Hi Christoph,
   This is a well-working code that computes conductance  for graphene with 2 leads (conductance is now commented in the end).  The issue appears at line
485.

Loading the large package warning  may be due to running from Eric6 Python IDE that I use.

I have now the latest 1.4 Kwant version installed via pip3  ,  which added the necessity to remove the default values from "args" parameter list, as it's no longer supported

As for ppa install,  I might be doing something wrong:   (Linux Mint 19 = Ubuntu bionic)
sudo add-apt-repository ppa:kwant-project/ppa
sudo apt-get update
sudo apt-get install kwant
returns:
"Unable to locate package kwant"

The test 
python3 -c 'import kwant; kwant.test(verbose=False)'

returns  21 warnings:  (see below)

.local/lib/python3.6/site-packages/kwant/tests/test_plotter.py::test_map
  /home/sergey/.local/lib/python3.6/site-packages/numpy/lib/function_base.py:3652: RuntimeWarning: Invalid value encountered in percentile
    interpolation=interpolation)
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1300: RuntimeWarning: invalid value encountered in greater
    overflow_pct = 100 * np.sum(unmasked_data > new_vmax) / len(unmasked_data)
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1301: RuntimeWarning: invalid value encountered in less
    underflow_pct = 100 * np.sum(unmasked_data < new_vmin) / len(unmasked_data)

.local/lib/python3.6/site-packages/kwant/tests/test_plotter.py::test_spectrum
  /home/sergey/.local/lib/python3.6/site-packages/mpl_toolkits/mplot3d/axes3d.py:1069: UserWarning: Axes3D.figure.canvas is 'None', mouse rotation disabled.  Set canvas then call Axes3D.mouse_init().
    "Axes3D.figure.canvas is 'None', mouse rotation disabled.  "
  /home/sergey/.local/lib/python3.6/site-packages/numpy/core/fromnumeric.py:83: RuntimeWarning: invalid value encountered in reduce
    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)

.local/lib/python3.6/site-packages/kwant/tests/test_plotter.py::test_density_interpolation
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns

.local/lib/python3.6/site-packages/kwant/tests/test_plotter.py::test_current_interpolation
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns
  /home/sergey/.local/lib/python3.6/site-packages/kwant/plotter.py:1684: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    field_out[field_slice] += magns

.local/lib/python3.6/site-packages/kwant/tests/test_plotter.py::test_current
  /home/sergey/.local/lib/python3.6/site-packages/kwant/tests/test_plotter.py:522: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    plotter.current(syst, current, file=out)
  /home/sergey/.local/lib/python3.6/site-packages/kwant/tests/test_plotter.py:526: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
    plotter.current(syst, current, ax=ax, file=out)

.local/lib/python3.6/site-packages/kwant/tests/test_wraparound.py::test_symmetry
  /home/sergey/.local/lib/python3.6/site-packages/kwant/tests/test_wraparound.py:169: RuntimeWarning: `particle_hole` and `time_reversal` symmetries are set on the input builder. However they are ignored for the wrapped system, since Kwant lacks a way to express the existence (or not) of a symmetry at k != 0.
    wrapped = wraparound(syst)

.local/lib/python3.6/site-packages/kwant/tests/test_wraparound.py::test_plot_2d_bands
  /home/sergey/.local/lib/python3.6/site-packages/numpy/core/fromnumeric.py:83: RuntimeWarning: invalid value encountered in reduce
    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)

-- Docs: http://doc.pytest.org/en/latest/warnings.html
=================== 282 passed, 21 warnings in 51.40 seconds ===================