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#!/usr/bin/env bash
pushd .
WORKDIR=`pwd`
#Install miniconda python
if [ $TRAVIS_OS_NAME == "osx" ]; then
wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O Miniconda3.sh
else
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O Miniconda3.sh --no-check-certificate # Default OS versions are old and have SSL / CERT issues
fi
bash Miniconda3.sh -b
# Create a new conda environment with the target python version
~/miniconda3/bin/conda install conda-build -y
~/miniconda3/bin/conda create -q -y --name testenv python=$CONDA_PY cython numpy nose psutil pip
# activate testenv environment
source ~/miniconda3/bin/activate testenv
conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda
conda install -y samtools bcftools htslib
# Need to make C compiler and linker use the anaconda includes and libraries:
export PREFIX=~/miniconda3/
export CFLAGS="-I${PREFIX}/include -L${PREFIX}/lib"
export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
samtools --version
htslib --version
bcftools --version
# Try building conda recipe first
~/miniconda3/bin/conda-build ci/conda-recipe/ --python=$CONDA_PY
# install code from the repository
python setup.py install
# find build/
# change into tests directory. Otherwise,
# 'import pysam' will import the repository,
# not the installed version. This causes
# problems in the compilation test.
cd tests
# create auxilliary data
echo
echo 'building test data'
echo
make -C pysam_data
make -C cbcf_data
# run nosetests
# -s: do not capture stdout, conflicts with pysam.dispatch
# -v: verbose output
nosetests -s -v
if [ $? != 0 ]; then
exit 1
fi
# build source tar-ball. Make sure to build so that .pyx files
# are cythonized.
cd ..
python setup.py build sdist
if [ $? != 0 ]; then
exit 1
fi
# check for presence of config.h files
echo "checking for presence of config.h files in tar-ball"
tar -tvzf dist/pysam-*.tar.gz | grep "config.h$"
if [ $? != 1 ]; then
exit 1
fi
# test pip installation from tar-ball with cython
echo "pip installing with cython"
pip install --verbose --no-deps --no-binary=:all: dist/pysam-*.tar.gz
if [ $? != 0 ]; then
exit 1
fi
# attempt pip installation without cython
echo "pip installing without cython"
~/miniconda3/bin/conda remove -y cython
~/miniconda3/bin/conda list
echo "python is" `which python`
pip install --verbose --no-deps --no-binary=:all: --force-reinstall --upgrade dist/pysam-*.tar.gz
if [ $? != 0 ]; then
exit 1
fi
# attempt pip installation without cython and without
# command line options
echo "pip installing without cython and no configure options"
export HTSLIB_CONFIGURE_OPTIONS=""
pip install --verbose --no-deps --no-binary=:all: --force-reinstall --upgrade dist/pysam-*.tar.gz
if [ $? != 0 ]; then
exit 1
fi
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