bamboo_build.sh

#!/bin/bash
type module >& /dev/null || . /mnt/software/Modules/current/init/bash
module load python/3
module load htslib  # since pysam was built against this
set -ex
nproc

export PATH=$PWD/build/bin:$PATH
export PYTHONUSERBASE=$PWD/build

PIP="pip --cache-dir=${bamboo_build_working_directory:-$PWD}/.pip"
if [[ -z ${bamboo_repository_branch_name+x} ]]; then
  WHEELHOUSE=/mnt/software/p/python/wheelhouse/develop
elif [[ ${bamboo_repository_branch_name} == develop ]]; then
  WHEELHOUSE=/mnt/software/p/python/wheelhouse/develop
elif [[ ${bamboo_repository_branch_name} == master ]]; then
  WHEELHOUSE=/mnt/software/p/python/wheelhouse/master
else
  WHEELHOUSE=/mnt/software/p/python/wheelhouse/develop
fi

rm -rf build
mkdir -p build/bin build/lib build/include build/share
$PIP install urllib3==1.21.1
$PIP install requests==2.29.0
$PIP install --user --no-index --find-link $WHEELHOUSE --no-compile -e '.[test]'

pytest --trace-config --collect-only

set +e
make pylint # way too many errors right now
set -e
make test

bash bamboo_wheel.sh