grond py3 clean

apps/grond

@@ -18,7 +18,7 @@ km = 1e3
 
 def d2u(d):
     if isinstance(d, dict):
-        return dict((k.replace('-', '_'), v) for (k, v) in d.iteritems())
+        return dict((k.replace('-', '_'), v) for (k, v) in d.items())
     else:
         return d.replace('-', '_')
 
@@ -102,7 +102,7 @@ def cl_parse(command, args, setup=None, details=None):
     usage = subcommand_usages[command]
     descr = subcommand_descriptions[command]
 
-    if isinstance(usage, basestring):
+    if isinstance(usage, str):
         usage = [usage]
 
     susage = '%s %s' % (program_name, usage[0])
@@ -284,7 +284,7 @@ region = Myanmar
         for fn in empty_files:
             open(p(fn), 'w').close()
     else:
-        print config
+        print(config)
 
 
 def command_events(args):
@@ -298,9 +298,9 @@ def command_events(args):
     config_path = args[0]
     config = grond.read_config(config_path)
 
-    print 'Available Events:'
+    print('Available Events:')
     for event_name in grond.get_event_names(config):
-        print '* %s' % event_name
+        print('* %s' % event_name)
 
 
 def command_check(args):
@@ -370,10 +370,10 @@ def command_go(args):
         config_path = args[0]
         config = grond.read_config(config_path)
 
-        print 'Available Events:'
+        print('Available Events:')
         for event_name in grond.get_event_names(config):
-            print '* %s' % event_name
-        print '\n'
+            print('* %s' % event_name)
+        print('\n')
 
         help_and_die(parser, 'missing arguments')
 
@@ -516,7 +516,7 @@ selected by specifying a comma-separated list.''' % (
             dirname, plotnames,
             save=options.save, formats=formats, dpi=options.dpi)
 
-    except grond.GrondError, e:
+    except grond.GrondError as e:
         die(str(e))
 
 
@@ -595,7 +595,7 @@ def command_export(args):
             type=options.type,
             pnames=pnames)
 
-    except grond.GrondError, e:
+    except grond.GrondError as e:
         die(str(e))
 
 

setup.cfg

+[metadata]
+description-file=README.md
+license-file=LICENSE
+
+[bdist_wheel]
+universal=1
+
+[build_ext]
+inplace=1
+
+[nosetests]
+verbosity=2
+detailed-errors=1
+with-coverage=1
+cover-erase=1
+cover-package=kite
+
+[coverage:report]
+exclude_lines =
+    def __repr__
+    def __str__
+    raise AssertionError
+    raise NotImplementedError
+    raise ValueError
+    raise
+    if __name__ == .__main__.:
+    logger.error

src/analysers/base.py

-
 import copy
 import numpy as num
 from pyrocko.guts import Object, Int
@@ -40,10 +39,10 @@ class Analyser(object):
         notifier.emit('progress_start', 'analysing problem', self.niter)
 
         isbad_mask = None
-        for iiter in xrange(self.niter):
+        for iiter in range(self.niter):
             while True:
                 x = []
-                for ipar in xrange(npar):
+                for ipar in range(npar):
                     v = rstate.uniform(xbounds[ipar, 0], xbounds[ipar, 1])
                     x.append(v)
 
@@ -70,7 +69,7 @@ class Analyser(object):
         weights = 1. / mean_ms
         groups, ngroups = wproblem.get_group_mask()
 
-        for igroup in xrange(ngroups):
+        for igroup in range(ngroups):
             weights[groups == igroup] /= (
                 num.nansum(weights[groups == igroup]) /
                 num.nansum(num.isfinite(weights[groups == igroup])))

src/baraddur/meta.py

@@ -7,7 +7,7 @@ class ColorCycler(list):
         list.__init__(self, *args, **kwargs)
         self.index = -1
 
-    def next(self):
+    def __next__(self):
         self.index += 1
         if self.index >= len(self):
             self.index = 0
@@ -20,4 +20,4 @@ def makeColorGradient(misfits, fr=1., fg=.5, fb=1.,
     r = num.sin(fr * misfits + pr) * 127 + 128
     g = num.sin(fg * misfits + pg) * 127 + 128
     b = num.sin(fb * misfits + pb) * 127 + 128
-    return ['#%02x%02x%02x' % (r[i], g[i], b[i]) for i in xrange(misfits.size)]
+    return ['#%02x%02x%02x' % (r[i], g[i], b[i]) for i in range(misfits.size)]

src/baraddur/server.py

@@ -164,10 +164,10 @@ class SmoothColumnDataSource(ColumnDataSource):
 
     def stream(self, data, **kwargs):
         sigma = self._gaussian_kw['sigma']
-        if data.keys() == self.data.keys():
+        if list(data.keys()) == list(self.data.keys()):
             raise AttributeError('streaming data must represent'
                                  ' existing column')
-        for key, arr in data.iteritems():
+        for key, arr in data.items():
             if arr.ndim > 1 or not isinstance(arr, num.ndarray):
                 raise AttributeError('data is not numpy.ndarray of 1d')
 
@@ -508,17 +508,17 @@ class Baraddur(BokehServer):
             if handler_docs is None:
                 continue
 
-            for url, bokeh_handler in handler_docs.iteritems():
+            for url, bokeh_handler in handler_docs.items():
                 bokeh_apps['/plots/%s' % url] = Application(bokeh_handler(
                     self.config))
         return bokeh_apps
 
     def get_tornado_handlers(self):
-        return [(r'/', pages.values()[0],
+        return [(r'/', list(pages.values())[0],
                  {'config': self.config})] +\
                [(r'/%s' % title, handler,
                  {'config': self.config})
-                for title, handler in pages.iteritems()] +\
+                for title, handler in pages.items()] +\
                [(r'/res/(.*)', StaticFileHandler,
                 {'path': op.join(op.dirname(__file__), 'res')})]
 

src/core.py

@@ -176,7 +176,7 @@ def load_problem_data(dirname, problem, skip_models=0):
             count=nmodels * problem.nparameters)\
             .astype(num.float)
 
-    nmodels = data1.size/problem.nparameters - skip_models
+    nmodels = data1.size//problem.nparameters - skip_models
     xs = data1.reshape((nmodels, problem.nparameters))
 
     fn = op.join(dirname, 'misfits')

src/listeners/curses.py

@@ -38,7 +38,7 @@ class CursesListener(object):
             parameter_names = ['Parameters'] + state.parameters
             col = 0
 
-            for icol in xrange(len(state.values) + 1):
+            for icol in range(len(state.values) + 1):
                 row = 0
 
                 if icol == 0:

src/listeners/terminal.py

@@ -41,40 +41,39 @@ class TerminalListener(Listener):
         lines = []
         self.current_state = state
 
-        def l(t):
-            lines.append(t)
+        ladd = lines.append
 
         def fmt(s):
-            return util.gform(s, significant_digits=(self.col_width-1-6)/2)
+            return util.gform(s, significant_digits=(self.col_width-1-6)//2)
 
         out_ln = self.row_name +\
             ''.join([self.parameter_fmt] * len(state.parameter_sets))
         col_param_width = max([len(p) for p in state.parameter_names]) + 2
 
-        l('Problem name: {s.problem_name}'
-          '\t({s.runtime:s} - remaining {s.runtime_remaining}'
-          ' @ {s.iter_per_second:.1f} iter/s)'
-            .format(s=state))
-        l('Iteration {s.iiter} / {s.niter}'
-          .format(s=state))
+        ladd('Problem name: {s.problem_name}'
+             '\t({s.runtime.seconds} - remaining {s.runtime_remaining}'
+             ' @ {s.iter_per_second:.1f} iter/s)'
+             .format(s=state))
+        ladd('Iteration {s.iiter} / {s.niter}'
+             .format(s=state))
 
-        l(out_ln.format(
-            *['Parameter'] + state.parameter_sets.keys(),
+        ladd(out_ln.format(
+            *['Parameter'] + list(state.parameter_sets.keys()),
             col_param_width=col_param_width,
             col_width=self.col_width,
             type='s'))
 
         for ip, parameter_name in enumerate(state.parameter_names):
-            l(out_ln.format(
-                parameter_name,
-                *[fmt(v[ip]) for v in state.parameter_sets.values()],
-                col_param_width=col_param_width,
-                col_width=self.col_width))
+            ladd(out_ln.format(
+                 parameter_name,
+                 *[fmt(v[ip]) for v in state.parameter_sets.values()],
+                 col_param_width=col_param_width,
+                 col_width=self.col_width))
 
-        l(state.extra_text.format(
+        ladd(state.extra_text.format(
             col_param_width=col_param_width,
             col_width=self.col_width,))
 
         lines[0:0] = ['\033[2J']
-        l('')
-        print '\n'.join(lines)
+        ladd('')
+        print('\n'.join(lines))

src/problems/base.py

@@ -188,7 +188,7 @@ class Problem(Object):
         ntargets = self.ntargets
         ws = num.zeros((nbootstrap, ntargets))
         rstate = num.random.RandomState(23)
-        for ibootstrap in xrange(nbootstrap):
+        for ibootstrap in range(nbootstrap):
             if type == 'classic':
                 ii = rstate.randint(0, ntargets, size=self.ntargets)
                 ws[ibootstrap, :] = num.histogram(
@@ -230,7 +230,7 @@ class Problem(Object):
         group, ngroups = self.get_group_mask()
 
         ws = num.zeros(self.ntargets)
-        for igroup in xrange(ngroups):
+        for igroup in range(ngroups):
             mask = group == igroup
             ws[mask] = 1.0 / root(num.nansum(exp(ns[mask])))
 
@@ -241,7 +241,7 @@ class Problem(Object):
 
         group, ngroups = self.get_group_mask()
         ws = num.zeros(ns.shape)
-        for igroup in xrange(ngroups):
+        for igroup in range(ngroups):
             mask = group == igroup
             ws[:, mask] = (1.0 / root(
                 num.nansum(exp(ns[:, mask]), axis=1)))[:, num.newaxis]

src/problems/double_dc.py

@@ -123,7 +123,7 @@ class DoubleDCProblem(Problem):
 
     def random_uniform(self, xbounds):
         x = num.zeros(self.nparameters)
-        for i in xrange(self.nparameters):
+        for i in range(self.nparameters):
             x[i] = num.random.uniform(xbounds[i, 0], xbounds[i, 1])
 
         return x.tolist()

src/problems/rectangular.py

@@ -92,7 +92,7 @@ class RectangularProblem(Problem):
 
     def random_uniform(self, xbounds):
         x = num.zeros(self.nparameters)
-        for i in xrange(self.nparameters):
+        for i in range(self.nparameters):
             x[i] = num.random.uniform(xbounds[i, 0], xbounds[i, 1])
 
         return x.tolist()

src/solvers/base.py

@@ -11,15 +11,13 @@ guts_prefix = 'grond'
 logger = logging.getLogger('grond.solver')
 
 
-class SimpleTimedelta(timedelta):
-    def __str__(self):
-        return timedelta.__str__(self).split('.')[0]
-
-
 class RingBuffer(num.ndarray):
+    def __new__(cls, *args, **kwargs):
+        cls = num.ndarray.__new__(cls, *args, **kwargs)
+        cls.fill(0.)
+        return cls
+
     def __init__(self, *args, **kwargs):
-        num.ndarray.__init__(self, *args, **kwargs)
-        self.fill(0.)
         self.pos = 0
 
     def put(self, value):
@@ -58,14 +56,14 @@ class SolverState(object):
 
     @property
     def runtime(self):
-        return SimpleTimedelta(seconds=time.time() - self.starttime)
+        return timedelta(seconds=time.time() - self.starttime)
 
     @property
     def runtime_remaining(self):
         if self.iter_per_second == 0.:
-            return SimpleTimedelta()
-        return SimpleTimedelta(seconds=(self.niter - self.iiter)
-                               / self.iter_per_second)
+            return timedelta()
+        return timedelta(seconds=(self.niter - self.iiter)
+                         / self.iter_per_second)
 
     @property
     def nparameters(self):

src/solvers/highscore.py

@@ -217,8 +217,8 @@ def solve(problem,
                     if sampler_distribution == 'normal':
                         ncandidates = 1
                         xcandidates = num.zeros((ncandidates, npar))
-                        for icandidate in xrange(ncandidates):
-                            for ipar in xrange(npar):
+                        for icandidate in range(ncandidates):
+                            for ipar in range(npar):
                                 ntry = 0
                                 while True:
                                     if local_sxs[ibootstrap_choice][ipar] > 0.:
@@ -300,7 +300,7 @@ def solve(problem,
 
         nlinks += 1
 
-        for ichain in xrange(chains_m.shape[0]):
+        for ichain in range(chains_m.shape[0]):
             isort = num.argsort(chains_m[ichain, :nlinks])
             chains_m[ichain, :nlinks] = chains_m[ichain, isort]
             chains_i[ichain, :nlinks] = chains_i[ichain, isort]
@@ -342,7 +342,7 @@ def solve(problem,
             mxs = []
             local_sxs = []
 
-            for i in xrange(1 + nbootstrap):
+            for i in range(1 + nbootstrap):
                 xs = xhist[chains_i[i, :nlinks], :]
                 mx = num.mean(xs, axis=0)
                 cov = num.cov(xs.T)
@@ -386,7 +386,7 @@ def solve(problem,
             matrix = (chains_i[:, :30] % 94 + 32).T
             for row in matrix[::-1]:
                 lines.append(''.join(chr(xxx) for xxx in row))
-            print '\n'.join(lines)
+            print('\n'.join(lines))
 
         if plot and plot.want_to_update(iiter):
             plot.update(

src/targets/waveform.py

@@ -365,7 +365,7 @@ class WaveformMisfitTarget(gf.Target, MisfitTarget):
 
             return mr
 
-        except NotFound, e:
+        except NotFound as e:
             logger.debug(str(e))
             raise gf.SeismosizerError('no waveform data, %s' % str(e))
 
@@ -419,7 +419,7 @@ tautoshift**2 / tautoshift_max**2``
             m, n = trace.Lx_norm(a, b, norm=exponent)
         else:
             mns = []
-            for ishift in xrange(-nshift_max, nshift_max+1):
+            for ishift in range(-nshift_max, nshift_max+1):
                 if ishift < 0:
                     a_cut = a[-ishift:]
                     b_cut = b[:ishift]

test/test_path.py

-import unittest
-from pyrocko import util
-from grond import HasPaths, Path
-
-
-class PathTestCase(unittest.TestCase):
-
-    def test_pathstuff(self):
-
-        class B(HasPaths):
-            p1 = Path.T()
-            p2 = Path.T()
-
-        class A(HasPaths):
-            p1 = Path.T()
-            p2 = Path.T()
-            b = B.T()
-
-        for path_prefix_a in (
-                None, 'relative_prefix_a', '/absolute_prefix_a'):
-            for path_prefix_b in (
-                    None, 'relative_prefix_b', '/absolute_prefix_b'):
-                a = A(
-                    path_prefix=path_prefix_a,
-                    p1='abc/x.txt',
-                    p2='/absolute/x.txt',
-                    b=B(
-                        path_prefix=path_prefix_b,
-                        p1='abc/y.txt',
-                        p2='/absolute/y.txt'))
-
-                a.set_basepath('rundir')
-
-                t1 = a.expand_path(a.p1)
-                t2 = a.expand_path(a.p2)
-                t3 = a.b.expand_path(a.b.p1)
-                t4 = a.b.expand_path(a.b.p2)
-
-                a.change_basepath('resultdir')
-
-                assert t1 == a.expand_path(a.p1)
-                assert t2 == a.expand_path(a.p2)
-                assert t3 == a.b.expand_path(a.b.p1)
-                assert t4 == a.b.expand_path(a.b.p2)
-
-
-if __name__ == '__main__':
-    util.setup_logging('test_path', 'warning')
-    unittest.main()