Merge pull request #13 from EPFL-LCSB/dev

VER: Bump to 0.7.0-b2

.gitignore

@@ -1,6 +1,8 @@
 # Pycharm folders
 .idea/*
 cobra_docker/work/.idea/*
+*___jb_old___
+*___jb_tmp___
 
 ###########################################
 ###	Standard Python	.gitignore	###

doc/conf.py

@@ -61,7 +61,8 @@
 # The short X.Y version.
 version = '0.7'
 # The full version, including alpha/beta/rc tags.
-release = '0.7.0-b1'
+
+release = '0.7.0-b2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.5
+FROM python:3.6
 # Warning: cplex 12.7.1 is only compatible with python 3.5, while
 # Gurobi 7.5 is only compatbile with with python 3.6. If you wan to
 # install both, I recommend downgrading the gurobi version.
@@ -11,30 +11,28 @@ USER root
 RUN apt-get update && apt-get install -y --no-install-recommends \
         libxml2-dev     \
         libxslt1-dev    \
-		less			\
+        less            \
     && rm -rf /var/lib/apt/lists/*
 
 ENV USER pytfa
 ENV HOME /home/$USER
 
+RUN useradd -ms "/bin/bash" "$USER"
+USER $USER
+WORKDIR $HOME
+
+USER root
+
 # Copy python package requirements
 COPY requirements.txt .
 
 # Install python packages
 RUN pip install -r requirements.txt
 
-RUN useradd -ms "/bin/bash" "$USER"
-USER $USER
-WORKDIR $HOME
-
 # Take care of the solvers
 COPY ./solvers /solvers
 COPY ./utils /utils
 
-# Fix permissions
-RUN ls -al /
-RUN find /utils -type f -iname "*.sh" -exec chmod +x {} \;
-
 # Install CPLEX
 RUN /utils/install_cplex.sh
 # Install gurobi
@@ -52,6 +50,7 @@ COPY src/ /src/
 RUN mkdir /src/pytfa
 
 COPY .bashrc $HOME
+RUN chown "$USER" "$HOME/.bashrc"
 
 #Finalizing installation
 

docker/requirements.txt

@@ -5,6 +5,7 @@ lxml
 openpyxl
 pymysql
 pytest
+python-libsbml
 scipy
 sqlalchemy
 tabulate

docker/utils/activate_gurobi.sh

@@ -2,8 +2,8 @@
 # Choose the GHOME variable depending on your gurobi version
 
 export GHOME_702="/opt/gurobi702/linux64"
-export GHOME_750="/opt/gurobi750/linux64"
-export GHOME=$GHOME_702
+export GHOME_752="/opt/gurobi752/linux64"
+export GHOME=$GHOME_752
 
 if [ -d $GHOME ]; then \
 	#$GHOME/bin/grbgetkey $LICENSE_KEY	&& \

docker/utils/install_cplex.sh

@@ -6,10 +6,15 @@
 
 echo "Installing and Moving CPLEX files"
 
-# Default Py3.4 install
-if [ -d /solvers/ibm ]; then cd /solvers/ibm/ILOG/CPLEX_Studio1271/cplex/python/3.5/x86-64_linux/ && \
+# Default Py3.5 install
+#if [ -d /solvers/ibm ]; then cd /solvers/ibm/ILOG/CPLEX_Studio1271/cplex/python/3.5/x86-64_linux/ && \#
+#	python3 setup.py install && \
+#	cp /solvers/ibm/ILOG/CPLEX_Studio1271/cplex/bin/x86-64_linux/cplex /usr/bin/; fi
+
+# Default Py3.6 install
+if [ -d /solvers/ibm ]; then cd /solvers/ibm/ILOG/CPLEX_Studio128/cplex/python/3.6/x86-64_linux/ && \
 	python3 setup.py install && \
-	cp /solvers/ibm/ILOG/CPLEX_Studio1271/cplex/bin/x86-64_linux/cplex /usr/bin/; fi
+	cp /solvers/ibm/ILOG/CPLEX_Studio128/cplex/bin/x86-64_linux/cplex /usr/bin/; fi
 
 # Tweaked Py2.6/2.7 install on conda Venv
 

docker/utils/install_gurobi.sh

@@ -3,20 +3,20 @@
 
 echo "Installing Gurobi"
 
-# if [ -f /solvers/gurobi7.5.0_linux64.tar.gz ]; then \
-# 	cp /solvers/gurobi7.5.0_linux64.tar.gz /opt	&&	\
-# 	cd /opt						&&	\
-# 	tar xvfz gurobi7.5.0_linux64.tar.gz		&&	\
-# 	cd /opt/gurobi750/linux64 			&& 	\
-# 	python3 setup.py install			&&	\
-# 	rm gurobi7.0.2_linux64.tar.gz; fi
-
-
-if [ -f /solvers/gurobi7.0.2_linux64.tar.gz ]; then \
-	cp /solvers/gurobi7.0.2_linux64.tar.gz /opt	&&	\
+if [ -f /solvers/gurobi7.5.2_linux64.tar.gz ]; then \
+	cp /solvers/gurobi7.5.2_linux64.tar.gz /opt	&&	\
 	cd /opt						&&	\
-	tar xvfz gurobi7.0.2_linux64.tar.gz		&&	\
-	cd /opt/gurobi702/linux64 			&& 	\
+	tar xvfz gurobi7.5.2_linux64.tar.gz		&&	\
+	cd /opt/gurobi752/linux64 			&& 	\
 	python3 setup.py install			&&	\
-	rm /opt/gurobi7.0.2_linux64.tar.gz; fi
+	rm /opt/gurobi7.5.2_linux64.tar.gz; fi
 
+
+#if [ -f /solvers/gurobi7.0.2_linux64.tar.gz ]; then \
+#	cp /solvers/gurobi7.0.2_linux64.tar.gz /opt	&&	\
+#	cd /opt						&&	\
+#	tar xvfz gurobi7.0.2_linux64.tar.gz		&&	\
+#	cd /opt/gurobi702/linux64 			&& 	\
+#	python3 setup.py install			&&	\
+#	rm /opt/gurobi7.0.2_linux64.tar.gz; fi
+#