Merge pull request #6 from satra/enh/sge

fix: parenthesis fixes

Author: hjmjohnson

.travis.yml

@@ -18,8 +18,10 @@ before_install:
 
 # Install packages
 install:
+  - conda update --yes conda
   - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
   - source activate testenv
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
   - conda install --yes numpy scipy nose traits networkx dateutil
   - pip install nibabel --use-mirrors
   - pip install python-coveralls --use-mirrors

nipype/pipeline/engine.py

@@ -205,11 +205,15 @@ def __repr__(self):
 
     def save(self, filename=None):
         if filename is None:
-            filename = 'temp.npz'
-        np.savez(filename, object=self)
+            filename = 'temp.pklz'
+        savepkl(filename, self)
 
     def load(self, filename):
-        return np.load(filename)
+        if '.npz' in filename:
+            DeprecationWarning(('npz files will be deprecated in the next '
+                                'release. you can use numpy to open them.'))
+            return np.load(filename)
+        return loadpkl(filename)
 
 
 class Workflow(WorkflowBase):

nipype/pipeline/plugins/base.py

@@ -6,6 +6,7 @@
 from copy import deepcopy
 from glob import glob
 import os
+import pickle
 import pwd
 import shutil
 from socket import gethostname
@@ -55,7 +56,7 @@ def report_crash(node, traceback=None, hostname=None):
                                      exc_traceback)
     timeofcrash = strftime('%Y%m%d-%H%M%S')
     login_name = pwd.getpwuid(os.geteuid())[0]
-    crashfile = 'crash-%s-%s-%s.npz' % (timeofcrash,
+    crashfile = 'crash-%s-%s-%s.pklz' % (timeofcrash,
                                         login_name,
                                         name)
     crashdir = node.config['execution']['crashdump_dir']
@@ -66,7 +67,8 @@ def report_crash(node, traceback=None, hostname=None):
     crashfile = os.path.join(crashdir, crashfile)
     logger.info('Saving crash info to %s' % crashfile)
     logger.info(''.join(traceback))
-    np.savez(crashfile, node=node, traceback=traceback)
+    savepkl(crashfile, dict(node=node, traceback=traceback))
+    #np.savez(crashfile, node=node, traceback=traceback)
     return crashfile
 
 
@@ -590,16 +592,17 @@ def _get_args(self, node, keywords):
             value = getattr(self, "_" + keyword)
             if keyword == "template" and os.path.isfile(value):
                 value = open(value).read()
-            if hasattr(node, "plugin_args") and
-             isinstance(node.plugin_args, dict) and keyword in node.plugin_args:
-                    if keyword == "template" and
-                                      os.path.isfile(node.plugin_args[keyword]):
+            if (hasattr(node, "plugin_args") and
+                    isinstance(node.plugin_args, dict) and
+                        keyword in node.plugin_args):
+                    if (keyword == "template" and
+                            os.path.isfile(node.plugin_args[keyword])):
                         tmp_value = open(node.plugin_args[keyword]).read()
                     else:
                         tmp_value = node.plugin_args[keyword]
 
-                    if 'overwrite' in node.plugin_args and
-                                                  node.plugin_args['overwrite']:
+                    if ('overwrite' in node.plugin_args and
+                            node.plugin_args['overwrite']):
                         value = tmp_value
                     else:
                         value += tmp_value

nipype/utils/filemanip.py

@@ -378,30 +378,21 @@ def load_json(filename):
     fp.close()
     return data
 
-
-def loadflat(infile, *args):
-    """Load an npz file into a dict
-    """
-    data = np.load(infile)
-    out = {}
-    if args:
-        outargs = np.setdiff1d(args, data.files)
-        if outargs:
-            raise IOError('File does not contain variables: '+str(outargs))
-    for k in data.files:
-        if k in args or not args:
-            out[k] = [f for f in data[k].flat]
-            if len(out[k]) == 1:
-                out[k] = out[k].pop()
-    return out
-
-
 def loadcrash(infile, *args):
     if '.pkl' in infile:
         return loadpkl(infile)
+    elif '.npz' in infile:
+        DeprecationWarning(('npz files will be deprecated in the next '
+                            'release. you can use numpy to open them.'))
+        data = np.load(infile)
+        out = {}
+        for k in data.files:
+            out[k] = [f for f in data[k].flat]
+            if len(out[k]) == 1:
+                out[k] = out[k].pop()
+        return out
     else:
-        return loadflat(infile, *args)
-
+        raise ValueError('Only pickled crashfiles are supported')
 
 def loadpkl(infile):
     """Load a zipped or plain cPickled file

nipype/utils/tests/test_filemanip.py

@@ -4,7 +4,7 @@
 from tempfile import mkstemp, mkdtemp
 
 from nipype.testing import assert_equal, assert_true, assert_false
-from nipype.utils.filemanip import (save_json, load_json, loadflat,
+from nipype.utils.filemanip import (save_json, load_json,
                                     fname_presuffix, fnames_presuffix,
                                     hash_rename, check_forhash,
                                     copyfile, copyfiles,
@@ -143,23 +143,6 @@ def test_json():
     os.unlink(name)
     yield assert_equal, sorted(adict.items()), sorted(new_dict.items())
 
-def test_loadflat():
-    alist = [dict(a='one', c='three', b='two'),
-             dict(a='one', c='three', b='two')]
-    fd, name = mkstemp(suffix='.npz')
-    np.savez(name,a=alist)
-    aloaded = loadflat(name)['a']
-    os.unlink(name)
-    yield assert_equal, len(aloaded), 2
-    yield assert_equal, sorted(aloaded[0].items()), sorted(alist[0].items())
-    adict = dict(a='one', c='three', b='two')
-    fd, name = mkstemp(suffix='.npz')
-    np.savez(name,a=adict)
-    aloaded = loadflat(name)['a']
-    os.unlink(name)
-    yield assert_true, isinstance(aloaded, dict)
-    yield assert_equal, sorted(aloaded.items()), sorted(adict.items())
-
 def test_related_files():
     file1 = '/path/test.img'
     file2 = '/path/test.hdr'