Source Code for Package mvpa.tests

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