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Package mvpa :: Package base :: Module externals

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Module externals

source code

Helper to verify presence of external libraries and modules

Functions

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__version_to_tuple(v)
Simple helper to convert version given as a string into a tuple.

source code

__check_scipy()
Check if scipy is present an if it is -- store its version

source code

__check_numpy()
Check if numpy is present (it must be) an if it is -- store its version

source code

__check_pywt(features=None)
Check for available functionality within pywt

source code

__check_libsvm_verbosity_control()
Check for available verbose control functionality

source code

__check_shogun(bottom_version, custom_versions=[])
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

__check_stablerdist()

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__check_in_ipython()

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__check_matplotlib()
Check for presence of matplotlib and set backend if requested.

source code

__check_pylab()
Check if matplotlib is there and then pylab

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__check_pylab_plottable()
Simple check either we can plot anything using pylab.

source code

__check_griddata()
griddata might be independent module or part of mlab

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exists(dep, force=False, raiseException=False, issueWarning=None)
Test whether a known dependency is installed on the system.

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testAllDependencies(force=False)
Test for all known dependencies.

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Variables

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versions = {}
Versions of available externals, as tuples

_KNOWN = {'libsvm': 'import mvpa.clfs.libsvmc._svm as __; x=__...

Imports: os, warning, cfg, debug

Function Details

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__version_to_tuple(v)

source code

Simple helper to convert version given as a string into a tuple.

Tuple of integers constructed by splitting at '.'.

__check_pywt(features=None)

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Check for available functionality within pywt

Parameters:

features (list of basestring) - List of known features to check such as 'wp reconstruct', 'wp reconstruct fixed'

__check_shogun(bottom_version, custom_versions=[])

source code

Check if version of shogun is high enough (or custom known) to be enabled in the testsuite

Parameters:

bottom_version (int) - Bottom version which must be satisfied
custom_versions (list of int) - Arbitrary list of versions which could got patched for a specific issue

__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

__check_pylab_plottable()

source code

Simple check either we can plot anything using pylab.

Primary use in unittests

exists(dep, force=False, raiseException=False, issueWarning=None)

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.
issueWarning (string or None or True) - If string, warning with given message would be thrown. If True, standard message would be used for the warning text.

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

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_KNOWN

Value:

{'libsvm': 'import mvpa.clfs.libsvmc._svm as __; x=__.convert2SVMNode'
, 'libsvm verbosity control': '__check_libsvm_verbosity_control();', '
nifti': 'from nifti import NiftiImage as __', 'nifti >= 0.20090205.1':
 'from nifti.clib import detachDataFromImage as __', 'ctypes': 'import
 ctypes as __', 'shogun': 'import shogun as __', 'shogun.mpd': 'import
 shogun.Classifier as __; x=__.MPDSVM', 'shogun.lightsvm': 'import sho
gun.Classifier as __; x=__.SVMLight', 'shogun.svrlight': 'from shogun.
Regression import SVRLight as __', 'numpy': "__check_numpy()", 'scipy'
...

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