roll sofia base to py2.7

Author: SpheMakh

stimela/cargo/base/sofia/Dockerfile

@@ -14,9 +14,11 @@ RUN pip install -U numpy>=1.8 \
         astro-tigger-lsm
 RUN git clone https://github.com/SoFiA-Admin/SoFiA.git /sofia
 RUN cd /sofia && git fetch && git fetch --tags
-RUN cd /sofia && git checkout v1.3.0
+RUN cd /sofia && git checkout v1.3.2
 RUN cd /sofia && python setup.py  install
 ENV SOFIA_MODULE_PATH /sofia/build/lib.linux-x86_64-2.7
 ENV SOFIA_PIPELINE_PATH /sofia/sofia_pipeline.py
 ENV PATH $PATH:/sofia:/sofia/gui
 RUN echo $PATH
+#RUN sed -i 's/from sofia import wavelet_finder/# from sofia import wavelet_finder/g' $SOFIA_PIPELINE_PATH
+#RUN cat $SOFIA_PIPELINE_PATH

stimela/cargo/cab/sofia/Dockerfile

@@ -1,4 +1,4 @@
-FROM stimela/sofia:1.2.5
+FROM stimela/sofia:1.2.5-1
 MAINTAINER <sphemakh@gmial.com>
 ADD src /scratch/code
 ENV LOGFILE ${OUTPUT}/logfile.txt

stimela/cargo/cab/sofia/parameters.json

@@ -1,7 +1,7 @@
 {
     "task": "sofia", 
     "base": "stimela/sofia", 
-    "tag": "1.2.5", 
+    "tag": "1.2.5-1", 
     "version" : "1.3.2",
     "description": "SoFiA, the Source Finding Application, is a new HI source finding pipeline intended to detect and parameterise galaxies in HI data cubes. While the software is still under development, several stable versions of SoFiA have already been released. This wiki contains user documentation and technical information on SoFiA and its individual modules.", 
     "prefix": "--", 

stimela/cargo/cab/sofia/src/run.py

@@ -3,6 +3,8 @@
 import Tigger
 import numpy
 import tempfile
+import json
+import codecs
 
 from astLib.astWCS import WCS
 from Tigger.Models import SkyModel, ModelClasses
@@ -17,7 +19,9 @@
 MSDIR = os.environ["MSDIR"]
 OUTPUT = os.environ["OUTPUT"]
 
-cab = utils.readJson(CONFIG)
+with codecs.open(CONFIG, "r", "utf8") as stdr:
+    cab = json.load(stdr)
+
 args = []
 msname = None
 

stimela/recipe.py

@@ -639,7 +639,7 @@ def docker_job(self, image, config=None,
                 build_label, image)]['DIR']
         except KeyError:
             raise StimelaCabParameterError(
-                'Cab {} has is uknown to stimela. Was it built?'.format(image))
+                'Cab {} is uknown to stimela. Was it built?'.format(image))
         parameter_file = cabpath+'/parameters.json'
 
         name = '{0}-{1}{2}'.format(self.name, id(image),