Merge branch 'release-1.10'

INSTALL

@@ -15,12 +15,6 @@ graphviz - http://www.graphviz.org/
 pygraphviz - http://pygraphviz.github.io/
 minc-stuffs - https://github.com/Mouse-Imaging-Centre/minc-stuffs
 
-The following environment variables should be set when running pydpiper code:
-
-PYRO_DETAILED_TRACEBACK=True
-PYRO_SERVERTYPE=multiplex
-PYRO_LOGLEVEL=INFO
-
 In Ubuntu (tested on 12.04), run: 
 	apt-get install python-networkx
 	pip install pyro

NEWS

@@ -1,3 +1,10 @@
+New in Version 1.10
+===================
+* PYRO environment variables are handled inside the code. The SERVERTYPE is 
+  set statically to multiplex (there are potential issues with the thread option)
+  and the LOGLEVEL and DETAILED_TRACEBACK can be overridden by environment 
+  variables (see the README)
+
 New in Version 1.9
 ==================
 * MAGeT uses the originally optimized defaults again. Hardcoded paths to the 

README

@@ -9,5 +9,9 @@ The code for executing the pipeline can be found in pipeline_executor.py.
 
 sge_batch is a perl script (written independently of this code) that is required to use the --queue=sge option currently written into pydpiper. It may be rewritten or moved to a separate subdirectory in the future. For now, this script should reside in a directory in the user's path. 
 
+You can use environment variables to override our configuration defaults for the underlying Pyro library, except for
+$PYRO_SERVERTYPE and $PYRO_LOGFILE; in particular, you may wish to change $PYRO_LOGLEVEL, since this also controls
+the verbosity of some of the application's own logging.  See the Pyro4 documentation for more options.
+
 Application modules that utilize the pipeline class definitions are currently in applications folder. These applications may be moved to a separate repository at a later date. 
 

pydpiper/pipeline.py

@@ -15,8 +15,14 @@
 import pipeline_executor as pe
 import logging
 import threading
+
+os.environ["PYRO_LOGLEVEL"] = os.getenv("PYRO_LOGLEVEL", "INFO")
+
 import Pyro4
 
+Pyro4.config.SERVERTYPE = pe.Pyro4.config.SERVERTYPE
+Pyro4.config.DETAILED_TRACEBACK = pe.Pyro4.config.DETAILED_TRACEBACK
+
 LOOP_INTERVAL = 5.0
 RESPONSE_LATENCY = 100
 

pydpiper/pipeline_executor.py

@@ -21,8 +21,13 @@
 G_log_file_name = G_prog_name + '-' + G_time_now + '-pid-' + G_proc_id + ".log"
 os.environ["PYRO_LOGFILE"] = G_log_file_name
 
+os.environ["PYRO_LOGLEVEL"] = os.getenv("PYRO_LOGLEVEL", "INFO")
+
 import Pyro4
 
+Pyro4.config.SERVERTYPE = "multiplex"
+Pyro4.config.DETAILED_TRACEBACK = os.getenv("PYRO_DETAILED_TRACEBACK", True)
+
 WAIT_TIMEOUT = 5.0
 HEARTBEAT_INTERVAL = 30.0
 

setup.py

@@ -3,7 +3,7 @@
 from distutils.core import setup
 
 setup(name='pydpiper',
-      version='1.9',
+      version='1.10',
       license='Modified BSD',
       description='Python code for flexible pipeline control',
       long_description = 'Python code for flexible pipeline control',