File: run_tests_travis.sh

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#!/usr/bin/env bash

# test script for pysam.
# The script performs the following tasks:
# 1. Setup a conda environment and install dependencies via conda
# 2. Build pysam via the conda recipe
# 3. Build pysam via setup.py from repository
# 4. Run tests on the setup.py version
# 5. Additional build tests
# 5.1 pip install with cython
# 5.2 pip install without cython
# 5.3 pip install without cython and without configure options

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 pytest psutil pip

# activate testenv environment
source ~/miniconda3/bin/activate testenv

conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

# pin versions, so that tests do not fail when pysam/htslib out of step
# add htslib dependencies
conda install -y "samtools=1.7" "bcftools=1.6" "htslib=1.7" xz curl bzip2

# 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 --disable-lzma"

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 via setup.py
echo "installing via setup.py from repository"
python setup.py install

# create auxilliary data
echo
echo 'building test data'
echo
make -C tests/pysam_data
make -C tests/cbcf_data

# echo any limits that are in place
ulimit -a

# run tests
pytest

if [ $? != 0 ]; then
    exit 1
fi

# build source tar-ball. Make sure to run 'build' target so that .pyx
# files are cythonized.
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
    echo "ERROR: found config.h in tar-ball"
    tar -tvzf dist/pysam-*.tar.gz | grep "config.h%"
    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