Merge 3c5a082 into 389ada4

.travis.yml

@@ -44,7 +44,7 @@ install:
 #  - pip install codecov
 
 script:
-   - travis_wait 60 py.test --cov=multiphonon tests
+   - py.test -s --cov=multiphonon tests
    - python examples/getdos-Al.py
    - python examples/getdos-Al-from-nparrs.py
 # the following were run standalone but now all included in the cmd above.

docs/conf.py

@@ -49,18 +49,18 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'multiphonon'
-copyright = u'2017, ORNL Neutron Data Sciences Group'
-author = u'Jiao Lin and Fahima Islam'
+project = 'multiphonon'
+copyright = '2017, ORNL Neutron Data Sciences Group'
+author = 'Jiao Lin and Fahima Islam'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u'0.1'
+version = '0.1'
 # The full version, including alpha/beta/rc tags.
-release = u'0.1.1'
+release = '0.1.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -227,8 +227,8 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'multiphonon.tex', u'multiphonon Documentation',
-     u'Jiao Lin', 'manual'),
+    (master_doc, 'multiphonon.tex', 'multiphonon Documentation',
+     'Jiao Lin', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -257,7 +257,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'multiphonon', u'multiphonon Documentation',
+    (master_doc, 'multiphonon', 'multiphonon Documentation',
      [author], 1)
 ]
 
@@ -271,7 +271,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'multiphonon', u'multiphonon Documentation',
+    (master_doc, 'multiphonon', 'multiphonon Documentation',
      author, 'multiphonon', 'One line description of project.',
      'Miscellaneous'),
 ]

examples/getdos-Al-from-nparrs.py

@@ -43,7 +43,7 @@
     C_ms=0.2, Ei=80., workdir=workdir)
 # process and plot
 for i, dos in enumerate(iterdos): 
-    print "* Iteration", i
+    print("* Iteration", i)
     if not headless:
         plt.plot(dos.E, dos.I, label='%d' % i)
     continue
@@ -52,4 +52,4 @@
     plt.legend()
     plt.show()
 
-print "Intermediate and final results are stored in directory %r" % workdir
+print("Intermediate and final results are stored in directory %r" % workdir)

examples/getdos-Al.py

@@ -35,7 +35,7 @@
 
 # process
 for i, dos in enumerate(iterdos):
-    print "* Iteration", i
+    print("* Iteration", i)
     if not headless:
         plt.plot(dos.E, dos.I, label='%d' % i)
     continue
@@ -44,4 +44,4 @@
     plt.legend()
     plt.show()
 
-print "Intermediate and final results are stored in directory %r" % workdir
+print("Intermediate and final results are stored in directory %r" % workdir)

examples/getdos2-graphite_Ei130meV-noUI.py

@@ -18,19 +18,19 @@
     from multiphonon.sqe import plot as plot_sqe
 
 
-print "* Reading DOS from $E_i=300$..."
+print("* Reading DOS from $E_i=300$...")
 dos_300 = hh.load('./data/graphite-Ei_300-dos.h5')
 #
 if not headless:
-    print "* Plotting DOS from $E_i=300$..."
+    print("* Plotting DOS from $E_i=300$...")
     plt.figure()
     plt.plot(dos_300.E, dos_300.I)
     plt.show()
 
-print "* Reading S(Q,E) from $E_i=130$..."
+print("* Reading S(Q,E) from $E_i=130$...")
 iqe_130 = hh.load('data/graphite-Ei_130-iqe.h5')
 if not headless:
-    print "* Plotting S(Q,E) from $E_i=130$..."
+    print("* Plotting S(Q,E) from $E_i=130$...")
     plt.figure()
     plot_sqe(iqe_130)
     plt.xlim(0, 18)
@@ -40,7 +40,7 @@
 # It is clear here only phonons with $E<120meV$ were measured in this dataset.
 
 
-print "* Processing and stitching..."
+print("* Processing and stitching...")
 iterdos = sqe2dos.sqe2dos(
     iqe_130, T=300, Ecutoff=100., 
     elastic_E_cutoff=(-30., 15), M=12.,
@@ -52,13 +52,13 @@
 # plot the partial DOS
 partial_dos = lastdos[(None, 100)]
 if not headless:
-    print "* Plotting the partial DOS from Ei=130 ..."
+    print("* Plotting the partial DOS from Ei=130 ...")
     plt.figure()
     plt.plot(partial_dos.E, partial_dos.I)
     plt.show()
 # plot the final DOS
 if not headless:
-    print "* Plotting the stitched DOS..."
+    print("* Plotting the stitched DOS...")
     plt.figure()
     plt.plot(lastdos.E, lastdos.I)
     plt.show()

multiphonon/backward/sqe2dos.py

@@ -293,7 +293,7 @@ def normalizeExpSQE_inelonly(sqe, dos, M, beta, elastic_E_cutoff):
 """
 
 # 
-from singlephonon_sqe2dos import sqe2dos as singlephonon_sqe2dos
+from .singlephonon_sqe2dos import sqe2dos as singlephonon_sqe2dos
 from ._sqe2dos_script_templates import \
     plot_intermediate_result_sqe_code,plot_intermediate_result_se_code, \
     plot_dos_iteration_code, plot_residual_code

multiphonon/dos/io.py

@@ -20,7 +20,7 @@ def fromascii(datapath, x_unit=None):
             continue
         tokens = line.split()
         try:
-            numbers = map(float, tokens)
+            numbers = list(map(float, tokens))
         except Exception as e:
             msg = 'Skip line %s' % line
             warnings.warn(msg)

multiphonon/dos/nice.py

@@ -47,7 +47,7 @@ def fit(N):
     if badfit:
         # import pylab; pylab.plot(E, g); pylab.show()
         raise ParabolicFittingError("Unable to fit DOS to parabolic")
-    print "DOS: fit first %s points to parbolic" % N
+    print("DOS: fit first %s points to parbolic" % N)
     E1 = E[:N]
     g[:N] = c * E1*E1
     return E,g
@@ -100,18 +100,18 @@ def smooth(x,window_len=11,window='hanning'):
     import numpy
 
     if x.ndim != 1:
-        raise ValueError, "smooth only accepts 1 dimension arrays."
+        raise ValueError("smooth only accepts 1 dimension arrays.")
 
     if x.size < window_len:
-        raise ValueError, "Input vector needs to be bigger than window size."
+        raise ValueError("Input vector needs to be bigger than window size.")
 
 
     if window_len<3:
         return x
 
 
     if not window in ['flat', 'hanning', 'hamming', 'bartlett', 'blackman']:
-        raise ValueError, "Window is on of 'flat', 'hanning', 'hamming', 'bartlett', 'blackman'"
+        raise ValueError("Window is on of 'flat', 'hanning', 'hamming', 'bartlett', 'blackman'")
 
 
     s=numpy.r_[x[window_len-1:0:-1],x,x[-1:-window_len:-1]]

multiphonon/getdos.py

@@ -1,5 +1,5 @@
 import histogram.hdf as hh, numpy as np
-import os
+import os, sys
 
 # hide the warnings on divide by zero etc
 np.seterr(divide='ignore', invalid='ignore')
@@ -256,9 +256,9 @@ def raw2iqe(eventnxs, iqe_h5, Eaxis, Qaxis, type):
     if not os.path.exists(iqe_h5):
         qaxis = Qmin, dQ, Qmax
         eaxis = Emin, dE, Emax
-        if isinstance(eventnxs, unicode):
+        if sys.version_info < (3,0) and isinstance(eventnxs, unicode):
             eventnxs = eventnxs.encode()
-        if isinstance(iqe_h5, unicode):
+        if sys.version_info < (3,0) and isinstance(iqe_h5, unicode):
             iqe_h5 = iqe_h5.encode()
         reduce(eventnxs, qaxis, iqe_h5, eaxis=eaxis, tof2E='guess', ibnorm='ByCurrent')
     else:

multiphonon/redutils.py

@@ -15,14 +15,14 @@ def _createDefaultMantidUserConfig(facility='SNS'):
 
 mantid_checked = False
 def _checkMantid():
-    print "* Checking Mantid ..."
+    print("* Checking Mantid ...")
     import subprocess as sp, shlex
     sp.call(shlex.split("python -c 'import matplotlib, mantid'"), stdout=sp.PIPE, stderr=sp.PIPE) # sometimes mantid import for the first time may fail
     if sp.call(shlex.split("python -c 'import matplotlib, mantid'")):
         raise RuntimeError("Please install mantid")
     global mantid_checked
     mantid_checked = True
-    print "  - Done."
+    print("  - Done.")
     return
 if not mantid_checked:
     _checkMantid()

multiphonon/ui/batch.py

@@ -29,7 +29,7 @@ def process(sample_nxs_list, mt_nxs_list, parameter_yaml):
             os.makedirs(workdir)
         log = open(os.path.join(workdir, 'log.getdos'), 'wt')
         kargs['workdir'] = workdir
-        print "* Processing %s, %s" % (sample_nxs, mt_nxs)
+        print("* Processing %s, %s" % (sample_nxs, mt_nxs))
         for msg in getDOS(**kargs):
             log.write('%s\n' % (msg,))
         continue

multiphonon/ui/getdos.py

@@ -122,7 +122,7 @@ def validate(self):
         return True
 
     def nextStep(self):
-        print "Done."
+        print("Done.")
 
 def round2(a, digits = 1):
     d = 10**(np.floor(np.log10(a)) - digits+1)
@@ -201,9 +201,9 @@ def nextStep(self):
             mt_nxs=context.mt_nxs,
             workdir=context.workdir,
         )
-        for msg in r2i:print msg
+        for msg in r2i:print(msg)
         context.iqe_h5, context.mtiqe_h5, context.Qaxis, context.Eaxis = msg
-        print "Done."
+        print("Done.")
 
 
 # Wizard: GetDOS 

multiphonon/ui/getdos0.py

@@ -84,7 +84,7 @@ def submit(b):
                   open(os.path.join(workdir, 'getdos-opts.yaml'), 'wt'))
         maxiter = 10
         close = lambda w: w.close()
-        map(close, w_all)
+        list(map(close, w_all))
         from ..getdos import getDOS
         log_progress(getDOS(samplenxs, mt_nxs=mtnxs, maxiter=maxiter, **kargs), every=1, size=maxiter+2)
         return
@@ -139,7 +139,7 @@ def log_progress(sequence, every=None, size=None):
                     label.value = 'Running: {index} / ?: {msg}...'.format(index=index, msg=msg)
                 else:
                     progress.value = index
-                    label.value = u'Running: {index} / {size}: {msg}...'.format(
+                    label.value = 'Running: {index} / {size}: {msg}...'.format(
                         index=index,
                         size=size,
                         msg=msg

tests/backward/singlephonon_sqe2dos_TestCase.py

@@ -32,7 +32,7 @@ def test1a(self):
         # compare to the original dos data
         E1, g1 = loadDOS()
         ginterp = np.interp(E1, E, g)
-        self.assert_(np.allclose(g1, ginterp))
+        self.assertTrue(np.allclose(g1, ginterp))
         # plot
         if interactive:
             import pylab
@@ -52,8 +52,8 @@ def test1b(self):
             newiqe, T=300, Ecutoff=65., elastic_E_cutoff=(-20., 6.7), M=50.94)
         path = os.path.join(here, 'expected_results', 'test1b-dos.h5')
         expected = hh.load(path)
-        self.assert_(np.allclose(DOS.I, expected.I))
-        self.assert_(np.allclose(DOS.E2, expected.E2))
+        self.assertTrue(np.allclose(DOS.I, expected.I))
+        self.assertTrue(np.allclose(DOS.E2, expected.E2))
         # plot
         if interactive:
             H.plot(DOS)
@@ -95,9 +95,9 @@ def test1c1(self):
         path = os.path.join(here, 'expected_results', 'test1c1-dos.h5')
         # hh.dump(newdos, path)
         expected = hh.load(path)
-        self.assert_(np.allclose(newdos.I, expected.I))
-        self.assert_(np.allclose(newdos.E, expected.E))
-        self.assert_(np.allclose(newdos.E2, expected.E2))
+        self.assertTrue(np.allclose(newdos.I, expected.I))
+        self.assertTrue(np.allclose(newdos.E, expected.E))
+        self.assertTrue(np.allclose(newdos.E2, expected.E2))
         # plot
         if interactive:
             pylab.errorbar(initdos.E, initdos.I, initdos.E2**.5, label='init')
@@ -117,8 +117,8 @@ def test1c2(self):
         path = os.path.join(here, 'expected_results', 'test1c2-dos.h5')
         # hh.dump(newdos, path)
         expected = hh.load(path)
-        self.assert_(np.allclose(newdos.I, expected.I))
-        self.assert_(np.allclose(newdos.E, expected.E))
+        self.assertTrue(np.allclose(newdos.I, expected.I))
+        self.assertTrue(np.allclose(newdos.E, expected.E))
         # self.assert_(np.allclose(newdos.E2, expected.E2))
         # plot
         if interactive:
@@ -142,7 +142,7 @@ def test1d(self):
             for w in ws:
                 has_scaling_factor_warning = has_scaling_factor_warning or ('Scaling factor' in str(w))
                 continue
-            self.assert_(has_scaling_factor_warning)
+            self.assertTrue(has_scaling_factor_warning)
         # plot
         if interactive:
             pylab.plot(initdos.E, initdos.I)

tests/backward/sqe2dos_TestCase.py

@@ -44,8 +44,8 @@ def test2a(self):
         path = os.path.join(here, 'expected_results', 'sqe2dos-test2a-final-dos.h5')
         # hh.dump(dos, path)
         expected = hh.load(path)
-        self.assert_(np.allclose(dos.I, expected.I))
-        self.assert_(np.allclose(dos.E2, expected.E2))
+        self.assertTrue(np.allclose(dos.I, expected.I))
+        self.assertTrue(np.allclose(dos.E2, expected.E2))
         if interactive:
             pylab.figure()
             pylab.errorbar(dos.E, dos.I+dos.I.max()/5., dos.E2**.5, label='new')
@@ -92,8 +92,8 @@ def test2b(self):
         path = os.path.join(here, 'expected_results', 'sqe2dos-test2b-final-dos.h5')
         # hh.dump(dos, path)
         expected = hh.load(path)
-        self.assert_(np.allclose(dos.I, expected.I))
-        self.assert_(np.allclose(dos.E2, expected.E2))
+        self.assertTrue(np.allclose(dos.I, expected.I))
+        self.assertTrue(np.allclose(dos.E2, expected.E2))
         if interactive:
             pylab.figure()
             pylab.errorbar(dos.E, dos.I + dos.I.max()/5, dos.E2**.5, label='new')
@@ -121,7 +121,7 @@ def test2c(self):
         path = os.path.join(here, 'expected_results', 'sqe2dos-test2c-final-dos.h5')
         # hh.dump(dos, path)
         expected = hh.load(path)
-        self.assert_(np.allclose(dos.I, expected.I))
+        self.assertTrue(np.allclose(dos.I, expected.I))
         # self.assert_(np.allclose(dos.E2, expected.E2))
         if interactive:
             pylab.figure()

tests/forward/phonon_TestCase.py

@@ -88,7 +88,7 @@ def test3(self):
 
 
     def _check(self, a1, a2):
-        self.assert_(np.allclose(a1, a2))
+        self.assertTrue(np.allclose(a1, a2))
 
     pass  # end of TestCase
 

tests/forward/phonon_TestCase2.py

@@ -25,7 +25,7 @@ def test1(self):
         T = 300
         beta = 1./(T*kelvin2mev)
         dwexp = DWExp(Q, M, E,g, beta, dE)
-        print dwexp
+        print(dwexp)
         return