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#!/bin/bash
set -e
pkg=snakemake
ROOT=$(pwd)
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
# Double quote below to expand the temporary directory variable now versus
# later is on purpose.
# shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
# copy the test tree so we're allowed to write to it
cd "${AUTOPKGTEST_TMP}"
cp -r ${ROOT}/tests .
export HOME="${AUTOPKGTEST_TMP}"
# workaround for #928826
. /etc/profile.d/modules.sh
#See debian/rules for why these are excluded
python3 -m pytest -v tests/test*.py -k 'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_modules_meta_wrapper and not test_tes and not test_deploy_script and not test_deploy_hashing and not test_peppy and not test_modules_peppy and not test_report_display_code and not test_wrapper_local_git_prefix and not test_github_issue1396 and not test_az_batch_executor and not test_modules_prefix and not test_env_modules and not test_github_issue1062 and not test_ancient and not test_symlink_time_handling and not test_github_issue1460 and not test_rule_inheritance_globals and not test_prebuilt_conda_script and not test_pipes_fail and not test_pipes and not test_multicomp_group_jobs and not test_group_job_resources_with_pipe'
#sometimes hangs, so use timeout and retry
python3 -m pytest -o faulthandler_timeout=60 -v tests/test*.py -k 'test_pipes_fail or test_pipes or test_multicomp_group_jobs or test_group_job_resources_with_pipe' || python3 -m pytest -o faulthandler_timeout=60 -v tests/test*.py -k 'test_pipes_fail or test_pipes or test_multicomp_group_jobs or test_group_job_resources_with_pipe' || python3 -m pytest -o faulthandler_timeout=60 -v tests/test*.py -k 'test_pipes_fail or test_pipes or test_multicomp_group_jobs or test_group_job_resources_with_pipe'
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