Merge pull request #14 from satra/nipypeclick

doc: update cli related docs

Author: satra

doc/users/cli.rst

@@ -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`.

doc/users/debug.rst

@@ -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

doc/users/index.rst

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