Refactor docker to make losoto work with python3

Docker/Dockerfile

@@ -98,7 +98,7 @@ ARG LoSoTo_TAG=master
 LABEL LoSoTo.version.tag=${LoSoTo_TAG}
     
 RUN apt-get update && apt-get install -y nodejs python3-pip git wsclean
-RUN python3 -m pip install cwltool cwl-runner -e "git://github.com/darafferty/LSMTool.git@${LSMTool_TAG}#egg=LSMTool" toil[cwl]==${TOIL_VERSION}
+RUN python3 -m pip install cwltool cwl-runner -e "git://github.com/darafferty/LSMTool.git@${LSMTool_TAG}#egg=LSMTool" "toil[cwl]"==${TOIL_VERSION} 
 
 RUN python3 -m pip install -e "git+https://github.com/revoltek/losoto.git@${LoSoTo_TAG}#egg=LoSoTo"
 
@@ -107,7 +107,8 @@ ADD skymodels.tar.gz /data/skymodels
 ADD test_data/A-Team_lowres.sourcedb /data/A-Team_lowres.sourcedb
 ADD test_data/example.h5 /data/example.h5
 ADD test_data/L570745_SB001_uv_MODEL.MS /data/L570745_SB001_uv_MODEL.MS
-
+ADD losoto.patch /home/lofaruser/losoto.patch
+RUN patch /src/losoto/losoto/operations/__init__.py /home/lofaruser/losoto.patch 
 ADD .entrypoint /home/lofaruser/.entrypoint
 RUN chown lofaruser:lofaruser /home/lofaruser/.entrypoint && \ 
     chmod +rx /home/lofaruser/.entrypoint

Docker/build_docker.sh

@@ -6,7 +6,7 @@ git_clone_or_pull () {
     BRANCH=$2
     DIR=$3
 
-    git clone --single-branch -b "${BRANCH}" "${REPO}" "${DIR}" 2> /dev/null || git -C "${DIR}" pull
+    git clone --depth 1 -b "${BRANCH}" "${REPO}" "${DIR}" 2> /dev/null || git -C "${DIR}" pull
 }
 
 # SOFTWARE VERSIONS

Docker/losoto.patch

+---  /src/losoto/losoto/operations/__init__.py      2019-11-07 12:43:46.220577945 +0000
++++  /src/losoto/losoto/operations/__init__.py      2019-11-07 12:43:34.401765786 +0000
+@@ -2,8 +2,7 @@
+ 
+ __all__ = [ os.path.basename(f)[:-3] for f in glob.glob(os.path.dirname(__file__)+"/*.py") if f[0] != '_']
+ 
+-for x in __all__:
+-    __import__(x, locals(), globals())
++from . import *
+ 
+ class Timer(object):
+     """
+