Electrostatics · nsoblath · Sep 25, 2021 · Sep 25, 2021 · Sep 25, 2021 · Sep 25, 2021
diff --git a/.build.sh b/.build.sh
@@ -1,60 +1,92 @@
 #!/bin/bash
-
+ 
 # echo "==================================== WHICH GCC ==================================== "
 # which gcc
 # ls /usr/local/bin/gcc*
-echo "==================================== WHICH GCC ==================================== "
-ostype="$(uname -s)"
-case "${ostype}" in
-      # NOTE: clang on Github Actions cannot fine Accelerate Framework
-      #       so you will get errors about not being able to find xerbla_
-      # Darwin*)    export CC=clang; export CXX=clang++;;
-      Darwin*)    export CC=gcc-9; export CXX=g++-9;;
-      Linux*)     export CC=gcc-9; export CXX=g++-9;;
-esac
-
-export CMAKE_C_COMPILER=$CC
-export CMAKE_CXX_COMPILER=$CXX
-export CMAKE_C_LINK_EXECUTABLE=$CC
-export CMAKE_CXX_LINK_EXECUTABLE=$CXX
-
+
+# Install prereqs with INSTALL_PREREQS=1 or turn off with INSTALL_PREREQS=0
+export INSTALL_PREREQS=1
+
+# Setup tests for APBS with TEST_APBS=1 or turn off with TEST_APBS=0
+export TEST_APBS=0
+
+# Create ZIP archive for APBS with PACKAGE_APBS=1 or turn off with PACKAGE_APBS=0
+export PACKAGE_APBS=0
+
+# Configure and Build pybind11 with BUILD_PYBIND=1 or turn off with BUILD_PYBIND=0
+export BUILD_PYBIND=0
+
+#echo "==================================== WHICH GCC ==================================== "
+#ostype="$(uname -s)"
+#case "${ostype}" in
+#      # NOTE: clang on Github Actions cannot fine Accelerate Framework
+#      #       so you will get errors about not being able to find xerbla_
+#      # Darwin*)    export CC=clang; export CXX=clang++;;
+#      Darwin*)    export CC=gcc-9; export CXX=g++-9;;# export CMAKE_C_FLAGS="-Wl,-rpath=@executable_path/../lib "; export CMAKE_CXX_FLAGS="-Wl,-rpath=@executable_path/../lib ";;
+#      Linux*)     export CC=gcc-9; export CXX=g++-9;;
+#esac
+
+#export CMAKE_C_COMPILER=$CC
+#export CMAKE_CXX_COMPILER=$CXX
+#export CMAKE_C_LINK_EXECUTABLE=$CC
+#export CMAKE_CXX_LINK_EXECUTABLE=$CXX
+
 export SRC_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 export COVERAGE="-g -O0 -fprofile-arcs -ftest-coverage"
 export COVERAGE=""
-export BUILD_DIR="$SRC_DIR/build"
-export INSTALL_DIR=$HOME/apbs
+: ${BUILD_DIR=$SRC_DIR/build}
+: ${INSTALL_DIR=$HOME/apbs}
 export PATH=$INSTALL_DIR:$PATH
-export RELEASE_TYPE=Debug
-export RELEASE_TYPE=Release
 
+# set variables only if they're not already set
+: ${RELEASE_TYPE:=Release}
+: ${BLA_VENDOR:=OpenBLAS}
+: ${BUILD_DOC:=ON}
+: ${BUILD_SHARED_LIBS:=OFF}
+: ${BUILD_TOOLS:=ON}
+: ${RELEASE_TYPE:=Release}
+: ${ENABLE_PYGBE:=ON}
+: ${ENABLE_BEM:=ON}
+: ${ENABLE_GEOFLOW:=ON}
+: ${ENABLE_FETK:=ON}
+: ${FETK_VERSION:="1.8.1"}
+: ${ENABLE_iAPBS:=ON}
+: ${ENABLE_OPENMP:=OFF}
+: ${ENABLE_PBAM:=ON}
+: ${ENABLE_PBSAM:=ON}
+: ${ENABLE_PYTHON:=OFF}
+: ${ENABLE_TESTS:=ON}
+: ${GET_NanoShaper:=ON}
+: ${PYTHON_MIN_VERSION:="3.9"}
+: ${PYTHON_MAX_VERSION:="3.10"}
+
 echo "==================================== WHERE AM I ==================================== "
 pwd
 echo "==================================== VERSIONS: ==================================== "
 echo "==================================== PYTHON VERSION"
 python -c "import sys; print(sys.version)"
 echo "==================================== CMAKE VERSION"
 cmake --version
-echo "==================================== C Compiler VERSION"
-$CMAKE_C_COMPILER --version
-echo "==================================== C++ Compiler VERSION"
-$CMAKE_CXX_COMPILER --version
+#echo "==================================== C Compiler VERSION"
+#$CMAKE_C_COMPILER --version
+#echo "==================================== C++ Compiler VERSION"
+#$CMAKE_CXX_COMPILER --version
 echo "==================================== SWIG VERSION"
 swig -version
-echo "==================================== Install Python requirements ==================================== "
-python -m pip install -U pip
-python -m pip install -U pytest
-python -m pip install -U virtualenv
-python -m pip install -U numpy
-python -m pip install -r requirements.txt
+
+if [ "${BUILD_PYBIND}" -ne "0" ]; then
+    echo "==================================== Install Python requirements ==================================== "
+    python -m pip install -U pip
+    python -m pip install -U pytest
+    python -m pip install -U virtualenv
+    python -m pip install -U numpy
+    python -m pip install -r requirements.txt
+fi
+
 #  Just build APBS for now
 echo "==================================== PWD FOR TOP DIR ==================================== "
 pwd
-echo "==================================== Get External SubModules ==================================== "
-git submodule init
-git submodule update
-git submodule sync
-git ls-tree HEAD externals
-
+
 echo "==================================== CLEAN =============================================== "
 rm -rf $BUILD_DIR                                         || exit 1
 rm -rf $INSTALL_DIR                                       || exit 1
@@ -64,58 +96,59 @@ echo "==================================== SETUP ENV ===========================
 export LD_LIBRARY_PATH=$HOME/apbs/lib:${LD_LIBRARY_PATH}
 export PATH=$HOME/apbs/bin:${PATH}
 
-export TEST_APBS=1
-export PACKAGE_APBS=1
-
-#  Build pybind11
-export BUILD_PYBIND=0
 if [ "${BUILD_PYBIND}" -ne "0" ]; then
-  echo "==================================== PYBIND =============================================== "
-  pushd $(pwd)/externals/pybind11
-  [ -d build ] || mkdir -p build
-  [ -d install ] || mkdir -p install
-  pushd build
-  cmake                              \
+    echo "==================================== PYBIND =============================================== "
+    pushd $(pwd)/externals/pybind11
+    [ -d build ] || mkdir -p build
+    [ -d install ] || mkdir -p install
+    pushd build
+    cmake                              \
         -DDOWNLOAD_CATCH=ON          \
         -DPYBIND11_TEST=OFF          \
         -DCMAKE_INSTALL_PREFIX=$(python3 -c "import os,sys; print(os.path.realpath(sys.argv[1]))" ../install) \
         ..
-  make -j install
-  popd
-  export pybind11_DIR=$(python3 -c "import os,sys; print(os.path.realpath(sys.argv[1]))" ./install)
-  echo "pybind11_DIR=${pybind11_DIR}"
-  popd
+    make -j install
+    popd
+    export pybind11_DIR=$(python3 -c "import os,sys; print(os.path.realpath(sys.argv[1]))" ./install)
+    echo "pybind11_DIR=${pybind11_DIR}"
+    popd
 fi
-
+ 
 echo "==================================== CONFIG =============================================== "
 cd $BUILD_DIR                                             || exit 1
 #cmake                                                     \
-cmake -S .. -B $BUILD_DIR --trace-source=../CMakeLists.txt --trace-expand \
-      -DCMAKE_INSTALL_INCLUDEDIR="include"                \
-      -DBUILD_DOC=ON                                      \
-      -DBUILD_SHARED_LIBS=ON                              \
-      -DBUILD_TOOLS=ON                                    \
+cmake -S .. -B $BUILD_DIR                                 \
+      -DBLA_VENDOR=${BLA_VENDOR}                          \
+      -DBUILD_DOC=${BUILD_DOC}                            \
+      -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}            \
+      -DBUILD_TOOLS=${BUILD_TOOLS}                        \
       -DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} ${COVERAGE}"      \
       -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} ${COVERAGE}"  \
-      -DCMAKE_BUILD_TYPE=$RELEASE_TYPE                    \
+      -DCMAKE_BUILD_TYPE=${RELEASE_TYPE}                  \
+      -DCMAKE_INSTALL_INCLUDEDIR="include"                \
       -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR                 \
-      -DENABLE_PYGBE=ON                                   \
-      -DENABLE_BEM=ON                                     \
-      -DENABLE_GEOFLOW=ON                                 \
-      -DENABLE_FETK=OFF                                   \
-      -DENABLE_OPENMP=ON                                  \
-      -DENABLE_PBAM=ON                                    \
-      -DENABLE_PBSAM=ON                                   \
-      -DENABLE_PYTHON=$BUILD_PYBIND                       \
-      -DENABLE_TESTS=ON                                   \
-      -DENABLE_TINKER=OFF                                 \
+      -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH}            \
+      -DENABLE_PYGBE=${ENABLE_PYGBE}                      \
+      -DENABLE_BEM=${ENABLE_BEM}                          \
+      -DENABLE_GEOFLOW=${ENABLE_GEOFLOW}                  \
+      -DENABLE_FETK=${ENABLE_FETK}                        \
+      -DENABLE_iAPBS=${ENABLE_iAPBS}                      \
+      -DENABLE_OPENMP=${ENABLE_OPENMP}                    \
+      -DENABLE_PBAM=${ENABLE_PBAM}                        \
+      -DENABLE_PBSAM=${ENABLE_PBSAM}                      \
+      -DENABLE_PYTHON=${ENABLE_PYBIND}                    \
+      -DENABLE_TESTS=${ENABLE_TESTS}                      \
+      -DFETK_VERSION="${FETK_VERSION}"                    \
+      -DPYTHON_MIN_VERSION="${PYTHON_MIN_VERSION}"        \
+      -DPYTHON_MAX_VERSION="${PYTHON_MAX_VERSION}"        \
       ..                                                  || exit 1
-
+ 
 echo "==================================== BUILD =============================================== "
-VERBOSE=1 make -j 1                                       || exit 1
-VERBOSE=1 make -j 1 install                               #|| exit 1
+VERBOSE=1 make -j                                       || exit 1
+VERBOSE=1 make -j install                               #|| exit 1
 export PATH="$INSTALL_DIR/bin:$PATH"
 
+
 if [ "${TEST_APBS}" -ne "0" ]; then
     # Run a single test if it fails using the following:
     # echo "==================================== VERBOSE TEST ======================================= "
@@ -124,6 +157,7 @@ if [ "${TEST_APBS}" -ne "0" ]; then
     ctest -C Release --output-on-failure                      #|| exit 1
 fi
 
+
 if [ "${PACKAGE_APBS}" -ne "0" ]; then
     echo "==================================== PACKAGE ============================================ "
     cpack -C Release -G ZIP                                   || exit 1

diff --git a/.extract_section.sh b/.extract_section.sh
@@ -0,0 +1,54 @@
+#! /bin/bash
+
+while getopts f:v: flag
+do
+    case "${flag}" in
+        f) filename=${OPTARG};;
+        v) version=${OPTARG};;
+    esac
+done
+
+if [ -z "$filename" ]; then
+    echo "Please specify a filename using '-f'"
+    exit 1
+fi
+
+if [ ! -f $filename ]; then
+
+    echo "File does not exist: ${filename}"
+    exit 1
+
+fi
+
+if [ -z "$version" ]; then
+    echo "Please specify a version using '-v'"
+    exit 1
+fi
+
+#echo "Analyzing file $filename"
+header="APBS[[:space:]]${version}"
+#echo "Section title: <${header}>"
+
+foundTitle=false
+foundFirstHyphens=false
+while read line; do
+    if [ "$foundTitle" == false ]; then
+        if [[ "$line" =~ ^${header} ]]; then
+            foundTitle=true
+        fi
+    else
+        if [[ $line =~ ^-+ ]]; then
+            if [ "$foundFirstHyphens" == false ]; then
+                foundFirstHyphens=true
+            else
+                break
+            fi
+        else
+            echo "$line"
+        fi
+    fi
+done <$filename
+
+if [ "$foundTitle" == false ]; then
+    echo "[No changes were documented]"
+fi