Source Code for Module mvpa.base.externals

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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  """Helper to verify presence of external libraries and modules 
 10  """ 
 11   
 12  __docformat__ = 'restructuredtext' 
 13   
 14  from mvpa.misc import warning 
 15   
 16  if __debug__: 
 17      from mvpa.misc import debug 
 18   
 19 -def __check_shogun(bottom_version, custom_versions=[2456]): 
 20      """Check if version of shogun is high enough (or custom known) to 
 21      be enabled in the testsuite""" 
 22      import shogun.Classifier as __sc 
 23      ver = __sc.Version_get_version_revision() 
 24      if (ver in custom_versions) or (ver >= bottom_version) : # custom built 
 25          return True 
 26      else: 
 27          raise ImportError, 'Version %s is smaller than needed %s' % \ 
 28                (ver, bottom_version) 
 29   
 30   
 31  # contains list of available (optional) external classifier extensions 
 32  _KNOWN = {'libsvm':'import mvpa.clfs.libsvm._svm as __; x=__.convert2SVMNode', 
 33            'nifti':'from nifti import NiftiImage as __', 
 34            'shogun':'import shogun as __', 
 35            'shogun.lightsvm': 'import shogun.Classifier as __; x=__.SVMLight', 
 36            'shogun.svrlight': 'from shogun.Regression import SVRLight as __', 
 37            'rpy': "import rpy", 
 38            'lars': "import rpy; rpy.r.library('lars')", 
 39            'pylab': "import pylab as __", 
 40            'sg_fixedcachesize': "__check_shogun(3043)", 
 41            } 
 42   
 43  _VERIFIED = {} 
 44   
 45  _caught_exceptions = [ImportError, AttributeError] 
 46  """Exceptions which are silently caught while running tests for externals""" 
 47  try: 
 48      import rpy 
 49      _caught_exceptions += [rpy.RException] 
 50  except: 
 51      pass 
 52   
 53 -def exists(dep, force=False): 
 54      """ 
 55      Test whether a known dependency is installed on the system. 
 56   
 57      This method allows us to test for individual dependencies without 
 58      testing all known dependencies. It also ensures that we only test 
 59      for a dependency once. 
 60   
 61      :Parameters: 
 62        dep : string 
 63          The dependency key to test. 
 64        force : boolean 
 65          Whether to force the test even if it has already been 
 66          performed. 
 67   
 68      """ 
 69      if _VERIFIED.has_key(dep) and not force: 
 70          # we have already tested for it, so return our previous result 
 71          return _VERIFIED[dep] 
 72      elif not _KNOWN.has_key(dep): 
 73          warning("%s is not a known dependency key." % (dep)) 
 74          return False 
 75      else: 
 76          # try and load the specific dependency 
 77          # default to false 
 78          _VERIFIED[dep] = False 
 79   
 80          if __debug__: 
 81              debug('EXT', "Checking for the presence of %s" % dep) 
 82   
 83          try: 
 84              exec _KNOWN[dep] 
 85              _VERIFIED[dep] = True 
 86          except tuple(_caught_exceptions): 
 87              pass 
 88   
 89          if __debug__: 
 90              debug('EXT', "Presence of %s is%s verified" % 
 91                    (dep, {True:'', False:' NOT'}[_VERIFIED[dep]])) 
 92   
 93          return _VERIFIED[dep] 
 94   
 95   
 96 -def testAllDependencies(force=False): 
 97      """ 
 98      Test for all known dependencies. 
 99   
100      :Parameters: 
101        force : boolean 
102          Whether to force the test even if it has already been 
103          performed. 
104   
105      """ 
106      # loop over all known dependencies 
107      for dep in _KNOWN: 
108          if not exists(dep, force): 
109              warning("Known dependency %s is not present, thus not available." \ 
110                      % dep) 
111   
112      if __debug__: 
113          debug('EXT', 'The following optional externals are present: %s' \ 
114                       % [ k for k in _VERIFIED.keys() if _VERIFIED[k]]) 
115