Added scripts for source packaging.

devtools/packaging/manifests/source/manifest.txt

 cmake_modules
 CMakeLists.txt
 docs-source
+docs
 examples
 libraries
 olla

devtools/packaging/scripts/source/build.sh

+#!/bin/bash
+
+# Build script for Linux distribution, for use in automated packaging.
+# Note that this must be run from outside the checked-out openmm/ directory.
+
+# Set relative workspace path.
+export WORKSPACE=`pwd`
+
+# Add conda binaries to path.
+PATH=$WORKSPACE/miniconda/bin:$PATH
+
+INSTALL=`pwd`/install
+if [ -e $INSTALL ]; then
+    rm -rf $INSTALL
+fi
+
+CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$INSTALL"
+
+# setting the rpath so that libOpenMMPME.so finds the right libfftw3
+#CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
+CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_AMOEBA_CUDA_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_CPU_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_CUDA_COMPILER_PLUGIN=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_CUDA_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_DRUDE_CUDA_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_DRUDE_OPENCL_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_OPENCL_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_RPMD_CUDA_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_RPMD_OPENCL_LIB=OFF"
+
+# Set location for FFTW3
+PREFIX="$WORKSPACE/miniconda"
+CMAKE_FLAGS+=" -DFFTW_INCLUDES=$PREFIX/include"
+CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.so"
+CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.so"
+
+# Build in subdirectory.
+if [ -e build ]; then
+    rm -rf build
+fi
+mkdir build
+cd build
+cmake ../openmm $CMAKE_FLAGS
+make -j4 all DoxygenApiDocs sphinxpdf
+
+# Install.
+make install

devtools/packaging/scripts/source/package.sh

+#!/bin/bash
+
+# Packaging script for Linux distribution, for use in automated packaging.
+# Note that this must be run from outside the checked-out openmm/ directory.
+
+# CONFIGURE HERE
+export PACKAGE_DIR="packaging" # directory to stuff packaged source distribution
+export VERSION=$(sed -nr "s/OPENMM_VERSION:STRING=(.*)/\1/p" build/CMakeCache.txt)
+export PACKAGE_SUBDIR="OpenMM-${VERSION}-Source" # directory where distribution will be unpacked
+export DISTRO_PREFIX="OpenMM-${VERSION}-Source" # prefix for source distribution (e.g. ${DISTRIBUTION_NAME}.zip)
+
+# Perform all work in a work directory.
+cd work
+
+# Clean up.
+rm -rf $PACKAGE_DIR
+
+# Make a directory to contain packaged source distribution
+mkdir $PACKAGE_DIR
+mkdir $PACKAGE_DIR/$PACKAGE_SUBDIR
+for filename in $( cat openmm/devtools/packaging/manifests/source/manifest.txt ); do
+   CMD="cp -r install/$filename $PACKAGE_DIR/$PACKAGE_SUBDIR"
+   echo $CMD
+   `$CMD`
+done
+
+# Add the install.sh script
+#CMD="cp -r openmm/devtools/packaging/install.sh $PACKAGE_DIR/$PACKAGE_SUBDIR"
+#echo $CMD
+#`$CMD`
+
+# Make Python source distribution.
+echo "Building Python source distribution..."
+pushd .
+cd build
+make PythonSdist
+cd python/dist
+tar zxf OpenMM-${VERSION}.tar.gz
+mv OpenMM-${VERSION} python
+popd
+cp -r build/python/dist/python $PACKAGE_DIR/$PACKAGE_SUBDIR
+
+# Create archives.
+cd $PACKAGE_DIR
+mkdir compressed
+tar zcf compressed/${DISTRO_PREFIX}.tgz $PACKAGE_SUBDIR
+zip -r compressed/${DISTRO_PREFIX}.zip $PACKAGE_SUBDIR
+cd ..

devtools/packaging/scripts/source/prepare.sh

+#!/bin/tcsh
+
+# Prepare for build by ensuring necessary prerequisites are locally installed.
+
+# Set relative workspace path.
+export WORKSPACE=`pwd`
+
+# Install miniconda
+export VERSION="Latest"
+export PLATFORM="Linux"
+export ARCH="x86_64"
+export MINICONDA="Miniconda-$VERSION-$PLATFORM-$ARCH.sh"
+if [ -f miniconda ];
+then
+   echo "miniconda already exists"
+else
+   echo "Downloading miniconda..."
+   rm -rf Miniconda-*
+   wget --quiet http://repo.continuum.io/miniconda/${MINICONDA}
+   bash ${MINICONDA} -b -p miniconda
+   PIP_ARGS="-U"
+fi
+
+# Add to path.
+export PATH=$WORKSPACE/miniconda/bin:$PATH
+
+# Ensure configuration is up to date.
+conda config --add channels http://conda.binstar.org/omnia
+conda install --yes --quiet swig fftw3f pip
+pip install sphinxcontrib-bibtex