MRG: Deprecate labs This PR reflects the recent mailing list discussion on the nipy.labs subpackage and implements two preliminary steps towards removal of the nipy dependency on Lapack: 1) deprecate all labs modules that depend on Lapack: bindings, glm, group and utils.routines. It is up to Bertrand and Gael to decide about the status of their labs modules and preferred migration strategies, given that the said modules are Lapack-free. 2) disable linking with system Lapack by default.
MRG: make SPM processing example for Open FMRI ds105 Example of how to batch script SPM8 preprocessing for the Open FMRI ds105 dataset.
Latest scipy assumes oned_as='row' default. Enforce in savemat call
MRG: Refactor group analysis A fast re-implementation of the parcel-based group analysis method proposed in Keller et al (Statistica Sinica 2008, MICCAI 2009); moving implementation from nipy.labs to nipy.algorithms.
SPM8 batch jobs need extra 'initcfg' step to spm_jobman Add SPM version check to decided whether to add this initcfg step.
…tica Sinica 2008; Roche, OHBM'12 talk)
MRG: depend on sympy 0.7.0; fix for sympy trunk Remove sympy 0.6.x compabibility fixes. Fix for changes in default sympy sorting in current trunk.
We've changed from using ``sort`` on sympy expressions, to using ``sort(expr, key=sympy.default_sort_key)``, in order to support sympy trunk (> 0.7.3). Unfortunately, these produce different results when sorting dummy variables, as in: In : a = sympy.Symbol('a') In : b = sympy.Dummy('b') In : sorted([a, b]) Out: [a, _b] In : sorted([a, b], key=sympy.default_sort_key) Out: [_b, a] I can't think of a way round this, so just change the failing doctest to use the new order.
Sympy > 0.7.3 raises an error attempting to sort sympy expressions without a key, but provides ``default_sort_key`` for backwards compatibility.
Sympy deprecated 'each_char' kwarg to symbols sometime >= 0.7.0, and removed for sympy > 0.7.3, but without raising an error. For safety, we raise an error.
Latest sympy lambdify needs the symbol on the left and the right hand side of a lambdified function to be the same. Hence we need 't' to be the term 't' not any sympy symbol 't'. At the moment we're using our own replacement for lambdify, but this change allows us to use the stock lambdify as of 0.7.3
Drop compatibility layer for sympy < 0.7.0
Older Numpies don't allow dtype= keyword to ``zeros_like``; use ``zeros`` instead.
MRG: clean HRF module and add SPM HRFs Some small cleanup to hrf module. This pull request adds the SPM HRF, the SPM temporal derivative, and the SPM spatial derivative, along with a function to replicate spm_hrf.m in the SPM distribution. Add SPM HRF, with temporal derivative and spatial derivative. Check against saved output from SPM code.
BF+TST: bug in nifti convert for 'unknown' space 'unknown' space should work if the header matches, but if there is no header, the zooms weren't being set, and the check was failing. Fix and test.
TST: add coveralls automated coverage Set up coveralls automated coverage report. Based partly on https://github.com/scipy/scipy/pulls/2907