Add Mac os x installation scripts

macosx.sh

@@ -0,0 +1,144 @@
+#!/bin/bash
+# This script contains common code for building PyNE on various Debian-derived systems
+#
+
+function check_repo() {
+
+    repo_name=$1
+
+    if [ -d ${repo_name} ] ; then
+        read -p "Delete the existing ${repo_name} directory and all contents? (y/n) " -n 1 -r
+        if [[ $REPLY =~ ^[Yy]$ ]] ; then
+            rm -rf ${repo_name}
+        fi
+    fi
+
+}
+
+function build_moab {
+
+    # Install MOAB
+    cd ${install_dir}
+    mkdir -p moab
+    cd moab
+    check_repo moab-repo
+    git clone --branch Version5.1.0 --single-branch https://bitbucket.org/fathomteam/moab moab-repo
+    cd moab-repo
+    mkdir -p build
+    cd build
+    cmake ../ -DENABLE_HDF5=ON \
+              -DBUILD_SHARED_LIBS=ON \
+              -DENABLE_PYMOAB=ON \
+              -DENABLE_BLASLAPACK=OFF \
+              -DENABLE_FORTRAN=OFF \
+              -DCMAKE_INSTALL_PREFIX=${install_dir}/moab
+    make
+    make install
+
+    echo "if [ -n \"\${LD_LIBRARY_PATH-}\" ]" >> ~/.bashrc
+    echo "then" >> ~/.bashrc 
+    echo "  export LD_LIBRARY_PATH=${install_dir}/moab/lib:\$LD_LIBRARY_PATH" >> ~/.bashrc
+    echo "else" >> ~/.bashrc
+    echo "  export LD_LIBRARY_PATH=${install_dir}/moab/lib" >> ~/.bashrc
+    echo "fi" >> ~/.bashrc
+
+    PYTHON_VERSION=$(python -c 'import sys; print(sys.version.split('')[0][0:3])')
+    echo "if [ -n \"\${PYTHONPATH-}\" ]" >> ~/.bashrc
+    echo "then" >> ~/.bashrc
+    echo "  export PYTHONPATH=${install_dir}/moab/lib/python${PYTHON_VERSION}/site-packages:\$PYTHONPATH" >> ~/.bashrc
+    echo "else" >> ~/.bashrc
+    echo "  export PYTHONPATH=${install_dir}/moab/lib/python${PYTHON_VERSION}/site-packages" >> ~/.bashrc
+    echo "fi" >> ~/.bashrc
+    source ~/.bashrc
+}
+
+function build_dagmc {
+
+    # Install DAGMC
+    cd ${install_dir}
+    check_repo dagmc
+    mkdir -p dagmc
+    cd dagmc
+    git clone https://github.com/svalinn/DAGMC.git dagmc-repo
+    cd dagmc-repo
+    git checkout develop
+    mkdir build
+    cd build
+    cmake .. -DMOAB_DIR=${install_dir}/moab \
+             -DBUILD_STATIC_LIBS=OFF \
+             -DCMAKE_INSTALL_PREFIX=${install_dir}/dagmc
+    make
+    make install
+}
+
+function install_pyne {
+
+    # Install PyNE
+    cd ${install_dir}
+    check_repo pyne
+    git clone https://github.com/pyne/pyne.git
+    cd pyne
+    if [ $1 == 'stable' ] ; then
+        TAG=$(git describe --abbrev=0 --tags)
+        git checkout tags/`echo ${TAG}` -b `echo ${TAG}`
+    fi
+
+
+	python setup.py install --user -- -DMOAB_LIBRARY=${install_dir}/moab/lib \
+                                      -DMOAB_INCLUDE_DIR=${install_dir}/moab/include \
+                                   --dagmc ${install_dir}/dagmc \
+                                   --clean    
+
+    echo "export PATH=${HOME}/.local/bin:\$PATH" >> ~/.bashrc
+    echo "export LD_LIBRARY_PATH=${HOME}/.local/lib:\$LD_LIBRARY_PATH" >> ~/.bashrc
+
+   PYTHON_VERSION=$(python -c 'import sys; print(sys.version.split('')[0][0:3])')
+    echo "if [ -n \"\${PYTHONPATH-}\" ]" >> ~/.bashrc
+    echo "then" >> ~/.bashrc
+    echo "  export PYTHONPATH=~/.local/lib/python${PYTHON_VERSION}/site-packages:\$PYTHONPATH" >> ~/.bashrc
+    echo "else" >> ~/.bashrc
+    echo "  export PYTHONPATH=~/.local/lib/python${PYTHON_VERSION}/site-packages" >> ~/.bashrc
+    echo "fi" >> ~/.bashrc
+    source ~/.bashrc
+}
+
+function run_nuc_data_make {
+
+    cd
+    # Generate nuclear data file
+    nuc_data_make
+
+}
+
+function test_pyne {
+
+    cd $install_dir/pyne
+    cd tests
+
+    ./travis-run-tests.sh python3
+}
+
+set -euo pipefail
+IFS=$'\n\t'
+
+# system update
+eval brew update
+eval brew install ${brew_package_list}
+export PATH="${HOME}/.local/bin:${PATH}"
+eval sudo pip3 install ${pip_package_list}
+
+install_dir=${HOME}/opt
+mkdir -p ${install_dir}
+
+build_moab
+
+build_dagmc
+
+install_pyne $1
+
+run_nuc_data_make
+
+test_pyne
+
+echo "Run 'source ~/.bashrc' to update environment variables. PyNE may not function correctly without doing so."
+echo "PyNE build complete."

osx_10.15.6.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+# This script builds the repo version of PyNE (with the MOAB optional
+# dependency) from scratch on MacOS 10.15.6. The folder $HOME/opt is created
+# and PyNE is installed within.
+#
+# Run this script from any directory by issuing the command where <version>
+# is either "dev" or "stable":
+# $ ./osx_10.15.6.sh <version>
+# After the build finishes run:
+#  $ source ~/.bashrc
+# or open a new terminal.
+
+# Use package manager for as many packages as possible
+brew_package_list="glib python3 wget eigen \
+             git cmake vim emacs gcc openblas \
+             lapack autoconf libtool make hdf5"
+
+pip_package_list="future numpy scipy cython nose tables matplotlib jinja2 \
+                  setuptools h5py"
+
+
+source macosx.sh $1

ubuntu_mint.sh

@@ -34,26 +34,20 @@ function build_moab {
               -DCMAKE_INSTALL_PREFIX=${install_dir}/moab
     make
     make install
-    export LD_LIBRARY_PATH=${install_dir}/moab/lib:$LD_LIBRARY_PATH
-    export LIBRARY_PATH=${install_dir}/moab/lib:$LIBRARY_PATH
-    if [ -z \$PYTHONPATH ]
-    then
-        export PYTHONPATH=${install_dir}/moab/lib/python2.7/site-packages
-    else
-        export PYTHONPATH=${install_dir}/moab/lib/python2.7/site-packages:\$PYTHONPATH
-    fi
+
     echo "export LD_LIBRARY_PATH=${install_dir}/moab/lib:\$LD_LIBRARY_PATH" >> ~/.bashrc
     echo "export LIBRARY_PATH=${install_dir}/moab/lib:\$LIBRARY_PATH" >> ~/.bashrc
     echo "export CPLUS_INCLUDE_PATH=${install_dir}/moab/include:\$CPLUS_INCLUDE_PATH" >> ~/.bashrc
     echo "export C_INCLUDE_PATH=${install_dir}/moab/include:\$C_INCLUDE_PATH" >> ~/.bashrc
 
     PYTHON_VERSION=$(python -c 'import sys; print(sys.version.split('')[0][0:3])')
     echo "if [ -z \$PYTHONPATH ]" >> ~/.bashrc
-    echo "then" >> ~/.bashrc >> ~/.bashrc
+    echo "then" >> ~/.bashrc
     echo "  export PYTHONPATH=$install_dir/moab/lib/python${PYTHON_VERSION}/site-packages" >> ~/.bashrc
     echo "else" >> ~/.bashrc
     echo "  export PYTHONPATH=$install_dir/moab/lib/python${PYTHON_VERSION}/site-packages:\$PYTHONPATH" >> ~/.bashrc
     echo "fi" >> ~/.bashrc
+    source ~/.bashrc
 }
 
 function build_dagmc {
@@ -92,31 +86,23 @@ function install_pyne {
                                --clean
     echo "export PATH=${HOME}/.local/bin:\$PATH" >> ~/.bashrc
     echo "export LD_LIBRARY_PATH=${HOME}/.local/lib:\$LD_LIBRARY_PATH" >> ~/.bashrc
-    echo "alias build_pyne='python setup.py install --user -- -DMOAB_LIBRARY=${install_dir}/moab/lib -DMOAB_INCLUDE_DIR=${install_dir}/moab/include'" >> ~/.bashrc
-
+    source ~/.bashrc
 }
 
-function nuc_data_make {
+function run_nuc_data_make {
 
+    cd
     # Generate nuclear data file
-    export LD_LIBRARY_PATH=${HOME}/.local/lib:${LD_LIBRARY_PATH}
-    ./scripts/nuc_data_make
+    nuc_data_make
 
 }
 
 function test_pyne {
 
+    cd $install_dir/pyne
     cd tests
 
-    # check which python version to run correct tests
-    version=`python -c 'import sys; print(sys.version_info[:][0])'`
-
-    # Run all the tests
-    if [ ${version} == '2' ] ; then
-        source ./travis-run-tests.sh python2
-    elif [ ${version} == '3' ] ; then
-        source ./travis-run-tests.sh python3
-    fi
+    ./travis-run-tests.sh python3
 }
 
 
@@ -144,9 +130,9 @@ build_dagmc
 
 install_pyne $1
 
-nuc_data_make
+run_nuc_data_make
 
 test_pyne
 
 echo "Run 'source ~/.bashrc' to update environment variables. PyNE may not function correctly without doing so."
-echo "PyNE build complete. PyNE can be rebuilt with the alias 'build_pyne' executed from ${install_dir}/pyne"
+echo "PyNE build complete."