Merge remote-tracking branch 'nipy/master' into clean-afni

Author: tsalo

.travis.yml

@@ -24,8 +24,8 @@ before_install:
   fsl afni elastix fsl-atlases; fi &&
   if $INSTALL_DEB_DEPENDECIES; then
     source /etc/fsl/fsl.sh;
-    source /etc/afni/afni.sh; fi &&
-  export FSLOUTPUTTYPE=NIFTI_GZ; }
+    source /etc/afni/afni.sh; 
+    export FSLOUTPUTTYPE=NIFTI_GZ; fi }
 - travis_retry bef_inst
 install:
 #  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi &&

CHANGES

@@ -1,11 +1,24 @@
 Upcoming release 0.13
 =====================
 
+* REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678)
+* ENH: Move nipype commands to group command using click (https://github.com/nipy/nipype/pull/1608)
 * FIX: AFNI Retroicor interface fixes (https://github.com/nipy/nipype/pull/1669)
+* FIX: Minor errors after migration to setuptools (https://github.com/nipy/nipype/pull/1671)
 * ENH: Add AFNI 3dNote interface (https://github.com/nipy/nipype/pull/1637)
+* ENH: Abandon distutils, only use setuptools (https://github.com/nipy/nipype/pull/1627)
 * FIX: Minor bugfixes related to unicode literals (https://github.com/nipy/nipype/pull/1656)
+* TST: Automatic retries in travis (https://github.com/nipy/nipype/pull/1659/files)
+* ENH: Add signal extraction interface (https://github.com/nipy/nipype/pull/1647)
 * ENH: Add a DVARS calculation interface (https://github.com/nipy/nipype/pull/1606)
 * ENH: New interface to b0calc of FSL-POSSUM (https://github.com/nipy/nipype/pull/1399)
+* ENH: Add CompCor (https://github.com/nipy/nipype/pull/1599)
+* ENH: Add duecredit entries (https://github.com/nipy/nipype/pull/1466)
+* FIX: Python 3 compatibility fixes (https://github.com/nipy/nipype/pull/1572)
+* REF: Improved PEP8 compliance for fsl interfaces (https://github.com/nipy/nipype/pull/1597)
+* REF: Improved PEP8 compliance for spm interfaces (https://github.com/nipy/nipype/pull/1593)
+* TST: Replaced coveralls with codecov (https://github.com/nipy/nipype/pull/1609)
+* ENH: More BrainSuite interfaces (https://github.com/nipy/nipype/pull/1554)
 * ENH: Convenient load/save of interface inputs (https://github.com/nipy/nipype/pull/1591)
 * ENH: Add a Framewise Displacement calculation interface (https://github.com/nipy/nipype/pull/1604)
 * FIX: Use builtins open and unicode literals for py3 compatibility (https://github.com/nipy/nipype/pull/1572)

bin/nipype2boutiques

@@ -0,0 +1,24 @@
+.. _cli:
+
+=============================
+Nipype Command Line Interface
+=============================
+
+The Nipype Command Line Interface allows a variety of operations::
+
+    $ nipypecli
+    Usage: nipypecli [OPTIONS] COMMAND [ARGS]...
+
+    Options:
+      -h, --help  Show this message and exit.
+
+    Commands:
+      convert  Export nipype interfaces to other formats.
+      crash    Display Nipype crash files.
+      run      Run a Nipype Interface.
+      search   Search for tracebacks content.
+      show     Print the content of Nipype node .pklz file.
+
+These have replaced previous nipype command line tools such as
+`nipype_display_crash`, `nipype_crash_search`, `nipype2boutiques`,
+`nipype_cmd` and `nipype_display_pklz`.

bin/nipype_cmd

@@ -20,7 +20,10 @@ performance issues.
       from nipype import config
       config.enable_debug_mode()
 
-   as the first import of your nipype script.
+   as the first import of your nipype script. To enable debug logging use::
+
+       from nipype import logging
+       logging.update_logging(config)
 
    .. note::
 
@@ -39,10 +42,10 @@ performance issues.
    node to fail without generating a crash file in the crashdump directory. In
    such cases, it will store a crash file in the `batch` directory.
 
-#. All Nipype crashfiles can be inspected with the `nipype_display_crash`
+#. All Nipype crashfiles can be inspected with the `nipypecli crash`
    utility.
 
-#. The `nipype_crash_search` command allows you to search for regular expressions
+#. The `nipypecli search` command allows you to search for regular expressions
    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
@@ -66,6 +69,6 @@ performance issues.
    PBS/LSF/SGE/Condor plugins in such cases the workflow may crash because it
    cannot retrieve the node result. Setting the `job_finished_timeout` can help::
 
-   workflow.config['execution']['job_finished_timeout'] = 65
+       workflow.config['execution']['job_finished_timeout'] = 65
 
 .. include:: ../links_names.txt

bin/nipype_crash_search

@@ -23,7 +23,7 @@
    plugins
    config_file
    debug
-
+   cli
 
 .. toctree::
    :maxdepth: 1