fix: resolved conflict

Author: satra

CHANGES

@@ -1,4 +1,4 @@
-Next release
+Release 0.9.0 (December 20, 2013)
 ============
 
 * ENH: SelectFiles: a streamlined version of DataGrabber

doc/_templates/sidebar_versions.html

@@ -17,7 +17,7 @@ <h3>{{ _('Versions') }}</h3>
                 <td align="left">Release</td><td align="right">Devel</td>
             </tr>
             <tr>
-                <td align="left">0.8.0</td><td align="right">pre-0.9</td>
+                <td align="left">0.9.0</td><td align="right">1.0-dev</td>
             </tr>
             <tr>
                 <td align="left"><a href="{{pathto('users/install')}}">Download</a></td>

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `0.7 <http://nipy.org/nipype/0.7>`_ `0.6 <http://nipy.org/nipype/0.6>`_
+Previous versions:  `0.8 <http://nipy.org/nipype/0.8>`_ `0.7 <http://nipy.org/nipype/0.7>`_
 
 .. container:: doc2
 

doc/users/install.rst

@@ -9,10 +9,10 @@ This page covers the necessary steps to install Nipype.
 Download
 --------
 
-Release 0.8.0: [`zip <https://github.com/nipy/nipype/archive/0.8.zip>`__ `tar.gz
-<https://github.com/nipy/nipype/archive/0.8.tar.gz>`__]
+Release 0.9.0: [`zip <https://github.com/nipy/nipype/archive/0.9.zip>`__ `tar.gz
+<https://github.com/nipy/nipype/archive/0.9.tar.gz>`__]
 
-Development: [`zip <http://github.com/nipy/nipype/zipball/master>`__ `tar.gz 
+Development: [`zip <http://github.com/nipy/nipype/zipball/master>`__ `tar.gz
 <http://github.com/nipy/nipype/tarball/master>`__]
 
 `Prior downloads <http://github.com/nipy/nipype/tags>`_
@@ -156,29 +156,29 @@ These are the software packages that nipype.interfaces wraps:
 FSL_
   4.1.0 or later
 
-matlab_ 
+matlab_
   2008a or later
 
 SPM_
   SPM5/8
 
 FreeSurfer_
   FreeSurfer version 4 and higher
-  
+
 AFNI_
   2009_12_31_1431 or later
 
 Slicer_
   3.6 or later
 
-Nipy_ 
+Nipy_
   0.1.2+20110404 or later
 
-Nitime_ 
+Nitime_
   (optional)
-  
+
 Camino_
-  
+
 Camino2Trackvis_
 
 ConnectomeViewer_

nipype/info.py

@@ -10,7 +10,7 @@
 _version_major = 0
 _version_minor = 9
 _version_micro = 0
-_version_extra = '.pre'
+_version_extra = ''
 
 def get_nipype_gitversion():
     """Nipype version as reported by the last commit in git

nipype/interfaces/fsl/model.py

@@ -1151,7 +1151,7 @@ def _run_interface(self, runtime):
         for cidx in range(npoints):
             mat_txt.append(' '.join(
                 ['%e' % self.inputs.regressors[key][cidx] for key in regs]))
-        mat_txt = '\n'.join(mat_txt)
+        mat_txt = '\n'.join(mat_txt) + '\n'
         # write t-con file
         con_txt = []
         counter = 0
@@ -1175,7 +1175,7 @@ def _run_interface(self, runtime):
                 convals[regs.index(reg)
                         ] = self.inputs.contrasts[idx][3][regidx]
             con_txt.append(' '.join(['%e' % val for val in convals]))
-        con_txt = '\n'.join(con_txt)
+        con_txt = '\n'.join(con_txt) + '\n'
         # write f-con file
         fcon_txt = ''
         if nfcons:
@@ -1190,6 +1190,7 @@ def _run_interface(self, runtime):
                         convals[tconmap[self.inputs.contrasts.index(tcon)]] = 1
                     fcon_txt.append(' '.join(['%d' % val for val in convals]))
                     fcon_txt = '\n'.join(fcon_txt)
+            fcon_txt += '\n'
         # write group file
         grp_txt = ['/NumWaves       1',
                    '/NumPoints      %d' % npoints,
@@ -1200,7 +1201,7 @@ def _run_interface(self, runtime):
                 grp_txt += ['%d' % self.inputs.groups[i]]
             else:
                 grp_txt += ['1']
-        grp_txt = '\n'.join(grp_txt)
+        grp_txt = '\n'.join(grp_txt) + '\n'
 
         txt = {'design.mat': mat_txt,
                'design.con': con_txt,
@@ -1702,7 +1703,7 @@ def _list_outputs(self):
 class GLMInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, argstr='-i %s', mandatory=True, position=1,
                    desc='input file name (text matrix or 3D/4D image file)')
-    out_file = File(name_template="%s_glm.txt", argstr='-o %s', position=3,
+    out_file = File(name_template="%s_glm", argstr='-o %s', position=3,
                     desc=('filename for GLM parameter estimates'
                           + ' (GLM betas)'),
                     name_source="in_file", keep_extension=True)
@@ -1799,23 +1800,17 @@ class GLM(FSLCommand):
     Example
     -------
     >>> import nipype.interfaces.fsl as fsl
-    >>> glm = fsl.GLM(in_file='functional.nii', design='maps.nii')
+    >>> glm = fsl.GLM(in_file='functional.nii', design='maps.nii', output_type='NIFTI')
     >>> glm.cmdline
-    'fsl_glm -i functional.nii -d maps.nii -o functional_glm.txt'
+    'fsl_glm -i functional.nii -d maps.nii -o functional_glm.nii'
 
     """
     _cmd = 'fsl_glm'
     input_spec = GLMInputSpec
     output_spec = GLMOutputSpec
 
     def _list_outputs(self):
-        outputs = self.output_spec().get()
-
-        outputs['out_file'] = self.inputs.out_file
-        # Generate an out_file if one is not provided
-        if not isdefined(outputs['out_file']) and isdefined(self.inputs.in_file):
-            outputs['out_file'] = self._gen_filename('out_file')
-        outputs['out_file'] = os.path.abspath(outputs['out_file'])
+        outputs = super(GLM, self)._list_outputs()
 
         if isdefined(self.inputs.out_cope):
             outputs['out_cope'] = os.path.abspath(self.inputs.out_cope)

nipype/interfaces/fsl/tests/test_auto_GLM.py

@@ -52,7 +52,7 @@ def test_GLM_inputs():
     out_file=dict(name_source='in_file',
     keep_extension=True,
     position=3,
-    name_template='%s_glm.txt',
+    name_template='%s_glm',
     argstr='-o %s',
     ),
     dat_norm=dict(argstr='--dat_norm',

nipype/interfaces/fsl/tests/test_model.py

@@ -33,12 +33,56 @@ def teardown_infile(tmp_dir):
 def test_MultipleRegressDesign():
     _, tp_dir = setup_infile()
     foo = fsl.MultipleRegressDesign()
-    foo.inputs.regressors = dict(reg1=[1,1,1],reg2=[0.2,0.4,0.5],reg3=[1,-1,2])
-    con1 = ['con1','T',['reg1','reg2'],[0.5,0.5]]
-    con2 = ['con2','T',['reg3'],[1]]
+    foo.inputs.regressors = dict(voice_stenght=[1,1,1],age=[0.2,0.4,0.5],BMI=[1,-1,2])
+    con1 = ['voice_and_age','T',['age','voice_stenght'],[0.5,0.5]]
+    con2 = ['just_BMI','T',['BMI'],[1]]
     foo.inputs.contrasts = [con1,con2,['con3','F',[con1,con2]]]
     res = foo.run()
     yield assert_equal, res.outputs.design_mat, os.path.join(os.getcwd(),'design.mat')
     yield assert_equal, res.outputs.design_con, os.path.join(os.getcwd(),'design.con')
     yield assert_equal, res.outputs.design_fts, os.path.join(os.getcwd(),'design.fts')
     yield assert_equal, res.outputs.design_grp, os.path.join(os.getcwd(),'design.grp')
+
+    design_mat_expected_content = """/NumWaves       3
+/NumPoints      3
+/PPheights      3.000000e+00 5.000000e-01 1.000000e+00
+
+/Matrix
+1.000000e+00 2.000000e-01 1.000000e+00
+-1.000000e+00 4.000000e-01 1.000000e+00
+2.000000e+00 5.000000e-01 1.000000e+00
+"""
+
+    design_con_expected_content = """/ContrastName1   voice_and_age
+/ContrastName2   just_BMI
+/NumWaves       3
+/NumContrasts   2
+/PPheights          1.000000e+00 1.000000e+00
+/RequiredEffect     100.000 100.000
+
+/Matrix
+0.000000e+00 5.000000e-01 5.000000e-01
+1.000000e+00 0.000000e+00 0.000000e+00
+"""
+
+    design_fts_expected_content = """/NumWaves       2
+/NumContrasts   1
+
+/Matrix
+1 1
+"""
+
+    design_grp_expected_content = """/NumWaves       1
+/NumPoints      3
+
+/Matrix
+1
+1
+1
+"""
+    yield assert_equal, open(os.path.join(os.getcwd(),'design.con'), 'r').read(), design_con_expected_content
+    yield assert_equal, open(os.path.join(os.getcwd(),'design.mat'), 'r').read(), design_mat_expected_content
+    yield assert_equal, open(os.path.join(os.getcwd(),'design.fts'), 'r').read(), design_fts_expected_content
+    yield assert_equal, open(os.path.join(os.getcwd(),'design.grp'), 'r').read(), design_grp_expected_content
+
+    teardown_infile(tp_dir)

setup.py

@@ -91,6 +91,7 @@ def main(**extra_args):
           author_email=INFO_VARS['AUTHOR_EMAIL'],
           platforms=INFO_VARS['PLATFORMS'],
           version=INFO_VARS['VERSION'],
+          install_requires=INFO_VARS['REQUIRES'],
           requires=INFO_VARS['REQUIRES'],
           configuration = configuration,
           cmdclass = cmdclass,