testbed/Project-MONAI__MONAI/runtests.sh

#! /bin/bash
set -e
# script for running all tests

# output formatting
separator=""
blue=""
green=""
red=""
noColor=""

if [[ -t 1 ]] # stdout is a terminal
then
    separator=$'--------------------------------------------------------------------------------\n'
    blue="$(tput bold; tput setaf 4)"
    green="$(tput bold; tput setaf 2)"
    red="$(tput bold; tput setaf 1)"
    noColor="$(tput sgr0)"
fi

# configuration values
doCoverage=false
doQuickTests=false
doNetTests=false
doDryRun=false
doZooTests=false

doUnitTests=true

doBlackFormat=false
doBlackFix=false
doIsortFormat=false
doIsortFix=false
doFlake8Format=false
doPytypeFormat=false
doMypyFormat=false
doCleanup=false

NUM_PARALLEL=1

function print_usage {
    echo "runtests.sh [--codeformat] [--autofix] [--black] [--isort] [--flake8] [--pytype] [--mypy]"
    echo "            [--nounittests] [--coverage] [--quick] [--net] [--dryrun] [-j number] [--clean] [--help] [--version]"
    echo ""
    echo "MONAI unit testing utilities."
    echo ""
    echo "Examples:"
    echo "./runtests.sh --codeformat --coverage     # run full tests (${green}recommended before making pull requests${noColor})."
    echo "./runtests.sh --codeformat --nounittests  # run coding style and static type checking."
    echo "./runtests.sh --quick                     # run minimal unit tests, for quick verification during code developments."
    echo "./runtests.sh --autofix --nounittests     # run automatic code formatting using \"isort\" and \"black\"."
    echo "./runtests.sh --clean                     # clean up temporary files and run \"python setup.py develop --uninstall\"."
    echo ""
    echo "Code style check options:"
    echo "    --black           : perform \"black\" code format checks"
    echo "    --autofix         : format code using \"isort\" and \"black\""
    echo "    --isort           : perform \"isort\" import sort checks"
    echo "    --flake8          : perform \"flake8\" code format checks"
    echo ""
    echo "Python type check options:"
    echo "    --pytype          : perform \"pytype\" static type checks"
    echo "    --mypy            : perform \"mypy\" static type checks"
    echo "    -j, --jobs        : number of parallel jobs to run \"pytype\" (default $NUM_PARALLEL)"
    echo ""
    echo "MONAI unit testing options:"
    echo "    --nounittests     : skip doing unit testing (i.e. only format lint testers)"
    echo "    --coverage        : peforms coverage analysis of code for tests run"
    echo "    -q, --quick       : disable long running tests"
    echo "    --net             : perform training/inference/eval integration testing"
    echo ""
    echo "Misc. options:"
    echo "    --dryrun          : display the commands to the screen without running"
    echo "    -f, --codeformat  : shorthand to run all code style and static analysis tests"
    echo "    -c, --clean       : clean temporary files from tests and exit"
    echo "    -h, --help        : show this help message and exit"
    echo "    -v, --version     : show MONAI and system version information and exit"
    echo ""
    echo "${separator}For bug reports, questions, and discussions, please file an issue at:"
    echo "    https://github.com/Project-MONAI/MONAI/issues/new/choose"
    echo ""
    exit 1
}

function print_version {
    ${cmdPrefix}python -c 'import monai; monai.config.print_config()'
}

function install_deps {
    echo "Pip installing MONAI development dependencies and compile MONAI cpp extensions..."
    ${cmdPrefix}python -m pip install -r requirements-dev.txt
}

function compile_cpp {
    echo "Compiling and installing MONAI cpp extensions..."
    ${cmdPrefix}python setup.py -v develop --uninstall
    if [[ "$OSTYPE" == "darwin"* ]];
    then  # clang for mac os
        CC=clang CXX=clang++ ${cmdPrefix}python setup.py -v develop
    else
        ${cmdPrefix}python setup.py -v develop
    fi
}

function clean_py {
    # uninstall the development package
    echo "Uninstalling MONAI development files..."
    ${cmdPrefix}python setup.py -v develop --uninstall

    # remove temporary files (in the directory of this script)
    TO_CLEAN="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
    echo "Removing temporary files in ${TO_CLEAN}"

    find ${TO_CLEAN} -type f -name "*.py[co]" -delete
    find ${TO_CLEAN} -type f -name ".coverage" -delete
    find ${TO_CLEAN} -type d -name "__pycache__" -delete

    find ${TO_CLEAN} -depth -type d -name ".eggs" -exec rm -r "{}" +
    find ${TO_CLEAN} -depth -type d -name "monai.egg-info" -exec rm -r "{}" +
    find ${TO_CLEAN} -depth -type d -name "build" -exec rm -r "{}" +
    find ${TO_CLEAN} -depth -type d -name "dist" -exec rm -r "{}" +
    find ${TO_CLEAN} -depth -type d -name ".mypy_cache" -exec rm -r "{}" +
    find ${TO_CLEAN} -depth -type d -name ".pytype" -exec rm -r "{}" +
    find ${TO_CLEAN} -depth -type d -name ".coverage" -exec rm -r "{}" +
}

function torch_validate {
    ${cmdPrefix}python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
}

function print_error_msg() {
    echo "${red}Error: $1.${noColor}"
    echo ""
}

function print_style_fail_msg() {
    echo "${red}Check failed!${noColor}"
    echo "Please run auto style fixes: ${green}./runtests.sh --autofix --nounittests${noColor}"
}

if [ -z "$1" ]
then
    print_error_msg "Too few arguments to $0"
    print_usage
fi

# parse arguments
while [[ $# -gt 0 ]]
do
    key="$1"
    case $key in
        --coverage)
            doCoverage=true
        ;;
        -q|--quick)
            doQuickTests=true
        ;;
        --net)
            doNetTests=true
        ;;
        --dryrun)
            doDryRun=true
        ;;
        --nou*)  # allow --nounittest | --nounittests | --nounittesting  etc.
            doUnitTests=false
        ;;
        -f|--codeformat)
            doBlackFormat=true
            doIsortFormat=true
            doFlake8Format=true
            doPytypeFormat=true
            doMypyFormat=true
        ;;
        --black)
            doBlackFormat=true
        ;;
        --autofix)
            doIsortFix=true
            doBlackFix=true
            doIsortFormat=true
            doBlackFormat=true
        ;;
        --isort)
            doIsortFormat=true
        ;;
        --flake8)
            doFlake8Format=true
        ;;
        --pytype)
            doPytypeFormat=true
        ;;
        --mypy)
            doMypyFormat=true
        ;;
        -j|--jobs)
            NUM_PARALLEL=$2
            shift
        ;;
        -c|--clean)
            doCleanup=true
        ;;
        -h|--help)
            print_usage
        ;;
        -v|--version)
            print_version
            exit 1
        ;;
        *)
            print_error_msg "Incorrect commandline provided, invalid key: $key"
            print_usage
        ;;
    esac
    shift
done

# home directory
homedir="$( cd -P "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
cd "$homedir"

# python path
export PYTHONPATH="$homedir:$PYTHONPATH"
echo "$PYTHONPATH"

# by default do nothing
cmdPrefix=""

if [ $doDryRun = true ]
then
    echo "${separator}${blue}dryrun${noColor}"

    # commands are echoed instead of ran
    cmdPrefix="dryrun "
    function dryrun { echo "    " "$@"; }
fi

if [ $doCleanup = true ]
then
    echo "${separator}${blue}clean${noColor}"

    clean_py

    echo "${green}done!${noColor}"
    exit
fi

# try to compile MONAI cpp
compile_cpp

# unconditionally report on the state of monai
print_version


if [ $doIsortFormat = true ]
then
    set +e  # disable exit on failure so that diagnostics can be given on failure
    if [ $doIsortFix = true ]
    then
        echo "${separator}${blue}isort-fix${noColor}"
    else
        echo "${separator}${blue}isort${noColor}"
    fi

    # ensure that the necessary packages for code format testing are installed
    if [[ ! -f "$(which isort)" ]]
    then
        install_deps
    fi
    ${cmdPrefix}isort --version

    if [ $doIsortFix = true ]
    then
        ${cmdPrefix}isort "$(pwd)"
    else
        ${cmdPrefix}isort --check "$(pwd)"
    fi

    isort_status=$?
    if [ ${isort_status} -ne 0 ]
    then
        print_style_fail_msg
        exit ${isort_status}
    else
        echo "${green}passed!${noColor}"
    fi
    set -e # enable exit on failure
fi


if [ $doBlackFormat = true ]
then
    set +e  # disable exit on failure so that diagnostics can be given on failure
    if [ $doBlackFix = true ]
    then
        echo "${separator}${blue}black-fix${noColor}"
    else
        echo "${separator}${blue}black${noColor}"
    fi

    # ensure that the necessary packages for code format testing are installed
    if [[ ! -f "$(which black)" ]]
    then
        install_deps
    fi
    ${cmdPrefix}black --version

    if [ $doBlackFix = true ]
    then
        ${cmdPrefix}black "$(pwd)"
    else
        ${cmdPrefix}black --check "$(pwd)"
    fi

    black_status=$?
    if [ ${black_status} -ne 0 ]
    then
        print_style_fail_msg
        exit ${black_status}
    else
        echo "${green}passed!${noColor}"
    fi
    set -e # enable exit on failure
fi


if [ $doFlake8Format = true ]
then
    set +e  # disable exit on failure so that diagnostics can be given on failure
    echo "${separator}${blue}flake8${noColor}"

    # ensure that the necessary packages for code format testing are installed
    if [[ ! -f "$(which flake8)" ]]
    then
        install_deps
    fi
    ${cmdPrefix}flake8 --version

    ${cmdPrefix}flake8 "$(pwd)" --count --statistics

    flake8_status=$?
    if [ ${flake8_status} -ne 0 ]
    then
        print_style_fail_msg
        exit ${flake8_status}
    else
        echo "${green}passed!${noColor}"
    fi
    set -e # enable exit on failure
fi


if [ $doPytypeFormat = true ]
then
    set +e  # disable exit on failure so that diagnostics can be given on failure
    echo "${separator}${blue}pytype${noColor}"

    # ensure that the necessary packages for code format testing are installed
    if [[ ! -f "$(which pytype)" ]]
    then
        install_deps
    fi
    ${cmdPrefix}pytype --version

    ${cmdPrefix}pytype -j ${NUM_PARALLEL} --python-version="$(python -c "import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')")"

    pytype_status=$?
    if [ ${pytype_status} -ne 0 ]
    then
        echo "${red}failed!${noColor}"
        exit ${pytype_status}
    else
        echo "${green}passed!${noColor}"
    fi
    set -e # enable exit on failure
fi


if [ $doMypyFormat = true ]
then
    set +e  # disable exit on failure so that diagnostics can be given on failure
    echo "${separator}${blue}mypy${noColor}"

    # ensure that the necessary packages for code format testing are installed
    if [[ ! -f "$(which mypy)" ]]
    then
        install_deps
    fi
    ${cmdPrefix}mypy --version

    if [ $doDryRun = true ]
    then
        ${cmdPrefix}MYPYPATH="$(pwd)"/monai mypy "$(pwd)"
    else
        MYPYPATH="$(pwd)"/monai mypy "$(pwd)" # cmdPrefix does not work with MYPYPATH
    fi

    mypy_status=$?
    if [ ${mypy_status} -ne 0 ]
    then
        : # mypy output already follows format
        exit ${mypy_status}
    else
        : # mypy output already follows format
    fi
    set -e # enable exit on failure
fi


# testing command to run
cmd="python3"

# When running --quick, require doCoverage as well and set QUICKTEST environmental
# variable to disable slow unit tests from running.
if [ $doQuickTests = true ]
then
    echo "${separator}${blue}quick${noColor}"
    doCoverage=true
    export QUICKTEST=True
fi

# set command and clear previous coverage data
if [ $doCoverage = true ]
then
    echo "${separator}${blue}coverage${noColor}"
    cmd="coverage run -a --source ."
    ${cmdPrefix}coverage erase
fi

# # download test data if needed
# if [ ! -d testing_data ] && [ "$doDryRun" != 'true' ]
# then
# fi

# unit tests
if [ $doUnitTests = true ]
then
    echo "${separator}${blue}unittests${noColor}"
    torch_validate
    ${cmdPrefix}${cmd} -m unittest -v
fi

# network training/inference/eval tests
if [ $doNetTests = true ]
then
    echo "${separator}${blue}coverage${noColor}"
    for i in tests/integration_*.py
    do
        echo "$i"
        ${cmdPrefix}${cmd} "$i"
    done
fi

# run model zoo tests
if [ $doZooTests = true ]
then
    echo "${separator}${blue}zoo${noColor}"
    print_error_msg "--zoo option not yet implemented"
    exit 255
fi

# report on coverage
if [ $doCoverage = true ]
then
    echo "${separator}${blue}coverage${noColor}"
    ${cmdPrefix}coverage report --skip-covered -m
fi