extra-foam.def

Bootstrap: library
From: centos:7.6.1810

%help
  EXtra-foam (previously known as karaboFAI) is an application that provides
  super fast on-line (real-time) and off-line data analysis and visualization
  for experiments at European XFEL that using 2D detectors, namely AGIPD, DSSC,
  LPD, FastCCD, JungFrau, etc., together with other 1D detectors (e.g. XGM,
  digitizer, etc.) and various control data.

  GitHub: https://github.com/European-XFEL/EXtra-foam
  Docs: https://extra-foam.readthedocs.io/en/latest/

%environment
  __conda_setup="$('/usr/local/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
  if [ $? -eq 0 ]; then
      eval "$__conda_setup"
  else
      if [ -f "/usr/local/etc/profile.d/conda.sh" ]; then
          . "/usr/local/etc/profile.d/conda.sh"
      else
          export PATH="/usr/local/bin:$PATH"
      fi
  fi
  unset __conda_setup

  conda activate base

%runscript
  extra-foam "$@"

%post
  export logpath=/.singularity.d/logs/
  mkdir -p $logpath

  #  Set default python version if missing
  PYTHON_VERSION="${PYTHON_VERSION:-3.7.5}"
  echo "Building for python version: $PYTHON_VERSION"

  #  Basic yum dependencies
  ##  Install and update
  yum update -y | tee $logpath/00-yum-update.log
  yum install -y epel-release | tee $logpath/01-yum-epel-release.log
  yum groupinstall -y 'Development Tools' | tee $logpath/02-yum-dev-tools.log
  yum install -y      \
    nano              \
    curl              \
    wget              \
    tar               \
    bzip2             \
    git               \
    e4fsprogs         \
    xeyes             \
    mesa-libGL        \
    qt5-qtbase        \
    libxkbcommon-x11  \
  | tee $logpath/03-yum-install.log

  ##  Log yum packages
  yum list installed | tee $logpath/04-yum-list-installed.log

  #  Install and setup miniconda
  ##  Download and install minconda
  curl -sSL http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o /tmp/miniconda.sh
  chmod +x /tmp/miniconda.sh
  /tmp/miniconda.sh -bfp /usr/local/
  rm -f /tmp/miniconda.sh
  source /usr/local/bin/activate

  ##  Install python dependencies
  conda install -y python=$PYTHON_VERSION
  conda install -y -c anaconda cmake numpy
  conda install -y -c omgarcia gcc-6

  ##  Download EXtra-foam source
  mkdir -p /usr/local/src/
  cd /usr/local/src/
  git clone https://github.com/European-XFEL/EXtra-foam
  cd EXtra-foam
  git checkout $GIT_COMMIT_HASH
  git submodule update --init | tee -a $logpath/05-extra-foam-submodules.log
  git log -n 1 | tee -a $logpath/06-extra-foam-clone.log

  pip install .

  ##  Export environment to concretise
  conda env export -n base -f /.singularity.d/logs/07-conda-env-export.log