add from builtins import open where needed, fixed some open and never closed files

Author: oesteban

Diff for: circle.yml

@@ -26,9 +26,9 @@ dependencies:
 
 test:
   override:
+    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
     - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh :
         timeout: 2600
-    - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
         timeout: 1600
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :

Diff for: doc/sphinxext/autosummary_generate.py

@@ -16,9 +16,9 @@
             ./ext/autosummary_generate.py -o source/generated source/*.rst
 
 """
+from __future__ import print_function, unicode_literals
+from builtins import open
 
-from __future__ import print_function
-import glob
 import re
 import inspect
 import os

Diff for: examples/fmri_ants_openfmri.py

@@ -12,35 +12,30 @@
     python fmri_ants_openfmri.py --datasetdir ds107
 """
 from __future__ import division, unicode_literals
-from builtins import range, str, bytes
-
-from nipype import config
-config.enable_provenance()
-
+from builtins import open, range, str, bytes
 
 from glob import glob
 import os
 
+from nipype import config
+from nipype import LooseVersion
+from nipype import Workflow, Node, MapNode
+from nipype.utils.filemanip import filename_to_list
 import nipype.pipeline.engine as pe
 import nipype.algorithms.modelgen as model
 import nipype.algorithms.rapidart as ra
 from nipype.algorithms.misc import TSNR
 from nipype.interfaces.c3 import C3dAffineTool
+from nipype.interfaces import fsl, Function, ants, freesurfer as fs
 import nipype.interfaces.io as nio
+from nipype.interfaces.io import FreeSurferSource
 import nipype.interfaces.utility as niu
+from nipype.interfaces.utility import Merge, IdentityInterface
 from nipype.workflows.fmri.fsl import (create_featreg_preproc,
                                        create_modelfit_workflow,
                                        create_fixed_effects_flow)
 
-from nipype import LooseVersion
-from nipype import Workflow, Node, MapNode
-from nipype.interfaces import (fsl, Function, ants, freesurfer)
-
-from nipype.interfaces.utility import Merge, IdentityInterface
-from nipype.utils.filemanip import filename_to_list
-from nipype.interfaces.io import FreeSurferSource
-import nipype.interfaces.freesurfer as fs
-
+config.enable_provenance()
 version = 0
 if fsl.Info.version() and \
         LooseVersion(fsl.Info.version()) > LooseVersion('5.0.6'):
@@ -56,7 +51,6 @@
            'from scipy.special import legendre'
            ]
 
-
 def median(in_files):
     """Computes an average of the median of each realigned timeseries
 

Diff for: examples/rsfmri_vol_surface_preprocessing.py

@@ -43,8 +43,7 @@
 - `MNI template <http://mindboggle.info/data/templates/ants/OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz>`_
 """
 
-from __future__ import division
-from __future__ import unicode_literals
+from __future__ import division, unicode_literals
 from builtins import open, range
 
 import os

Diff for: examples/rsfmri_vol_surface_preprocessing_nipy.py

@@ -44,8 +44,7 @@
 
 """
 
-from __future__ import division
-from __future__ import unicode_literals
+from __future__ import division, unicode_literals
 from builtins import open, range
 
 import os

Diff for: examples/smri_ants_build_template.py

@@ -12,7 +12,8 @@
 1. Tell python where to find the appropriate functions.
 """
 
-from __future__ import print_function
+from __future__ import print_function, unicode_literals
+from builtins import open
 from future import standard_library
 standard_library.install_aliases()
 

Diff for: examples/smri_ants_registration.py

@@ -11,8 +11,9 @@
 
 1. Tell python where to find the appropriate functions.
 """
+from __future__ import print_function, unicode_literals
+from builtins import open
 
-from __future__ import print_function
 from future import standard_library
 standard_library.install_aliases()
 

Diff for: nipype/algorithms/misc.py

@@ -12,7 +12,7 @@
 
 '''
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import str, zip, range
+from builtins import str, zip, range, open
 from future.utils import raise_from
 
 import os
@@ -236,15 +236,17 @@ def _gen_output_file_name(self):
         return os.path.abspath(base + ".nii")
 
     def _run_interface(self, runtime):
-        hdr = nb.AnalyzeHeader.from_fileobj(
-            open(self.inputs.header_file, 'rb'))
+        with open(self.inputs.header_file, 'rb') as hdr_file:
+            hdr = nb.AnalyzeHeader.from_fileobj(hdr_file)
 
         if isdefined(self.inputs.affine):
             affine = self.inputs.affine
         else:
             affine = None
 
-        data = hdr.data_from_fileobj(open(self.inputs.data_file, 'rb'))
+        with open(self.inputs.header_file, 'rb') as data_file:
+            data = hdr.data_from_fileobj(data_file)
+
         img = nb.Nifti1Image(data, affine, hdr)
         nb.save(img, self._gen_output_file_name())
 
@@ -364,11 +366,9 @@ def _gen_output_file_name(self):
 
     def _run_interface(self, runtime):
         import gzip
-        in_file = gzip.open(self.inputs.in_file, 'rb')
-        out_file = open(self._gen_output_file_name(), 'wb')
-        out_file.write(in_file.read())
-        out_file.close()
-        in_file.close()
+        with gzip.open(self.inputs.in_file, 'rb') as in_file:
+            with open(self._gen_output_file_name(), 'wb') as out_file:
+                out_file.write(in_file.read())
         return runtime
 
     def _list_outputs(self):
@@ -501,8 +501,9 @@ def merge_csvs(in_list):
             try:
                 in_array = np.loadtxt(in_file, delimiter=',', skiprows=1)
             except ValueError as ex:
-                first = open(in_file, 'r')
-                header_line = first.readline()
+                with open(in_file, 'r') as first:
+                    header_line = first.readline()
+
                 header_list = header_line.split(',')
                 n_cols = len(header_list)
                 try:
@@ -681,8 +682,8 @@ def _run_interface(self, runtime):
             ext = '.csv'
 
         out_file = op.abspath(name + ext)
-        file_handle = open(out_file, 'w')
-        file_handle.write(csv_headings)
+        with open(out_file, 'w') as file_handle:
+            file_handle.write(csv_headings)
 
         shape = np.shape(output_array)
         typelist = maketypelist(
@@ -711,8 +712,9 @@ def _run_interface(self, runtime):
             output[extraheading] = extrafieldlist
         iflogger.info(output)
         iflogger.info(fmt)
-        np.savetxt(file_handle, output, fmt, delimiter=',')
-        file_handle.close()
+        with open(out_file, 'a') as file_handle:
+            np.savetxt(file_handle, output, fmt, delimiter=',')
+
         return runtime
 
     def _list_outputs(self):
@@ -774,6 +776,8 @@ def _run_interface(self, runtime):
             new_line = line.replace('\n', '')
             new_line = new_line + ',' + self.inputs.extra_field + '\n'
             out_file.write(new_line)
+        in_file.close()
+        out_file.close()
         return runtime
 
     def _list_outputs(self):

Diff for: nipype/caching/memory.py

@@ -10,7 +10,7 @@
    >>> os.chdir(datadir)
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import object
+from builtins import object, open
 
 import os
 import hashlib
@@ -106,11 +106,13 @@ def __repr__(self):
 def read_log(filename, run_dict=None):
     if run_dict is None:
         run_dict = dict()
-    for line in open(filename, 'r'):
-        dir_name, job_name = line[:-1].split('/')
-        jobs = run_dict.get(dir_name, set())
-        jobs.add(job_name)
-        run_dict[dir_name] = jobs
+
+    with open(filename, 'r') as logfile:
+        for line in logfile:
+            dir_name, job_name = line[:-1].split('/')
+            jobs = run_dict.get(dir_name, set())
+            jobs.add(job_name)
+            run_dict[dir_name] = jobs
     return run_dict
 
 
@@ -226,8 +228,9 @@ def _log_name(self, dir_name, job_name):
         # Every counter is a file opened in append mode and closed
         # immediately to avoid race conditions in parallel computing:
         # file appends are atomic
-        open(os.path.join(base_dir, 'log.current'),
-             'a').write('%s/%s\n' % (dir_name, job_name))
+        with open(os.path.join(base_dir, 'log.current'), 'a') as currentlog:
+            currentlog.write('%s/%s\n' % (dir_name, job_name))
+
         t = time.localtime()
         year_dir = os.path.join(base_dir, 'log.%i' % t.tm_year)
         try:
@@ -239,8 +242,9 @@ def _log_name(self, dir_name, job_name):
             os.mkdir(month_dir)
         except OSError:
             "Dir exists"
-        open(os.path.join(month_dir, '%02i.log' % t.tm_mday),
-             'a').write('%s/%s\n' % (dir_name, job_name))
+
+        with open(os.path.join(month_dir, '%02i.log' % t.tm_mday), 'a') as rotatefile:
+            rotatefile.write('%s/%s\n' % (dir_name, job_name))
 
     def clear_previous_runs(self, warn=True):
         """ Remove all the cache that where not used in the latest run of

Diff for: nipype/interfaces/cmtk/cmtk.py

@@ -10,7 +10,7 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import range
+from builtins import range, open
 
 import pickle
 import os.path as op
@@ -711,9 +711,8 @@ def _run_interface(self, runtime):
 
         if write_dict:
             iflogger.info('Saving Dictionary File to {path} in Pickle format'.format(path=dict_file))
-            file = open(dict_file, 'w')
-            pickle.dump(labelDict, file)
-            file.close()
+            with open(dict_file, 'w') as f:
+                pickle.dump(labelDict, f)
         return runtime
 
     def _list_outputs(self):

Diff for: nipype/interfaces/diffusion_toolkit/dti.py

@@ -11,7 +11,7 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import range
+from builtins import range, open
 
 import os
 import re
@@ -71,16 +71,16 @@ class DTIRecon(CommandLine):
 
     def _create_gradient_matrix(self, bvecs_file, bvals_file):
         _gradient_matrix_file = 'gradient_matrix.txt'
-        bvals = [val for val in re.split('\s+', open(bvals_file).readline().strip())]
-        bvecs_f = open(bvecs_file)
-        bvecs_x = [val for val in re.split('\s+', bvecs_f.readline().strip())]
-        bvecs_y = [val for val in re.split('\s+', bvecs_f.readline().strip())]
-        bvecs_z = [val for val in re.split('\s+', bvecs_f.readline().strip())]
-        bvecs_f.close()
-        gradient_matrix_f = open(_gradient_matrix_file, 'w')
-        for i in range(len(bvals)):
-            gradient_matrix_f.write("%s, %s, %s, %s\n" % (bvecs_x[i], bvecs_y[i], bvecs_z[i], bvals[i]))
-        gradient_matrix_f.close()
+        with open(bvals_file) as fbvals:
+            bvals = [val for val in re.split('\s+', fbvals.readline().strip())]
+        with open(bvecs_file) as fbvecs:
+            bvecs_y = [val for val in re.split('\s+', fbvecs.readline().strip())]
+            bvecs_z = [val for val in re.split('\s+', fbvecs.readline().strip())]
+            bvecs_x = [val for val in re.split('\s+', fbvecs.readline().strip())]
+
+        with open(_gradient_matrix_file, 'w') as gradient_matrix_f:
+            for i in range(len(bvals)):
+                gradient_matrix_f.write("%s, %s, %s, %s\n" % (bvecs_x[i], bvecs_y[i], bvecs_z[i], bvals[i]))
         return _gradient_matrix_file
 
     def _format_arg(self, name, spec, value):

Diff for: nipype/interfaces/elastix/utils.py

@@ -9,6 +9,7 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import open
 
 import os.path as op
 

Diff for: nipype/interfaces/freesurfer/tests/test_utils.py

@@ -1,6 +1,8 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import open
 
 import os
 from tempfile import mkdtemp

Diff for: nipype/interfaces/fsl/dti.py

@@ -13,7 +13,7 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import range
+from builtins import range, open
 
 import os
 import warnings

Diff for: nipype/interfaces/fsl/model.py

@@ -12,7 +12,7 @@
     >>> os.chdir(datadir)
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import range
+from builtins import range, open
 
 import os
 from glob import glob

Diff for: nipype/interfaces/fsl/preprocess.py

@@ -12,7 +12,7 @@
     >>> os.chdir(datadir)
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import range
+from builtins import range, open
 
 import os
 import os.path as op

Diff for: nipype/interfaces/minc/minc.py

@@ -17,6 +17,7 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import open
 
 import glob
 import os

Diff for: nipype/interfaces/mrtrix/convert.py

@@ -10,6 +10,7 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import open
 
 import os.path as op
 import nibabel as nb

Diff for: nipype/interfaces/nipy/preprocess.py

@@ -8,6 +8,7 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import open
 
 import os
 

Diff for: nipype/interfaces/nitime/analysis.py

@@ -11,8 +11,7 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-
-from builtins import zip, object
+from builtins import zip, object, open
 
 import numpy as np
 import tempfile