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runtests.sh
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runtests.sh
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#! /bin/bash
# Copyright 2020 MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# script for running all tests
set -e
# 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="$(tput sgr0)"
fi
# configuration values
doCoverage=false
doQuickTests=false
doNetTests=false
doDryRun=false
doZooTests=false
doUnitTests=true
doBlackFormat=false
doBlackFix=false
doIsortFormat=false
doIsortFix=false
doFlake8Format=false
doClangFormat=false
doPytypeFormat=false
doMypyFormat=false
doCleanup=false
NUM_PARALLEL=1
PY_EXE=${MONAI_PY_EXE:-$(which python)}
function print_usage {
echo "runtests.sh [--codeformat] [--autofix] [--black] [--isort] [--flake8] [--clangformat] [--pytype] [--mypy]"
echo " [--nounittests] [--coverage] [--quick] [--net] [--dryrun] [-j number] [--clean] [--help] [--version]"
echo ""
echo "MONAI unit testing utilities."
echo ""
echo "Examples:"
echo "./runtests.sh --codeformat --coverage # run full tests (${green}recommended before making pull requests${noColor})."
echo "./runtests.sh --codeformat --nounittests # run coding style and static type checking."
echo "./runtests.sh --quick # run minimal unit tests, for quick verification during code developments."
echo "./runtests.sh --autofix --nounittests # run automatic code formatting using \"isort\" and \"black\"."
echo "./runtests.sh --clean # clean up temporary files and run \"${PY_EXE} 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 " --clangformat : format csrc code using \"clang-format\""
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 ""
echo "To choose an alternative python executable, set the environmental variable, \"MONAI_PY_EXE\"."
exit 1
}
function check_import {
echo "python: ${PY_EXE}"
${cmdPrefix}${PY_EXE} -c "import monai"
}
function print_version {
${cmdPrefix}${PY_EXE} -c 'import monai; monai.config.print_config()'
}
function install_deps {
echo "Pip installing MONAI development dependencies and compile MONAI cpp extensions..."
${cmdPrefix}${PY_EXE} -m pip install -r requirements-dev.txt
}
function compile_cpp {
echo "Compiling and installing MONAI cpp extensions..."
# depends on setup.py behaviour for building
# currently setup.py uses environment variables: BUILD_MONAI and FORCE_CUDA
${cmdPrefix}${PY_EXE} setup.py develop --user --uninstall
if [[ "$OSTYPE" == "darwin"* ]];
then # clang for mac os
CC=clang CXX=clang++ ${cmdPrefix}${PY_EXE} setup.py develop --user
else
${cmdPrefix}${PY_EXE} setup.py develop --user
fi
}
function clang_format {
echo "Running clang-format..."
${cmdPrefix}${PY_EXE} -m tests.clang_format_utils
clang_format_tool='.clang-format-bin/clang-format'
# Verify .
if ! type -p "$clang_format_tool" >/dev/null; then
echo "'clang-format' not found, skipping the formatting."
exit 1
fi
find monai/csrc -type f | while read i; do $clang_format_tool -style=file -i $i; done
}
function clean_py {
# uninstall the development package
echo "Uninstalling MONAI development files..."
${cmdPrefix}${PY_EXE} setup.py develop --user --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}/monai -type f -name "*.py[co]" -delete
find ${TO_CLEAN}/monai -type f -name "*.so" -delete
find ${TO_CLEAN}/monai -type d -name "__pycache__" -delete
find ${TO_CLEAN} -maxdepth 1 -type f -name ".coverage" -delete
find ${TO_CLEAN} -depth -maxdepth 1 -type d -name ".eggs" -exec rm -r "{}" +
find ${TO_CLEAN} -depth -maxdepth 1 -type d -name "monai.egg-info" -exec rm -r "{}" +
find ${TO_CLEAN} -depth -maxdepth 1 -type d -name "build" -exec rm -r "{}" +
find ${TO_CLEAN} -depth -maxdepth 1 -type d -name "dist" -exec rm -r "{}" +
find ${TO_CLEAN} -depth -maxdepth 1 -type d -name ".mypy_cache" -exec rm -r "{}" +
find ${TO_CLEAN} -depth -maxdepth 1 -type d -name ".pytype" -exec rm -r "{}" +
find ${TO_CLEAN} -depth -maxdepth 1 -type d -name ".coverage" -exec rm -r "{}" +
}
function torch_validate {
${cmdPrefix}${PY_EXE} -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}"
}
function is_pip_installed() {
return $(${PY_EXE} -c "import sys, pkgutil; sys.exit(0 if pkgutil.find_loader(sys.argv[1]) else 1)" $1)
}
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
;;
--clangformat)
doClangFormat=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: $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 " " "$@"; }
else
check_import
fi
if [ $doCleanup = true ]
then
echo "${separator}${blue}clean${noColor}"
clean_py
echo "${green}done!${noColor}"
exit
fi
if [ $doClangFormat = true ]
then
echo "${separator}${blue}clang-formatting${noColor}"
clang_format
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 ! is_pip_installed isort
then
install_deps
fi
${cmdPrefix}isort --version
if [ $doIsortFix = true ]
then
${cmdPrefix}${PY_EXE} -m isort "$(pwd)"
else
${cmdPrefix}${PY_EXE} -m 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 ! is_pip_installed black
then
install_deps
fi
${cmdPrefix}${PY_EXE} -m black --version
if [ $doBlackFix = true ]
then
${cmdPrefix}${PY_EXE} -m black "$(pwd)"
else
${cmdPrefix}${PY_EXE} -m 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 ! is_pip_installed flake8
then
install_deps
fi
${cmdPrefix}${PY_EXE} -m flake8 --version
${cmdPrefix}${PY_EXE} -m 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 ! is_pip_installed pytype
then
install_deps
fi
${cmdPrefix}${PY_EXE} -m pytype --version
${cmdPrefix}${PY_EXE} -m pytype -j ${NUM_PARALLEL} --python-version="$(${PY_EXE} -c "import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')")"
pytype_status=$?
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 ! is_pip_installed mypy
then
install_deps
fi
${cmdPrefix}${PY_EXE} -m mypy --version
if [ $doDryRun = true ]
then
${cmdPrefix}MYPYPATH="$(pwd)"/monai ${PY_EXE} -m mypy "$(pwd)"
else
MYPYPATH="$(pwd)"/monai ${PY_EXE} -m mypy "$(pwd)" # cmdPrefix does not work with MYPYPATH
fi
mypy_status=$?
if [ ${mypy_status} -ne 0 ]
then
: # mypy output already follows format
exit ${mypy_status}
else
: # mypy output already follows format
fi
set -e # enable exit on failure
fi
# testing command to run
cmd="${PY_EXE}"
# 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="${PY_EXE} -m coverage run -a --source ."
${cmdPrefix}${PY_EXE} -m 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}"
${cmdPrefix}${PY_EXE} -m coverage report --skip-covered -m
fi