install.sh

#!/bin/bash

# Install script for SEIDART toolbox

# ----------------------------- Anaconda install ------------------------------
VER="v0.2"
echo "--------------------------------------------
SeidarT Anaconda-based installer $VER
Univ. of Maine / Univ. of Washington, 2020
--------------------------------------------
This installer will check for Anaconda/Miniconda
and install a SeidarT environment prior to compiling from
source.
You will have the option to install Miniconda
if no existing conda is found.

Please follow instructions in prompts.
"
read -rp $'Press Enter to continue...\n'


echo '
Do you wish to delete source files after installation?
This will not affect how the program runs, but you will
not be able to edit source code.
'
# ask if we should enable pure end-user mode and delete the source scripts
read -rp $'Type "yes" and press Enter to delete source files. (default: no)\n' EUMODE

if [[ "$EUMODE" == "yes" || "$EUMODE" == "Yes" || "$EUMODE" == "YES" ]] ; then
        # end-user mode
        EUMODE="yes"
else
        # developer mode
        unset EUMODE
        echo "Developer mode enabled. Source scripts will not be deleted."
fi

bash conda_deps.sh ||
echo "Conda installation failed. Try installing dependencies the run the noconda_install script." ||
exit 1

`grep etc/profile.d/conda.sh ~/.bashrc` &&
conda activate SeidarT &&
echo "conda activate SeidarT : Successfully activated SeidarT environment." ||
echo "Could not find SeidarT conda environment. Exiting." ||
exit 1

echo ""
echo "Starting compiling/installation process..."

# -----------------------------------------------------------------------------
# Make sure we have a folder to put everything in
if [ ! -d "bin" ]; then
	mkdir bin
fi

# --------------------------------- Clean Up ----------------------------------
# Typically, install will overwrite everything but when there is a compile 
# error this can make debugging difficult if it goes unnoticed. Not everyone 
# can read the f2py or gfortran outputs

# Just clean up if specified 
CLEAN=${1:-"none"}
if [[ $CLEAN == "clean" ]] ; then 
        # Clear the bin folder
        rm -rf bin/* 
        # Remove .mod and .o (if any) files generated during the fortran compile
        rm fdtd/*.mod
        rm fdtd/*.o
        exit 1
fi

# -----------------------------------------------------------------------------
# Make sure everything is in unix format 
dos2unix vis/* 
dos2unix survey_wrappers/*
dos2unix exe/* 
dos2unix materials/*
dos2unix fdtd/*

# Compile the fortran code
#2D
cd fdtd
f2py3 -c --fcompiler=gnu95 -DNPY_NO_DEPRECATED_API -m emfdtd2d emFDTD2D.f95
f2py3 -c --fcompiler=gnu95 -DNPY_NO_DEPRECATED_API -m seismicfdtd2d seismicFDTD2D.f95
f2py3 -c --fcompiler=gnu95 -DNPY_NO_DEPRECATED_API -m emfdtd25d emFDTD25D.f95
f2py3 -c --fcompiler=gnu95 -DNPY_NO_DEPRECATED_API -m seismicfdtd25d seismicFDTD25D.f95
mv *.so ../bin
cd ..

# Synthetic microstructure
cd materials
f2py3 -c --fcompiler=gnu95 -m orientsynth orientsynth.f95
mv *.so ../bin
cd ..

# --------------------------- Create the executables --------------------------
# Start with the python scripts
cp exe/prjbuild.py bin/prjbuild
cp exe/prjrun.py bin/prjrun
cp exe/sourcefunction.py bin/sourcefunction
cp materials/orientation_tensor.py bin/orientation_tensor

# Move the visualization tools
cp vis/arraybuild.py bin/arraybuild
cp vis/rcxdisplay.py bin/rcxdisplay
cp vis/im2anim.py bin/im2anim
cp vis/vtkbuild.py bin/vtkbuild 
cp vis/wiggleplot.py bin/wiggleplot 
cp vis/imgen.py bin/imgen.py # The generalized image functions module
cp vis/imvector.py bin/imvector
cp vis/vectoranim.py bin/vectoranim
cp vis/implot.py bin/implot

# move the conversion scripts
cp io/array2segy.py bin/array2segy

# Change them to executables
chmod +x bin/prjbuild \
        bin/prjrun \
        bin/sourcefunction \
        bin/arraybuild \
        bin/rcxdisplay \
        bin/wiggleplot \
        bin/im2anim \
        bin/orientation_tensor \
        bin/array2segy \
	bin/vtkbuild \
        bin/imvector \
        bin/vectoranim \
        bin/implot



# Now do the bash scripts
cp survey_wrappers/common_offset bin/common_offset
cp survey_wrappers/common_midpoint bin/common_midpoint

cp io/array2sac bin/array2sac

chmod +x bin/common_offset bin/common_midpoint bin/array2sac


# ---------------- Move all other required files to bin folder ----------------
cp materials/material_functions.py bin/material_functions.py
cp materials/definitions.py bin/definitions.py

if [ ! -z ${EUMODE+x} ]; then
        echo "Deleting source files..."
        rm -rfv exe materials vis io survey_wrappers
        echo '
[end user mode]:
Source files deleted. You will need to download the
software again if you would like to edit source files.
Developers should not commit changes on this branch as
this will cause unwanted consequences in source control.
Developers can also use the git command "git restore ."
to restore all deleted files to source control.'
        unset EUMODE
fi

echo '
Done!
Type "conda activate SeidarT" to access the SeidarT environment.'