diff --git a/AUTHORS.rst b/AUTHORS.rst
index 594c40914a38bffd1801722a523d12c9bdb491f9..03819f1087205c7e3225e22a80e743e1f6892cfc 100644
--- a/AUTHORS.rst
+++ b/AUTHORS.rst
@@ -4,19 +4,22 @@ Authors of Kwant
The principal developers of Kwant are
-* Christoph W. Groth (SPSMS-INAC-CEA Grenoble)
+* Christoph W. Groth (INAC/CEA Grenoble)
* Michael Wimmer (TU Delft)
* Anton R. Akhmerov (TU Delft)
-* Xavier Waintal (SPSMS-INAC-CEA Grenoble)
+* Xavier Waintal (INAC/CEA Grenoble)
The authors can be reached at authors@kwant-project.org.
-Other people that have contributed to Kwant include
+Other contributors to Kwant include
-* Daniel Jaschke (SPSMS-INAC-CEA Grenoble)
-* Joseph Weston (SPSMS-INAC-CEA Grenoble)
+* Mathieu Istas (INAC/CEA Grenoble)
+* Daniel Jaschke (INAC/CEA Grenoble)
+* Michał Nowak (TU Delft)
+* Adrien Sorgniard (INAC/CEA Grenoble)
+* Joseph Weston (INAC/CEA Grenoble)
-We thank Christoph Gohlke for the creation of Windows installers.
+We thank Christoph Gohlke for the creation of installers for Microsoft Windows.
`CEA <http://cea.fr>`_ is the French Commissariat à l'énergie atomique et aux
énergies alternatives. The CEA is the copyright holder for the contributions of
diff --git a/CONTRIBUTE.rst b/CONTRIBUTE.rst
index 978d5fd3c4149a89cf5b6ba0a6d7a8d0237a7daf..128c9b22ab2794f9ec7bdd314da1920422f08e54 100644
--- a/CONTRIBUTE.rst
+++ b/CONTRIBUTE.rst
@@ -9,76 +9,6 @@ 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
-<http://kwant-project.org/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
-:doc:`suggested acknowledgements <citing>`. 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
-<http://kwant-project.org/community.html>`__, or directly by `email
-<mailto:authors@kwant-project.org>`_ for matters that you prefer to not discuss
-publicly.
-
-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
-<http://kwant-project.org/community.html>`__.
-
-If the problem is not known yet, please email a bug report to the `Kwant mailing
-list <http://kwant-project.org/community.html>`__. 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.
-
-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 :doc:`installation instructions <install>`.
-
-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.
+fixing/improving the documentation. Please see the `Kwant website
+<http://kwant-project.org/community>`_ for information on how to get in touch
+with the Kwant community.
diff --git a/INSTALL.rst b/INSTALL.rst
index ca806ea0cd77f8537ae67866fbf81041ca1fa535..2a0be39d0b85d5f67615ecc4f8af60fc252eb787 100644
--- a/INSTALL.rst
+++ b/INSTALL.rst
@@ -1,313 +1,32 @@
-=========================
-Installation instructions
-=========================
+=====================
+Installation of Kwant
+=====================
-Kwant can be installed either using prepared packages (Debian, Ubuntu, and Arch
-variants of GNU/Linux, Mac OS X, Microsoft Windows), or it can be built and
-installed from source.
+Ready-to-use Kwant packages are available for many platforms (like GNU/Linux,
+Mac OS X, Microsoft Windows). See the `installation page of the Kwant website
+<http://kwant-project.org/install>`_ for instructions on how to install Kwant
+on your platform. This is the recommended way for new users.
-In general, installation from packages is advisable, especially for novice
-users. Expert users may find it helpful to build Kwant from source, as this
-will also allow them to customize Kwant to use certain optimized versions of
-libraries.
+The remainder of this section documents how to build Kwant from source. This
+information is mostly of interest to contributors and packagers.
-************************
-Installing from packages
-************************
-
-Debian and derivatives
-======================
-
-The easiest way to install Kwant on a Debian system is using the pre-built
-packages we provide. Our packages are known to work with Debian "wheezy" and
-Debian "jessie", but they may also work on many other recent Debian-derived
-sytems as well. (For example, the following works with recent Ubuntu versions.)
-
-The lines prefixed with ``sudo`` have to be run as root.
-
-1. Add the following lines to ``/etc/apt/sources.list``::
-
- deb http://downloads.kwant-project.org/debian/ stable main
- deb-src http://downloads.kwant-project.org/debian/ stable main
-
-2. (Optional) Add the OpenPGP key used to sign the repositories by executing::
-
- sudo apt-key adv --keyserver pool.sks-keyservers.net --recv-key C3F147F5980F3535
-
- The fingerprint of the key is 5229 9057 FAD7 9965 3C4F 088A C3F1 47F5 980F
- 3535.
-
-3. Update the package data, and install Kwant::
-
- sudo apt-get update
- sudo apt-get install python-kwant python-kwant-doc
-
- The ``python-kwant-doc`` package is optional and installs the HTML
- documentation of Kwant in the directory ``/usr/share/doc/python-kwant-doc``.
-
-Should the last command (``apt-get install``) fail due to unresolved
-dependencies, you can try to build and install your own packages, which is
-surprisingly easy::
-
- cd /tmp
-
- sudo apt-get build-dep tinyarray
- apt-get source --compile tinyarray
- sudo dpkg -i python-tinyarray_*.deb
-
- sudo apt-get build-dep kwant
- apt-get source --compile kwant
- sudo dpkg -i python-kwant_*.deb python-kwant-doc_*.deb
-
-This method should work for virtually all Debian-derived systems, even on exotic
-architectures.
-
-
-Ubuntu and derivatives
-======================
-
-Execute the following commands::
-
- sudo apt-add-repository ppa:kwant-project/ppa
- sudo apt-get update
- sudo apt-get install python-kwant python-kwant-doc
-
-This should provide Kwant for all versions of Ubuntu >= 12.04. The HTML
-documentation will be installed locally in the directory
-``/usr/share/doc/python-kwant-doc``.
-
-
-Arch Linux
-==========
-
-`Arch install scripts for Kwant
-<https://aur.archlinux.org/packages/python2-kwant/>`_ are kindly provided by
-Jörg Behrmann (formerly by Max Schlemmer). To install, follow the `Arch User
-Repository installation instructions
-<https://wiki.archlinux.org/index.php/Arch_User_Repository#Installing_packages>`_.
-Note that for checking the validity of the package you need to add the key
-used for signing to your user's keyring via::
-
- gpg --keyserver pool.sks-keyservers.net --recv-key C3F147F5980F3535
-
-The fingerprint of the key is 5229 9057 FAD7 9965 3C4F 088A C3F1 47F5 980F
-3535.
-
-
-Mac OS X
-========
-
-There is a number of different package managers for bringing software from the
-Unix/Linux world to Mac OS X. Since the community is quite split, we provide
-Kwant and its dependencies both via the `homebrew <http://brew.sh>`_ and the
-`MacPorts <http://www.macports.org>`_ systems.
-
-
-Mac OS X: homebrew
-==================
-
-homebrew is a recent addition to the package managers on Mac OS X. It is
-lightweight, tries to be as minimalistic as possible and give the user
-freedom than Macports. We recommend this option if you have no preferences.
-
-1. Open a terminal and install homebrew as described on the `homebrew
- homepage <http://brew.sh>`_ (instructions are towards the end of
- the page)
-
-2. Run ::
-
- brew doctor
-
- and follow its directions. It will ask for a few prerequisites to be
- installed, in particular
-
- * the Xcode developer tools (compiler suite for Mac OS X) from
- `<http://developer.apple.com/downloads>`_. You will need an Apple ID to
- download. Note that if you have one already from using the App store on the
- Mac/Ipad/Iphone/... you can use that one. Downloading the command line
- tools (not the full Xcode suite) is sufficient. If you have the full Xcode
- suite installed, you might need to download the command line tools manually
- if you have version 4 or higher. In this case go to `Xcode->Preferences`,
- click on `Download`, go to `Components`, select `Command Line Tools` and
- click on `Install`.
- * although `brew doctor` might not complain about it right away, while we're
- at it, you should also install the X11 server from the `XQuartz project
- <http://xquartz.macosforge.org>`_ if you have Mac OS X 10.8 or higher.
-
-3. Add permanently ``/usr/local/bin`` before ``/usr/bin/`` in the ``$PATH$``
- environment variable of your shell, for example by adding ::
-
- export PATH=/usr/local/bin:$PATH
-
- at the end of your ``.bash_profile`` or ``.profile``. Then close
- the terminal and reopen it again.
-
-4. Install a few prerequisites ::
-
- brew install gfortran python
-
-5. Add additional repositories ::
-
- brew tap homebrew/science
- brew tap samueljohn/python
- brew tap michaelwimmer/kwant
-
-6. Install Kwant and its prerequisites ::
-
- pip install nose
- brew install numpy scipy matplotlib
- brew install kwant
-
-Notes:
-
-- If something does not work as expected, use ``brew doctor`` for
- instructions (it will find conflicts and things like that).
-- As mentioned, homebrew allows for quite some freedom. In particular,
- if you are an expert, you don't need necessarily to install
- numpy/scipy/matplotlib from homebrew, but can use your own installation.
- The only prerequisite is that they are importable from python. (the
- Kwant installation will in any case complain if they are not)
-- In principle, you need not install the homebrew python, but could use
- Apple's already installed python. Homebrew's python is more up-to-date,
- though.
-
-
-Mac OS X: MacPorts
-==================
-
-MacPorts is a full-fledged package manager that recreates a whole Linux-like
-environment on your Mac.
-
-In order to install Kwant using MacPorts, you have to
-
-1. Install a recent version of MacPorts, as explained in the
- `installation instructions of MacPorts
- <http://www.macports.org/install.php>`_.
- In particular, as explained there, you will have to install also a
- few prerequisites, namely
-
- * the Xcode developer tools (compiler suite for Mac OS X) from
- `<http://developer.apple.com/downloads>`_. You will need an Apple ID to
- download. Note that if you have one already from using the App store
- on the Mac/Ipad/Iphone/... you can use that one. You will also need the
- command line tools: Within Xcode 4, you have to download them by going to
- `Xcode->Preferences`, click on `Download`, go to `Components`,
- select `Command Line Tools` and click on `Install`. Alternatively, you can
- also directly download the command line tools from the
- Apple developer website.
- * if you have Mac OS X 10.8 or higher, the X11 server from the
- `XQuartz project <http://xquartz.macosforge.org>`_.
-
-2. After the installation, open a terminal and execute ::
-
- echo http://downloads.kwant-project.org/macports/ports.tar |\
- sudo tee -a /opt/local/etc/macports/sources.conf >/dev/null
-
- (this adds the Kwant MacPorts download link
- `<http://downloads.kwant-project.org/macports/ports.tar>`_ at the end of the
- ``sources.conf`` file.)
-
-3. Execute ::
-
- sudo port selfupdate
-
-4. Now, install Kwant and its prerequisites ::
-
- sudo port install py27-kwant
-
-5. Finally, we choose python 2.7 to be the default python ::
-
- sudo port select --set python python27
-
- After that, you will need to close and reopen the terminal to
- have all changes in effect.
-
-Notes:
-
-* If you have problems with macports because your institution's firewall
- blocks macports (more precisely, the `rsync` port), resulting in
- errors from ``sudo port selfupdate``, follow
- `these instructions <https://trac.macports.org/wiki/howto/PortTreeTarball>`_.
-* Of course, if you already have macports installed, you can skip step 1
- and continue with step 2.
-
-
-Microsoft Windows
-=================
-
-There are multiple distributions of scientific Python software for Windows that
-provide the prerequisites for Kwant. We recommend to use the packages kindly
-provided by Christoph Gohlke. To install Kwant on Windows
-
-1. Determine whether you have a 32-bit or 64-bit Windows installation by
- following these `instructions <http://support.microsoft.com/kb/827218>`_.
-
-2. Download and install Python 2.7 for the appropriate architecture (32-bit or
- 64-bit) from the official `Python download site
- <http://www.python.org/download/>`_.
-
-3. Open a command prompt, as described in "How do I get a command prompt" at
- the `Microsoft Windows website
- <http://windows.microsoft.com/en-us/windows/command-prompt-faq>`_.
-
-4. In the command prompt window, execute::
-
- C:\Python27\python.exe C:\Python27\Tools\Scripts\win_add2path.py
-
- (Instead of typing this command, you can also just copy it from here and
- paste it into the command prompt window). If you did not use the default
- location to install Python in step 2, then replace ``C:\Python27`` by the
- actual location where Python is installed.
-
-5. Reboot your computer.
-
-6. Download the necessary packages (with the ending ``.whl``) for your
- operating system (32 or 64 bit) and Python version (e.g. ``cp27`` for Python
- 2.7) from the `website of Christoph Gohlke
- <http://www.lfd.uci.edu/~gohlke/pythonlibs/>`_. For Kwant, we recommend to
- download at least `NumPy
- <http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy>`__, `SciPy
- <http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy>`__, `Matplotlib
- <http://www.lfd.uci.edu/~gohlke/pythonlibs/#matplotlib>`__, `Nose
- <http://www.lfd.uci.edu/~gohlke/pythonlibs/#nose>`__, `Tinyarray
- <http://www.lfd.uci.edu/~gohlke/pythonlibs/#tinyarray>`__, and `Kwant
- <http://www.lfd.uci.edu/~gohlke/pythonlibs/#kwant>`__ itself.
-
-7. Now open a command prompt with administrator rights, as described in "How do
- I run a command with elevated permissions" at the `Microsoft Windows website
- <http://windows.microsoft.com/en-us/windows/command-prompt-faq>`_.
-
- In this new command prompt window, execute ::
-
- pip install <filename>
-
- for each of the downloaded files (replacing ``<filename>`` with it).
-
- Now you are done, you can ``import kwant`` from within Python scripts.
-
-(Note that many other userful scientific packages are available in Gohlke’s
-repository. For example, you might want to install `IPython
-<http://www.lfd.uci.edu/~gohlke/pythonlibs/#ipython>`_ and its various
-dependencies so that you can use the `IPython notebook
-<http://ipython.org/notebook.html>`_.)
-
-
-***********************************
-Building and installing from source
-***********************************
+********************
+Generic instructions
+********************
Prerequisites
=============
Building Kwant requires
- * `Python <http://python.org>`_ 2.6 or 2.7 (Python 3 is not supported yet),
+ * `Python <http://python.org>`_ 2.6 or 2.7 (Python 3 is supported by
+ Kwant 1.2 and above),
* `SciPy <http://scipy.org>`_ 0.9 or newer,
* `LAPACK <http://netlib.org/lapack/>`_ and `BLAS <http://netlib.org/blas/>`_,
(For best performance we recommend the free `OpenBLAS
<http://xianyi.github.com/OpenBLAS/>`_ or the nonfree `MKL
<http://software.intel.com/en-us/intel-mkl>`_.)
- * `Tinyarray <http://git.kwant-project.org/tinyarray/about/>`_, a NumPy-like
+ * `Tinyarray <https://gitlab.kwant-project.org/kwant/tinyarray>`_, a NumPy-like
Python package optimized for very small arrays,
* An environment which allows to compile Python extensions written in C and
C++.
@@ -320,27 +39,27 @@ The following software is highly recommended though not strictly required:
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 `nose <http://nose.readthedocs.org/>`_ testing framework for running the
+ * The `nose testing framework <http://nose.readthedocs.org/>`_ for running the
tests included with Kwant.
In addition, to build a copy of Kwant that has been checked-out directly from
-`its Git repository <http://git.kwant-project.org/kwant>`_, you will also need
-`Cython <http://cython.org/>`_ 0.22 or newer. You do not need Cython to build
-Kwant that has been unpacked from a source .tar.gz-file.
+version control, you will also need `Cython <http://cython.org/>`_ 0.22 or
+newer. You do not need Cython to build Kwant that has been unpacked from a
+source .tar.gz-file.
-Generic instructions
-====================
+Building and installing Kwant
+=============================
Kwant can be built and installed following the `usual Python conventions
<http://docs.python.org/install/index.html>`_ by running the following commands
in the root directory of the Kwant distribution. ::
- pip install .
+ python setup.py build
+ python setup.py install
Depending on your system, you might have to run the second command with
-administrator privileges (e.g. prefixing it with ``sudo``). If you use Python
-older than 2.7.9, see `pip installation instructions <https://docs.python.org/2/installing/#install-pip-in-versions-of-python-prior-to-python-2-7-9>`_.
+administrator privileges (e.g. prefixing it with ``sudo``).
After installation, tests can be run with::
@@ -349,12 +68,83 @@ After installation, tests can be run with::
The tutorial examples can be found in the directory ``tutorial`` inside the root
directory of the Kwant source distribution.
+(Cython will be run automatically when the source tree has been checked out of
+version control. Kwant tarballs include the Cython-generated files, and
+cythonization is disabled when building not from git. If ever necessary, this
+default can be overridden by giving the ``--cython`` option to setup.py.)
+
+
+Build configuration
+===================
+
+The setup script of Kwant has to know how to link against LAPACK & BLAS, and,
+optionally, MUMPS. By default it will assume that LAPACK and BLAS can be found
+under their usual names. MUMPS will be not linked against by default, except
+on Debian-based systems when the package ``libmumps-scotch-dev`` is installed.
+
+All these settings can be configured by creating/editing the file
+``build.conf`` in the root directory of the Kwant distribution. This
+configuration file consists of sections, one for each dependency, led by a
+[dependency-name] header and followed by name = value entries. Possible names
+are keyword arguments for ``distutils.core.Extension`` (For a complete list,
+see its `documentation
+<http://docs.python.org/2/distutils/apiref.html#distutils.core.Extension>`_).
+The corresponding values are whitespace-separated lists of strings.
+
+The two currently possible sections are [lapack] and [mumps]. The former
+configures the linking against LAPACK _AND_ BLAS, the latter against MUMPS
+(without LAPACK and BLAS).
+
+Example ``build.conf`` for linking Kwant against a self-compiled MUMPS, `SCOTCH
+<http://www.labri.fr/perso/pelegrin/scotch/>`_ and `METIS
+<http://glaros.dtc.umn.edu/gkhome/metis/metis/overview>`_::
+
+ [mumps]
+ libraries = zmumps mumps_common pord metis esmumps scotch scotcherr mpiseq gfortran
+
+Example ``build.conf`` for linking Kwant with Intel MKL.::
+
+ [lapack]
+ libraries = mkl_intel_lp64 mkl_sequential mkl_core mkl_def
+ library_dirs = /opt/intel/mkl/lib/intel64
+ extra_link_args = -Wl,-rpath=/opt/intel/mkl/lib/intel64
+
+The detailed syntax of ``build.conf`` is explained in the `documentation of
+Python's configparser module
+<http://docs.python.org/3/library/configparser.html#supported-ini-file-structure>`_.
+
+
+Building the documentation
+==========================
+
+To build the documentation, the `Sphinx documentation generator
+<http://sphinx.pocoo.org/>`_ is required with ``numpydoc`` extension
+(version 0.5 or newer). If PDF documentation is to be built, the tools
+from the `libRSVG <http://live.gnome.org/LibRsvg>`_ (Debian/Ubuntu package
+``librsvg2-bin``) are needed to convert SVG drawings into the PDF format.
+
+As a prerequisite for building the documentation, Kwant must have been built
+successfully using ``python setup.py build`` as described above (or Kwant must
+be already installed in Python's search path). HTML documentation is built by
+entering the ``doc`` subdirectory of the Kwant package and executing ``make
+html``. PDF documentation is generated by executing ``make latex`` followed
+by ``make all-pdf`` in ``doc/build/latex``.
+
+Because of some quirks of how Sphinx works, it might be necessary to execute
+``make clean`` between building HTML and PDF documentation. If this is not
+done, Sphinx may mistakenly use PNG files for PDF output or other problems may
+appear.
+
+
+****************************
+Hints for specific platforms
+****************************
Unix-like systems (GNU/Linux)
=============================
Kwant should run on all recent Unix-like systems. The following instructions
-have been verified to work on Debian 7 (Wheezy) or newer, and on Ubuntu 12.04 or
+have been verified to work on Debian 8 (Jessie) or newer, and on Ubuntu 14.04 or
newer. For other distributions step 1 will likely have to be adapted. If
Ubuntu-style ``sudo`` is not available, the respective command must be run as
root.
@@ -366,15 +156,16 @@ root.
2. Unpack Tinyarray, enter its directory. To build and install, run ::
- sudo pip install .
+ python setup.py build
+ sudo python setup.py install
3. Inside the Kwant source distribution's root directory run ::
- sudo pip install .
+ python setup.py build
+ sudo python setup.py install
-By default the package will be installed under ``/usr/local``. Type ``pip help
-install`` for installation options and see `pip documentation
-<https://pip.readthedocs.org>`_ for a detailed description of ``pip``.
+By default the package will be installed under ``/usr/local``. Run ``python
+setup.py --help install`` for installation options.
Mac OS X: MacPorts
@@ -385,8 +176,12 @@ systems. Here we only consider the case of `MacPorts
<http://www.macports.org>`_ in detail. Some remarks for homebrew are given
below.
-1. In order to set up MacPorts or homebrew, follow steps 1 - 3 of
- the respective instructions of `MacPorts`_
+1. Install a recent version of MacPorts, as explained in the `installation
+ instructions of MacPorts <http://www.macports.org/install.php>`_. `The
+ MacPorts section of the Kwant website
+ <http://kwant-project.org/install#mac-os-x-macports>`_ may be also of
+ interest. (Note that it describes how to install Kwant using a ports file,
+ while the aim here is to install from source manually.)
2. Install the required dependencies::
@@ -429,18 +224,18 @@ installed as ::
brew install gcc python
brew tap homebrew/science
brew tap homebrew/python
- brew tap michaelwimmer/kwant
+ brew tap kwant-project/kwant
pip install nose six
brew install numpy scipy matplotlib
Note that during the installation you will be told which paths to add when you
want to compile/link against scotch/metis/mumps; you need to add these to the
-build.conf file. Also, when linking against mumps, one needs also to link
-against metis (in addition to the libraries needed for MacPorts).
+build.conf file. Also, when linking against MUMPS, one needs also to link
+against METIS (in addition to the libraries needed for MacPorts).
-Windows
-=======
+Microsoft Windows
+=================
Our efforts to compile Kwant on Windows using only free software (MinGW) were
only moderately successful. At the end of a very complicated process we
@@ -452,66 +247,3 @@ It is possible to compile Kwant on Windows using non-free compilers, however we
(the authors of Kwant) have no experience with this. The existing Windows
binary installers of Kwant and Tinyarray were kindly prepared by Christoph
Gohlke.
-
-
-Build configuration
-===================
-
-The setup script of Kwant has to know how to link against LAPACK & BLAS, and,
-optionally, MUMPS. By default it will assume that LAPACK and BLAS can be found
-under their usual names. MUMPS will be not linked against by default, except
-on Debian-based systems when the package ``libmumps-scotch-dev`` is installed.
-
-All these settings can be configured by creating/editing the file
-``build.conf`` in the root directory of the Kwant distribution. This
-configuration file consists of sections, one for each dependency, led by a
-[dependency-name] header and followed by name = value entries. Possible names
-are keyword arguments for ``distutils.core.Extension`` (For a complete list,
-see its `documentation
-<http://docs.python.org/2/distutils/apiref.html#distutils.core.Extension>`_).
-The corresponding values are whitespace-separated lists of strings.
-
-The two currently possible sections are [lapack] and [mumps]. The former
-configures the linking against LAPACK _AND_ BLAS, the latter against MUMPS
-(without LAPACK and BLAS).
-
-Example ``build.conf`` for linking Kwant against a self-compiled MUMPS, `SCOTCH
-<http://www.labri.fr/perso/pelegrin/scotch/>`_ and `METIS
-<http://glaros.dtc.umn.edu/gkhome/metis/metis/overview>`_::
-
- [mumps]
- libraries = zmumps mumps_common pord metis esmumps scotch scotcherr mpiseq
- gfortran
-
-Example ``build.conf`` for linking Kwant with Intel MKL.::
-
- [lapack]
- libraries = mkl_intel_lp64 mkl_sequential mkl_core mkl_def
- library_dirs = /opt/intel/mkl/lib/intel64
- extra_link_args = -Wl,-rpath=/opt/intel/mkl/lib/intel64
-
-The detailed syntax of ``build.conf`` is explained in the `documentation of
-Python's configparser module
-<http://docs.python.org/3/library/configparser.html#supported-ini-file-structure>`_.
-
-
-Building the documentation
-==========================
-
-To build the documentation, the `Sphinx documentation generator
-<http://sphinx.pocoo.org/>`_ is required with ``numpydoc`` extension
-(version 0.5 or newer). If PDF documentation is to be built, the tools
-from the `libRSVG <http://live.gnome.org/LibRsvg>`_ (Debian/Ubuntu package
-``librsvg2-bin``) are needed to convert SVG drawings into the PDF format.
-
-As a prerequisite for building the documentation, Kwant must have been built
-successfully using ``./setup.py build`` as described above (or Kwant must be
-already installed in Python's search path). HTML documentation is built by
-entering the ``doc`` subdirectory of the Kwant package and executing ``make
-html``. PDF documentation is generated by executing ``make latex`` followed by
-``make all-pdf`` in ``doc/build/latex``.
-
-Because of some quirks of how Sphinx works, it might be necessary to execute
-``make clean`` between building HTML and PDF documentation. If this is not
-done, Sphinx may mistakenly use PNG files for PDF output or other problems may
-appear.
diff --git a/README.rst b/README.rst
index 0c25092f0dab316f867e3015f2100131ef3ca898..3b6ec5805bc39b0329191d13d62c1e0119143a01 100644
--- a/README.rst
+++ b/README.rst
@@ -28,10 +28,14 @@ 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 version. A
-`mailing list <http://kwant-project.org/community>`_ is available for
-discussions, questions, and reporting bugs. The development of Kwant can be
-followed via the `public git repository <http://git.kwant-project.org/kwant>`_.
+See the `Kwant web site <http://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
+discussions related to Kwant. Please report bugs and other issues using the
+`issue tracker <https://gitlab.kwant-project.org/kwant/kwant/issues>`_.
See also in this directory: `<INSTALL.rst>`_, `<LICENSE.rst>`_, `<AUTHORS.rst>`_,
`<CITING.rst>`_, `<CONTRIBUTE.rst>`_.
diff --git a/kwant/plotter.py b/kwant/plotter.py
index 3564eca591c27e7f1078f9dc69c7968c283e5b5f..31cc1e9df0981d0fad8849f1f9eea61f06f690c3 100644
--- a/kwant/plotter.py
+++ b/kwant/plotter.py
@@ -1156,6 +1156,12 @@ def plot(sys, num_lead_cells=2, unit='nn',
end_pos = resize_to_dim(end_pos)
start_pos = resize_to_dim(start_pos)
+ # Apply transformations to the data
+ if pos_transform is not None:
+ sites_pos = np.apply_along_axis(pos_transform, 1, sites_pos)
+ end_pos = np.apply_along_axis(pos_transform, 1, end_pos)
+ start_pos = np.apply_along_axis(pos_transform, 1, start_pos)
+
# Determine the reference length.
if unit == 'pt':
reflen = None
@@ -1187,12 +1193,6 @@ def plot(sys, num_lead_cells=2, unit='nn',
except:
raise ValueError('Invalid value of unit argument.')
- # Apply transformations to the data
- if pos_transform is not None:
- sites_pos = np.apply_along_axis(pos_transform, 1, sites_pos)
- end_pos = np.apply_along_axis(pos_transform, 1, end_pos)
- start_pos = np.apply_along_axis(pos_transform, 1, start_pos)
-
# make all specs proper: either constant or lists/np.arrays:
def make_proper_site_spec(spec, fancy_indexing=False):
if callable(spec):
diff --git a/setup.py b/setup.py
index 012de36a5e36670bf169c607d9fd5c08a9bcfc38..99c978c1e65aa69c6d8e098a49aef6e0e94ad0aa 100755
--- a/setup.py
+++ b/setup.py
@@ -11,6 +11,15 @@
from __future__ import print_function
import sys
+
+v = sys.version_info
+if v[:2] not in [(2, 7), (2, 6)]:
+ error = "This version of Kwant requires Python 2.6 or 2.7.\n"
+ if v[0] >= 2:
+ error += "Please use Kwant 1.2 or above."
+ print(error, file=sys.stderr)
+ sys.exit(1)
+
import re
import os
import glob