public release 3.0.0 - see README and CHANGES for details

extras/singularity/singularity_python3

@@ -3,10 +3,11 @@ OSVersion: bionic
 MirrorURL: http://ch.archive.ubuntu.com/ubuntu/
 
 %help
-a singularity container for PMSCO.
+A singularity container for PMSCO.
 
-git clone requires an ssh key for git.psi.ch.
-try agent forwarding (-A option to ssh).
+singularity run -e pmsco.sif path/to/pmsco -r path/to/your-runfile
+
+path/to/pmsco must point to the directory that contains the __main__.py file.
 
 #%setup
 # executed on the host system outside of the container before %post
@@ -34,22 +35,25 @@ try agent forwarding (-A option to ssh).
     Python_Version 3
 
 %environment
-    export PATH="/usr/local/miniconda3/bin:$PATH"
-    export PYTHON_VERSION=3
-    export SINGULAR_BRANCH="singular"
     export LC_ALL=C
+    export PYTHON_VERSION=3
+    export CONDA_ROOT=/opt/miniconda
+    export PLANTUML_JAR_PATH=/opt/plantuml/plantuml.jar
+    export SINGULAR_BRANCH="singular"
 
 %post
-    export PYTHON_VERSION=3
     export LC_ALL=C
+    export PYTHON_VERSION=3
+    export CONDA_ROOT=/opt/miniconda
+    export PLANTUML_ROOT=/opt/plantuml
 
     sed -i 's/$/ universe/' /etc/apt/sources.list
     apt-get update
     apt-get -y install \
         binutils \
         build-essential \
+        default-jre \
         doxygen \
-        doxypy \
         f2c \
         g++ \
         gcc \
@@ -67,11 +71,11 @@ try agent forwarding (-A option to ssh).
     apt-get clean
 
     wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
-    bash ~/miniconda.sh -b -p /usr/local/miniconda3
-    export PATH="/usr/local/miniconda3/bin:$PATH"
+    bash ~/miniconda.sh -b -p ${CONDA_ROOT}
 
+    . ${CONDA_ROOT}/bin/activate
     conda create -q --yes -n pmsco python=${PYTHON_VERSION}
-    . /usr/local/miniconda3/bin/activate pmsco
+    conda activate pmsco
     conda install -q --yes -n pmsco \
         pip \
         "numpy>=1.13" \
@@ -82,35 +86,36 @@ try agent forwarding (-A option to ssh).
         mock \
         future \
         statsmodels \
-        swig
+        swig \
+        gitpython
     conda clean --all -y
-    /usr/local/miniconda3/envs/pmsco/bin/pip install periodictable attrdict fasteners mpi4py
+    pip install periodictable attrdict commentjson fasteners mpi4py doxypypy
 
+    mkdir ${PLANTUML_ROOT}
+    wget -O ${PLANTUML_ROOT}/plantuml.jar https://sourceforge.net/projects/plantuml/files/plantuml.jar/download
 
 #%test
 # test the image after build
 
 %runscript
-    # executes command from command line
-    source /usr/local/miniconda3/bin/activate pmsco
-    exec echo "$@"
+    . ${CONDA_ROOT}/etc/profile.d/conda.sh
+    conda activate pmsco
+    exec python "$@"
 
 %apprun install
-    source /usr/local/miniconda3/bin/activate pmsco
+    . ${CONDA_ROOT}/etc/profile.d/conda.sh
+    conda activate pmsco
     cd ~
     git clone https://git.psi.ch/pearl/pmsco.git pmsco
     cd pmsco
-    git checkout develop
+    git checkout master
     git checkout -b ${SINGULAR_BRANCH}
 
+    make all
+    nosetests -w tests/
+
+%apprun compile
+    . ${CONDA_ROOT}/etc/profile.d/conda.sh
+    conda activate pmsco
     make all
     nosetests
-
-%apprun python
-    source /usr/local/miniconda3/bin/activate pmsco
-    exec python "${@}"
-
-%apprun conda
-    source /usr/local/miniconda3/bin/activate pmsco
-    exec conda "${@}"
-