Merge remote-tracking branch 'upstream/master'

Author: jason-wg

.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 +1,12 @@
-Release 0.12.0-rc1 (April 20, 2016)
+Release 0.12.0-rc2 (June 19, 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)
 * ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
@@ -31,6 +37,8 @@ Release 0.12.0-rc1 (April 20, 2016)
 * ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
 * FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
 * ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
+* ENH: Added interfaces for AFNI 3dDegreeCentrality, 3dECM, 3dLFCD, 3dClipLevel, 3dmask_tool, and 3dSeg
+       (https://github.com/nipy/nipype/pull/1460)
 
 Release 0.11.0 (September 15, 2015)
 ============

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
 

Makefile

@@ -15,8 +15,6 @@ sdist: zipdoc
 	python setup.py sdist
 	@echo "Done building source distribution."
 	# XXX copy documentation.zip to dist directory.
-	# XXX Somewhere the doc/_build directory is removed and causes
-	# this script to fail.
 
 egg: zipdoc
 	@echo "Building egg..."
@@ -45,7 +43,10 @@ clean-build:
 clean-ctags:
 	rm -f tags
 
-clean: clean-build clean-pyc clean-so clean-ctags
+clean-doc:
+	rm -rf doc/_build
+
+clean: clean-build clean-pyc clean-so clean-ctags clean-doc
 
 in: inplace # just a shortcut
 inplace:

doc/links_names.txt

@@ -56,7 +56,7 @@
 .. _doctest-mode: http://www.cis.upenn.edu/~edloper/projects/doctestmode/
 .. _bazaar: http://bazaar-vcs.org/
 .. _subversion: http://subversion.tigris.org/
-.. _nose: http://somethingaboutorange.com/mrl/projects/nose
+.. _nose: http://nose.readthedocs.io/en/latest/
 .. _`python coverage tester`: http://nedbatchelder.com/code/modules/coverage.html
 
 .. Other python projects

doc/sphinxext/numpy_ext/numpydoc.py

@@ -40,7 +40,7 @@ def mangle_docstrings(app, what, name, obj, options, lines,
 
     if what == 'module':
         # Strip top title
-        title_re = re.compile(ur'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*',
+        title_re = re.compile(r'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*',
                               re.I | re.S)
         lines[:] = title_re.sub(u'', u"\n".join(lines)).split(u"\n")
     else:
@@ -61,7 +61,7 @@ def mangle_docstrings(app, what, name, obj, options, lines,
     references = []
     for line in lines:
         line = line.strip()
-        m = re.match(ur'^.. \[([a-z0-9_.-])\]', line, re.I)
+        m = re.match(r'^.. \[([a-z0-9_.-])\]', line, re.I)
         if m:
             references.append(m.group(1))
 
@@ -70,7 +70,7 @@ def mangle_docstrings(app, what, name, obj, options, lines,
     if references:
         for i, line in enumerate(lines):
             for r in references:
-                if re.match(ur'^\d+$', r):
+                if re.match(r'^\d+$', r):
                     new_r = u"R%d" % (reference_offset[0] + int(r))
                 else:
                     new_r = u"%s%d" % (r, reference_offset[0])

doc/users/debug.rst

@@ -43,7 +43,7 @@ performance issues.
    utility.
 
 #. The `nipype_crash_search` command allows you to search for regular expressions
-in the tracebacks of the Nipype crashfiles within a log folder.
+   in the tracebacks of the Nipype crashfiles within a log folder.
 
 #. Nipype determines the hash of the input state of a node. If any input
    contains strings that represent files on the system path, the hash evaluation

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/images/gantt_chart.png

@@ -9,10 +9,9 @@ This page covers the necessary steps to install Nipype.
 Download
 --------
 
-Release 0.10.0: [`zip <https://github.com/nipy/nipype/archive/0.10.0.zip>`__ `tar.gz
-<https://github.com/nipy/nipype/archive/0.10.0.tar.gz>`__]
+Current release: `<https://github.com/nipy/nipype/releases/latest>`_.
 
-Development: [`zip <http://github.com/nipy/nipype/zipball/master>`__ `tar.gz
+Development version: [`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>`_
@@ -21,13 +20,18 @@ To check out the latest development version::
 
         git clone git://github.com/nipy/nipype.git
 
+or::
+
+        git clone https://github.com/nipy/nipype.git
+
+Check out the list of nipype's `current dependencies <https://github.com/shoshber/nipype/blob/master/nipype/info.py#L105>`_.
+
 Install
 -------
 
 The installation process is similar to other Python packages.
 
-If you already have a Python environment setup that has the dependencies listed
-below, you can do::
+If you already have a Python environment set up, you can do::
 
 	easy_install nipype
 
@@ -46,9 +50,8 @@ Mac OS X
 ~~~~~~~~
 
 The easiest way to get nipype running on Mac OS X is to install Anaconda_ or
-Canopy_ and then add nibabel and nipype by executing::
+Canopy_ and then add nipype by executing::
 
-	easy_install nibabel
 	easy_install nipype
 
 From source
@@ -58,7 +61,7 @@ If you downloaded the source distribution named something
 like ``nipype-x.y.tar.gz``, then unpack the tarball, change into the
 ``nipype-x.y`` directory and install nipype using::
 
-    python setup.py install
+    pip install -e .
 
 **Note:** Depending on permissions you may need to use ``sudo``.
 
@@ -72,8 +75,18 @@ nose_ installed, then do the following::
 
 you can also test with nosetests::
 
-    nosetests --with-doctest /software/nipy-repo/masternipype/nipype
-    --exclude=external --exclude=testing
+    nosetests --with-doctest <installation filepath>/nipype  --exclude=external --exclude=testing
+
+or::
+
+    nosetests --with-doctest nipype
+
+A successful test run should complete in a few minutes and end with
+something like::
+
+    Ran 13053 tests in 126.618s
+
+    OK (SKIP=66)
 
 All tests should pass (unless you're missing a dependency). If SUBJECTS_DIR
 variable is not set some FreeSurfer related tests will fail. If any tests
@@ -85,9 +98,9 @@ tests::
 
        export MATLABCMD=$pathtomatlabdir/bin/$platform/MATLAB
 
-where, $pathtomatlabdir is the path to your matlab installation and
-$platform is the directory referring to x86 or x64 installations
-(typically glnxa64 on 64-bit installations).
+where ``$pathtomatlabdir`` is the path to your matlab installation and
+``$platform`` is the directory referring to x86 or x64 installations
+(typically ``glnxa64`` on 64-bit installations).
 
 Avoiding any MATLAB calls from testing
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -98,37 +111,9 @@ On unix systems, set an empty environment variable::
 
 This will skip any tests that require matlab.
 
-Dependencies
+Recommended Software
 ------------
 
-Below is a list of required dependencies, along with additional software
-recommendations.
-
-Must Have
-~~~~~~~~~
-
-Python_ 2.7
-
-Nibabel_ 1.0 - 1.4
-  Neuroimaging file i/o library
-
-NetworkX_ 1.0 - 1.8
-  Python package for working with complex networks.
-
-NumPy_ 1.3 - 1.7
-
-SciPy_ 0.7 - 0.12
-  Numpy and Scipy are high-level, optimized scientific computing libraries.
-
-Enthought_ Traits_ 4.0.0 - 4.3.0
-
-Dateutil 1.5 -
-
-.. note::
-
-    Full distributions such as Anaconda_ or Canopy_ provide the above packages,
-    except Nibabel_.
-
 Strong Recommendations
 ~~~~~~~~~~~~~~~~~~~~~~
 
@@ -140,18 +125,22 @@ Matplotlib_ 1.0 - 1.2
   Plotting library
 
 `RDFLib <http://rdflib.readthedocs.org/en/latest/>`_ 4.1
-RDFLibrary required for provenance export as RDF
+  RDFLibrary required for provenance export as RDF
 
 Sphinx_ 1.1
   Required for building the documentation
 
 `Graphviz <http://www.graphviz.org/>`_
-  Required for building the documentation
+  Required for building the documentation. The python wrapper package (``graphviz``)
+  and the program itself both need to be installed.
 
 Interface Dependencies
 ~~~~~~~~~~~~~~~~~~~~~~
 
-These are the software packages that nipype.interfaces wraps:
+You might not need some of the following packages, depending on what exactly you
+want to use nipype for. If you do need any of them, install nipype's wrapper package
+(``nipype.interfaces``), then install the programs separately onto your computer, just
+like you would install any other app.
 
 FSL_
   4.1.0 or later