Package mvpa :: Package base :: Module externals
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Module externals

source code

Helper to verify presence of external libraries and modules
Functions [hide private]
 
__check_shogun(bottom_version, custom_versions=[2456])
Check if version of shogun is high enough (or custom known) to be enabled in the testsuite
source code
 
__check_weave()
Apparently presence of scipy is not sufficient since some versions experience problems.
source code
 
__check_atlas_family(family) source code
 
exists(dep, force=False, raiseException=False)
Test whether a known dependency is installed on the system.
source code
 
testAllDependencies(force=False)
Test for all known dependencies.
source code
Variables [hide private]
  _KNOWN = {'libsvm': 'import mvpa.clfs.libsvmc._svm as __; x=__...
  _caught_exceptions = [ImportError, AttributeError, RuntimeError]
Exceptions which are silently caught while running tests for externals

Imports: os, warning, cfg, debug, rpy


Function Details [hide private]

__check_weave()

source code 

Apparently presence of scipy is not sufficient since some versions experience problems. E.g. in Sep,Oct 2008 lenny's weave failed to work. May be some other converter could work (? See http://lists.debian.org/debian-devel/2008/08/msg00730.html for a similar report.

Following simple snippet checks compilation of the basic code using weave

exists(dep, force=False, raiseException=False)

source code 

Test whether a known dependency is installed on the system.

This method allows us to test for individual dependencies without testing all known dependencies. It also ensures that we only test for a dependency once.

Parameters:
  • dep (string or list of string) - The dependency key(s) to test.
  • force (boolean) - Whether to force the test even if it has already been performed.
  • raiseException (boolean) - Whether to raise RuntimeError if dependency is missing.

testAllDependencies(force=False)

source code 
Test for all known dependencies.
Parameters:
  • force (boolean) - Whether to force the test even if it has already been performed.

Variables Details [hide private]

_KNOWN

Value:
{'libsvm': 'import mvpa.clfs.libsvmc._svm as __; x=__.convert2SVMNode'\
, 'nifti': 'from nifti import NiftiImage as __', 'nifti >= 0.20081017.\
1': 'from nifti.nifticlib import detachDataFromImage as __', 'ctypes':\
 'import ctypes as __', 'shogun': 'import shogun as __', 'shogun.mpd':\
 'import shogun.Classifier as __; x=__.MPDSVM', 'shogun.lightsvm': 'im\
port shogun.Classifier as __; x=__.SVMLight', 'shogun.svrlight': 'from\
 shogun.Regression import SVRLight as __', 'scipy': "import scipy as _\
_", 'weave': "__check_weave()", 'pywt': "import pywt as __", 'rpy': "i\
...