Merge branch 'master' into doc/Install4Developers

Author: oesteban

.travis.yml

@@ -55,8 +55,7 @@ install:
   pip install https://github.com/dmsurti/mayavi/archive/4d4aaf315a29d6a86707dd95149e27d9ed2225bf.zip;
   pip install -e git+https://github.com/enthought/ets.git#egg=ets;
   fi
-- pip install -r requirements.txt  # finish remaining requirements
-- python setup.py install
+- pip install -e .
 script:
 - python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-cov --cover-package nipype --cov-config .coveragerc --logging-level=DEBUG --verbosity=3
 after_success:
@@ -70,4 +69,4 @@ deploy:
     tags: true
     repo: nipy/nipype
     branch: master
-  distributions: "sdist bdist_wheel"
+  distributions: "sdist"

CHANGES

@@ -1,6 +1,11 @@
-Release 0.12.0-rc1 (April 20, 2016)
-============
-
+Release 0.12.0 (July 12, 2016)
+==============================
+
+* ENH: New interface for Bruker to Nifti converter (https://github.com/nipy/nipype/pull/1523)
+* FIX: output file naming for FIRST outputs (https://github.com/nipy/nipype/pull/1524)
+* ENH: Adds `fslmaths -Tstd` to maths interfaces (https://github.com/nipy/nipype/pull/1518)
+* FIX: Selecting "gamma" in FSL Level1Design now does what the name says (https://github.com/nipy/nipype/pull/1500)
+* ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(https://github.com/nipy/nipype/pull/1493)
 * ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372)
 * ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
 * ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
@@ -36,7 +41,7 @@ Release 0.12.0-rc1 (April 20, 2016)
        (https://github.com/nipy/nipype/pull/1460)
 
 Release 0.11.0 (September 15, 2015)
-============
+===================================
 
 * API: Change how hash values are computed (https://github.com/nipy/nipype/pull/1174)
 * ENH: New algorithm: mesh.WarpPoints applies displacements fields to point sets
@@ -122,7 +127,7 @@ Release 0.11.0 (September 15, 2015)
        (https://github.com/nipy/nipype/pull/1142)
 
 Release 0.10.0 (October 10, 2014)
-============
+=================================
 
 * ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
        to enable parallel processing of very large images.
@@ -166,19 +171,19 @@ Release 0.10.0 (October 10, 2014)
 * FIX: Update for FSL 5.0.7 which deprecated Contrast Manager
 
 Release 0.9.2 (January 31, 2014)
-============
+================================
 
 * FIX: DataFinder was broken due to a typo
 * FIX: Order of DataFinder outputs was not guaranteed, it's human sorted now
 * ENH: New interfaces: Vnifti2Image, VtoMat
 
 Release 0.9.1 (December 25, 2013)
-============
+=================================
 
 * FIX: installation issues
 
 Release 0.9.0 (December 20, 2013)
-============
+=================================
 
 * ENH: SelectFiles: a streamlined version of DataGrabber
 * ENH: new tools for defining workflows: JoinNode, synchronize and itersource

CONTRIBUTING.md

@@ -10,10 +10,16 @@
 * Pull Requests should be tested, if feasible:
     - bugfixes should include regression tests
     - new behavior should at least get minimal exercise
-* Use a descriptive prefix for your PR: ENH, FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
-* After submiting the PR, include an update to the CHANGES file: prefix: description (URL of pull request)
-* `make specs`
-* do: `make check-before-commit` before submitting the PR. This will require you to either install or be in developer mode with: `python setup.py install/develop`.
+* Use a descriptive prefix for your PR: ENH (enhancement), FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
+* The person who accepts/merges your PR will include an update to the CHANGES file: prefix: description (URL of pull request)
+* Run `make check-before-commit` before submitting the PR.
+  This will require you to either install or be in developer mode with: `python setup.py install/develop`.
+* In general, do not catch exceptions without good reason. 
+  * catching non-fatal exceptions. 
+    Log the exception as a warning.
+  * adding more information about what may have caused the error.
+    Raise a new exception using ``raise_from(NewException("message"), oldException)`` from ``future``.
+    Do not log this, as it creates redundant/confusing logs.
 
 ## Contributing issues
 

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "0.11.0"
+release = "0.12.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/links_names.txt

@@ -95,7 +95,9 @@
 .. _Camino: http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php
 .. _Camino2Trackvis: http://camino-trackvis.sourceforge.net/
 .. _MRtrix: http://www.brain.org.au/software/mrtrix/index.html
+.. _MRtrix3: http://www.mrtrix.org/
 .. _MNE: https://martinos.org/mne/index.html
+.. _ANTS: http://stnava.github.io/ANTs/
 
 .. General software
 .. _gcc: http://gcc.gnu.org

doc/users/grabbing_and_sinking.rst

@@ -58,6 +58,7 @@ DataGrabber stores its outputs in a field called outfiles.
   datasource1 = nio.DataGrabber()
   datasource1.inputs.base_directory = os.getcwd()
   datasource1.inputs.template = 'data/s1/f3.nii'
+  datasource1.inputs.sort_filelist = True
   results = datasource1.run()
 
 Or you can get at all uncompressed NIfTI files starting with the letter 'f' in
@@ -67,6 +68,7 @@ all directories starting with the letter 's'.
 
   datasource2.inputs.base_directory = '/mass'
   datasource2.inputs.template = 'data/s*/f*.nii'
+  datasource1.inputs.sort_filelist = True
 
 Two special inputs were used in these previous cases. The input `base_directory`
 indicates in which directory to search, while the input `template` indicates the
@@ -89,6 +91,7 @@ then used to set the template (see %d in the template).
   datasource3 = nio.DataGrabber(infields=['run'])
   datasource3.inputs.base_directory = os.getcwd()
   datasource3.inputs.template = 'data/s1/f%d.nii'
+  datasource1.inputs.sort_filelist = True
   datasource3.inputs.run = [3, 7]
 
 This will return files `basedir/data/s1/f3.nii` and `basedir/data/s1/f7.nii`. We
@@ -98,6 +101,7 @@ can take this a step further and pair subjects with runs.
 
   datasource4 = nio.DataGrabber(infields=['subject_id', 'run'])
   datasource4.inputs.template = 'data/%s/f%d.nii'
+  datasource1.inputs.sort_filelist = True
   datasource4.inputs.run = [3, 7]
   datasource4.inputs.subject_id = ['s1', 's3']
 
@@ -115,6 +119,7 @@ wish to retrieve all the functional runs and the structural image for the subjec
   datasource = nio.DataGrabber(infields=['subject_id'], outfields=['func', 'struct'])
   datasource.inputs.base_directory = 'data'
   datasource.inputs.template = '*'
+  datasource1.inputs.sort_filelist = True
   datasource.inputs.field_template = dict(func='%s/f%d.nii',
                                           struct='%s/struct.nii')
   datasource.inputs.template_args = dict(func=[['subject_id', [3,5,7,10]]],

doc/users/install.rst

@@ -176,10 +176,14 @@ Nipy_
 Nitime_
   (optional)
 
+ANTS_
+
+MRtrix_ and MRtrix3_
+
 Camino_
 
 Camino2Trackvis_
 
 ConnectomeViewer_
 
-.. include:: ../links_names.txt
+.. include:: ../links_names.txt

doc/users/resource_sched_profiler.rst

@@ -144,17 +144,17 @@ The pandas_ Python package is required to use this feature.
 	from nipype.pipeline.plugins.callback_log import log_nodes_cb
 	args_dict = {'n_procs' : 8, 'memory_gb' : 10, 'status_callback' : log_nodes_cb}
 	workflow.run(plugin='MultiProc', plugin_args=args_dict)
-	
+
 	# ...workflow finishes and writes callback log to '/home/user/run_stats.log'
-	
+
 	from nipype.utils.draw_gantt_chart import generate_gantt_chart
 	generate_gantt_chart('/home/user/run_stats.log', cores=8)
 	# ...creates gantt chart in '/home/user/run_stats.log.html'
 
 The ``generate_gantt_chart`` function will create an html file that can be viewed
 in a browser. Below is an example of the gantt chart displayed in a web browser.
 Note that when the cursor is hovered over any particular node bubble or resource
-bubble, some additional information is shown in a pop-up. 
+bubble, some additional information is shown in a pop-up.
 
  * -  .. image:: images/gantt_chart.png
          :width: 100 %

nipype/__init__.py

@@ -55,26 +55,10 @@ def test(self, label='fast', verbose=1, extra_argv=['--exe'],
     test = _NoseTester().test
 del nosetester
 
-
-def _test_local_install():
-    """ Warn the user that running with nipy being
-        imported locally is a bad idea.
-    """
-    if os.getcwd() == os.sep.join(
-            os.path.abspath(__file__).split(os.sep)[:-2]):
-        import warnings
-        warnings.warn('Running the tests from the install directory may '
-                      'trigger some failures')
-
-_test_local_install()
-
 # Set up package information function
 from .pkg_info import get_pkg_info as _get_pkg_info
 get_info = lambda: _get_pkg_info(os.path.dirname(__file__))
 
-# Cleanup namespace
-del _test_local_install
-
 # If this file is exec after being imported, the following lines will
 # fail
 try:

nipype/algorithms/misc.py

@@ -15,6 +15,7 @@
 from __future__ import division
 from builtins import zip
 from builtins import range
+from future.utils import raise_from
 
 import os
 import os.path as op
@@ -857,9 +858,9 @@ def __init__(self, infields=None, force_run=True, **kwargs):
     def _run_interface(self, runtime):
         try:
             import pandas as pd
-        except ImportError:
-            raise ImportError(('This interface requires pandas '
-                               '(http://pandas.pydata.org/) to run.'))
+        except ImportError as e:
+            raise_from(ImportError('This interface requires pandas '
+                                    '(http://pandas.pydata.org/) to run.'), e)
 
         try:
             import lockfile as pl