Merge pull request #27 from yarikoptic/rf-changes-from-datalad

Rf changes from datalad

.travis.yml

@@ -11,16 +11,12 @@ env:
     - PYTHON=python PYSUF=''
     # - PYTHON=python3 PYSUF=3 : python3-numpy not currently available
 install:
-    - sudo rmdir /dev/shm
-    - sudo ln -Tsf /{run,dev}/shm
-    - sudo apt-get update -qq
-    - sudo apt-get install lsb-release
-    - source /etc/lsb-release
-    - echo ${DISTRIB_CODENAME}
-    - wget -O- http://neuro.debian.net/lists/${DISTRIB_CODENAME}.de-md.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
-    - sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9
-    - sudo apt-get update -qq
+    # to prevent IPv6 being used for APT
+    - sudo bash -c "echo 'Acquire::ForceIPv4 \"true\";' > /etc/apt/apt.conf.d/99force-ipv4"
+    # The ultimate one-liner setup for NeuroDebian repository
+    - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
     #- sudo apt-get install $PYTHON-dev
+    - sudo pip install six
     - sudo apt-get install -qq $PYTHON-numpy
     - sudo apt-get install -qq $PYTHON-scipy
     - sudo apt-get install -qq $PYTHON-nibabel

testkraut/__init__.py

@@ -28,17 +28,11 @@ def __call__(mcs, sid, instance, *args):
             mcs._instances[sid] = instance
         return mcs._instances[sid]
 
-class __Singleton:
-    """To ensure single instance of a class instantiation (object)
-
-    """
-
-    __metaclass__ = _SingletonType
-    def __init__(self, *args):
-        pass
-    # Provided __call__ just to make silly pylint happy
-    def __call__(self):
-        raise NotImplementedError
+# Awkward way to define Python2 and Python3 compatible use of metaclasses
+# Ref: https://wiki.python.org/moin/PortingToPy3k/BilingualQuickRef#metaclasses
+__Singleton = _SingletonType(str('__Singleton'), (), {
+        '__doc__': "To ensure single instance of a class instantiation (object)"
+    })
 
 #
 # As the very first step: Setup configuration registry instance and

testkraut/config.py

@@ -10,7 +10,9 @@
 
 __docformat__ = 'restructuredtext'
 
-from ConfigParser import SafeConfigParser
+from six.moves.configparser import SafeConfigParser
+from six import iteritems
+
 import os.path
 from os.path import join as opj
 
@@ -92,9 +94,9 @@ def __init__(self, filenames=None):
             self.__cfg_filenames = []
 
         # set critical defaults
-        for sec, vars in ConfigManager._DEFAULTS.iteritems():
+        for sec, vars in iteritems(ConfigManager._DEFAULTS):
             self.add_section(sec)
-            for key, value in vars.iteritems():
+            for key, value in iteritems(vars):
                 self.set(sec, key, value)
 
         # now get the setting
@@ -191,11 +193,11 @@ def get(self, section, option, default=None, **kwargs):
 
         try:
             return SafeConfigParser.get(self, section, option, **kwargs)
-        except ValueError, e:
+        except ValueError as e:
             # provide somewhat descriptive error
-            raise ValueError, \
-                  "Failed to obtain value from configuration for %s.%s. " \
-                  "Original exception was: %s" % (section, option, e)
+            raise ValueError(
+                  "Failed to obtain value from configuration for %s.%s. "
+                  "Original exception was: %s" % (section, option, e))
 
 
     def getboolean(self, section, option, default=None):
@@ -215,7 +217,7 @@ def getboolean(self, section, option, default=None):
                 else:
                     boolean_states = self.BOOLEAN_STATES
                 if default.lower() not in boolean_states:
-                    raise ValueError, 'Not a boolean: %s' % default
+                    raise ValueError('Not a boolean: %s' % default)
                 return boolean_states[default.lower()]
 
         return SafeConfigParser.getboolean(self, section, option)
@@ -235,8 +237,8 @@ def get_as_dtype(self, section, option, dtype, default=None):
             return default
         try:
             return SafeConfigParser._get(self, section, dtype, option)
-        except ValueError, e:
+        except ValueError as e:
             # provide somewhat descriptive error
-            raise ValueError, \
-                  "Failed to obtain value from configuration for %s.%s. " \
-                  "Original exception was: %s" % (section, option, e)
+            raise ValueError(
+                  "Failed to obtain value from configuration for %s.%s. "
+                  "Original exception was: %s" % (section, option, e))

testkraut/spec.py

@@ -14,6 +14,9 @@
 import difflib
 from uuid import uuid1 as uuid
 
+from six import string_types, iteritems
+from six.moves import xrange
+
 __allowed_spec_keys__ = [
         'assertions',
         'authors',
@@ -38,9 +41,14 @@ def _raise(exception, why, input=None):
 
 def _verify_tags(struct, tags, name):
     for tag in tags:
-        if not tag in struct:
-            _raise(ValueError,
-                        "mandatory key '%s' is not in %s" % (tag, name))
+        if isinstance(tag, set):
+            if not tag.intersection(struct):
+                _raise(ValueError,
+                       "at least one of the keys %s must be in %s" % (tag, name))
+        else:
+            if not tag in struct:
+                _raise(ValueError,
+                       "mandatory key '%s' is not in %s" % (tag, name))
 
 def _verify_spec_tags(specs, tags, name):
     for i, os_id in enumerate(specs):
@@ -67,7 +75,7 @@ def __init__(self, src=None):
         dict.__init__(self)
         if isinstance(src, file):
             self.update(json.load(src))
-        elif isinstance(src, basestring):
+        elif isinstance(src, string_types):
             self.update(json.loads(src))
         elif isinstance(src, dict):
             self.update(src)
@@ -79,8 +87,10 @@ def __init__(self, src=None):
         self._check()
 
     def _check(self):
+        # Late import to prevent circular imports
+        from .testcase import __spec_matchers__
         _verify_tags(self, ('id', 'version', 'tests'), 'SPEC')
-        _verify_spec_tags(self.get('outputs', {}), ('type', 'value'),
+        _verify_spec_tags(self.get('outputs', {}), ('type', set(__spec_matchers__.keys())),
                           'outputs')
         _verify_spec_tags(self.get('inputs', {}), ('type', 'value'),
                           'inputs')
@@ -111,7 +121,7 @@ def save(self, filename, minimize=False):
         spec_file = open(filename, 'w')
         if minimize:
             # don't write empty containers
-            towrite = dict([(k, v) for k, v in self.iteritems()
+            towrite = dict([(k, v) for k, v in iteritems(self)
                                 if not (isSequenceType(v) or isMappingType(v)) \
                                    or len(v)])
         else:
@@ -194,7 +204,7 @@ def diff(fr, to, recursive_list=False, min_abs_numdiff=None,
             return dtree
         else:
             return None
-    elif isinstance(fr, basestring):
+    elif isinstance(fr, string_types):
         # any string
         if not fr == to:
             return {'ndiff': difflib.ndiff(('%s\n' % fr).splitlines(True),

testkraut/testcase.py

@@ -16,14 +16,30 @@
 from json import dumps as jds
 from functools import wraps
 
+from six import string_types, iteritems, text_type
+
 import logging
 lgr = logging.getLogger(__name__)
 
 from testtools import TestCase, RunTest
 from testtools.content import Content, text_content
 from testtools.content_type import ContentType, UTF8_TEXT
 from testtools import matchers as tm
-from testtools.matchers import Equals, Annotate, FileExists, Contains, DirExists
+from testtools.matchers import Equals, Annotate, FileExists, Contains, DirExists, \
+     MatchesRegex, StartsWith, EndsWith
+     # To be added whenever testtools gets upgraded (1.5.0 has those already exposed)
+     #DoesNotEndWith, DoesNotStartWith
+
+__spec_matchers__ = {
+    'value': Equals,
+    'contains': Contains,
+    'matches': MatchesRegex,
+    'startswith': StartsWith,
+    'endswith': EndsWith,
+#    'doesnotstartwith': DoesNotStartWith,
+#    'doesnotendwith': DoesNotEndWith,
+    }
+
 import testtools.matchers as tt_matchers
 from . import matchers as tk_matchers
 
@@ -81,7 +97,7 @@ def __new__(cls, name, bases, attr):
             if hasattr(attr[method_name], "template"):
                 source = attr[method_name]
                 source_name = method_name.lstrip("_")
-                for test_name, args in source.template.items():
+                for test_name, args in list(source.template.items()):
                     parg, kwargs = args
                     new_name = "test_%s" % test_name
                     new_methods[new_name] = _method_partial(source, *parg, **kwargs)
@@ -122,12 +138,15 @@ def discover_specs(paths=None):
             # we actually found a new one
             lgr.debug("discovered test SPEC '%s'" % spec_id)
             discovered[spec_id] = spec_fname
-        except Exception, e:
+        # TODO: provide configuration variable allowing to avoid this
+        # swallow-everything catcher to troubleshoot problems in the code
+        # inside
+        except Exception as e:
             # not a valid SPEC
             lgr.warning("ignoring '%s': no a valid SPEC file: %s (%s)"
                       % (spec_fname, str(e), e.__class__.__name__))
     # wrap spec file locations in TestArgs
-    return dict([(k, TestArgs(v)) for k, v in discovered.iteritems()])
+    return dict([(k, TestArgs(v)) for k, v in iteritems(discovered)])
 
 
 class TestFromSPEC(TestCase):
@@ -279,12 +298,12 @@ def _execute_python_test(self, testid, testspec):
             sys.stderr = capture_stderr = StringIO()
             try:
                 if 'code' in testspec:
-                    exec testspec['code'] in {}, {}
+                    exec(testspec['code'], {}, {})
                 elif 'file' in testspec:
                     execfile(testspec['file'], {}, {})
                 else:
                     raise ValueError("no test code found")
-            except Exception, e:
+            except Exception as e:
                 execinfo['exception'] = dict(type=e.__class__.__name__,
                                              info=str(e))
                 if not 'shouldfail' in testspec or testspec['shouldfail'] == False:
@@ -333,7 +352,7 @@ def _execute_shell_test(self, testid, testspec):
                 texec.returncode,
                 Annotate("test shell command '%s' yielded non-zero exit code" % cmd,
                          Equals(0)))
-        except OSError, e:
+        except OSError as e:
             lgr.error("%s: %s" % (e.__class__.__name__, str(e)))
             if not 'shouldfail' in testspec or testspec['shouldfail'] == False:
                 self.assertThat(e,
@@ -364,7 +383,7 @@ def _execute_nipype_test(self, testid, testspec):
         locals = dict()
         try:
             execfile(testwffilepath, dict(), locals)
-        except Exception, e:
+        except Exception as e:
             lgr.error("%s: %s" % (e.__class__.__name__, str(e)))
             self.assertThat(e,
                 Annotate("test workflow setup failed: %s (%s)"
@@ -388,7 +407,7 @@ def _execute_nipype_test(self, testid, testspec):
             sys.stderr = capture_stderr = StringIO()
             try:
                 exec_graph = workflow.run()
-            except Exception, e:
+            except Exception as e:
                 execinfo['exception'] = dict(type=e.__class__.__name__,
                                              info=str(e))
                 if not 'shouldfail' in testspec or testspec['shouldfail'] == False:
@@ -435,10 +454,22 @@ def _check_output_presence(self, spec):
             elif ospectype == 'string' and ospec_id.startswith('tests'):
                 execinfo = self._details['exec_info']
                 sec, idx, field = ospec_id.split('::')
-                self.assertThat(
-                    execinfo[idx][field],
-                    Annotate("unexpected output for '%s'" % ospec_id,
-                             Equals(ospec['value'])))
+                for f, matcher in iteritems(__spec_matchers__):
+                    if f in ospec:
+                        # allow for multiple target values (given a matcher) being
+                        # specified.  For some matchers it might make no sense
+                        # (e.g. "endswith")
+                        targets = ospec[f]
+                        for target in (targets if isinstance(targets, list) else [targets]):
+                            target = text_type.replace(target, "<NEWLINE>", os.linesep)
+                            # TODO: This replacement may be should be done elsewhere
+                            # to have a general solution. It's now affecting string-type only.
+                            # Additionally, "<NEWLINE>" may appear in some output intentionally,
+                            # so let's find sth closer to be 'unique'.
+                            self.assertThat(
+                                 execinfo[idx][field],
+                                 Annotate("unexpected output for '%s'" % ospec_id,
+                                           matcher(target)))
             else:
                 raise NotImplementedError(
                         "dunno how to handle output type '%s' yet"
@@ -447,7 +478,7 @@ def _check_output_presence(self, spec):
 
     def _compute_metrics(self, spec, info):
         metricspecs = spec.get('metrics', {})
-        for mid, mspec in metricspecs.iteritems():
+        for mid, mspec in iteritems(metricspecs):
             metric = mspec.get('metric', None)
             if metric is None:
                 lgr.warning("broken metric spec '%s': no metric given" % mid)
@@ -472,7 +503,7 @@ def _compute_metrics(self, spec, info):
 
     def _check_assertions(self, spec, metric_info):
         specs = spec.get('assertions', {})
-        for aid, aspec in specs.iteritems():
+        for aid, aspec in iteritems(specs):
             lgr.debug("check assertion '%s'" % aid)
             # preconditions
             self.assertThat(aspec, Contains('value'))
@@ -497,7 +528,7 @@ def _check_assertions(self, spec, metric_info):
                 assertion = matcher(
                         **dict(
                             zip([(k, _resolve_metric_value(v, metric_info))
-                                            for k, v in args.iteritems()])))
+                                            for k, v in iteritems(args)])))
             else:
                 assertion = matcher(_resolve_metric_value(args, metric_info))
             # value to match
@@ -547,7 +578,7 @@ def _get_system_info(self):
         return TestFromSPEC._system_info
 
     def _verify_dependencies(self, spec):
-        for dep_id, depspec in spec.get('dependencies', {}).iteritems():
+        for dep_id, depspec in iteritems(spec.get('dependencies', {})):
             if not 'type' in depspec or not 'location' in depspec:
                 raise ValueError("dependency SPEC '%s' contains no 'type' or no 'location' field"
                                  % dep_id)
@@ -577,7 +608,7 @@ def _prepare_environment(self, spec):
                 # unset if null
                 if env in os.environ:
                     del os.environ[env]
-            elif isinstance(env_spec[env], basestring):
+            elif isinstance(env_spec[env], string_types):
                 # set if string
                 # set the new one
                 os.environ[env] = str(env_spec[env])
@@ -599,7 +630,7 @@ def _prepare_environment(self, spec):
     def _restore_environment(self):
         if self._environ_restore is None:
             return
-        for env, val in self._environ_restore.iteritems():
+        for env, val in iteritems(self._environ_restore):
             if val is None:
                 if env in os.environ:
                     del os.environ[env]
@@ -614,7 +645,7 @@ def _get_dep_info(self):
                           default=False):
             return
         spec = self._cur_spec
-        for dep_id, depspec in spec.get('dependencies', {}).iteritems():
+        for dep_id, depspec in iteritems(spec.get('dependencies', {})):
             if not 'type' in depspec or not 'location' in depspec:
                 raise ValueError("dependency SPEC '%s' contains no 'type' or no 'location' field"
                                  % dep_id)