CosmoSIS installation script for conda

cosmosis-conda.sh

#!/bin/bash -i
cat << EOF && read -n1 -srp "press key to start, Ctrl+C to abort" && echo
---

to get this script:

    $ curl -OL https://git.io/cosmosis-conda.sh
    $ chmod +x cosmosis-conda.sh

to run this script:

    $ ./cosmosis-conda.sh

after the script runs, you should have a conda environment called
"cosmosis" which you can activate to run cosmosis:

    $ conda activate cosmosis
    $ cosmosis --help

if the installation fails, you can remove the "cosmosis" environment
and start from the beginning:

    $ conda env remove -n cosmosis

---
EOF

# ------------------
# user configuration
# ------------------

# name of the cosmosis environment
COSMOSIS_ENV=cosmosis

# set the cosmosis branch to check out (leave empty for release)
COSMOSIS_BRANCH=develop

# use OpenMP in cosmosis (=1) or don't (=0)
COSMOSIS_OMP=1

# conda BLAS and LAPACK versions: mkl, openblas, blis, netlib
CONDA_BLAS="mkl"
CONDA_LAPACK="mkl"


# --------------------
# detect some settings
# --------------------

# get operating system name
OS=$(uname -s)


# -----------
# get to work
# -----------

# halt on error
set -e

# create environment file
ENVFILE=cosmosis-conda.yml

# write conda environment
cat << EOF > ${ENVFILE}
name: ${COSMOSIS_ENV}
channels:
  - conda-forge
  - nodefaults
dependencies:
  - compilers
  - mpi
  - python=3
  - future
  - mpi4py
  - numpy
  - scipy
  - matplotlib-base
  - astropy
  - libblas=*=*${CONDA_BLAS}
  - liblapack=*=*${CONDA_LAPACK}
  - emcee
  - minuit2
  - nose
  - pyyaml
  - gsl
  - fftw
  - cfitsio
EOF

# load conda integration
eval "$(conda shell.bash hook)"

# create environment from file
conda env create -f ${ENVFILE}

# activate the environment
conda activate "${COSMOSIS_ENV}"

# change to environment directory
cd ${CONDA_PREFIX}

# install SDK on macOS
if [ "$OS" == "Darwin" ]; then
    mkdir opt
    cd opt
    curl -L https://github.com/phracker/MacOSX-SDKs/releases/download/10.13/MacOSX10.13.sdk.tar.xz | tar -xJ
    cd ..
    echo "export CONDA_BUILD_SYSROOT=\${CONDA_PREFIX}/opt/MacOSX10.13.sdk" > etc/conda/activate.d/sysroot.sh
    source etc/conda/activate.d/sysroot.sh
    echo "sysroot set to ${CONDA_BUILD_SYSROOT}"
fi

# clone cosmosis repositories
git clone https://bitbucket.org/joezuntz/cosmosis
cd cosmosis
git checkout ${COSMOSIS_BRANCH}
git clone https://bitbucket.org/joezuntz/cosmosis-standard-library
cd cosmosis-standard-library
git checkout ${COSMOSIS_BRANCH}
cd ..

# write setup script
cat << EOF > setup-my-cosmosis
export COSMOSIS_SRC_DIR=\${CONDA_PREFIX}/cosmosis
export COSMOSIS_OMP=${COSMOSIS_OMP}
export COSMOSIS_ALT_COMPILERS=1

export CC="\${CC} \${CFLAGS} \${LDFLAGS}"
export CXX="\${CXX} \${CXXFLAGS} \${LDFLAGS}"
export FC="\${FC} \${FFLAGS} \${LDFLAGS}"
export MPIFC="mpif90 \${FFLAGS} \${LDFLAGS}"

export GSL_INC=\${CONDA_PREFIX}/include
export GSL_LIB=\${CONDA_PREFIX}/lib

export CFITSIO_INC=\${CONDA_PREFIX}/include
export CFITSIO_LIB=\${CONDA_PREFIX}/lib

export FFTW_LIBRARY=\${CONDA_PREFIX}/lib
export FFTW_INCLUDE_DIR=\${CONDA_PREFIX}/include

export MINUIT2_INC=\${CONDA_PREFIX}/include/Minuit2
export MINUIT2_LIB=\${CONDA_PREFIX}/lib

export LAPACK_LINK="-L\${CONDA_PREFIX}/lib -lblas -llapack"

export DYLD_LIBRARY_PATH=\${COSMOSIS_SRC_DIR}/cosmosis/datablock/:\${COSMOSIS_SRC_DIR}/cosmosis-standard-library/likelihood/:\${COSMOSIS_SRC_DIR}/cosmosis-standard-library/likelihood/planck/plc-1.0/lib/:\${COSMOSIS_SRC_DIR}/cosmosis-standard-library/likelihood/planck2015/plc-2.0/lib/:\${DYLD_LIBRARY_PATH}

export LD_LIBRARY_PATH=\${COSMOSIS_SRC_DIR}/cosmosis/datablock/:\${COSMOSIS_SRC_DIR}/cosmosis-standard-library/likelihood/planck/plc-1.0/lib/:\${COSMOSIS_SRC_DIR}/cosmosis-standard-library/likelihood/planck2015/plc-2.0/lib/:\${LD_LIBRARY_PATH}

export PYTHONPATH=\${COSMOSIS_SRC_DIR}:\${PYTHONPATH}
export PATH=\${COSMOSIS_SRC_DIR}/bin:/path/to/gcc:/path/to/python/:\${PATH}

alias cd_cosmosis="cd \${COSMOSIS_SRC_DIR}"
EOF

# load the new setup script
source setup-my-cosmosis

# link setup script to run when environment is activated
mkdir -p ${CONDA_PREFIX}/etc/conda/activate.d
ln -s ${COSMOSIS_SRC_DIR}/setup-my-cosmosis ${CONDA_PREFIX}/etc/conda/activate.d/cosmosis.sh

# build cosmosis
make

# all done!
cat << EOF
---

activate the new environment:

    $ conda activate ${COSMOSIS_ENV}

change to the cosmosis source directory:

    $ cd_cosmosis

run the first cosmosis demo:

    $ cosmosis demos/demo1.ini

---
EOF