Source Code for Package mvpa.tests

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  4  # 
  5  #   See COPYING file distributed along with the PyMVPA package for the 
  6  #   copyright and license terms. 
  7  # 
  8  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## 
  9  """Unit test interface for PyMVPA""" 
 10   
 11  import unittest 
 12  import numpy as np 
 13  from mvpa import _random_seed, cfg 
 14  from mvpa.base import externals, warning 
 15   
 16   
 17 -def collectTestSuites(): 
 18      """Runs over all tests it knows and composes a dictionary with test suite 
 19      instances as values and IDs as keys. IDs are the filenames of the unittest 
 20      without '.py' extension and 'test_' prefix. 
 21   
 22      During collection this function will run a full and verbose test for all 
 23      known externals. 
 24      """ 
 25      # list all test modules (without .py extension) 
 26      tests = [ 
 27          # Basic data structures/manipulators 
 28          'test_externals', 
 29          'test_base', 
 30          'test_dochelpers', 
 31          'test_dataset', 
 32          'test_arraymapper', 
 33          'test_boxcarmapper', 
 34          'test_som', 
 35          'test_neighbor', 
 36          'test_maskeddataset', 
 37          'test_metadataset', 
 38          'test_splitter', 
 39          'test_state', 
 40          'test_params', 
 41          'test_eepdataset', 
 42          # Misc supporting utilities 
 43          'test_config', 
 44          'test_stats', 
 45          'test_support', 
 46          'test_verbosity', 
 47          'test_report', 
 48          'test_datasetfx', 
 49          'test_cmdline', 
 50          'test_args', 
 51          'test_eepdataset', 
 52          'test_meg', 
 53          # Classifiers (longer tests) 
 54          'test_kernel', 
 55          'test_clf', 
 56          'test_regr', 
 57          'test_knn', 
 58          'test_gnb', 
 59          'test_svm', 
 60          'test_plr', 
 61          'test_smlr', 
 62          # Various algorithms 
 63          'test_svdmapper', 
 64          'test_procrust', 
 65          'test_hyperalignment', 
 66          'test_samplegroupmapper', 
 67          'test_transformers', 
 68          'test_transerror', 
 69          'test_clfcrossval', 
 70          'test_searchlight', 
 71          'test_rfe', 
 72          'test_ifs', 
 73          'test_datameasure', 
 74          'test_perturbsensana', 
 75          'test_splitsensana', 
 76          # And the suite (all-in-1) 
 77          'test_suite', 
 78          ] 
 79   
 80      # provide people with a hint about the warnings that might show up in a 
 81      # second 
 82      warning('Testing for availability of external software packages. Test ' 
 83              'cases depending on missing packages will not be part of the test ' 
 84              'suite.') 
 85   
 86      # So we could see all warnings about missing dependencies 
 87      warning.maxcount = 1000 
 88      # fully test of externals 
 89      externals.testAllDependencies() 
 90   
 91   
 92      __optional_tests = [ ('scipy', 'ridge'), 
 93                           ('scipy', 'stats_sp'), 
 94                           ('scipy', 'datasetfx_sp'), 
 95                           (['lars','scipy'], 'lars'), 
 96                           ('nifti', 'niftidataset'), 
 97                           ('mdp', 'icamapper'), 
 98                           ('scipy', 'zscoremapper'), 
 99                           ('pywt', 'waveletmapper'), 
100                           (['cPickle', 'gzip'], 'hamster'), 
101                           ('nose', 'iohelpers'), 
102      #                     ('mdp', 'pcamapper'), 
103                         ] 
104   
105      if not cfg.getboolean('tests', 'lowmem', default='no'): 
106          __optional_tests += [(['nifti', 'lxml'], 'atlases')] 
107   
108   
109      # and now for the optional tests 
110      optional_tests = [] 
111   
112      for external, testname in __optional_tests: 
113          if externals.exists(external): 
114              optional_tests.append('test_%s' % testname) 
115   
116   
117      # finally merge all of them 
118      tests += optional_tests 
119   
120      # import all test modules 
121      for t in tests: 
122   
123          # TODO: exclude tests which fail to import: e.g. on Windows 
124          # could get WindowsError due to missing msvcr90.dll 
125   
126          exec 'import ' + t 
127   
128      # instanciate all tests suites and return dict of them (with ID as key) 
129      return dict([(t[5:], eval(t + '.suite()')) for t in tests ]) 
130   
131   
132   
133 -def run(limit=None, verbosity=None): 
134      """Runs the full or a subset of the PyMVPA unittest suite. 
135   
136      :Parameters: 
137        limit: None | list 
138          If None, the full test suite is run. Alternatively, a list with test IDs 
139          can be provides. IDs are the base filenames of the test implementation, 
140          e.g. the ID for the suite in 'mvpa/tests/test_niftidataset.py' is 
141          'niftidataset'. 
142        verbosity: None | int 
143          Verbosity of unittests execution. If None, controlled by PyMVPA 
144          configuration tests/verbosity.  Values higher than 2 enable all Python,  
145          NumPy and PyMVPA warnings 
146      """ 
147      if __debug__: 
148          from mvpa.base import debug 
149          # Lets add some targets which provide additional testing 
150          debug.active += ['CHECK_.*'] 
151   
152      # collect all tests 
153      suites = collectTestSuites() 
154   
155      if limit is None: 
156          # make global test suite (use them all) 
157          ts = unittest.TestSuite(suites.values()) 
158      else: 
159          ts = unittest.TestSuite([suites[s] for s in limit]) 
160   
161   
162      class TextTestRunnerPyMVPA(unittest.TextTestRunner): 
163          """Extend TextTestRunner to print out random seed which was 
164          used in the case of failure""" 
165          def run(self, test): 
166              """Run the bloody test and puke the seed value if failed""" 
167              result = super(TextTestRunnerPyMVPA, self).run(test) 
168              if not result.wasSuccessful(): 
169                  print "MVPA_SEED=%s" % _random_seed 
170   
171      if verbosity is None: 
172          verbosity = int(cfg.get('tests', 'verbosity', default=1)) 
173   
174      if verbosity < 3: 
175          # no MVPA warnings during whole testsuite (but restore handlers later on) 
176          handler_backup = warning.handlers 
177          warning.handlers = [] 
178   
179          # No python warnings (like ctypes version for slmr) 
180          import warnings 
181          warnings.simplefilter('ignore') 
182   
183          # No numpy 
184          np_errsettings = np.geterr() 
185          np.seterr(**dict([(x, 'ignore') for x in np_errsettings])) 
186   
187      # finally run it 
188      TextTestRunnerPyMVPA(verbosity=verbosity).run(ts) 
189   
190      if verbosity < 3: 
191          # restore warning handlers 
192          warning.handlers = handler_backup 
193          np.seterr(**np_errsettings) 
194