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Oct 8, 2016
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doc: update cli related docs #14

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24 changes: 24 additions & 0 deletions doc/users/cli.rst
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@@ -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`.
11 changes: 7 additions & 4 deletions doc/users/debug.rst
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Expand Up @@ -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::

Expand All @@ -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
Expand All @@ -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
2 changes: 1 addition & 1 deletion doc/users/index.rst
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Expand Up @@ -23,7 +23,7 @@
plugins
config_file
debug

cli

.. toctree::
:maxdepth: 1
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