Add script to build and install pre-requisites for macOS

target/patches/dep_build_macOS.sh

@@ -0,0 +1,374 @@
+#!/bin/bash
+
+# Exit immediately if a command exits with a non-zero status
+set -e
+
+# Check the number of arguments
+if [ "$#" -lt 2 ] || [ "$#" -gt 3 ]; then
+    echo "Usage: $0 <interspec_src_dir> <working_directory> <install_directory>"
+    exit 1
+fi
+
+# Set proxy, if you need it
+export http_proxy=http://proxy.sandia.gov:80
+export https_proxy=http://proxy.sandia.gov:80
+
+working_directory=$2
+install_directory=$3
+
+if [ ! -d "$1" ]; then
+  echo "The first argument to the InterSpec source code directory is not valid"
+  exit 1
+fi
+
+interspec_src=$(realpath "$1")
+PATCH_DIR="${interspec_src}/target/patches/"
+if [ ! -d "${PATCH_DIR}" ]; then
+  echo "The InterSpec patch directory at '${PATCH_DIR}' is invalid."
+  exit 1
+fi
+
+# Create the working directory if it doesn't exist
+if [ ! -d "$working_directory" ]; then
+    mkdir -p "$working_directory"
+    if [ $? -ne 0 ]; then
+        echo "Error: Failed to create working directory '$working_directory'."
+        exit 1
+    fi
+    echo "Created working directory: $working_directory"
+else
+    echo "Working directory already exists: $working_directory"
+fi
+
+# Create the install directory if it doesn't exist
+if [ ! -d "$install_directory" ]; then
+    mkdir -p "$install_directory"
+    if [ $? -ne 0 ]; then
+        echo "Error: Failed to create install directory '$install_directory'."
+        exit 1
+    fi
+    echo "Created install directory: $install_directory"
+else
+    echo "Install directory already exists: $install_directory"
+fi
+
+# Assign arguments to variables
+working_directory=$(realpath "$working_directory")
+install_directory=$(realpath "$install_directory")
+
+# Output the assigned variables
+echo "Working Directory: $working_directory"
+echo "Install Directory: $install_directory"
+
+
+# git patching will fail if our working directory is a sub-directory of the InterSpec source code
+if [[ "$working_directory" == "$interspec_src"* ]]; then
+  echo "The working directory (second argument) must not be a subdirectory of the InterSpec source directory (first argument)."
+  exit 1
+fi
+
+export MACOSX_DEPLOYMENT_TARGET=10.13 # MacOS High Sierra (2017, supported through 2020)
+export MY_WT_PREFIX=$install_directory
+
+
+# Define a function to download a file and check its hash
+download_file() {
+  local file_url="$1"
+  local file_name="$2"
+  local expected_sha256="$3"
+
+  if [ -f "$file_name" ]; then
+    echo "File '$file_name' already exists. Skipping download."
+  else
+    curl -L "${file_url}" --output "${file_name}"
+  fi
+
+  downloaded_sha256=$(shasum -a 256 "$file_name" | awk '{ print $1 }')
+  if [ "$downloaded_sha256" != "$expected_sha256" ]; then
+    echo "Error: SHA-256 hash mismatch for '$file_name'."
+    echo "Expected: $expected_sha256"
+    echo "Got: $downloaded_sha256"
+    exit 1
+  else
+    echo "SHA-256 hash verified for '$file_name'."
+  fi
+}
+
+
+# Change to the working directory
+cd "$working_directory"
+if [ $? -ne 0 ]; then
+    echo "Error: Failed to change to working directory '$working_directory'."
+    exit 1
+fi
+
+
+## Build boost 1.78
+if [ -f "${working_directory}/boost.installed" ]; then
+    echo "Boost already installed (as indicated by existance of boost.installed file) - skipping."
+else
+  # Download the file using curl
+  file_url="https://sourceforge.net/projects/boost/files/boost/1.78.0/boost_1_78_0.zip/download"
+  file_name="boost_1_78_0.zip"
+  expected_sha256="f22143b5528e081123c3c5ed437e92f648fe69748e95fa6e2bd41484e2986cc3"
+
+  download_file "${file_url}" "${file_name}" "${expected_sha256}"
+
+  # unzip and change into resulting directory
+  if [ -e "${working_directory}/boost.unzipped" ]; then
+    echo "Boost already unzipped."
+  else
+    unzip "${file_name}"
+    touch "${working_directory}/boost.unzipped"
+  fi
+
+  cd "${file_name%.*}"
+
+  if [ -e "${working_directory}/boost.built" ]; then
+    echo "Boost already built - not rebuilding."
+  else
+    # build the b2 executable
+    ./bootstrap.sh cxxflags="-arch x86_64 -arch arm64 -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}" cflags="-arch x86_64 -arch arm64 -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}" linkflags="-arch x86_64 -arch arm64 -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}" --prefix=${MY_WT_PREFIX}
+
+    # build and stage boost for arm64
+    ./b2 toolset=clang-darwin target-os=darwin architecture=arm abi=aapcs cxxflags="-stdlib=libc++ -arch arm64 -std=c++14 -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}" cflags="-arch arm64  -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}" linkflags="-stdlib=libc++ -arch arm64 -std=c++14 -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}" link=static variant=release threading=multi --build-dir=macOS_arm64_build --prefix=${MY_WT_PREFIX} -a stage
+
+    # copy arm libraries to a separate directory
+    mkdir -p arm64 && cp stage/lib/libboost_* arm64/
+
+    # build boost for x86_64 and install it (we'll copy over the libraries later)
+    ./b2 toolset=clang-darwin target-os=darwin architecture=x86 cxxflags="-stdlib=libc++ -arch x86_64 -std=c++14 -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}" cflags="-arch x86_64 -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}" linkflags="-stdlib=libc++ -arch x86_64 -std=c++14 -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}" abi=sysv binary-format=mach-o link=static variant=release threading=multi --build-dir=macOS_x64_build --prefix=${MY_WT_PREFIX} -a install
+
+    # move x86 libraries to a seperate directory
+    mkdir x86_64 && mv ${MY_WT_PREFIX}/lib/libboost_* x86_64/
+
+    # Now lipo libraries together
+    mkdir -p universal
+    for dylib in arm64/*; do 
+      lipo -create -arch arm64 $dylib -arch x86_64 x86_64/$(basename $dylib) -output universal/$(basename $dylib); 
+    done
+
+    touch "${working_directory}/boost.built"
+  fi
+
+  # And finally copy the fat libraries to the prefix location
+  cp universal/libboost_* ${MY_WT_PREFIX}/lib/
+
+  touch "${working_directory}/boost.installed"
+fi #if boost.installed exists / else
+
+
+cd "${working_directory}"
+
+
+## Build libpng
+if [ -f "${working_directory}/libpng.installed" ]; then
+    echo "libpng already installed (as indicated by existance of libpng.installed file) - skipping."
+else
+  # libpng is only necessary if you are going to build the macOS packaged app, with the Quick Look utility that provides previews of spectrum files in the Finder and various places throughout the OS.
+  # We will build once for arm64, and then x86_64 and lipo the libraries together to create a fat library.
+  file_url="http://prdownloads.sourceforge.net/libpng/libpng-1.6.37.tar.gz"
+  file_name="libpng-1.6.37.tar.gz"
+  expected_sha256="daeb2620d829575513e35fecc83f0d3791a620b9b93d800b763542ece9390fb4"
+  src_dir="libpng-1.6.37"
+
+  download_file "${file_url}" "${file_name}" "${expected_sha256}"
+
+
+  if [ -d "${src_dir}" ]; then
+    echo "libpng already unzipped, not doing again."
+  else
+    tar -xzvf "${file_name}"
+  fi
+
+  cd "${src_dir}"
+
+  if [ -d build ]; then
+    rm -r build
+    echo "Deleted previous libpng build directory."
+  fi
+
+  mkdir build
+  cd build
+
+  # First build for arm64 (-DCMAKE_OSX_ARCHITECTURES="x86_64;arm64" doesnt seem to work)
+  cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET}" -DPNG_SHARED=OFF -DCMAKE_INSTALL_PREFIX="${MY_WT_PREFIX}" -DCMAKE_OSX_ARCHITECTURES="arm64" -DPNG_ARM_NEON=on ..
+  make -j10 install
+  rm -rf ./*
+
+  # Then build for x86_64
+  cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET}" -DPNG_SHARED=OFF -DCMAKE_INSTALL_PREFIX="${MY_WT_PREFIX}" -DCMAKE_OSX_ARCHITECTURES="x86_64" ..
+  make -j10
+
+  # And now lipo the libraries together
+  mkdir universal
+  lipo -create -arch x86_64 libpng16.a -arch arm64 "${MY_WT_PREFIX}/lib/libpng16.a" -output universal/libpng16.a
+  cp universal/libpng16.a "${MY_WT_PREFIX}/lib/"
+
+  touch "${working_directory}/libpng.installed"
+fi #if libpng.installe exists / else
+
+cd "${working_directory}"
+
+
+## Build libharu
+if [ -f "${working_directory}/libharu.installed" ]; then
+    echo "libharu already installed (as indicated by existance of libharu.installed file) - skipping."
+else
+  # libharu is only necessary if you are going to build the macOS packaged app, with the Quick Look utility.
+  file_url="https://github.com/libharu/libharu/archive/RELEASE_2_3_0.zip"
+  file_name="libharu_2.3.0.zip"
+  expected_sha256="34de0ed4e994d9c704339292740b8019c33e8538814e104d882508a33517d1a8"
+  src_dir="libharu-RELEASE_2_3_0"
+
+  download_file "${file_url}" "${file_name}" "${expected_sha256}"
+
+  if [ -d "${src_dir}" ]; then
+    echo "libharu already unzipped, not doing again."
+  else
+    unzip "${file_name}"
+  fi
+
+  cd "${src_dir}"
+
+  if [ -d build ]; then
+    rm -r build
+    echo "Deleted previous libharu build directory."
+  fi
+
+  mkdir build
+  cd build
+
+  # CMake will take care of building for x86_64 and arm64 at the same time
+  cmake -DLIBHPDF_SHARED=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET}" -DPNG_LIBRARY_RELEASE= -DPNG_LIBRARY_RELEASE=${MY_WT_PREFIX}/lib/libpng.a -DPNG_PNG_INCLUDE_DIR=${MY_WT_PREFIX}/include -DCMAKE_INSTALL_PREFIX=${MY_WT_PREFIX} -DCMAKE_OSX_ARCHITECTURES="x86_64;arm64" ..
+  make -j10 install
+
+  touch "${working_directory}/libharu.installed"
+fi #if libharu.installe exists / else
+
+
+cd "${working_directory}"
+
+
+## Build Wt 3.7.1
+if [ -f "${working_directory}/wt.installed" ]; then
+    echo "Wt already installed (as indicated by existance of wt.installed file) - skipping."
+else
+  # InterSpec code will only compile with exactly version 3.3.4 or 3.7.1.  
+  # For 3.3.4, see version of this file from before Dec 26th 2021 for pathc and build instructions.
+
+  file_url="https://github.com/emweb/wt/archive/3.7.1.tar.gz"
+  file_name="wt-3.7.1.tar.gz"
+  expected_sha256="232a2f0a2f3c4174c96872ab15ef7bc0a544d9401486a4c496a6b37f27cc10e7"
+  src_dir="wt-3.7.1"
+
+  download_file "${file_url}" "${file_name}" "${expected_sha256}"
+
+  if [ -d "${src_dir}" ]; then
+    echo "Wt already unzipped, not doing again."
+  else
+    tar -xzvf "${file_name}"
+  fi
+
+  cd "${src_dir}"
+
+  if [ -f "wt.patched" ]; then
+    echo "Wt already pated, not doing again."
+  else
+    git apply --reject --ignore-space-change --ignore-whitespace "${PATCH_DIR}/wt/3.7.1/NormalBuild/wt_3.7.1_git.patch"
+    touch wt.patched
+  fi
+
+  if [ -d build ]; then
+    rm -r build
+    echo "Deleted previous libharu build directory."
+  fi
+
+  mkdir build
+  cd build
+
+  cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET}" -DCMAKE_PREFIX_PATH="${MY_WT_PREFIX}" -DBoost_INCLUDE_DIR="${MY_WT_PREFIX}/include" -DBOOST_PREFIX="${MY_WT_PREFIX}" -DSHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX="${MY_WT_PREFIX}" -DHARU_PREFIX="${MY_WT_PREFIX}" -DHARU_LIB="${MY_WT_PREFIX}/lib/libhpdfs.a" -DENABLE_SSL=OFF -DCONNECTOR_FCGI=OFF -DBUILD_EXAMPLES=OFF -DBUILD_TESTS=OFF -DENABLE_MYSQL=OFF -DENABLE_POSTGRES=OFF -DENABLE_PANGO=OFF -DINSTALL_FINDWT_CMAKE_FILE=ON -DHTTP_WITH_ZLIB=OFF -DWT_CPP_11_MODE="-std=c++14" -DCONFIGURATION=data/config/wt_config_osx.xml -DWTHTTP_CONFIGURATION=data/config/wthttpd -DCONFIGDIR="${MY_WT_PREFIX}/etc/wt" -DCMAKE_OSX_ARCHITECTURES="x86_64;arm64" -S ..
+  make -j10 install
+  touch "${working_directory}/wt.installed"
+fi #if wt.installed exists / else
+
+
+cd "${working_directory}"
+
+
+## Install Eigen
+if [ -f "${working_directory}/Eigen.installed" ]; then
+    echo "Eigen already installed (as indicated by existance of Eigen.installed file) - skipping."
+else
+  # Build Eigen, which is required by ceres-solver, and used a few other places
+  # in InterSpec if its available
+  file_url="https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz"
+  file_name="eigen-3.4.0.tar.gz"
+  expected_sha256="8586084f71f9bde545ee7fa6d00288b264a2b7ac3607b974e54d13e7162c1c72"
+  src_dir="eigen-3.4.0"
+
+  download_file "${file_url}" "${file_name}" "${expected_sha256}"
+
+  if [ -d "${src_dir}" ]; then
+    echo "Eigen already unzipped, not doing again."
+  else
+    tar -xzvf "${file_name}"
+  fi
+
+  cd "${src_dir}"
+
+  if [ -d build ]; then
+    rm -r build
+    echo "Deleted previous libharu build directory."
+  fi
+
+  mkdir build
+  cd build
+
+  cmake -DCMAKE_INSTALL_PREFIX="${MY_WT_PREFIX}" -DCMAKE_BUILD_TYPE=Release -DEIGEN_MPL2_ONLY=1 -DEIGEN_BUILD_SHARED_LIBS=OFF -DEIGEN_BUILD_DOC=OFF -DEIGEN_BUILD_TESTING=OFF ..
+  cmake --build . --config Release --target install
+
+  touch "${working_directory}/Eigen.installed"
+fi #if Eigen.installed exists / else
+
+
+cd "${working_directory}"
+
+## Build Ceres-Solver
+if [ -f "${working_directory}/Ceres.installed" ]; then
+    echo "Ceres-Solver already installed (as indicated by existance of Ceres.installed file) - skipping."
+else
+  # Build ceres-solver; this is the optimizer used for the relative efficiency
+  # tool, and a small amount of the peak fitting.
+  file_url="http://ceres-solver.org/ceres-solver-2.1.0.tar.gz"
+  file_name="ceres-solver-2.1.0.tar.gz"
+  expected_sha256="f7d74eecde0aed75bfc51ec48c91d01fe16a6bf16bce1987a7073286701e2fc6"
+  src_dir="ceres-solver-2.1.0"
+
+  download_file "${file_url}" "${file_name}" "${expected_sha256}"
+
+  if [ -d "${src_dir}" ]; then
+    echo "Ceres-Solver already unzipped, not doing again."
+  else
+    tar -xzvf "${file_name}"
+  fi
+
+  cd "${src_dir}"
+
+  if [ -d build_macos ]; then
+    rm -r build_macos
+    echo "Deleted previous Ceres-Solver build_macos directory."
+  fi
+
+  mkdir build_macos
+  cd build_macos
+
+  cmake -DCMAKE_PREFIX_PATH="${MY_WT_PREFIX}" -DCMAKE_OSX_DEPLOYMENT_TARGET="${MACOSX_DEPLOYMENT_TARGET}" -DCMAKE_INSTALL_PREFIX="${MY_WT_PREFIX}" -DMINIGLOG=ON -DGFLAGS=OFF -DCXSPARSE=OFF -DACCELERATESPARSE=OFF -DCUDA=OFF -DEXPORT_BUILD_DIR=ON -DBUILD_TESTING=ON -DBUILD_EXAMPLES=OFF -DPROVIDE_UNINSTALL_TARGET=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_OSX_ARCHITECTURES="x86_64;arm64" ..
+  cmake --build . --config Release --target install -j 16
+
+  touch "${working_directory}/Ceres.installed"
+fi #if Ceres.installed exists / else
+
+cd "${working_directory}"
+
+echo "Have successfully installed all libraries to ${install_directory}"