fixed #1

Dockerfile

@@ -1,39 +1,35 @@
 
 # Install all the cheminformatic packages
-FROM mdstudio/mdstudio_docker_conda
+FROM mdstudio/mdstudio_docker_conda:0.0.2
 
 RUN apt-get update -y && apt-get install swig wget gcc g++ gfortran cmake libxrender-dev -y
 
 COPY . /home/mdstudio/lie_structures
 
 RUN chown mdstudio:mdstudio /home/mdstudio/lie_structures
 
-RUN conda upgrade --all --yes
+RUN conda install -c openbabel openbabel && \
+    conda install -c bioconda java-jdk && \
+    conda install -c conda-forge jpype1 && \
+    conda install -c speleo3 indigo 
 
-RUN conda install -c openbabel openbabel
-#     # conda install -c bioconda java-jdk && \
-#     # conda install -c conda-forge jpype1 && \
-#     # conda install -c speleo3 indigo 
+RUN pip install pydpi
 
-RUN python -c "import pybel"
+WORKDIR /home/mdstudio
 
-# RUN pip install pydpi
+RUN wget https://github.com/cdk/cdk/releases/download/cdk-2.1.1/cdk-2.1.1.jar
 
-# WORKDIR /home/mdstudio
+RUN wget https://bitbucket.org/dan2097/opsin/downloads/opsin-1.3.0-jar-with-dependencies.jar
 
-# # RUN wget https://github.com/cdk/cdk/releases/download/cdk-2.1.1/cdk-2.1.1.jar
+ENV CLASSPATH=/home/mdstudio/cdk-2.1.1.jar:/home/mdstudio/opsin-1.3.0-jar-with-dependencies.jar:$CLASSPATH
 
-# # RUN wget https://bitbucket.org/dan2097/opsin/downloads/opsin-1.3.0-jar-with-dependencies.jar
+ENV JPYPE_JVM=/usr/local/jre/lib/amd64/server/libjvm.so
 
-# # ENV CLASSPATH=/home/mdstudio/cdk-2.1.1.jar:/home/mdstudio/opsin-1.3.0-jar-with-dependencies.jar:$CLASSPATH
 
-# # ENV JPYPE_JVM=/usr/local/jre/lib/amd64/server/libjvm.so
+RUN pip install "https://github.com/cinfony/cinfony/tarball/master#egg=cinfony-1.2"
 
+WORKDIR /home/mdstudio/lie_structures
 
-# RUN pip install "https://github.com/cinfony/cinfony/tarball/master#egg=cinfony-1.2"
+RUN pip install -e .
 
-# WORKDIR /home/mdstudio/lie_structures
-
-# RUN pip install -e .
-
-# CMD ["bash", "entry_point_lie_structures.sh"]
+CMD ["bash", "entry_point_lie_structures.sh"]

lie_structures/__init__.py

@@ -3,18 +3,13 @@
 package:  lie_structures
 LIEStudio small molecule cheminformatics functions
 """
-
+# Pandas and Openbabel share a common json library name
+# Adding the pandas import here avoids a REALLY NASTY race condition
+# If you remove the pandas import all the HELL may break loose
+import pandas
 import os
 
-__module__ = 'lie_structures'
-__docformat__ = 'restructuredtext'
-__version__ = '{major:d}.{minor:d}'.format(major=0, minor=2)
-__author__ = 'Marc van Dijk'
-__status__ = 'pre-release beta1'
-__date__ = '5 august 2016'
 __licence__ = 'Apache Software License 2.0'
-__url__ = 'https://github.com/NLeSC/LIEStudio'
-__copyright__ = "Copyright (c) VU University, Amsterdam"
 __rootpath__ = os.path.dirname(__file__)
 
 from .cheminfo_pkgmanager import CinfonyPackageManager

lie_structures/wamp_services.py

@@ -5,7 +5,6 @@
 
 WAMP service methods the module exposes.
 """
-
 import os
 import tempfile