Merge pull request #658 from jbarnoud/issue-260-python-3

Issue #260 Partial python 3 compatibility

.travis.yml

@@ -1,17 +1,23 @@
-env:
-   global:
-      - secure: "HIj3p+p2PV8DBVg/KGUx6n83KwB0ASE5FwOn0SMB9zxnzAqe8sapwdBQdMdq0sXB7xT1spJqRxuxOMVEVn35BNLu7bxMLfa4287C8YXcomnvmv9xruxAsjsIewnNQ80vtPVbQddBPxa4jKbqgPby5QhhAP8KANAqYe44pIV70fY="
-      - GH_DOC_BRANCH: develop
-      - GH_REPOSITORY: github.com/MDAnalysis/mdanalysis.git
-      - GIT_CI_USER: TravisCI
-      - GIT_CI_EMAIL: [email protected]
-      - MDA_DOCDIR: package/doc/html
-   matrix:
-   - SETUP=full CYTHONIZE=true
-   - SETUP=minimal CYTHONIZE=false
 language: python
-python:
-  - "2.7"
+env:
+  global:
+    - secure: "HIj3p+p2PV8DBVg/KGUx6n83KwB0ASE5FwOn0SMB9zxnzAqe8sapwdBQdMdq0sXB7xT1spJqRxuxOMVEVn35BNLu7bxMLfa4287C8YXcomnvmv9xruxAsjsIewnNQ80vtPVbQddBPxa4jKbqgPby5QhhAP8KANAqYe44pIV70fY="
+    - GH_DOC_BRANCH: develop
+    - GH_REPOSITORY: github.com/MDAnalysis/mdanalysis.git
+    - GIT_CI_USER: TravisCI
+    - GIT_CI_EMAIL: [email protected]
+    - MDA_DOCDIR: package/doc/html
+matrix:
+  allow_failures:
+     - python: "3.3"
+       env: SETUP=full CYTHONIZE=true
+  include:
+     - python: "2.7"
+       env: SETUP=minimal CYTHONIZE=false
+     - python: "2.7"
+       env: SETUP=full CYTHONIZE=true
+     - python: "3.3"
+       env: SETUP=full CYTHONIZE=true
 # command to install dependencies
 addons:
   apt:
@@ -41,7 +47,7 @@ install:
   - chmod +x testsuite/MDAnalysisTests/mda_nosetests
 # command to run tests
 script:
-  - ./testsuite/MDAnalysisTests/mda_nosetests --with-coverage --cover-package MDAnalysis --processes=2 --process-timeout=300 --with-memleak
+  - ./testsuite/MDAnalysisTests/mda_nosetests --with-coverage --cover-package MDAnalysis --processes=2 --process-timeout=300 $( if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then echo '--with-memleak'; fi )
   - |
      test ${TRAVIS_PULL_REQUEST} == "false" && \
      test ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} && \

README.rst

@@ -28,7 +28,7 @@ lists of  supported `trajectory formats`_ and `topology formats`_.)
    
    # Iterate through trajectories
    for ts in u.trajectory:
-       print ag.center_of_mass()
+       print(ag.center_of_mass())
 
 Source code
 ===========

package/MDAnalysis/__init__.py

@@ -172,3 +172,12 @@
 del weakref
 
 from .migration.ten2eleven import ten2eleven
+
+import six
+if six.PY3:
+    warnings.warn('''\
+#####
+MDAnalysis on python 3 is highly experimental!
+It is mostly non functional and dramatically untested.
+Use at your own risks!!!
+''')

package/MDAnalysis/analysis/density.py

@@ -82,15 +82,13 @@
 
 """
 from __future__ import print_function
-
 from six.moves import range
 
 import numpy as np
 import sys
 import os
 import os.path
 import errno
-import cPickle
 import warnings
 
 try:

package/MDAnalysis/analysis/gnm.py

@@ -80,6 +80,7 @@
 
 # import copy #unused
 
+from __future__ import print_function
 from six.moves import range
 
 import numpy as np
@@ -113,7 +114,7 @@ def backup_file(filename):
                     failure = False
                     break
         if failure:
-            print "Too many backups. Clean up and try again"
+            print("Too many backups. Clean up and try again")
             exit()
 
 
@@ -195,7 +196,8 @@ def generate_output(self, w, v, outputobject, time, matrix, nmodes=2, ReportVect
         if ReportVector:
             with open(ReportVector, "a") as oup:
                 for item in enumerate(v[list_map[1]]):
-                    print >> oup, "", counter, time, item[0] + 1, w[list_map[1]], item[1]
+                    print("", counter, time, item[0] + 1,
+                          w[list_map[1]], item[1], file=oup)
         outputobject.append((time, w[list_map[1]], v[list_map[1]]))
         #outputobject.append((time, [ w[list_map[i]] for i in range(nmodes) ], [ v[list_map[i]] for i in range(
         # nmodes) ] ))
@@ -288,7 +290,8 @@ def _get_timestep():
             try:
                 [u, w, v] = linalg.svd(matrix)
             except linalg.LinAlgError:
-                print "\nFrame skip at", timestep, "(SVD failed to converge). Cutoff", self.cutoff
+                print("\nFrame skip at", timestep,
+                      "(SVD failed to converge). Cutoff", self.cutoff)
                 continue
             #Save the results somewhere useful in some useful format. Usefully.
             self.generate_output(w, v, self.results, timestep, matrix, ReportVector=self.ReportVector, counter=counter)

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -1,5 +1,5 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #
 # MDAnalysis --- http://www.MDAnalysis.org
 # Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
@@ -309,10 +309,10 @@ class HydrogenBondAnalysis_OtherFF(HydrogenBondAnalysis):
    .. automethod:: _get_bonded_hydrogens_list
 
 """
-
+import six
+from six.moves import range, zip, map, cPickle
 
 from collections import defaultdict
-from six.moves import range, zip, map
 import numpy as np
 import warnings
 import logging
@@ -984,8 +984,6 @@ def save_table(self, filename="hbond_table.pickle"):
 
         .. SeeAlso:: :mod:`cPickle` module and :class:`numpy.recarray`
         """
-        import cPickle
-
         if self.table is None:
             self.generate_table()
         cPickle.dump(self.table, open(filename, 'wb'), protocol=cPickle.HIGHEST_PROTOCOL)
@@ -1050,7 +1048,7 @@ def count_by_type(self):
 
         # float because of division later
         tsteps = float(len(self.timesteps))
-        for cursor, (key, count) in enumerate(hbonds.iteritems()):
+        for cursor, (key, count) in enumerate(six.iteritems(hbonds)):
             out[cursor] = key + (count / tsteps,)
 
         # return array as recarray
@@ -1109,7 +1107,7 @@ def timesteps_by_type(self):
         out = np.empty((out_nrows,), dtype=dtype)
 
         out_row = 0
-        for (key, times) in hbonds.iteritems():
+        for (key, times) in six.iteritems(hbonds):
             for tstep in times:
                 out[out_row] = key + (tstep,)
                 out_row += 1

package/MDAnalysis/analysis/helanal.py

@@ -109,7 +109,7 @@
 .. autofunction:: helanal_main
 
 """
-
+from __future__ import print_function
 from six.moves import range
 
 import os
@@ -316,31 +316,32 @@ def helanal_trajectory(universe, selection="name CA", start=None, end=None, begi
 
         #print out rotations across the helix to a file
         with open(twist_filename, "a") as twist_output:
-            print >> twist_output, frame,
+            print(frame, end='', file=twist_output)
             for loc_twist in twist:
-                print >> twist_output, loc_twist,
-            print >> twist_output, ""
+                print(loc_twist, end='', file=twist_output)
+            print("", file=twist_output)
 
         with open(bend_filename, "a") as bend_output:
-            print >> bend_output, frame,
+            print(frame, end='', file=bend_output)
             for loc_bend in bending_angles:
-                print >> bend_output, loc_bend,
-            print >> bend_output, ""
+                print(loc_bend, end='', file=bend_output)
+            print("", file=bend_output)
 
         with open(screw_filename, "a") as rot_output:
-            print >> rot_output, frame,
+            print(frame, end='', file=rot_output)
             for rotation in local_screw_angles:
-                print >> rot_output, rotation,
-            print >> rot_output, ""
+                print(rotation, end='', file=rot_output)
+            print("", file=rot_output)
 
         with open(tilt_filename, "a") as tilt_output:
-            print >> tilt_output, frame,
+            print(frame, end='', file=tilt_output)
             for tilt in local_helix_axes:
-                print >> tilt_output, np.rad2deg(mdamath.angle(tilt, ref_axis)),
-            print >> tilt_output, ""
+                print(np.rad2deg(mdamath.angle(tilt, ref_axis)),
+                      end='', file=tilt_output)
+            print("", file=tilt_output)
 
         with open(fitted_tilt_filename, "a") as tilt_output:
-            print >> tilt_output, frame, np.rad2deg(fit_tilt)
+            print(frame, np.rad2deg(fit_tilt), file=tilt_output)
 
         if len(global_bending) == 0:
             global_bending = [[] for item in bending_angles]
@@ -360,26 +361,26 @@ def helanal_trajectory(universe, selection="name CA", start=None, end=None, begi
 
     bending_statistics_matrix = [[stats(col) for col in row] for row in global_bending_matrix]
     with open(matrix_filename, 'w') as mat_output:
-        print >> mat_output, "Mean"
+        print("Mean", file=mat_output)
         for row in bending_statistics_matrix:
             for col in row:
                 formatted_angle = "{0:6.1f}".format(col[0])
-                print >> mat_output, formatted_angle,
-            print >> mat_output, ''
+                print(formatted_angle, end='', file=mat_output)
+            print('', file=mat_output)
 
-        print >> mat_output, "\nSD"
+        print('\nSD', file=mat_output)
         for row in bending_statistics_matrix:
             for col in row:
                 formatted_angle = "{0:6.1f}".format(col[1])
-                print >> mat_output, formatted_angle,
-            print >> mat_output, ''
+                print(formatted_angle, end='', file=mat_output)
+            print('', file=mat_output)
 
-        print >> mat_output, "\nABDEV"
+        print("\nABDEV", file=mat_output)
         for row in bending_statistics_matrix:
             for col in row:
                 formatted_angle = "{0:6.1f}".format(col[2])
-                print >> mat_output, formatted_angle,
-            print >> mat_output, ''
+                print(formatted_angle, end='', file=mat_output)
+            print('', file=mat_output)
 
     logger.info("Height: %g  SD: %g  ABDEV: %g  (Angstroem)", height_mean, height_sd, height_abdev)
     logger.info("Twist: %g  SD: %g  ABDEV: %g", twist_mean, twist_sd, twist_abdev)
@@ -401,29 +402,31 @@ def helanal_trajectory(universe, selection="name CA", start=None, end=None, begi
         logger.info(output)
 
     with open(summary_filename, 'w') as summary_output:
-        print >> summary_output, "Height:", height_mean, "SD", height_sd, "ABDEV", height_abdev, '(nm)'
-        print >> summary_output, "Twist:", twist_mean, "SD", twist_sd, "ABDEV", twist_abdev
-        print >> summary_output, "Residues/turn:", rnou_mean, "SD", rnou_sd, "ABDEV", rnou_abdev
-        print >> summary_output, "Local bending angles:"
-        residue_statistics = zip(*bending_statistics)
+        print("Height:", height_mean, "SD", height_sd, "ABDEV", height_abdev, '(nm)', file=summary_output)
+        print("Twist:", twist_mean, "SD", twist_sd, "ABDEV", twist_abdev,
+              file=summary_output)
+        print("Residues/turn:", rnou_mean, "SD", rnou_sd, "ABDEV", rnou_abdev,
+              file=summary_output)
+        print("Local bending angles:", file=summary_output)
+        residue_statistics = list(zip(*bending_statistics))
         measure_names = ["Mean ", "SD   ", "ABDEV"]
-        print >> summary_output, "ResID",
+        print("ResID", end='', file=summary_output)
         if start is None:
             for item in range(4, len(residue_statistics[0]) + 4):
                 output = "{0:8d}".format(item)
-                print >> summary_output, output,
+                print(output, end='', file=summary_output)
         else:
             for item in range(start + 3, len(residue_statistics[0]) + start + 3):
                 output = "{0:8d}".format(item)
-                print >> summary_output, output,
-        print >> summary_output, ""
+                print(output, end='', file=summary_output)
+        print('', file=summary_output)
 
         for measure, name in zip(residue_statistics, measure_names):
-            print >> summary_output, name,
+            print(name, end='', file=summary_output)
             for residue in measure:
                 output = "{0:8.1f}".format(residue)
-                print >> summary_output, output,
-            print >> summary_output, ''
+                print(output, end='', file=summary_output)
+            print('', file=summary_output)
 
 
 def tilt_correct(number):
@@ -596,9 +599,9 @@ def origin_pdb(origins, pdbfile):
         i = 1
         for xyz in origins:
             tmp = "ATOM    {0:3d}  CA  ALA   {1:3d}    {2:8.3f}{3:8.3f}{4:8.3f}  1.00  0.00".format(i, i, xyz[0], xyz[1], xyz[2])
-            print >> output, tmp
+            print(tmp, file=output)
             i += 1
-        print >> output, "TER\nENDMDL"
+        print("TER\nENDMDL", file=output)
 
 
 def main_loop(positions, ref_axis=None):

package/MDAnalysis/analysis/hole.py

@@ -101,8 +101,8 @@
 iterate over the sorted profiles (see :meth:`HOLEtraj.sorted_profiles_iter`) ::
 
   for q, profile in H:
-     print "orderparameter = %g" % q
-     print "min(R) = %g" % profile.radius.min()
+     print("orderparameter = %g" % q)
+     print("min(R) = %g" % profile.radius.min())
 
 
 Data structures

package/MDAnalysis/analysis/psa.py

@@ -1,5 +1,5 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #
 # MDAnalysis --- http://www.MDAnalysis.org
 # Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
@@ -217,16 +217,15 @@
 .. |Np| replace:: :math:`N_p`
 
 """
-
-from six.moves import range
+import six
+from six.moves import range, cPickle
 
 import numpy as np
 
 import MDAnalysis
 import MDAnalysis.analysis.align
 from MDAnalysis import NoDataError
 
-import cPickle as pickle
 import os
 
 import logging
@@ -1144,7 +1143,7 @@ def __init__(self, universes, reference=None, ref_select='name CA',
                          'paths' : '/paths',
                          'distance_matrices' : '/distance_matrices',
                          'plots' : '/plots'}
-        for dir_name, directory in self.datadirs.iteritems():
+        for dir_name, directory in six.iteritems(self.datadirs):
             try:
                 full_dir_name = os.path.join(self.targetdir, dir_name)
                 os.makedirs(full_dir_name)
@@ -1173,11 +1172,11 @@ def __init__(self, universes, reference=None, ref_select='name CA',
         self._labels_pkl = os.path.join(self.targetdir, "psa_labels.pkl")
         # Pickle topology and trajectory filenames for this analysis to curdir
         with open(self._top_pkl, 'wb') as output:
-            pickle.dump(self.top_name, output)
+            cPickle.dump(self.top_name, output)
         with open(self._trjs_pkl, 'wb') as output:
-            pickle.dump(self.trj_names, output)
+            cPickle.dump(self.trj_names, output)
         with open(self._labels_pkl, 'wb') as output:
-            pickle.dump(self.labels, output)
+            cPickle.dump(self.labels, output)
 
         self.natoms = None
         self.npaths = None
@@ -1259,7 +1258,7 @@ def generate_paths(self, **kwargs):
         self.fit_trj_names = fit_trj_names
         if save:
             with open(self._fit_trjs_pkl, 'wb') as output:
-                pickle.dump(self.fit_trj_names, output)
+                cPickle.dump(self.fit_trj_names, output)
         if store:
             filename = kwargs.pop('filename', None)
             self.save_paths(filename=filename)
@@ -1407,7 +1406,7 @@ def save_paths(self, filename=None):
             logger.info("Wrote path to file %r", current_outfile)
         self.path_names = path_names
         with open(self._paths_pkl, 'wb') as output:
-            pickle.dump(self.path_names, output)
+            cPickle.dump(self.path_names, output)
         return filename