merge commits from the 1.2 branch that should have rather gone to 1.1

CONTRIBUTE.rst

@@ -75,13 +75,10 @@ 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 --cython
+    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.
-
-The option ``--cython`` enables the translation of .pyx files into .c files.
-It is only needed if any .pyx files have been modified.

doc/source/images/ab_ring.py.diff

@@ -8,27 +8,7 @@
  from cmath import exp
  from math import pi
  
-@@ -40,12 +41,13 @@
-     sys[lat.shape(ring, (0, r1 + 1))] = 4 * t
-     sys[lat.neighbors()] = -t
- 
--    # In order to introduce a flux through the ring, we introduce a phase on
--    # the hoppings on the line cut through one of the arms.  Since we want to
--    # change the flux without modifying the Builder instance repeatedly, we
--    # define the modified hoppings as a function that takes the flux as its
--    # parameter phi.
--    def fluxphase(site1, site2, phi):
-+    # In order to introduce a flux through the ring, we introduce a phase
-+    # on the hoppings on the line cut through one of the arms
-+
-+    # since we want to change the flux without modifying Builder repeatedly,
-+    # we define the modified hoppings as a function that takes the flux
-+    # through the argument phi.
-+    def fluxphase(site1, site2, phi=0):
-         return exp(1j * phi)
- 
-     def crosses_branchcut(hop):
-@@ -81,6 +83,50 @@
+@@ -81,6 +82,50 @@
      return sys
  
  
@@ -79,7 +59,7 @@
  def plot_conductance(sys, energy, fluxes):
      # compute conductance
  
-@@ -90,18 +136,31 @@
+@@ -90,18 +135,31 @@
          smatrix = kwant.smatrix(sys, energy, args=[flux])
          data.append(smatrix.transmission(1, 0))
  
@@ -116,7 +96,7 @@
  
      # Finalize the system.
      sys = sys.finalized()
-@@ -111,6 +170,17 @@
+@@ -111,6 +169,17 @@
                                                  for i in xrange(100)])
  
  

doc/source/tutorial/ab_ring.py

@@ -50,8 +50,8 @@ def make_system(a=1, t=1.0, W=10, r1=10, r2=20):
     # define the modified hoppings as a function that takes the flux as its
     # parameter phi.
 #HIDDEN_BEGIN_lvkt
-    def fluxphase(site1, site2, phi):
-        return exp(1j * phi)
+    def hopping_phase(site1, site2, phi):
+        return -t * exp(1j * phi)
 
     def crosses_branchcut(hop):
         ix0, iy0 = hop[0].tag
@@ -65,7 +65,7 @@ def make_system(a=1, t=1.0, W=10, r1=10, r2=20):
         for hop in kwant.builder.HoppingKind((1, 0), lat, lat)(sys):
             if crosses_branchcut(hop):
                 yield hop
-    sys[hops_across_cut] = fluxphase
+    sys[hops_across_cut] = hopping_phase
 #HIDDEN_END_lvkt
 
     #### Define the leads. ####

setup.py

@@ -62,7 +62,7 @@ try:
     sys.argv.remove(CYTHON_OPTION)
     use_cython = True
 except ValueError:
-    use_cython = False
+    use_cython = version_is_from_git
 
 if use_cython:
     try:
@@ -355,7 +355,7 @@ def complain_cython_unavailable():
         ver = '.'.join(str(e) for e in REQUIRED_CYTHON_VERSION)
         print(msg.format(ver), file=sys.stderr)
     else:
-        print("Run setup.py without {}.".format(NO_CYTHON_OPTION),
+        print("Run setup.py with the {} option.".format(CYTHON_OPTION),
               file=sys.stderr)