Fix pycodestyle E305 using autopep8 (scipy#8391)

* Fix pycodestyle E305 using autopep8

Using pycodestyle v2.3.1 (successor to the tool pep8) to check
coding style, there were hundreds of cases of:

E305 expected 2 blank lines after class or function definition

These were fixed using:

autopep8 --select E305 --in-place ...

This would close issue scipy#8388, cross reference scipy#8384 for updating
TravisCI to use pycodestyle inplace of pep8 for style checks.

* TravisCI/tox can now enforce pep8 E305

benchmarks/benchmarks/spatial.py

@@ -55,6 +55,7 @@ def time_build(self, mnr, cls_name):
         else:
             self.cls(self.data)
 
+
 LEAF_SIZES = [8, 128]
 BOX_SIZES = [None, 0.0, 1.0]
 

benchmarks/benchmarks/test_functions.py

@@ -154,6 +154,7 @@ def der(self, coords):
                 2. * (2.625 - x + x * y**3) * (3. * x * y**2))
         return np.array([dfdx, dfdy])
 
+
 """
 Global Test functions for minimizers.
 

doc/postprocess.py

@@ -56,5 +56,6 @@ def process_tex(lines):
             new_lines.append(line)
     return new_lines
 
+
 if __name__ == "__main__":
     main()

doc/source/tutorial/examples/newton_krylov_preconditioning.py

@@ -89,5 +89,6 @@ def main():
     plt.colorbar()
     plt.show()
 
+
 if __name__ == "__main__":
     main()

doc/source/tutorial/stats/plots/kde_plot2.py

@@ -11,6 +11,7 @@ def my_kde_bandwidth(obj, fac=1./5):
     """We use Scott's Rule, multiplied by a constant factor."""
     return np.power(obj.n, -1./(obj.d+4)) * fac
 
+
 fig = plt.figure()
 ax = fig.add_subplot(111)
 

doc/source/tutorial/stats/plots/kde_plot5.py

@@ -9,6 +9,7 @@ def measure(n):
     m2 = np.random.normal(scale=0.5, size=n)
     return m1+m2, m1-m2
 
+
 m1, m2 = measure(2000)
 xmin = m1.min()
 xmax = m1.max()

runtests.py

@@ -406,6 +406,7 @@ def gcov_reset_counters():
 # LCOV support
 #
 
+
 LCOV_OUTPUT_FILE = os.path.join(ROOT_DIR, 'build', 'lcov.out')
 LCOV_HTML_DIR = os.path.join(ROOT_DIR, 'build', 'lcov')
 

scipy/_lib/decorator.py

@@ -77,6 +77,7 @@ def getargspec(f):
     spec = getfullargspec(f)
     return ArgSpec(spec.args, spec.varargs, spec.varkw, spec.defaults)
 
+
 DEF = re.compile(r'\s*def\s*([_\w][_\w\d]*)\s*\(')
 
 
@@ -282,6 +283,7 @@ def __call__(self, func):
             func, "with _self_: return _func_(%(shortsignature)s)",
             dict(_self_=self, _func_=func), __wrapped__=func)
 
+
 init = getfullargspec(_GeneratorContextManager.__init__)
 n_args = len(init.args)
 if n_args == 2 and not init.varargs:  # (self, genobj) Python 2.7

scipy/cluster/vq.py

@@ -264,6 +264,7 @@ def py_vq(obs, code_book, check_finite=True):
     min_dist = dist[np.arange(len(code)), code]
     return code, min_dist
 
+
 # py_vq2 was equivalent to py_vq
 py_vq2 = np.deprecate(py_vq, old_name='py_vq2', new_name='py_vq')
 
@@ -515,6 +516,7 @@ def _krandinit(data, k):
     x += mu
     return x
 
+
 _valid_init_meth = {'random': _krandinit, 'points': _kpoints}
 
 
@@ -529,6 +531,7 @@ def _missing_raise():
     raise ClusterError("One of the clusters is empty. "
                        "Re-run kmeans with a different initialization.")
 
+
 _valid_miss_meth = {'warn': _missing_warn, 'raise': _missing_raise}
 
 

scipy/constants/codata.py

@@ -1353,6 +1353,7 @@ def find(sub=None, disp=False):
     else:
         return result
 
+
 # Table is lacking some digits for exact values: calculate from definition
 c = value('speed of light in vacuum')
 mu0 = 4e-7 * pi

scipy/fftpack/basic.py

@@ -95,6 +95,7 @@ def _fake_cfftnd(x, shape, *a, **kw):
     else:
         return _fftpack.zfftnd(x, shape, *a, **kw).astype(numpy.complex64)
 
+
 _DTYPE_TO_FFT = {
 #        numpy.dtype(numpy.float32): _fftpack.crfft,
         numpy.dtype(numpy.float32): _fake_crfft,

scipy/fftpack/pseudo_diffs.py

@@ -78,6 +78,8 @@ def kernel(k,order=order,c=c):
     overwrite_x = _datacopied(tmp, x)
     return convolve.convolve(tmp,omega,swap_real_imag=order % 2,
                              overwrite_x=overwrite_x)
+
+
 del _cache
 
 
@@ -146,6 +148,8 @@ def kernel(k, h=h):
 
     overwrite_x = _datacopied(tmp, x)
     return convolve.convolve(tmp,omega,swap_real_imag=1,overwrite_x=overwrite_x)
+
+
 del _cache
 
 
@@ -186,6 +190,8 @@ def kernel(k,h=h):
         _cache[(n,h)] = omega
     overwrite_x = _datacopied(tmp, x)
     return convolve.convolve(tmp,omega,swap_real_imag=1,overwrite_x=overwrite_x)
+
+
 del _cache
 
 
@@ -251,6 +257,8 @@ def kernel(k):
         _cache[n] = omega
     overwrite_x = _datacopied(tmp, x)
     return convolve.convolve(tmp,omega,swap_real_imag=1,overwrite_x=overwrite_x)
+
+
 del _cache
 
 
@@ -323,6 +331,8 @@ def kernel(k,a=a,b=b):
         _cache[(n,a,b)] = omega
     overwrite_x = _datacopied(tmp, x)
     return convolve.convolve(tmp,omega,swap_real_imag=1,overwrite_x=overwrite_x)
+
+
 del _cache
 
 
@@ -377,6 +387,8 @@ def kernel(k,a=a,b=b):
         _cache[(n,a,b)] = omega
     overwrite_x = _datacopied(tmp, x)
     return convolve.convolve(tmp,omega,swap_real_imag=1,overwrite_x=overwrite_x)
+
+
 del _cache
 
 
@@ -430,6 +442,8 @@ def kernel(k,a=a,b=b):
         _cache[(n,a,b)] = omega
     overwrite_x = _datacopied(tmp, x)
     return convolve.convolve(tmp,omega,overwrite_x=overwrite_x)
+
+
 del _cache
 
 
@@ -485,6 +499,8 @@ def kernel(k,a=a,b=b):
         _cache[(n,a,b)] = omega
     overwrite_x = _datacopied(tmp, x)
     return convolve.convolve(tmp,omega,overwrite_x=overwrite_x)
+
+
 del _cache
 
 
@@ -537,4 +553,5 @@ def kernel_imag(k,a=a):
     return convolve.convolve_z(tmp,omega_real,omega_imag,
                                overwrite_x=overwrite_x)
 
+
 del _cache

scipy/fftpack/tests/gen_fftw_ref.py

@@ -26,6 +26,7 @@ def gen_data(dt):
 
     return arrays
 
+
 # generate single precision data
 data = gen_data(np.float32)
 filename = 'fftw_single_ref'

scipy/integrate/odepack.py

@@ -10,6 +10,7 @@
 class ODEintWarning(Warning):
     pass
 
+
 _msgs = {2: "Integration successful.",
          1: "Nothing was done; the integration time was 0.",
          -1: "Excess work done on this call (perhaps wrong Dfun type).",

scipy/integrate/quadrature.py

@@ -29,6 +29,8 @@ def _cached_roots_legendre(n):
 
     _cached_roots_legendre.cache[n] = roots_legendre(n)
     return _cached_roots_legendre.cache[n]
+
+
 _cached_roots_legendre.cache = dict()
 
 

scipy/interpolate/_fitpack_impl.py

@@ -310,6 +310,7 @@ def splprep(x, w=None, u=None, ub=None, ue=None, k=3, task=0, s=None, t=None,
     else:
         return tcku
 
+
 _curfit_cache = {'t': array([], float), 'wrk': array([], float),
                  'iwrk': array([], intc)}
 
@@ -792,6 +793,7 @@ def spalde(x, tck):
 # def _curfit(x,y,w=None,xb=None,xe=None,k=3,task=0,s=None,t=None,
 #           full_output=0,nest=None,per=0,quiet=1):
 
+
 _surfit_cache = {'tx': array([], float), 'ty': array([], float),
                  'wrk': array([], float), 'iwrk': array([], intc)}
 

scipy/interpolate/setup.py

@@ -48,6 +48,7 @@ def configuration(parent_package='',top_path=None):
 
     return config
 
+
 if __name__ == '__main__':
     from numpy.distutils.core import setup
     setup(**configuration(top_path='').todict())

scipy/interpolate/tests/test_polyint.py

@@ -51,6 +51,7 @@ def check_shape(interpolator_cls, x_shape, y_shape, deriv_shape=None, axis=0,
         yi, y = np.broadcast_arrays(yi, yv)
         assert_allclose(yi, y)
 
+
 SHAPES = [(), (0,), (1,), (6, 2, 5)]
 
 

scipy/io/arff/arffread.py

@@ -659,6 +659,7 @@ def test_weka(filename):
     for i in meta:
         print_attribute(i, meta[i], data[i])
 
+
 # make sure nose does not find this as a test
 test_weka.__test__ = False
 

scipy/io/arff/setup.py

@@ -7,6 +7,7 @@ def configuration(parent_package='io',top_path=None):
     config.add_data_dir('tests')
     return config
 
+
 if __name__ == '__main__':
     from numpy.distutils.core import setup
     setup(**configuration(top_path='').todict())

scipy/io/harwell_boeing/setup.py

@@ -8,6 +8,7 @@ def configuration(parent_package='',top_path=None):
 
     return config
 
+
 if __name__ == '__main__':
     from numpy.distutils.core import setup
     setup(**configuration(top_path='').todict())

scipy/io/matlab/setup.py

@@ -10,6 +10,7 @@ def configuration(parent_package='io',top_path=None):
     config.add_data_dir('tests')
     return config
 
+
 if __name__ == '__main__':
     from numpy.distutils.core import setup
     setup(**configuration(top_path='').todict())

scipy/io/matlab/tests/test_mio.py

@@ -45,6 +45,7 @@ def mlarr(*args, **kwargs):
     arr.shape = matdims(arr)
     return arr
 
+
 # Define cases to test
 theta = np.pi/4*np.arange(9,dtype=float).reshape(1,9)
 case_table4 = [

scipy/io/setup.py

@@ -14,6 +14,7 @@ def configuration(parent_package='',top_path=None):
     config.add_subpackage('harwell_boeing')
     return config
 
+
 if __name__ == '__main__':
     from numpy.distutils.core import setup
     setup(**configuration(top_path='').todict())

scipy/linalg/_cython_signature_generator.py

@@ -79,6 +79,7 @@ def sigs_from_dir(directory, outfile, manual_wrappers=None, exclusions=None):
 # The other manual signatures are used because the signature generating
 # functions don't work when function pointer arguments are used.
 
+
 lapack_manual_wrappers = '''void cgees(char *jobvs, char *sort, cselect1 *select, int *n, c *a, int *lda, int *sdim, c *w, c *vs, int *ldvs, c *work, int *lwork, s *rwork, bint *bwork, int *info)
 void cgeesx(char *jobvs, char *sort, cselect1 *select, char *sense, int *n, c *a, int *lda, int *sdim, c *w, c *vs, int *ldvs, s *rconde, s *rcondv, c *work, int *lwork, s *rwork, bint *bwork, int *info)
 void cgges(char *jobvsl, char *jobvsr, char *sort, cselect2 *selctg, int *n, c *a, int *lda, c *b, int *ldb, int *sdim, c *alpha, c *beta, c *vsl, int *ldvsl, c *vsr, int *ldvsr, c *work, int *lwork, s *rwork, bint *bwork, int *info)