Adds installation instructions and scripts

name: agile

channels:

  - conda-forge

  - defaults

dependencies:

  - python=3.11

  - astropy

  - fitsio

  - matplotlib

  - numpy

  - scipy

  - pandas

  - pyvo

name: imSim

channels:

  - conda-forge

  - defaults

dependencies:

  - python>=3.11

  - stackvana>=0.2023.32

  - rubin-sim

  - pip

  - pip:

    - -r /home/aetviita/Projects/agile/opt/imsim/imSim/etc/standalone_conda_requirements.txt

    - -e /home/aetviita/Projects/agile/opt/imsim/imSim

    - -e /home/aetviita/Projects/agile/opt/imsim/skyCatalogs

vars:

  RUBIN_SIM_DATA_DIR=/home/aetviita/Projects/agile/opt/imsim/rubin_sim_data

  SIMS_SED_LIBRARY_DIR=/home/aetviita/Projects/agile/opt/rubin_sim_data/sims_sed_library

#!/bin/sh -ex

#

# Author: Akke Viitanen

# Email: akke.viitanen@helsinki.fi

# Initializes the agile environment

install_agile () {

    conda env remove -yn agile

    conda create -c conda-forge -yn agile python=3.10 pip

    conda run -n agile python3 -m pip install -r requirements.txt

}

# Install egg and vif

install_vif () {

    #sudo apt update

    #sudo apt install -y libcfitsio-dev wcslib-dev liblapack-dev libgsl0-dev libfftw3-dev libgoogle-perftools-dev libdwarf-dev libunwind8-dev libelf-dev

    #sudo apt install -y clang-18 llvm-18-dev libclang-18-dev

    rm -rf opt/vif

    git clone git@github.com:cschreib/vif.git opt/vif

    cd opt/vif

    # NOTE: patch clang

    filename_limits=$(find /usr/lib/llvm-* -name limits.h | head -n1)

    echo "$filename_limits" # Always quote your variables, especially when echoing

    sed -ie "s|if (EXISTS \"\${CLANG_ROOT}/lib/clang/\${CLANG_VERSION}/include/limits.h\")|if (EXISTS $filename_limits)|g" cmake/FindLibClang.cmake

    sed -ie "s|set(CLANG_SYSTEM_INCLUDE \"\${CLANG_ROOT}/lib/clang/\${CLANG_VERSION}/include/\")|set(CLANG_SYSTEM_INCLUDE $filename_limits)|g" cmake/FindLibClang.cmake

    rm -rfv build

    mkdir -vp build

    cd build

    cmake ..

    make

    sudo make install

    if ! grep "source ~/.vifrc" ~/.bashrc ; then

        echo "source ~/.vifrc" >> ~/.bashrc

    fi

}

install_egg () {

    git clone git@github.com:cschreib/egg.git opt/egg

    cd opt/egg

    rm -rfv build

    mkdir -vp build

    cd build

    cmake ..

    make

    sudo make install

    sudo chmod -Rv a+r /usr/local/share/egg

    sudo chmod -Rv a+x /usr/local/share/egg

}

install_imsim () {

	# NOTE: only download the data

    # https://lsstdesc.org/imSim/install.html#method-2-conda-and-the-stackvana-package

    mkdir -vp opt/imsim

    cd opt/imsim

    git clone https://github.com/LSSTDESC/imSim.git

    git clone https://github.com/LSSTDESC/skyCatalogs

    # install sims_sed_library

    mkdir -p rubin_sim_data/sims_sed_library

    curl 'https://s3df.slac.stanford.edu/groups/rubin/static/sim-data/rubin_sim_data/skybrightness_may_2021.tgz' | tar -C rubin_sim_data -xz

    curl .https://s3df.slac.stanford.edu/groups/rubin/static/sim-data/rubin_sim_data/throughputs_2023_09_07.tgz. | tar -C rubin_sim_data -xz

    curl .https://s3df.slac.stanford.edu/groups/rubin/static/sim-data/sed_library/seds_170124.tar.gz.  | tar -C rubin_sim_data/sims_sed_library -xz

}

install_lsst_science_pipelines () {

	# https://pipelines.lsst.io/install/lsstinstall.html

	mkdir -vp opt/lsst_stack

	cd opt/lsst_stack

	curl -OL 'https://ls.st/lsstinstall'

	chmod u+x lsstinstall

	./lsstinstall -T v29_1_1

	. loadLSST.sh

	eups distrib install -t v29_1_1 lsst_distrib

	curl -sSL 'https://raw.githubusercontent.com/lsst/shebangtron/main/shebangtron' | python

	setup lsst_distrib

}

#install_agile

#install_vif

#install_egg

#install_imsim

install_lsst_science_pipelines