Merge branch 'master' into 'future_imports'

Conflicts:
	vistrails/core/interpreter/noncached.py
	vistrails/gui/application.py
	vistrails/gui/job_monitor.py
	vistrails/packages/JobSubmission/__init__.py
	vistrails/packages/JobSubmission/common_definitions.py
	vistrails/packages/JobSubmission/init.py
	vistrails/packages/JobSubmission/machine.py
	vistrails/packages/RemoteQ/hdfs.py
	vistrails/packages/RemoteQ/streaming.py
	vistrails/packages/analytics/init.py

doc/usersguide/conf.py

@@ -22,7 +22,7 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.ifconfig', 'sphinx.ext.extlinks']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.ifconfig', 'sphinx.ext.extlinks', 'sphinxarg.ext']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

doc/usersguide/example.rst

@@ -48,6 +48,7 @@ Intermediate Concepts and VisTrails Packages
 .. toctree::
    :maxdepth: 2
 
+   parameter_widgets
    controlflow
    cfassistant
    list_handling

doc/usersguide/mashups.rst

@@ -67,7 +67,7 @@ A Simple Example
 
    * Open :vtl:`brain_vistrail.vt`
    * Choose ``Save As`` and rename the file if you do not want to overwrite the original.
-   * Select the "counter 4" version
+   * Select the "contour 3" version
    * Press execute to ensure any necessary upgrades are made
    * Select ``Mashup`` from the toolbar.
    * In the Mashup Pipeline tab, look under ``vtkProperty`` :math:`\rightarrow` ``SetOpacity`` and double-click on ``Float``.  

doc/usersguide/parameter_widgets.rst

@@ -0,0 +1,73 @@
+.. _chap-parameter-widgets:
+
+*****************
+Parameter Widgets
+*****************
+
+.. index::  parameter widgets
+
+Introduction to Parameter Widgets
+=================================
+
+Parameter widgets are editable parameters inside modules in the pipeline
+view. They can be used to give an overview of the parameters in a workflow, or to
+quickly edit parameters without the usual clicking on a module and selecting
+the parameter in the 'Module Info' panel.
+:ref:`Figure 1 <fig-edit-widgets-example>` shows a complete workflow
+using parameter widgets. :vtl:`(open in vistrails) <parameter_widgets.vt>`
+
+.. _fig-edit-widgets-example:
+
+.. figure:: figures/edit_widgets/edit-widgets.png
+   :align: center
+   :width: 100%
+
+   Figure 1 - Complex Workflow with Parameter Widgets.
+
+Enabling Parameter Widgets
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Parameter widgets are hidden by default, but can be enabled by toggling the
+pencil icon in the 'Module Info' panel (See :ref:`Figure 2 <fig-enabling-edit-widgets>`).
+This will show all existing parameter widgets as well as the pencil icons
+in 'Module Info' for adding new ones.
+
+.. _fig-enabling-edit-widgets:
+
+.. figure:: figures/edit_widgets/enabling-edit-widgets.png
+   :align: center
+   :width: 30%
+
+   Figure 2 - How to enable/disable the Parameter Widgets mode.
+
+Adding a parameter widget to a module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A parameter widget can be enabled or disabled in the 'Module Info' panel by
+toggling the pencil icon (See :ref:`Figure 3 <fig-edit-widget>`). Only
+parameters of constant type that have widgets for editing can be added.
+
+Constant modules such as String and Integer show a parameter widget for 'value'
+by default, but it can be removed using the 'Module Info' panel if needed.
+
+.. _fig-edit-widget:
+
+.. figure:: figures/edit_widgets/edit-widget.png
+   :align: center
+   :width: 60%
+
+   Figure 3 - How to add/remove Parameter Widgets from modules.
+
+Limitations
+^^^^^^^^^^^
+
+On some platforms (Such as Mac) some parameter widgets may look unsharp or
+pixelated. This is because no widget for that type has been created for use
+in the pipeline view, and the default one from the 'Module Info' pane has been used instead.
+
+Only one parameter widget per port can be visible right now. In the 'Module Info' pane it is
+possible to specify several function parameters for each port.
+
+Zooming out will hide all the edit widgets for performance reasons, it would also
+be difficult to edit anything in that size.
+

doc/usersguide/vtl/parameter_widgets.vtl

@@ -0,0 +1 @@
+<vtlink filename="@examples/terminator.vt" version="parameter widgets"/>

requirements.txt

@@ -14,6 +14,7 @@ python-dateutil
 scipy
 scp
 Sphinx
+sphinx-argparse
 SQLAlchemy
 suds
 unittest2

scripts/delete_from_db.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 ###############################################################################
 ##
 ## Copyright (C) 2011-2014, NYU-Poly.

scripts/diff_package.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 ###############################################################################
 ##
 ## Copyright (C) 2011-2014, NYU-Poly.

scripts/dist/mac/Input/README

@@ -13,15 +13,6 @@ To run it, open the folder in finder and double-click on the VisTrails icon.
 
 Please see the About Message for Licensing and Disclaimers.
 
-Using VisTrails.command
----------------------------
-
-If you would like to see the messages sent to standard output while executing
-VisTrails, you may use the VisTrails.command file. If you dragged the VisTrails
-folder to a place other than /Applications folder, you might need to execute 
-path/to/VisTrails/scripts/update_vistrails_command.py script from where your 
-folder is located.
-
 
 Release Name: v2.1.4 build 269e4808eca3 from v2.1 branch
 

scripts/dist/mac/Input/VisTrails.command

@@ -2,7 +2,9 @@
 #If you get an error saying:
 #Found another instance of VisTrails running
 #Sending parameters to main instance  []
-#Failed:  QLocalSocket::connectToServer: Connection refused 
+#Failed:  QLocalSocket::connectToServer: Connection refused
 #make sure VisTrails is not already running and simply try to run the script again
-#This might indicate that VisTrails did not quit properly 
-DYLD_LIBRARY_PATH= /Applications/VisTrails/VisTrails.app/Contents/MacOS/vistrails
+#This might indicate that VisTrails did not quit properly
+
+cd "$(dirname "$0")"
+DYLD_LIBRARY_PATH= VisTrails.app/Contents/MacOS/vistrails

scripts/extract.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 ###############################################################################
 ##
 ## Copyright (C) 2011-2014, NYU-Poly.
@@ -36,23 +37,25 @@
 import imp
 import sys
 
-def copyDir(src, dst):
+
+def copy_dir(src, dst):
     for info in src.entryInfoList():
         if info.isDir():
             dst.mkdir(info.fileName())
             src.cd(info.fileName())
             dst.cd(info.fileName())
-            copyDir(src, dst)
+            copy_dir(src, dst)
             src.cd('..')
             dst.cd('..')
         elif info.isFile():
             QtCore.QFile.copy(info.filePath(), dst.filePath(info.fileName()))
-
-if __name__=="__main__":
-    if len(sys.argv)!=2:
+
+
+if __name__ == "__main__":
+    if len(sys.argv) != 2:
         print "Usage: python extract.py resource_rc"
         sys.exit(0)
 
-    moduleName = sys.argv[1]
-    imp.load_source('resModule', moduleName)
-    copyDir(QtCore.QDir(":"), QtCore.QDir("."))
+    module_name = sys.argv[1]
+    imp.load_source('resModule', module_name)
+    copy_dir(QtCore.QDir(":"), QtCore.QDir("."))

scripts/generate_pkg_doc.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 import itertools
 import sys
 

scripts/mac_update_bin.sh

@@ -62,27 +62,27 @@ for dir in $OLD_DIRS
 do
     if [ -e "$2/$BIN_PATH/$dir" ]
     then
-        rm -r $2/$BIN_PATH/$dir
+        rm -r "$2/$BIN_PATH/$dir"
     fi
 done
 
 if [ -e "$2/$BIN_PATH/$ROOT_DIR_NAME" ]
 then
-    rm -r $2/$BIN_PATH/$ROOT_DIR_NAME
+    rm -r "$2/$BIN_PATH/$ROOT_DIR_NAME"
 fi
-ln -s -f -F $1/$ROOT_DIR_NAME $2/$BIN_PATH/$ROOT_DIR_NAME
+ln -s -f -F "$1/$ROOT_DIR_NAME" "$2/$BIN_PATH/$ROOT_DIR_NAME"
 
 if [ -e "$2/$BIN_PATH/../../run.py" ]
 then
-    rm $2/$BIN_PATH/../../run.py
+    rm "$2/$BIN_PATH/../../run.py"
 fi
-ln -s -f -F $1/$ROOT_DIR_NAME/run.py $2/$BIN_PATH/../../run.py
+ln -s -f -F "$1/$ROOT_DIR_NAME/run.py" "$2/$BIN_PATH/../../run.py"
 
 if [ -e "$2/../$EXAMPLES_DIR_NAME" ]
 then
-    rm -r $2/../$EXAMPLES_DIR_NAME
+    rm -r "$2/../$EXAMPLES_DIR_NAME"
 fi
-ln -s -f -F $1/$EXAMPLES_DIR_NAME $2/../$EXAMPLES_DIR_NAME
+ln -s -f -F "$1/$EXAMPLES_DIR_NAME" "$2/../$EXAMPLES_DIR_NAME"
 
 
 exit 0

scripts/sql_delete.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 ###############################################################################
 ##
 ## Copyright (C) 2011-2014, NYU-Poly.

scripts/sql_to_xml.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 ###############################################################################
 ##
 ## Copyright (C) 2011-2014, NYU-Poly.

scripts/start_vistrails.sh

@@ -36,12 +36,12 @@
 #settings
 LOG_DIR=/server/vistrails/logs
 
-VISTRAILS_DIR=/server/vistrails/trunk/vistrails
-ADDRESS="crowdlabs.sci.utah.edu"
+VISTRAILS_DIR=../vistrails
+ADDRESS="localhost"
 PORT="8081"
 CONF_FILE="server.cfg"
 NUMBER_OF_OTHER_VISTRAILS_INSTANCES="2"
-MULTI_OPTION="-M"
+MULTI_OPTION="--multithread"
 if (("$#" > "0")); then
     VIRTUAL_DISPLAY="$1"
 fi
@@ -58,7 +58,7 @@ if (("$#" == "5")); then
    if(("$5" == "0")); then
        MULTI_OPTION=""
    else
-       MULTI_OPTION="-M"
+       MULTI_OPTION="--multithread"
    fi
 fi
 
@@ -77,6 +77,6 @@ kill -9 `cat $PID`
 
 export PYTHONPATH=/home/emanuele/src/titan/build/lib:$PYTHONPATH
 export LD_LIBRARY_PATH=/home/emanuele/src/titan/build/lib:$LD_LIBRARY_PATH
-python vistrails_server.py -T $ADDRESS -R $PORT -C $CONF_FILE -O$NUMBER_OF_OTHER_VISTRAILS_INSTANCES $MULTI_OPTION&
+python vistrails_server.py --rpc-server $ADDRESS --rpc-port $PORT --rpc-config $CONF_FILE --rpc-instances $NUMBER_OF_OTHER_VISTRAILS_INSTANCES $MULTI_OPTION&
 echo $! > $PID
 

scripts/start_vistrails_xvfb.sh

@@ -42,7 +42,7 @@ ADDRESS="vis-7.sci.utah.edu"
 PORT="8081"
 CONF_FILE="server.cfg"
 NUMBER_OF_OTHER_VISTRAILS_INSTANCES="1"
-MULTI_OPTION="-M"
+MULTI_OPTION="--multithread"
 if (("$#" > "0")); then
     VIRTUAL_DISPLAY="$1"
 fi
@@ -59,7 +59,7 @@ if (("$#" == "5")); then
    if(("$5" == "0")); then
        MULTI_OPTION=""
    else
-       MULTI_OPTION="-M"
+       MULTI_OPTION="--multithread"
    fi
 fi
 
@@ -104,6 +104,6 @@ sleep 5
 #finally kill it if it still did not respond because it was hanging
 kill -9 `cat $PID`
 
-python vistrails_server.py -T $ADDRESS -R $PORT -C $CONF_FILE -O$NUMBER_OF_OTHER_VISTRAILS_INSTANCES $MULTI_OPTION&
+python vistrails_server.py --rpc-server=$ADDRESS --rpc-port $PORT --rpc-config $CONF_FILE --rpc-instances $NUMBER_OF_OTHER_VISTRAILS_INSTANCES $MULTI_OPTION&
 echo $! > $PID
 

scripts/update_db.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 ###############################################################################
 ##
 ## Copyright (C) 2011-2014, NYU-Poly.

scripts/update_vistrails_command.py

@@ -33,31 +33,34 @@
 ## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
 ##
 ###############################################################################
-""" This script assumes that VisTrails.command file is located at ../ 
-Run this script after you copied the VisTrails folder and run from where it 
-is located. 
+""" This script assumes that VisTrails.command file is located at ../
+Run this script after you copied the VisTrails folder and run from where it
+is located.
 
 """
 import os, os.path
+import sys
 
 if __name__ == "__main__":
+    sys.stderr.write("Running the update_vistrails_command.py script is not required anymore.\n"
+                     "It will be removed in future releases.\n")
+    # TODO : Remove this file after 2.2
+
     # get VisTrails folder
     vt_folder = os.path.abspath(os.path.join(os.path.dirname(__file__),'..'))
-    app_command = os.path.join(vt_folder,'VisTrails.app/Contents/MacOS/vistrails')
     command_file = os.path.join(vt_folder, 'VisTrails.command')
-    
-    file_header = """#This will execute VisTrails in a separate terminal window
+
+    file_contents = """#This will execute VisTrails in a separate terminal window
 #If you get an error saying:
 #Found another instance of VisTrails running
 #Sending parameters to main instance  []
-#Failed:  QLocalSocket::connectToServer: Connection refused 
+#Failed:  QLocalSocket::connectToServer: Connection refused
 #make sure VisTrails is not already running and simply try to run the script again
-#This might indicate that VisTrails did not quit properly 
+#This might indicate that VisTrails did not quit properly
 
+cd "$(dirname "$0")"
+DYLD_LIBRARY_PATH= VisTrails.app/Contents/MacOS/vistrails
 """
-    file_contents = "DYLD_LIBRARY_PATH= " + app_command
     f = open(command_file, 'w')
-    f.write(file_header)
     f.write(file_contents)
     f.close()
-

vistrails/core/analogy/__init__.py

@@ -127,7 +127,7 @@ def name_remap(d):
                     a_connect.destination.spec == c_connect.destination.spec):
                     break
         if match is not None:
-            connection_remap[a_connect.id] = c_connect.id
+            connection_remap[a_connect.id] = match.id
         elif _debug:
             print "failed to find connection match", a_connect.id, a_source, \
                 a_dest