Merge pull request #1608 from alexsavio/master

WIP: Move nipype commands to a group command

Author: satra

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

bin/nipype_display_crash

@@ -112,6 +112,7 @@ def get_nipype_gitversion():
 FUTURE_MIN_VERSION = '0.15.2'
 SIMPLEJSON_MIN_VERSION = '3.8.0'
 PROV_MIN_VERSION = '1.4.0'
+CLICK_MIN_VERSION = '6.6.0'
 
 NAME = 'nipype'
 MAINTAINER = 'nipype developers'
@@ -141,6 +142,7 @@ def get_nipype_gitversion():
     'future>=%s' % FUTURE_MIN_VERSION,
     'simplejson>=%s' % SIMPLEJSON_MIN_VERSION,
     'prov>=%s' % PROV_MIN_VERSION,
+    'click>=%s' % CLICK_MIN_VERSION,
     'xvfbwrapper',
     'funcsigs'
 ]

bin/nipype_display_pklz

@@ -0,0 +1 @@
+