/
run_tests.sh
executable file
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run_tests.sh
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#!/bin/bash
# run_tests.sh -- created 2016-04-28, Renato Alves
source bash_colors.sh
export TOP_PID=$$
# If a command in a pipe fails, the whole command fails
set -o pipefail
REAL=true
PLATFORM='unknown'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
PLATFORM='Linux'
elif [[ "$unamestr" == 'Darwin' ]]; then
PLATFORM='Darwin'
fi
function run {
clr_bold " $@"
if [ $REAL == true ]; then
eval $@ || (clr_red "ERRORS FOUND!" && exit 1)
fi
}
usage() {
echo >&2 ""
echo >&2 "This script runs the test suite provided with ete3."
echo >&2 "Without any optional parameters it defaults to running the api tests"
echo >&2 "on a Python 3.5 environment."
echo >&2 ""
echo >&2 "Usage:"
echo >&2 " $0 [option] [-v version] [testset]"
echo >&2 ""
echo >&2 "Optional parameters:"
echo >&2 " -h|--help = help: shows the current information"
echo >&2 " --setup-only = setup-only: configures and updates the testing environment but skips tests"
echo >&2 " --test-only = test-only: skips configuration of environment and runs tests"
echo >&2 " -l = enable logging to tests.log"
echo >&2 " -s = show the content of tests.log at the end of execution (implies -l)"
echo >&2 " -x = install ete3 external apps in the test environment"
echo >&2 " -v = python version to use for running tests. (default: 3.5)"
echo >&2 " --qt4 = qt4 is used for running tests. (default: qt5)"
echo >&2 " testset = set of tests to run. (default: api) (for full testsuite use all)"
echo >&2 ""
}
valid_version() {
if [ -z "$1" ]; then
echo "$2" # No version was specified
else
if ! [[ $1 =~ ^[2-3](\.[0-9]|\.[1-9][0-9]){0,2}$ ]]; then
echo >&2 -e "\nERROR: Python version should be in one of the following formats: 3, 3.5, 3.5.12 not $1"
usage
kill -s TERM $TOP_PID
else
echo "$1"
fi
fi
}
handle_error() {
if [ "$1" != "0" ]; then
echo >&2 -e "\n$2"
echo >&2 "$3"
# NOTE Not sure why this isn't working anymore.
# It should send a non-zero exit code but it always reports 0
# which is super bad because it silences errors in the testsuite
#kill -s TERM $TOP_PID
# We workaround using exit and the exitcode seen by handle_error
exit "$1"
fi
}
optional() {
if [ "x$1" == "x" ]; then
echo "$2"
else
echo "$1"
fi
}
setup_miniconda3() {
if ! [ -f "${CONDA}/bin/conda" ]; then
clr_green ">>> Downloading miniconda for $PLATFORM... "
echo "${CONDA}/bin/conda"
if [[ $PLATFORM == 'Linux' ]]; then
run "wget -nv https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to download miniconda installation script" "$wget_output"
clr_green "DONE"
elif [[ $PLATFORM == 'Darwin' ]]; then
run "wget -nv https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to download miniconda installation script" "$wget_output"
clr_green "DONE"
else
handle_error "1" "OS not supported"
fi
clr_green ">>> Installing miniconda... "
run "bash miniconda.sh -b -p "${CONDA}" 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to install miniconda" "$install_output"
clr_green "DONE"
clr_green ">>> Updating miniconda packages and package information... "
run "${CONDA}/bin/conda update -q -y conda 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to update conda packages" "$conda_update_output"
clr_green "DONE"
clr_green ">>> Cleaning up miniconda installation files... "
run "rm -f miniconda.sh 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to remove miniconda.sh" "$clean_output"
clr_green "DONE"
fi
clr_green ">>> Collecting information about conda... "
run "${CONDA}/bin/conda info -a 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to collect information about conda" "$info_output"
clr_green "DONE"
}
setup_miniconda2() {
if ! [ -f "${CONDA}/bin/conda" ]; then
clr_green ">>> Downloading miniconda for $PLATFORM... "
echo "${CONDA}/bin/conda"
if [[ $PLATFORM == 'Linux' ]]; then
run "wget -nv https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to download miniconda installation script" "$wget_output"
clr_green "DONE"
elif [[ $PLATFORM == 'Darwin' ]]; then
run "wget -nv https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh -O miniconda.sh 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to download miniconda installation script" "$wget_output"
clr_green "DONE"
else
handle_error "1" "OS not supported"
fi
clr_green ">>> Installing miniconda... "
run "bash miniconda.sh -b -p "${CONDA}" 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to install miniconda" "$install_output"
clr_green "DONE"
clr_green ">>> Updating miniconda packages and package information... "
run "${CONDA}/bin/conda update -q -y conda 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to update conda packages" "$conda_update_output"
clr_green "DONE"
clr_green ">>> Cleaning up miniconda installation files... "
run "rm -f miniconda.sh 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to remove miniconda.sh" "$clean_output"
clr_green "DONE"
fi
clr_green ">>> Collecting information about conda... "
run "${CONDA}/bin/conda info -a 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to collect information about conda" "$info_output"
clr_green "DONE"
}
create_env_qt4() {
# env_output=$("${CONDA}/bin/conda" env list | grep "test_${VERSION}")
# if [ $? == 0 ]; then
# # Env already created. Nothing to do
# echo >&2 "### Using existing conda environment test_${VERSION}."
# return 0
# fi
clr_green ">>> Creating test environment for version ${VERSION}... "
run "${CONDA}/bin/conda env remove -y -n test_${VERSION} || true"
run "${CONDA}/bin/conda create -q -y -n test_${VERSION} python=${VERSION} pip=10 pyqt=4 qt=4 numpy=1.16.4 six lxml coverage scikit-bio biopython=1.74 scipy=1.2.1"
clr_green "DONE"
}
create_env() {
# env_output=$("${CONDA}/bin/conda" env list | grep "test_${VERSION}")
# if [ $? == 0 ]; then
# # Env already created. Nothing to do
# echo >&2 "### Using existing conda environment test_${VERSION}."
# return 0
# fi
clr_green ">>> Creating test environment for version ${VERSION}... "
run "${CONDA}/bin/conda env remove -y -n test_${VERSION} || true"
run "${CONDA}/bin/conda create -q -y -n test_${VERSION} python=${VERSION} pyqt numpy six lxml coverage scikit-bio biopython scipy"
clr_green "DONE"
# clr_green ">>> Updating conda packages in environment test_${VERSION}... "
# run "source ${CONDA}/bin/activate test_${VERSION} 2>&1 && ${CONDA}/bin/conda update -y --all 2>&1 | tee -a ${LOG}"
# handle_error "$?" "ERROR: Failed to update packages in the conda environment" "$update_conda_output"
# clr_green "DONE"
}
create_env_27() {
clr_green ">>> Creating test environment for version ${VERSION}... "
run "${CONDA}/bin/conda env remove -y -n test_${VERSION} || true"
run "${CONDA}/bin/conda create -q -y -n test_${VERSION} python=${VERSION} pyqt qt numpy six lxml coverage scikit-bio biopython scipy -c conda-forge"
clr_green "DONE"
}
install_external_apps() {
if [ "$EXTERNAL_APPS" == "1" ]; then
clear_green ">>> Installing external packages in environment test_${VERSION}... "
run "${CONDA}/bin/activate test_${VERSION} 2>&1 && ${CONDA}/bin/conda install -c etetoolkit ete3_external_apps -y 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to install ete3 external apps in the conda environment" "$external_apps_output"
clear_green "DONE"
fi
}
install_ete() {
clr_green ">>> Installing latest ete in test environment... "
run "source ${CONDA}/bin/activate test_${VERSION} 2>&1 && python setup.py install --donottrackinstall 2>&1 | tee -a ${LOG}"
handle_error "$?" "ERROR: Failed to install/update ete to the latest commit on test_${VERSION}" "$update_output"
clr_green "DONE"
}
showlog() {
if [ "$SHOWLOG" == "1" ]; then
echo -e ">>> Showing contents of test log:\n"
[ -f "${LOG}" ] && cat "${LOG}"
fi
}
run_tests() {
#clr_green ">>> Obtaining deployed python version... "
#run "${CONDA}/bin/activate test_${VERSION} &>/dev/null && python --version 2>&1"
#handle_error "$?" "ERROR: couldn't obtain python version" "$py_version_output"
#echo "DONE"
clr_green ">>> Obtaining ete3 version... "
run "source ${CONDA}/bin/activate test_${VERSION} &>/dev/null && ete3 version 2>&1"
handle_error "$?" "ERROR: couldn't obtain ete3 version" "$ete_version_output"
echo "DONE"
clr_green ">>> Running tests on ete ${ete_version_output} using ${py_version_output}... "
run "source ${CONDA}/bin/activate test_${VERSION} 2>&1 && coverage run -m ete3.test.test_${TESTSET}"
handle_error "$?" "ERROR: One or more tests failed on test_${VERSION}" "$tests_output"
echo "DONE"
echo "### All tests passed successfully"
}
# Location of current script
FILEDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
EXTERNAL_APPS=0
SETUP=1
TEST=1
QT4=0
# Logfile
NULL_LOG="/dev/null"
LOG="${NULL_LOG}"
DEFAULT_LOG="${FILEDIR}/tests.log"
SHOWLOG=0
# Parse args using getopt (instead of getopts) to allow arguments before options
if [[ $PLATFORM == 'Linux' ]]; then
ARGS="$(getopt -o v:lshx -l help,test-only,setup-only,qt4 -n "$0" -- "$@" 2>/dev/null)"
elif [[ $PLATFORM == 'Darwin' ]]; then
ARGS="$(/usr/local/opt/gnu-getopt/bin/getopt -o v:lshx -l help,test-only,setup-only,qt4 -n "$0" -- "$@" 2>/dev/null)"
else
handle_error "1" "OS not supported"
fi
if [ "$?" != "0" ]; then
usage
handle_error "1" "ERROR: Check the arguments passed. At least one was not valid."
fi
# reorganize arguments as returned by getopt
eval set -- "$ARGS"
echo OPTIONS:$ARGS
while true; do
case "$1" in
# Shift before to throw away option
# Shift after if option has a required positional argument
-l)
shift
LOG="${DEFAULT_LOG}"
;;
-s)
shift
SHOWLOG=1
LOG="${DEFAULT_LOG}"
;;
-v)
shift
# Validate provided python version to use for tests
VERSION="$1"
shift
;;
-x)
shift
EXTERNAL_APPS=1
;;
--setup-only) # setup/install only
shift
TEST=0
;;
--test-only) # test only
shift
SETUP=0
;;
--qt4) # qt4
shift
QT4=1
;;
-h|--help)
usage
exit
;;
--)
shift
break
;;
esac
done
VERSION="$(valid_version "${VERSION}" 3.5)"
TESTSET="$(optional "$1" api)"
SLEEP=2 # Time to wait for xvfb to start and be functional
[ ! -f "ete3/test/test_${TESTSET}.py" ] && usage && handle_error "1" "ERROR: Invalid testset selected ${TESTSET}"
if [ "${LOG}" == "${NULL_LOG}" ]; then
echo "### Running ${TESTSET} tests with Python ${VERSION}"
else
echo "### Running ${TESTSET} tests with Python ${VERSION} and logging to ${LOG}"
fi
# Empty logfile
echo -n > "${LOG}"
# At any of these signals conditionally show the contents of the logfile
trap 'exitcode=$? ; showlog ; exit $exitcode' EXIT HUP INT QUIT TERM
if [ "$VERSION" == "2.7" ]; then
CONDA="${FILEDIR}/test_tmp/miniconda2"
else
CONDA="${FILEDIR}/test_tmp/miniconda3"
fi
if [ "${SETUP}" == "1" ]; then
if [ "$QT4" == "1" ]; then
setup_miniconda3
create_env_qt4
elif [ "$VERSION" == "2.7" ]; then
setup_miniconda2
create_env_27
else
setup_miniconda3
create_env
fi
install_external_apps
install_ete
fi
if [ "${TEST}" == "1" ]; then
run_tests
fi
showlog