provision_ubuntu18.sh

#!/bin/bash

sudo apt-get update

sudo apt-get install -y libxml2-dev gdb g++ git make libxml++2.6-dev valgrind libboost-dev libboost-filesystem-dev zip python3 zip default-jre-headless python3-lxml curl mpich rapidjson-dev npm libhdf5-dev

# RISC-V toolchain (not sure exactly how much is needed)
# TODO: which parts are needed?
#sudo apt-get install -y autoconf automake autotools-dev curl libmpc-dev libmpfr-dev libgmp-dev gawk build-essential bison flex texinfo gperf libtool patchutils bc zlib1g-dev

# Needed for POEMS
sudo apt-get install -y libmetis-dev libtbb-dev

# Testing.
# npm has the most recent version of bats, because life is like that
# OLD: This version does not support parallel jobs though...
# OLD: sudo npm install -g bats
if [[ "$(which bats)" == "" ]] ; then
    git clone https://github.com/bats-core/bats-core.git
    (cd bats-core && sudo ./install.sh /usr/local )
fi

# Graph partitioning
sudo apt-get install -y metis 

# Visualisation
sudo apt-get install -y graphviz imagemagick ffmpeg

# Editors
sudo apt-get install -y emacs-nox screen

# Algebraic multigrid, plus others
# TODO: Do this in a more pip oriented way
sudo apt-get install -y python3-pip python3-numpy python3-scipy python3-ujson
sudo pip3 install pyamg
sudo pip3 install svgwrite
sudo pip3 install h5py

# Creating meshes
sudo apt-get install -y octave octave-msh octave-geometry hdf5-tools

# TODO: This line eeds changing or removing for ubuntu 18
# Fix a bug in geometry package for svg.
# Note that sed is _not_ using extended regular expressions (no "-r")
#sudo sed -i -e 's/,{0},/,"{0}",/g' -e 's/,{1},/,"{1}",/g'  /usr/share/octave/packages/geometry-2.1.0/io/@svg/parseSVGData.py

# Used to support generation of documentation from schema
#TODO: No longer needed?
#sudo apt-get install -y xsltproc ant libsaxon-java docbook docbook-xsl-ns pandoc