public release 3.0.0 - see README and CHANGES for details

extras/singularity/singularity_python2

@@ -1,117 +0,0 @@
-BootStrap: debootstrap
-OSVersion: bionic
-MirrorURL: http://ch.archive.ubuntu.com/ubuntu/
-
-%help
-a singularity container for PMSCO.
-
-git clone requires an ssh key for git.psi.ch.
-try agent forwarding (-A option to ssh).
-
-#%setup
-# executed on the host system outside of the container before %post
-#
-# this will be inside the container
-#    touch ${SINGULARITY_ROOTFS}/tacos.txt
-# this will be on the host
-#    touch avocados.txt
-
-#%files
-# files are copied before %post
-#
-# this copies to root
-#    avocados.txt
-# this copies to /opt
-#    avocados.txt /opt
-#
-# this does not work
-#    ~/.ssh/known_hosts /etc/ssh/ssh_known_hosts
-#    ~/.ssh/id_rsa /etc/ssh/id_rsa
-
-%labels
-    Maintainer Matthias Muntwiler
-    Maintainer_Email matthias.muntwiler@psi.ch
-    Python_Version 2.7
-
-%environment
-    export PATH="/usr/local/miniconda3/bin:$PATH"
-    export PYTHON_VERSION=2.7
-    export SINGULAR_BRANCH="singular"
-    export LC_ALL=C
-
-%post
-    export PYTHON_VERSION=2.7
-    export LC_ALL=C
-
-    sed -i 's/$/ universe/' /etc/apt/sources.list
-    apt-get update
-    apt-get -y install \
-        binutils \
-        build-essential \
-        doxygen \
-        doxypy \
-        f2c \
-        g++ \
-        gcc \
-        gfortran \
-        git \
-        graphviz \
-        libblas-dev \
-        liblapack-dev \
-        libopenmpi-dev \
-        make \
-        nano \
-        openmpi-bin \
-        openmpi-common \
-        sqlite3 \
-        wget
-    apt-get clean
-
-    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
-    bash ~/miniconda.sh -b -p /usr/local/miniconda3
-    export PATH="/usr/local/miniconda3/bin:$PATH"
-
-    conda create -q --yes -n pmsco python=${PYTHON_VERSION}
-    . /usr/local/miniconda3/bin/activate pmsco
-    conda install -q --yes -n pmsco \
-        pip \
-        "numpy>=1.13" \
-        scipy \
-        ipython \
-        matplotlib \
-        nose \
-        mock \
-        future \
-        statsmodels \
-        swig
-    conda clean --all -y
-    /usr/local/miniconda3/envs/pmsco/bin/pip install periodictable attrdict fasteners mpi4py
-    
-    
-#%test
-# test the image after build
-
-%runscript
-    # executes command from command line
-    . /usr/local/miniconda3/bin/activate pmsco
-    exec echo "$@"
-
-%apprun install
-    . /usr/local/miniconda3/bin/activate pmsco
-    cd ~
-    git clone https://git.psi.ch/pearl/pmsco.git pmsco
-    cd pmsco
-    git checkout develop
-    git checkout -b ${SINGULAR_BRANCH}
-
-    make all
-    nosetests
-
-%apprun python
-    . /usr/local/miniconda3/bin/activate pmsco
-    exec python "${@}"
-
-%apprun conda
-    . /usr/local/miniconda3/bin/activate pmsco
-    exec conda "${@}"
-

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 "${@}"
-

extras/vagrant/Vagrantfile

@@ -12,8 +12,8 @@ Vagrant.configure("2") do |config|
 
   # Every Vagrant development environment requires a box. You can search for
   # boxes at https://vagrantcloud.com/search.
-  config.vm.box = "singularityware/singularity-2.4"
-  config.vm.box_version = "2.4"
+  config.vm.box = "sylabs/singularity-3.7-ubuntu-bionic64"
+  config.vm.box_version = "3.7"
 
   # Disable automatic box update checking. If you disable this, then
   # boxes will only be checked for updates when the user runs