build_pipeline.sh

command=$1
if [ $# -eq 0 ] ; then 
    command=none
fi

if [[ ! -f src/alphaimpute2/tinyhouse/Pedigree.py ]] ; then
    echo Pedigree.py file not found. Check that the tinyhouse submodule is up to date
    exit 
fi

# Create python wheel.
rm -r build
rm -r dist
python setup.py bdist_wheel

if [ $command == "install" ] ; then
    pip uninstall AlphaImpute2 -y
    pip install dist/AlphaImpute2-0.0.3-py3-none-any.whl
fi

#Compile manual
 ( cd docs; make latexpdf )


target=AlphaImpute2
rm -rf $target
mkdir $target
cp dist/* $target
cp docs/build/latex/AlphaImpute2.pdf $target
cp -r example $target

cp MIT_License.txt $target


version=`git describe --tags --abbrev=0`
commit=`git rev-parse --short HEAD`
date=$(date '+%d-%m-%Y')

rm src/alphaimpute2/version.py
echo version = \"$version\" > src/alphaimpute2/Imputation/version.py
echo commit = \"$commit\" >> src/alphaimpute2/Imputation/version.py
echo date = \"$date\" >> src/alphaimpute2/Imputation/version.py



zip -r $target.zip $target