http://antonakhmerov.org>`_ (TU Delft)
 * `Xavier Waintal <http://inac.cea.fr/Pisp/xavier.waintal/>`_ (SPSMS-INAC-CEA
   Grenoble)
 

content/citing.txt → content/cite.rst

-Citing kwant
+Citing Kwant
 ============
 
 We provide Kwant as free software under a `BSD license </license.html>`_ as a
-service to the physics community.  If you have used Kwant for work that has lead
-to a scientific publication, please mention this explicitly in the text body.
-In addition, we ask you to cite the main paper that introduces Kwant:
+service to the physics community.  If you have used Kwant for work that has
+lead to a scientific publication, please mention the fact that you used it
+explicitly in the text body.  For example, you may add
 
-  The reference will be provided here once it is available (soon).
+  *the numerical calculations were performed using the Kwant code*
+
+to the description of your numerical calculations.  In addition, we ask you to
+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)
+  <http://iopscience.iop.org/1367-2630/16/6/063065/article>`_.
+
+
+Other references we ask you to consider
+---------------------------------------
 
 If you have profited from the quantum transport functionality of Kwant, please
 also cite the upcoming paper that describes the relevant algorithms. The
@@ -17,9 +29,9 @@ Kwant owes much of its current performance to the use of the `MUMPS
 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
-  Anal. & Appl. **23** (1), 15 (2001).
+  Anal. & Appl. 23 (1), 15 (2001).
 
 Finally, if you use the routine for generation of circular ensembles of random
 matrices, please cite
 
-  \F. Mezzadri, Notices Am. Math. Soc. **54**, 592 (2007).
+  \F. Mezzadri, Notices Am. Math. Soc. 54, 592 (2007).

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content/common/kwant.css

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-    overflow-y: scroll;
-}
-
-body {
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content/community.rst

+The Kwant community
+===================
+
+The Kwant project is an international collaboration.
+Everybody is welcome to participate in the community
+by asking and replying to questions, reporting bugs, providing suggestions,
+and `contributing to the code and documentation </contribute.html>`_.
+
+The Kwant community uses three public communication channels:
+the mailing list for generic discussions, questions, and announcements;
+the gitlab instance for development discussions and reporting bugs;
+and the chat for real-time discussions related to development.
+
+A list of `Kwant authors </authors>`_ is included in the documentation.
+Please contact the authors directly only for matters that cannot be discussed on the public channels.
+
+
+Mailing list
+------------
+
+The kwant-discuss mailing list is the main public communication platform for anything related to Kwant:
+questions, discussions, development, and announcements.
+It may be used both as a web forum and as a classical mailing list.
+
+The `kwant-discuss web interface <https://mail.python.org/archives/list/kwant-discuss@python.org/>`_
+allows to follow discussions and search the archives.
+
+To start a new discussion thread, you may either use the web interface
+(sign-in required)
+or write directly to
+kwant-discuss@python.org.
+In order to avoid spam,
+messages of unsubscribed participants are held for moderation.
+
+Similarly, replying is possible either by mail
+(if you received the post to which you want reply by mail),
+or using the web interface:
+the “reply” button under each message allows to compose directly
+(for signed-in users),
+or triggers a reply by mail (otherwise).
+
+You may subscribe to receive posts to the list by mail.
+Subscription is done either through the
+`kwant-discuss info page
+<https://mail.python.org/mailman3/lists/kwant-discuss.python.org/>`_
+or by sending any message to
+kwant-discuss-join@python.org.
+(The subject and content are ignored and may be empty.)
+To unsubscribe, either use the info page,
+or send any message to kwant-discuss-leave@python.org.
+
+List etiquette :
+
+- When asking questions,
+  `help others to help you <https://stackoverflow.com/help/how-to-ask>`_.
+  In particular, use the search function before posting.
+
+- When replying, please avoid quoting the complete original message.
+  Instead, consider
+  `bottom-posting <https://en.wikipedia.org/wiki/Posting_style#Bottom-posting>`_.
+
+
+Announcements mailing list
+--------------------------
+
+This read-only list is used for important announcements like new releases of Kwant.
+Only a few messages are sent per year.
+These announcements are also posted on the main mailing list,
+so there is no need to subscribe to both lists.
+We recommend every user of Kwant to subscribe at least to this list in order to stay informed about new developments.
+
+The `kwant-announce archives <https://mail.python.org/archives/list/kwant-announce@python.org/>`_
+are available on the web.
+
+To subscribe, either use the form on the `kwant-announce info page <https://mail.python.org/mailman3/lists/kwant-announce.python.org/>`_
+or simply send any message to kwant-announce-join@python.org.
+(The subject and content are ignored and may be empty.)
+To unsubscribe, either use the info page, or send any message to kwant-announce-leave@python.org.
+
+
+Development chat
+----------------
+
+The Kwant developer chat is accessible to the community via `Gitter <https://gitter.im/kwant-project/Lobby>`_.
+Come say hi if you would like to get involved with developing Kwant!
+
+
+Gitlab instance
+---------------
+
+The Kwant project runs a `gitlab instance <https://gitlab.kwant-project.org/>`_
+that hosts the `main Kwant code repository <https://gitlab.kwant-project.org/kwant/kwant>`_
+as well as the `repositories of related projects <https://gitlab.kwant-project.org/kwant>`_.
+The gitlab instance is used for reporting bugs (see next section) and `development </contribute.html>`_
+
+
+Reporting bugs
+--------------
+
+If you encounter a problem with Kwant,
+first try to reproduce it with as simple a system as possible.
+Double-check with the documentation that what you observe is actually a bug in Kwant.
+If you think it is, please check `the list of known bugs in Kwant <https://gitlab.kwant-project.org/kwant/kwant/issues?label_name=bug>`_.
+It may be also a good idea to search or ask on the general mailing list.
+(You can use the search box at the top of this page.)
+
+If after checking you still think that you have found a bug, please add it to
+the above-mentioned list of bugs by creating an issue with the “bug” label.  A
+useful bug report should contain:
+
+- The versions of software you are using: Kwant, Python, operating system, etc.
+
+- A description of the problem, i.e. what exactly goes wrong.  This should
+  include any relevant error messages.
+
+- Enough information to reproduce the bug, preferably in the form of a simple
+  script.

content/community.txt

-Getting help, contributing and reporting problems
-=================================================
-
-Mailing list
-------------
-
-The mailing list is (meant to become) the main communication platform for
-anything related to Kwant: asking questions, reporting bugs, and discussing
-further development.  You can use it in various ways:
-
-- `Subscribe <https://mailman-mail5.webfaction.com/listinfo/kwant-discuss>`_ and
-  use it along with your regular email.  (You can unsubscribe at any moment.)
-
-- Follow through the `Gmane web interface
-  <http://news.gmane.org/gmane.comp.science.kwant.user>`_.  It is both possible
-  to write new messages (action: post) and to reply (action: followup).
-
-- .. raw:: html
-
-      <p><form id="searchgmane" method="get" action="http://search.gmane.org/">
-      <input type="text" name="query" />
-      <input type="hidden" name="group" value="gmane.comp.science.kwant.user" />
-      <input type="submit" value="Search the Kwant mailing list" />
-      </form></p>
-
-- Send a message directly to kwant-discuss@kwant-project.org.  (If you are not
-  subscribed, it is not guaranteed that any replies will reach you by email.)
-
-
-Reporting bugs
---------------
-
-If you encounter a problem with Kwant, first try to reproduce it with as simple
-a system as possible.  Double-check with the documentation that what you
-observe is actually a bug in Kwant. If you think it is, please check whether
-the problem is already known by searching the mailing list.
-
-If the problem is not known yet, please send a bug report to the mailing list.
-A report should contain:
-
-* The versions of software you are using (Kwant, Python, operating system, etc.)
-
-* A description of the problem, i.e. what exactly goes wrong.
-
-* Enough information to reproduce the bug, preferably in the form of a simple
-  script.
-
-
-Contributing
-------------
-
-We see Kwant not just as a package with fixed functionality, but rather as a
-framework for implementing different physics-related algorithms using a common
-set of concepts and, if possible, a shared interface.  We have designed it
-leaving room for growth, and plan to keep extending it.
-
-External contributions to Kwant are highly welcome.  You can help to advance
-the project not only by writing code, but also by reporting bugs, and
-fixing/improving the documentation.  A `mailing list
-</community.html>`_ is available for discussions.
-
-If you have some code that works well with Kwant, or extends it in some useful
-way, please consider sharing it.  Any external contribution will be clearly
-marked as such, and relevant papers will be added to the list of `suggested
-acknowledgements </citing.html>`_.  The complete development history is also
-made available through a `web interface <http://git.kwant-project.org/kwant>`_.
-If you plan to contribute, it is best to coordinate with us in advance either
-through the mailing list, or directly at authors@kwant-project.org for matters
-that you prefer to not discuss publicly.
-
-
-How to contribute
-.................
-
-We use the version control system `Git <http://git-scm.com/>`_ to coordinate the
-development of Kwant.  If you are new to Git, we invite you to learn its basics.
-(There's a plethora of information available on the Web.)  Kwant's Git
-repository contains not only the source code, but also all of the reference
-documentation and the tutorial.
-
-It is best to base your work on the latest version of Kwant::
-
-    git clone http://git.kwant-project.org/kwant
-
-Then you can modify the code, and build Kwant and the documentation as
-described in the `build instructions
-</doc/1.0/pre/install.html#building-and-installing-from-source>`_.
-
-Some things to keep in mind:
-
-* Please keep the code consistent by adhering to the prevailing naming and
-  formatting conventions.  We generally follow the `"Style Guide for Python
-  Code" <http://www.python.org/dev/peps/pep-0008/>`_ For docstrings, we follow
-  `NumPy's "Docstring Standard"
-  <http://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>`_ and
-  `Python's "Docstring Conventions"
-  <http://www.python.org/dev/peps/pep-0257/>`_.
-
-* Write tests for all the important functionality you add.  Be sure not to
-  break existing tests.
-
-A useful trick for working on the source code is to build in-place so that there
-is no need to re-install after each change.  This can be done with the following
-command ::
-
-    python setup.py build_ext -i
-
-The ``kwant`` subdirectory of the source distribution will be thus turned into
-a proper Python package that can be imported.  To be able to import Kwant from
-within Python, one can either work in the root directory of the distribution
-(where the subdirectory ``kwant`` is located), or make a (symbolic) link from
-somewhere in the Python search path to the the package subdirectory.

content/contribute.rst

+Contributing to Kwant
+=====================
+
+We see Kwant not just as a package with fixed functionality, but rather as a
+framework for implementing different physics-related algorithms using a common
+set of concepts.  Contributions to Kwant are highly welcome.  You can help the
+project not only by writing code, but also by reporting bugs, and
+fixing/improving the website and the documentation.
+
+
+Where help is needed
+--------------------
+
+The `Kwant issue tracker
+<https://gitlab.kwant-project.org/kwant/kwant/issues>`_ serves to track bugs
+in Kwant, but most issues are in fact ideas for enhancements.  The issues are
+categorized with labels, so that it is possible to view `all the “easy” issues
+<https://gitlab.kwant-project.org/kwant/kwant/issues?label_name=difficulty%3A+easy>`_
+for example.
+
+Please do feel free to enter new issues yourself.  If you are unsure about some aspect It may be a good idea to discuss your idea on the mailing list kwant-discuss@kwant-project.org before filing an issue.
+
+If you already have some code that extends Kwant in a useful way, please
+consider sharing it.  If your extension fits well with Kwant and is of wide
+enough interest, we will be happy to include it into Kwant proper.  For more
+specialized cases, we will find a solution as well.  (We could, for example,
+add a list of Kwant-related modules to this website.)  In any case, external
+contributions will be clearly marked as such, and relevant papers will be
+added to the list of `suggested acknowledgements </cite.html>`_.
+
+
+Getting the source code
+-----------------------
+
+The source code of released versions of Kwant is available for `download
+<http://downloads.kwant-project.org/kwant/>`_.  You can follow the development
+through the `Kwant page of our GitLab instance
+<https://gitlab.kwant-project.org/kwant/kwant>`_.  The `Git
+<http://git-scm.com/>`_ repository of Kwant can be cloned directly with the
+command ::
+
+    git clone https://gitlab.kwant-project.org/kwant/kwant.git
+
+The Kwant git repository has two main branches: The branch *master*
+contains the development towards the next release.  The branch *stable* contains
+the most recent release that is considered stable, and only bugfixes are applied
+to it.
+
+
+Setting up for development
+--------------------------
+
+When working with the Kwant source, regular `build instructions
+</doc/1/pre/install.html#building-and-installing-from-source>`_ apply.  It
+would be tiresome, however, to have to reinstall the modified Kwant after each
+modification.
+
+One easy way to avoid this is to build in-place so that there is no need to
+reinstall after each change.  This can be done with the following command ::
+
+    python3 setup.py build_ext -i
+
+No further installation is necessary.  The “inner” ``kwant`` subdirectory has
+been turned into a proper Python package that can be imported from the “outer”
+directory, i.e. the directory where ``setup.py`` is located.  Any script
+inside that directory that imports Kwant will get the modified version.  (To
+be able to import the modified Kwant from another directory one can create a
+symbolic link to the package.)
+
+The above ``build_ext`` command does not have to be rerun when a Python file
+is modified.  Recompilation is only necessary whenever a Cython file
+(``.pyx``) has been changed.
+
+
+Modifying the source code
+-------------------------
+
+We recommend that you keep each of your changes to Kwant on a separate “topic
+branch” that starts at *master*.  Try to not mix up unrelated changes in a
+single branch.  To create a topic branch, use the command::
+
+    git checkout -b my_topic master
+
+Now you can begin to implement your idea.  As you go, register your changes
+with Git as explained, for example, in the `Pro Git book
+<https://git-scm.com/book/en/v2/Git-Basics-Recording-Changes-to-the-Repository>`_
+that is freely available online.
+
+Once you feel that you would like to show your work to other interested people
+(because you would like to receive feedback, or because you consider it
+ready), it's time to inspect your branch.  Run ``git status`` to make sure
+that you have committed all of your changes, then use a tool like ``gitk`` to
+view your branch.
+
+In the following, two methods to share your commits are described.  The first
+will be familiar if you have experience with the popular GitHub service.  If
+you do not, you might prefer the second method, since it is simpler.
+
+
+Method 1: Using the Kwant GitLab instance
+.........................................
+
+Go the `GitLab page of the official Kwant repository
+<https://gitlab.kwant-project.org/kwant/kwant>`_.  Since you do not have write
+access to this repository, you have to create an own “fork” of it by clicking
+on the button just right of the “star” button.
+
+You created a public copy of the Kwant repository that is controlled by you.
+Add it as a remote repository to the clone of Kwant on your computer::
+
+    git remote add own https://gitlab.kwant-project.org/<USERNAME>/kwant.git
+
+You can copy-and-paste your own version of the above URL from the main page of
+your repository.  (If you know about SSH, you may also prefer to upload your
+public ssh key to GitLab and to use SSH as transport.)  The string ``own`` is
+the local name you give to the remote, it can be anything.
+
+Now you can push your topic branch to your repository::
+
+    git push own my_branch
+
+This will make your branch appear in GitLab.  Now you can let us know about
+your branch by `creating a merge request in GitLab
+<https://gitlab.kwant-project.org/help/workflow/forking_workflow.md>`_ or by
+sending a message to kwant-discuss@kwant-project.org.
+
+
+Method 2: Sending patches to the mailing list
+.............................................
+
+Run the command ::
+
+    git format-patch origin/master
+
+This will create a “patch” file for each commit on your branch.  Now simply
+send these patches as email attachments to kwant-discuss@kwant-project.org,
+together with an explanation of your idea.  You do not have to be subscribed
+to the mailing list.
+
+(Or, even better, use ``git send-email`` as shown in this `example of usage
+<https://kernel.org/pub/software/scm/git/docs/git-send-email.html#_example>`_
+and this `git send-email howto
+<http://www.freedesktop.org/wiki/Software/PulseAudio/HowToUseGitSendEmail/>`_.)
+
+
+Coding style
+------------
+
+* Please keep the code consistent by adhering to the prevailing naming and
+  formatting conventions.  We generally respect the `"Style Guide for Python
+  Code" <http://www.python.org/dev/peps/pep-0008/>`_.  For docstrings, we
+  follow `NumPy's "Docstring Standard"
+  <http://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>`_ and
+  `Python's "Docstring Conventions"
+  <http://www.python.org/dev/peps/pep-0257/>`_.
+
+* Write tests for all the important functionality you add.  Be sure not to
+  break existing tests.
+
+* Create a logical sequence of commits with clear commit messages.  Each
+  commit message consists of a summary line, and, whenever necessary, a
+  more detailed explanation.  Both parts are separated by a blank line
+  and wrapped to 72 characters (unless quoting error messages and such).
+  The summary line should be as clear as possible.  The detailed
+  explanation should be included whenever it helps to motivate or
+  understand the commit.  Bear in mind that the merge request text and
+  discussions are not part of a commit.

content/doc/index.rst

+Documentation
+=============
+
+Tutorial and reference manual
+-----------------------------
+
+.. class:: docs-list, button-links
+
+* **Online**:
+
+  + `stable version </doc/1/>`_
+  + `development version </doc/dev/>`_
+
+* **Downloads**:
+
+  + `PDF <http://downloads.kwant-project.org/doc/latest.pdf>`_
+  + `zipped HTML <http://downloads.kwant-project.org/doc/latest.zip>`_
+
+Interactive online course
+-------------------------
+The APS March meeting 2016 tutorial “Introduction to Computational Quantum Nanoelectronics” focuses on the physics, but also serves as a crash course on Kwant.  `All the materials are available online </mm16.html>`_ and can be run directly in a web browser, without installing Kwant locally.
+
+Screencast
+----------
+
+.. raw:: html
+
+   A brief video introduction of Kwant:
+
+   <ul class="button-links inline-list">
+       <li> <a href="kwant-screencast-2014.html">watch</a> </li>
+       <li> <a href="http://downloads.kwant-project.org/doc/kwant-screencast-2014.mp4" download>download</a> </li>
+   </ul>
+
+Article
+-------
+
+This paper (`download PDF <http://downloads.kwant-project.org/doc/kwant-paper.pdf>`__) introduces Kwant in a systematic way and discusses its design and performance (`New J. Phys. 16, 063065 (2014) <http://iopscience.iop.org/1367-2630/16/6/063065/article>`_).

content/doc/index.txt

-Kwant documentation
-===================
-
-The two available resources for learning Kwant are its tutorial, and the paper
-inctroducing Kwant structure and design. The tutorial is hands-on, and mainly
-explains how to use Kwant, and its various features, while the paper presents a
-more general perspective, useful to kwow for extending Kwant functionality.
-
-Kwant tutorial:
-
-* `browse online </doc/1.0>`_
-* `download pdf <http://downloads.kwant-project.org/doc/kwant-doc-1.0.0.pdf>`_
-* `download html+zip
-  <http://downloads.kwant-project.org/doc/kwant-doc-1.0.0.zip>`_
-
-Kwant paper:
-
-* `download pdf <http://downloads.kwant-project.org/doc/kwant-paper.pdf>`__

content/extensions/index.rst

+================
+Kwant extensions
+================
+
+Going beyond the core package, there are several tools that extend Kwant in useful ways.
+You can check these out below.
+
+If you have some re-usable code that you think would be useful to the wider Kwant community,
+post to the `Kwant development mailing list <mailto:kwant-discuss@kwant-project.org>`_ with a
+link to the code and a couple of sentences describing it, and we'll add it to this page.
+
+
+Semicon: k·p simulations made easy
+----------------------------------
+**Get the code**: https://gitlab.kwant-project.org/semicon/semicon
+
+A package of tools for doing k·p simulations. Contains: model definitions, material parameters,
+and helper functions for generating template Kwant systems.
+
+Generating quasicrystals
+------------------------
+**Get the code**: https://arxiv.org/src/1510.06035v2/anc/quasicrystal.py
+
+Code for reproducing numerics from the paper "`Aperiodic Weak Topological Superconductors <https://arxiv.org/abs/1510.06035>`_"
+by Fulga et al.
+Contains functionality for building 2D Ammann-Beenker tilings, an example of a quasicrystal, and
+Kwant systems constructed from such tilings.
+
+Time-dependent transport
+------------------------
+**Get the code**: https://gitlab.kwant-project.org/kwant/tkwant
+
+A package for defining time-dependent systems with Kwant, and calculating
+time-dependent quantities. Details of the algorithm can be found in the
+following two papers:
+
++ `Towards realistic time-resolved simulations of quantum devices <https://dx.doi.org/10.1007/s10825-016-0855-9>`_
++ `Numerical simulations of time resolved quantum electronics <https://dx.doi.org/10.1016/j.physrep.2013.09.001>`_
+
+Qsymm: Symmetry finder and symmetric Hamiltonian generator
+----------------------------------------------------------
+**Get the code**: https://gitlab.kwant-project.org/qt/qsymm
+
+A package that makes symmetry analysis simple. It automatically generates model Hamiltonians from symmetry constraints and finds the full symmetry group of your Hamiltonian. Works with tight-binging and k dot p Hamiltonians and supports all kinds of symmetries, including conserved quantities, space group symmetries, time reversal, particle-hole and all combinations of these.
+
++ `Qsymm: algorithmic symmetry finding and symmetric Hamiltonian generation <http://dx.doi.org/10.1088/1367-2630/aadf67>`_

content/harvard-only_trial.rst

+Trial pre-release of Kwant
+==========================
+
+With the release of Kwant the instructions that were here were rendered
+obsolete. Please go to the `installation instructions </install.html>`_ for the
+latest Kwant release.

content/harvard-only_trial/index.txt

-Harvard-only trial pre-release of kwant
-=======================================
-
-kwant is made available as a special preview **exclusively** to the audience of
-the 30 April 2013 presentation at Harvard University by Anton Akhmerov.  Please
-do not spread the link to this page.  Instead, you are welcome show the link to
-the `kwant website <http://kwant-project.org/>`_.
-
-You may use kwant for your personal evaluation.  Any other use, **explicitly
-including further distribution**, is not allowed.  Please wait for the release
-of the final version that we expect to occur very soon.
-
-So far, kwant is running on the following platforms: GNU/Linux, Mac OS, and
-Windows.  The usage experience on GNU/Linux is best (this is the platform
-recommended by the authors of kwant), followed by Mac OS.  Support for Windows
-is highly experimental (help wanted).
-
-
-Installation from source
-------------------------
-
-This method of installation is described in the documentation.  It is extremely
-easy on Debian-based GNU/Linux distributions (e.g. Ubuntu).  On Mac OS and
-Windows it is more involved, but documented as well.  Please download the files
-and follow the `installation instructions </docs/install.html>`_.
-
-* kwant: `tar-gz-archive <kwant-0.3pre4.tar.gz>`__, `zip-archive <kwant-0.3pre4.zip>`__
-* tinyarray (needed by kwant): `tar-gz-archive <tinyarray-0.0.tar.gz>`__, `zip-archive <tinyarray-0.0.zip>`__
-
-
-Binary installation instructions for Windows
---------------------------------------------
-
-**Warning:** These packages are highly experimental and likely not to work
-fully.  In a test with Windows XP, most tutorial examples ran.  In another test
-with Windows 7, most did not.  We would appreciate the help of people
-experienced with the Windows platform.
-
-**Important note**: The provided binary packages are compiled for 32-bit
-Microsoft Windows (win32).  They can be installed on a 64-bit Windows as well,
-but for them to work all the other required packages (like Python itself) have
-to be present in their win32 versions.
-
-1. Install the official Python 2.7 distribution from the official `Python
-   download page <http://python.org/download/>`_. Bear in mind the note above:
-   Choose "Python 2.7.x Windows Installer", not the 64 bit version.
-
-2. Install the Python packages required by kwant (NumPy, SciPy, matplotlib).  An
-   easy way to do so is to install the `scipy-stack package
-   <http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy-stack>`_ (win32-py2.7)
-   kindly provided by Christoph Gohlke.  Please also note the instructions
-   at the top of that page.
-
-3. Download and execute the `tinyarray installer <tinyarray-0.0.win32-py2.7.exe>`__.
-
-4. Download and execute the `kwant installer <kwant-0.3pre2.win32-py2.7.exe>`__.
-
-5. kwant and tinyarray require four libraries (DLLs) that can be downloaded
-   `here <kwant-dlls.zip>`__.  For these libraries to be found by kwant, they
-   have either to be in the current directory, or in a directory that belongs to
-   ``PATH``, or in ``C:\WINDOWS\SYSTEM32``.  You have the following alternative
-   possibilities:
-
-   (a) Unpack the 4 files into some directory and launch all your kwant Python
-       scripts from the same directory.
-
-   (b) Like (a), but add that directory to the ``PATH`` environment variable
-       (The Web knows how to do that.).  Now you should be able to launch kwant
-       scripts from everywhere.
-
-   (c) Copy the four DLL files directly to ``C:\WINDOWS\SYSTEM32``.
-
-Please note that the kwant binary packages do not include any kwant examples or
-documentation.  Use the `online documentation </docs/>`_.

content/index.rst

+Quantum transport simulations made easy
+=======================================
+
+.. raw:: html
+
+    <div class="workflow-image">
+    <object type="image/svg+xml" data="kwant-workflow.svgz" class="img-responsive">kwant-workflow.svgz</object>
+    </div>
+
+Kwant is a `free (open source) <https://gitlab.kwant-project.org/kwant/kwant>`_,
+powerful, and easy to use Python package for numerical calculations on tight-binding
+models with a strong focus on quantum transport.
+
+.. raw:: html
+
+    <div id="recent-posts" class="section col-sm-6">
+    <h2> Recent blog posts </h2>
+
+.. post-list::
+    :stop: 4
+
+.. raw:: html
+
+    </div>
+
+.. raw:: html
+
+    <div id="kwant-uses" class="section col-sm-5">
+    <h2> Use Kwant to... </h2>
+    <ul id="kwant-uses-list">
+        <li>
+        <a href="/about#quantum-hall-effect"> Compute differential conductance </a>
+        </li>
+        <li>
+        <a href="/about#graphene-flake"> Visualize edge states </a>
+        </li>
+        <li>
+        <a href="/about#numerical-experiment-flying-qubit"> Conduct numerical experiments </a>
+        </li>
+        <li>
+        <a href="/doc/1/tutorial/spectrum#band-structure-calculations"> Explore band structure </a>
+        </li>
+        <li>
+        <a href="https://tkwant.kwant-project.org/"> Simulate time-dependent problems </a>
+        </li>
+    </div>

content/index.txt

-Quantum transport simulations made easy
-=======================================
-
-Kwant is a Python package for numerical calculations on tight-binding models
-with a strong focus on quantum transport.  It is designed to be flexible and
-easy to use, while not sacrificing performance.
-
-Tight-binding models are ubiquitous in quantum physics and they can be used to
-describe a vast variety of systems and phenomena, such as semiconductors,
-metals, graphene, topological insulators, quantum Hall effect,
-superconductivity, spintronics, molecular electronics, any combination of the
-above and many other things.  While all these systems exhibit very distinct
-physical behavior, the underlying mathematical description is very similar.
-Kwant has been designed so that the computer simulation of various physical
-systems and phenomena is within reach of one software package.
-
-Kwant does not use the traditional input files often found in scientific
-software packages. Instead, one writes simple Python programs (using the
-Python's simple and very expressive syntax) to define the system and calculate
-its quantum properties (conductance, density of states, etc). This workflow is
-summarized as follows:
-
-.. image:: kwant-workflow.svgz
-    :width: 90%
-
-Kwant was designed to be easy to use: for example the program that generates
-the right panel of the image above is only 42 lines long (including detailed
-comments). Kwant is also accessible for people without expertise in
-numerics. To aid that, it is provided along with a detailed hand-on `tutorial
-</doc/1.0/tutorial/>`_ and the Kwant `paper </paper>`_, which describes the
-guiding principles underlying its design.
-
-
-Examples of Kwant usage
------------------------
-
-The following examples are mostly taken from real research projects done with
-Kwant.  The tutorial_ and the `Kwant paper
-<http://downloads.kwant-project.org/doc/kwant-paper.pdf>`_ each contain several
-pedagogical examples with line-by-line explanations (`zipfile of all examples
-<http://downloads.kwant-project.org/examples/kwant-examples.zip>`_).
-
-
-Graphene flake
-..............
-
-.. container:: rightside
-
-   .. image:: graphene-edgestate.svgz
-      :width: 15em
-
-Wave function of a low energy eigenstate of a graphene flake. The size of each
-circle is proportional to the wave function probability amplitude on that site.
-It is clearly seen that the wave function is peaked near the zigzag segments of
-the boundary, as can be `expected <http://arxiv.org/abs/1003.4602>`_ for
-graphene quantum dots. The image is taken from the Kwant `plotting tutorial
-<doc/1.0/tutorial/tutorial6.html>`_.
-
-
-3-d system: Majorana states
-...........................
-
-.. container:: rightside
-
-   .. image:: quantum-wire.png
-
-Kwant allows systems of any dimensionality, for example three-dimensional ones.
-This image shows a 3-d model of a semiconducting quantum wire (gray cylinder).
-The red region is a tunnel barrier, used to measure tunneling conductance, the
-blue region is a superconducting electrode.  In this simulated device, a
-Majorana bound state appears close to the superconducting-normal interface.
-
-Taken from: S. Mi, A. R. Akhmerov, M. Wimmer (to be published).
-
-
-Numerical experiment: flying qubit
-..................................
-
-.. container:: rightside
-
-   .. image:: flying-qubit.png
-
-Numerical simulations and experimental results for a flying qubit sample made in
-a GaAs/GaAlAs heterostrucutre. The Kwant simulations were performed with
-particular attention to a realistic model of the confining potential seen by the
-electrons.  This allows for rather subtle aspects of the experiment could be
-reproduced.  Such "numerical experiments" can not only be used to interpret the
-experimental data but also can help to design the sample geometry and in to
-choose the right materials.
-
-Taken from T. Bautze et al., to be submitted to Phys. Rev. B.  See Yamamoto et
-al., `Nature Nanotechnology 7, 247 (2012)
-<http://dx.doi.org/doi:10.1038/nnano.2012.28>`_ for details about the
-experiment.
-
-
-conductance of a Corbino disk in a quantum Hall regime
-......................................................
-
-.. container:: leftside
-
-   .. image:: corbino-layout.svgz
-      :width: 15em
-
-
-.. container:: rightside
-
-   .. image:: corbino-conductance.png
-
-Transport properties of a Corbino disk across a quantum Hall transition. Left:
-geometry of the sample consisting of a ring-shaped two-dimensional electron gas
-(grey) in a perpendicular magnetic field.  Right: conductance across the
-transition, showing quantized conductance peaks.
-
-Taken from I. C. Fulga, F. Hassler, A. R. Akhmerov, C. W. J. Beenakker,
-`Phys. Rev. B 84, 245447 (2011)
-<http://link.aps.org/doi/10.1103/PhysRevB.84.245447>`_; `arXiv:1110.4280
-<http://arxiv.org/abs/1110.4280>`_.