Merge branch 'flakes' into 'master'

Flakes for CI

* I've switched on flakes in CI so that it can catch some simple errors.
* Among cruft pyflakes has identified two actual bugs.

Right now pyflakes is too simple-minded to digest dynamic formation of `__all__` in `__init__.py`, should we do something about it or should we rather silence pyflakes like I did?

See merge request !29

.gitlab-ci.yml

@@ -3,4 +3,4 @@ job:
     - python3 setup.py build
     - python3 setup.py build_ext -i
     - make -C doc clean && make -C doc html
-    - py.test --cov=kwant kwant
\ No newline at end of file
+    - py.test --cov=kwant --flakes kwant

kwant/digest.py

@@ -22,7 +22,6 @@ this module.
 from math import pi, log, sqrt, cos
 from hashlib import md5
 from struct import unpack
-import sys
 
 __all__ = ['uniform', 'gauss', 'test']
 

kwant/linalg/mumps.py

@@ -14,6 +14,7 @@ __all__ = ['MUMPSContext', 'schur_complement', 'AnalysisStatistics',
 import time
 import numpy as np
 import scipy.sparse
+import warnings
 from . import _mumps
 from .fortran_helpers import prepare_for_fortran
 

kwant/linalg/tests/test_mumps.py

@@ -81,3 +81,10 @@ def test_error_minus_9(r=10):
 
     # No need to check result, it's enough if no exception is raised
     MUMPSContext().factor(ham)
+
+
+def test_factor_warning():
+    """Test that a warning is raised if factor is asked without analysis."""
+    a = sp.identity(10, dtype=complex)
+    with pytest.warns(RuntimeWarning):
+        MUMPSContext().factor(a, reuse_analysis=True)

kwant/solvers/default.py

@@ -6,7 +6,7 @@
 # the file AUTHORS.rst at the top-level directory of this distribution and at
 # http://kwant-project.org/authors.
 
-__all__ = ['smatrx', 'ldos', 'wave_function', 'greens_function']
+__all__ = ['smatrix', 'ldos', 'wave_function', 'greens_function']
 
 # MUMPS usually works best.  Use SciPy as fallback.
 import warnings

kwant/solvers/sparse.py

@@ -8,7 +8,6 @@
 
 __all__ = ['smatrix', 'greens_function', 'ldos', 'wave_function', 'Solver']
 
-import warnings
 import numpy as np
 import scipy.sparse as sp
 from . import common

kwant/solvers/tests/test_sparse.py

@@ -7,7 +7,6 @@
 # http://kwant-project.org/authors.
 
 from  kwant.solvers.sparse import smatrix, greens_function, ldos, wave_function
-import kwant.solvers.sparse
 from . import _test_sparse
 
 def test_output():

kwant/system.py

@@ -11,7 +11,6 @@
 __all__ = ['System', 'FiniteSystem', 'InfiniteSystem']
 
 import abc
-import types
 from copy import copy
 from . import _system
 

kwant/tests/test_plotter.py

@@ -15,7 +15,7 @@ import pytest
 
 if plotter.mpl_enabled:
     from mpl_toolkits import mplot3d
-    from matplotlib import pyplot
+    from matplotlib import pyplot  # pragma: no flakes
 
 
 def test_importable_without_matplotlib():

pytest.ini

 [pytest]
 testpaths = kwant
+flakes-ignore =
+    __init__.py UnusedImport
+    graph/tests/test_scotch.py UndefinedName
+    graph/tests/test_dissection.py UndefinedName