buildwheels.sh

#!/bin/bash
#
# Build manylinux1 wheels for pysam. Based on the example at
# <https://github.com/pypa/python-manylinux-demo>
#
# It is best to run this in a fresh clone of the repository!
#
# Run this within the repository root:
#   docker run --rm -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /io/buildwheels.sh
#
# The wheels will be put into the wheelhouse/ subdirectory.
#
# For interactive tests:
#   docker run -it -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /bin/bash

set -xeuo pipefail

# For convenience, if this script is called from outside of a docker container,
# it starts a container and runs itself inside of it.
if ! grep -q docker /proc/1/cgroup; then
  # We are not inside a container
  exec docker run --rm -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /io/$0
fi

yum install -y zlib-devel

# Python 2.6 is not supported
rm -r /opt/python/cp26*

# Python 3.3 builds fail with:
#  /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-CentOS-linux/4.8.2/ld: cannot find -lchtslib
rm -r /opt/python/cp33*

# Without libcurl support, htslib can open files from HTTP and FTP URLs.
# With libcurl support, it also supports HTTPS and S3 URLs, but libcurl needs a
# current version of OpenSSL, and we do not want to be responsible for
# updating the wheels as soon as there are any security issues. So disable
# libcurl for now.
# See also <https://github.com/pypa/manylinux/issues/74>.
#
export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"

PYBINS="/opt/python/*/bin"
for PYBIN in ${PYBINS}; do
    ${PYBIN}/pip install -r /io/requirements.txt
    ${PYBIN}/pip wheel /io/ -w wheelhouse/
done

# Bundle external shared libraries into the wheels
#
# The '-L .' option is a workaround. By default, auditwheel puts all external
# libraries (.so files) into a .libs directory and sets the RUNPATH to $ORIGIN/.libs.
# When HTSLIB_MODE is 'shared' (now the default), then all so libraries part of
# pysam require that RUNPATH is set to $ORIGIN (without the .libs). It seems
# auditwheel overwrites $ORIGIN with $ORIGIN/.libs. This workaround makes
# auditwheel set the RUNPATH to "$ORIGIN/." and it will work as desired.
#
for whl in wheelhouse/*.whl; do
    auditwheel repair -L . $whl -w /io/wheelhouse/
done

# Created files are owned by root, so fix permissions.
chown -R --reference=/io/setup.py /io/wheelhouse/

# TODO Install packages and test them
#for PYBIN in ${PYBINS}; do
#    ${PYBIN}/pip install pysam --no-index -f /io/wheelhouse
#    (cd $HOME; ${PYBIN}/nosetests ...)
#done