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#!/bin/bash
#
# Copyright 2021 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.
init_globals() {
if [ "$0" != "/bin/bash" ]; then
SCRIPT_DIR=$(dirname "$(readlink -f "$0")")
export RUN_SCRIPT_FILE="$(readlink -f "$0")"
else
export RUN_SCRIPT_FILE="$(readlink -f "${BASH_SOURCE[0]}")"
fi
export TOP=$(git rev-parse --show-toplevel || $(dirname "${RUN_SCRIPT_FILE}"))
MONAI_PY_EXE=${MONAI_PY_EXE:-"python3"}
export MONAI_PY_EXE
DO_DRY_RUN="false" # print commands but do not execute them. Used by run_command
}
################################################################################
# Utility functions
################################################################################
#######################################
# Get list of available commands from a given input file.
#
# Available commands and command summary are extracted by checking a pattern
# "_desc() { c_echo '".
# Section title is extracted by checking a pattern "# Section: ".
# This command is used for listing available commands in CLI.
#
# e.g.)
# "# Section: String/IO functions"
# => "# String/IO functions"
# "to_lower_desc() { c_echo 'Convert to lower case"
# => "to_lower ----------------- Convert to lower case"
#
# Arguments:
# $1 - input file that defines commands
# Returns:
# Print list of available commands from $1
#######################################
get_list_of_available_commands() {
local mode="color"
if [ "${1:-}" = "color" ]; then
mode="color"
shift
elif [ "${1:-}" = "nocolor" ]; then
mode="nocolor"
shift
fi
local file_name="$1"
if [ ! -e "$1" ]; then
echo "$1 doesn't exist!"
fi
local line_str='--------------------------------'
local IFS= cmd_lines="$(IFS= cat "$1" | grep -E -e "^(([[:alpha:]_[:digit:]]+)_desc\(\)|# Section: )" | sed "s/_desc() *{ *c_echo '/ : /")"
local line
while IFS= read -r line; do
local cmd=$(echo "$line" | cut -d":" -f1)
local desc=$(echo "$line" | cut -d":" -f2-)
if [ "$cmd" = "# Section" ]; then
c_echo ${mode} B "${desc}"
else
# there is no substring operation in 'sh' so use 'cut'
local dash_line="$(echo "${line_str}" | cut -c ${#cmd}-)" # = "${line_str:${#cmd}}"
c_echo ${mode} Y " ${cmd}" w " ${dash_line} ${desc}"
fi
# use <<EOF, not '<<<"$cmd_lines"' to be executable in sh
done <<EOF
$cmd_lines
EOF
}
my_cat_prefix() {
local IFS
local prefix="$1"
local line
while IFS= read -r line; do
echo "${prefix}${line}" # -e option doesn't work in 'sh' so disallow escaped characters
done <&0
}
c_str() {
local old_color=39
local old_attr=0
local color=39
local attr=0
local text=""
local mode="color"
if [ "${1:-}" = "color" ]; then
mode="color"
shift
elif [ "${1:-}" = "nocolor" ]; then
mode="nocolor"
shift
fi
for i in "$@"; do
case "$i" in
r|R)
color=31
;;
g|G)
color=32
;;
y|Y)
color=33
;;
b|B)
color=34
;;
p|P)
color=35
;;
c|C)
color=36
;;
w|W)
color=37
;;
z|Z)
color=0
;;
esac
case "$i" in
l|L|R|G|Y|B|P|C|W)
attr=1
;;
n|N|r|g|y|b|p|c|w)
attr=0
;;
z|Z)
attr=0
;;
*)
text="${text}$i"
esac
if [ "${mode}" = "color" ]; then
if [ ${old_color} -ne ${color} ] || [ ${old_attr} -ne ${attr} ]; then
text="${text}\033[${attr};${color}m"
old_color=$color
old_attr=$attr
fi
fi
done
/bin/echo -en "$text"
}
c_echo() {
# Select color/nocolor based on the first argument
local mode="color"
if [ "${1:-}" = "color" ]; then
mode="color"
shift
elif [ "${1:-}" = "nocolor" ]; then
mode="nocolor"
shift
else
if [ ! -t 1 ]; then
mode="nocolor"
fi
fi
local old_opt="$(shopt -op xtrace)" # save old xtrace option
set +x # unset xtrace
if [ "${mode}" = "color" ]; then
local text="$(c_str color "$@")"
/bin/echo -e "$text\033[0m"
else
local text="$(c_str nocolor "$@")"
/bin/echo -e "$text"
fi
eval "${old_opt}" # restore old xtrace option
}
echo_err() {
>&2 echo "$@"
}
c_echo_err() {
>&2 c_echo "$@"
}
printf_err() {
>&2 printf "$@"
}
get_item_ranges() {
local indexes="$1"
local list="$2"
echo -n "$(echo "${list}" | xargs | cut -d " " -f "${indexes}")"
return $?
}
get_unused_ports() {
local num_of_ports=${1:-1}
local start=${2:-49152}
local end=${3:-61000}
comm -23 \
<(seq ${start} ${end} | sort) \
<(ss -tan | awk '{print $4}' | while read line; do echo ${line##*\:}; done | grep '[0-9]\{1,5\}' | sort -u) \
| shuf | tail -n ${num_of_ports} # use tail instead head to avoid broken pipe in VSCode terminal
}
newline() {
echo
}
info() {
c_echo W "$(date -u '+%Y-%m-%d %H:%M:%S') [INFO] " Z "$@"
}
error() {
echo R "$(date -u '+%Y-%m-%d %H:%M:%S') [ERROR] " Z "$@"
}
fatal() {
echo R "$(date -u '+%Y-%m-%d %H:%M:%S') [FATAL] " Z "$@"
echo
if [ -n "${SCRIPT_DIR}" ]; then
exit 1
fi
}
run_command() {
local status=0
local cmd="$*"
if [ "${DO_DRY_RUN}" != "true" ]; then
c_echo B "$(date -u '+%Y-%m-%d %H:%M:%S') " W "\$ " G "${cmd}"
else
c_echo B "$(date -u '+%Y-%m-%d %H:%M:%S') " C "[dryrun] " W "\$ " G "${cmd}"
fi
[ "$(echo -n "$@")" = "" ] && return 1 # return 1 if there is no command available
if [ "${DO_DRY_RUN}" != "true" ]; then
"$@"
status=$?
fi
return $status
}
retry() {
local retries=$1
shift
local count=0
until run_command "$@"; do
exit=$?
wait=$((2 ** count))
count=$((count + 1))
if [ $count -lt $retries ]; then
info "Retry $count/$retries. Exit code=$exit, Retrying in $wait seconds..."
sleep $wait
else
fatal "Retry $count/$retries. Exit code=$exit, no more retries left."
return 1
fi
done
return 0
}
#==================================================================================
# Section: Inspect
#==================================================================================
get_package_info_desc() { c_echo 'Get package info from app(& model) path
Arguments:
$1 - Application folder or file path
$2 - Model path (optional)
'
}
get_package_info() {
local app_path="${1:-}"
local model_path="${2:-}"
[ -z "${app_path}" ] && c_echo_err R "No application path specified." && return 1
${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py get_package_info ${app_path} ${model_path}
}
#==================================================================================
# Section: Build
#==================================================================================
install_python_dev_deps() {
local config="${1:-dev}"
if [ -n "${VIRTUAL_ENV}" ] || [ -n "${CONDA_PREFIX}" ]; then
# Read the Docs site is using specific setuptools version so should not upgrade it.
if [ "$config" = "read_the_docs" ]; then
run_command ${MONAI_PY_EXE} -m pip install -q -U pip wheel build
else
run_command ${MONAI_PY_EXE} -m pip install -q -U setuptools pip wheel build
fi
run_command ${MONAI_PY_EXE} -m pip install -q -r ${TOP}/requirements-dev.txt
run_command ${MONAI_PY_EXE} -m pip install -q -r ${TOP}/requirements-examples.txt
else
c_echo_err R "You must be in a virtual environment to install dependencies."
if [ ! -e "$TOP/.venv/dev/bin/python3" ]; then
c_echo_err W "Installing a virtual environment at " G "$TOP/.venv/dev" W " ..."
run_command ${MONAI_PY_EXE} -m venv "$TOP/.venv/dev"
fi
c_echo_err W "Please activate the virtual environment at " G "$TOP/.venv/dev" W " and execute the setup command again."
c_echo_err
c_echo_err G " source $TOP/.venv/dev/bin/activate"
c_echo_err G " $0 $CMD $ARGS"
exit 1
fi
install_edit_mode
}
install_edit_mode() {
# Create a symlink to the virtual environment.
# This solves an issue with separate package folders for 'monai' and 'monai-deploy-app-sdk' like below:
# - 'monai': installed with 'pip install monai'
# - 'monai-deploy-app-sdk': installed with 'pip install -e . # installed with development(edit) mode
local monai_package_path=$(${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py dist_module_path monai)
local sdk_package_path=$(${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py dist_module_path monai-deploy-app-sdk)
local is_sdk_editable="false"
if ${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py is_dist_editable monai-deploy-app-sdk; then
is_sdk_editable="true"
fi
c_echo b "monai_package_path: " Z "${monai_package_path}"
c_echo b "sdk_package_path : " Z "${sdk_package_path}"
c_echo b "is_sdk_editable : " Z "${is_sdk_editable}"
if [ "${is_sdk_editable}" == "false" ]; then
c_echo W "Installing monai-deploy-app-sdk in edit mode..."
if [ -n "${VIRTUAL_ENV}" ] || [ -n "${CONDA_PREFIX}" ]; then
run_command ${MONAI_PY_EXE} -m pip install -e ${TOP}
else
c_echo_err R "You must be in a virtual environment to install monai-deploy-app-sdk in edit mode."
fi
if ${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py is_dist_editable monai-deploy-app-sdk; then
is_sdk_editable="true"
fi
sdk_package_path=$(${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py dist_module_path monai-deploy-app-sdk)
c_echo b "sdk_package_path : " Z "${sdk_package_path}"
c_echo b "is_sdk_editable : " Z "${is_sdk_editable}"
fi
if [ "${is_sdk_editable}" = "false" ]; then
c_echo W "Installing monai-deploy-app-sdk in edit mode..."
fi
if [ "$is_sdk_editable" = "true" ] && [ -n "${monai_package_path}" ] && [ ! -L ${monai_package_path}/monai/deploy ]; then
c_echo W "Creating a symbolic link... " b "'${monai_package_path}/monai/deploy' " Z "->" b " '${sdk_package_path}/monai/deploy'"
run_command ln -sfn ${sdk_package_path}/monai/deploy ${monai_package_path}/monai/deploy
fi
# Refresh command-line tools
hash -r
}
setup_desc() { c_echo 'Setup development environment
Arguements:
$1 - configuration (default: "dev")
'
}
setup() {
local config="${1:-dev}"
install_python_dev_deps "${config}"
}
clean_desc() { c_echo 'Clean up temporary files and uninstall monai-deploy-app-sdk
'
}
clean() {
c_echo W 'Cleaning up temporary files and run "' "${MONAI_PY_EXE}" ' -m pip uninstall monai-deploy-app-sdk"...'
# Remove coverage history
run_command rm -f junit-monai-deploy-app-sdk.xml monai-deploy-app-sdk-coverage.xml
# Uninstall the development package
if [ -n "${VIRTUAL_ENV}" ] || [ -n "${CONDA_PREFIX}" ]; then
c_echo W "Uninstalling MONAI Deploy App SDK installation..."
run_command ${MONAI_PY_EXE} -m pip uninstall monai-deploy-app-sdk
fi
local monai_package_path=$(${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py dist_module_path monai)
local sdk_package_path=$(${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py dist_module_path monai-deploy-app-sdk)
local is_sdk_editable="false"
if ${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py is_dist_editable monai-deploy-app-sdk; then
is_sdk_editable="true"
fi
c_echo b "monai_package_path: " Z "${monai_package_path}"
c_echo b "sdk_package_path : " Z "${sdk_package_path}"
c_echo b "is_sdk_editable : " Z "${is_sdk_editable}"
if [ "$is_sdk_editable" = "false" ] && [ -n "${monai_package_path}" ] && [ -L ${monai_package_path}/monai/deploy ]; then
c_echo W "Deleting a symbolic link at " b "'${monai_package_path}/monai/deploy'... "
run_command rm ${monai_package_path}/monai/deploy
fi
# Remove temporary files (in the directory of this script)
c_echo W "Removing temporary files in ${TOP}"
run_command find ${TOP}/monai -type f -name "*.py[co]" -delete
run_command find ${TOP}/monai -type f -name "*.so" -delete
run_command find ${TOP}/monai -type d -name "__pycache__" -delete
run_command find ${TOP} -depth -maxdepth 1 -type d -name "monai_deploy_app_sdk.egg-info" -exec rm -r "{}" +
run_command find ${TOP} -depth -maxdepth 1 -type d -name "build" -exec rm -r "{}" +
run_command find ${TOP} -depth -maxdepth 1 -type d -name "dist" -exec rm -r "{}" +
run_command find ${TOP} -depth -maxdepth 1 -type d -name ".mypy_cache" -exec rm -r "{}" +
run_command find ${TOP} -depth -maxdepth 1 -type d -name ".pytype" -exec rm -r "{}" +
run_command find ${TOP} -depth -maxdepth 1 -type d -name "__pycache__" -exec rm -r "{}" +
}
build_desc() { c_echo 'Build distribution package
Build a distribution package for this SDK using
"build" (https://pypa-build.readthedocs.io/en/stable/index.html).
Arguements:
$1 - destination folder (default: ${TOP}/dist)
'
}
build() {
local dest_path="${1:-${TOP}/dist}"
install_python_dev_deps
run_command rm -rf ${dest_path}/monai-deploy-app-sdk-*.gz ${dest_path}/monai_deploy_app_sdk-*.whl
# Somehow, 'build' package causes an issue without `PIP_NO_CACHE_DIR=off` at Python 3.6 (with pyenv)
# (https://github.com/pypa/pip/issues/2897)
PIP_NO_CACHE_DIR=off run_command ${MONAI_PY_EXE} -m build -o "${dest_path}"
}
#==================================================================================
# Section: Test
#==================================================================================
get_platform_name() {
${MONAI_PY_EXE} -c "import platform; print(platform.system().lower())"
}
get_python_version() {
${MONAI_PY_EXE} -c "from sys import version_info; print(f'{version_info.major}.{version_info.minor}')"
}
check_import() {
[ -z "${1:-}" ] && c_echo_err R "No module specified." && return 1
local module_name="${1:-}"
c_echo W "Checking import of module '" b "${module_name}" W "'..."
run_command ${MONAI_PY_EXE} -c "import ${1}"
}
is_module_installed() {
local module_name="${1:-}"
local result=0
[ -z "${module_name}" ] && c_echo_err R "No module name specified." && return 1
${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py is_module_installed "${module_name}"
result=$?
return ${result}
}
# Edit 'setup.cfg' ([isort] section) if you want to skip formatting for particular files.
isort_format() {
local command="${1:-}"
local result=0
local old_opt="$(shopt -op xtrace)" # save old xtrace option
set +e # unset error trap
if [ "${command}" = "fix" ]; then
c_echo W "Fixing import order..."
else
c_echo W "Checking import order..."
fi
# Ensure that the necessary packages for code format testing are installed
if ! is_module_installed isort; then
install_python_dev_deps
fi
run_command ${MONAI_PY_EXE} -m isort --version
if [ "${command}" = "fix" ]; then
run_command ${MONAI_PY_EXE} -m isort "${TOP}"
else
run_command ${MONAI_PY_EXE} -m isort --check "${TOP}"
fi
result=$?
if [ ${result} -ne 0 ]; then
c_echo_err R "isort check failed!"
c_echo_err W "Please run auto style fixes: " G "./run check --autofix"
exit ${result}
else
c_echo_err G "isort check passed!"
fi
eval "${old_opt}" # restore old xtrace option
}
# Edit 'pyproject.toml' ([tool.black] section) if you want to skip formatting for particular files.
black_format() {
local command="${1:-}"
local result=0
local old_opt="$(shopt -op xtrace)" # save old xtrace option
set +e # unset error trap
if [ "${command}" = "fix" ]; then
c_echo W "Fixing styles using black..."
else
c_echo W "Checking styles using black..."
fi
# Ensure that the necessary packages for code format testing are installed
if ! is_module_installed black; then
install_python_dev_deps
fi
run_command ${MONAI_PY_EXE} -m black --version
if [ "${command}" = "fix" ]; then
run_command ${MONAI_PY_EXE} -m black "${TOP}"
else
run_command ${MONAI_PY_EXE} -m black --check "${TOP}"
fi
result=$?
if [ ${result} -ne 0 ]; then
c_echo_err R "black check failed!"
c_echo_err W "Please run auto style fixes: " G "./run check --autofix"
exit ${result}
else
c_echo_err G "black check passed!"
fi
eval "${old_opt}" # restore old xtrace option
}
# Edit 'setup.cfg' ([flake8] section) if you want to skip formatting for particular files.
flake8_format() {
local command="${1:-}"
local result=0
local old_opt="$(shopt -op xtrace)" # save old xtrace option
set +e # unset error trap
c_echo W "Checking styles using flake8..."
# Ensure that the necessary packages for code format testing are installed
if ! is_module_installed flake8; then
install_python_dev_deps
fi
run_command ${MONAI_PY_EXE} -m flake8 --version
run_command ${MONAI_PY_EXE} -m flake8 "${TOP}" --count --statistics
result=$?
if [ ${result} -ne 0 ]; then
c_echo_err R "flake8 check failed!"
exit ${result}
else
c_echo_err G "flake8 check passed!"
fi
eval "${old_opt}" # restore old xtrace option
}
# Edit 'setup.cfg' ([pytype] section) if you want to skip formatting for particular files.
# You can use '# type: ignore' to ignore a specific line in a file.
pytype_format() {
local num_workers="${1:-$(nproc)}"
local result=0
local old_opt="$(shopt -op xtrace)" # save old xtrace option
set +e # unset error trap
c_echo W "Checking styles using pytype..."
local platform_name="$(get_platform_name)"
# Skip if it is MacOS
if [ "${platform_name}" = "darwin" ]; then
c_echo_err R "pytype does not work on MacOS (https://github.com/google/pytype/issues/661), skipping the checking."
return 0
fi
# Ensure that the necessary packages for code format testing are installed
if ! is_module_installed pytype; then
install_python_dev_deps
fi
run_command ${MONAI_PY_EXE} -m pytype --version
local python_version="$(get_python_version)"
pushd "${TOP}" > /dev/null
run_command ${MONAI_PY_EXE} -m pytype -j "${num_workers}" --python-version="${python_version}"
result=$?
popd > /dev/null
if [ ${result} -ne 0 ]; then
c_echo_err R "pytype check failed!"
exit ${result}
else
c_echo_err G "pytype check passed!"
fi
eval "${old_opt}" # restore old xtrace option
}
# Edit 'setup.cfg' ([mypy] section) if you want to skip formatting for particular files.
# You can use '# type: ignore' to ignore a specific line in a file.
mypy_format() {
local command="${1:-}"
local result=0
local old_opt="$(shopt -op xtrace)" # save old xtrace option
set +e # unset error trap
c_echo W "Checking styles using mypy..."
local platform_name="$(get_platform_name)"
# Ensure that the necessary packages for code format testing are installed
if ! is_module_installed mypy; then
install_python_dev_deps
fi
run_command ${MONAI_PY_EXE} -m mypy --version
local python_version="$(get_python_version)"
#MYPYPATH="${TOP}/monai/deploy"
# https://github.com/python/mypy/issues/8584: Redesign import handling
# https://github.com/python/mypy/issues/10172: Issue with `pip install -e .`
# - https://mypy.readthedocs.io/en/stable/command_line.html#cmdoption-mypy-explicit-package-bases
# - https://mypy.readthedocs.io/en/stable/running_mypy.html#mapping-paths-to-modules
# - Using `--namespace-packages --explicit-package-bases` solves the issue with the current folder structure.
run_command ${MONAI_PY_EXE} -m mypy --namespace-packages --explicit-package-bases "${TOP}"
result=$?
if [ ${result} -ne 0 ]; then
c_echo_err R "mypy check failed!"
exit ${result}
else
c_echo_err G "mypy check passed!"
fi
eval "${old_opt}" # restore old xtrace option
}
check_desc() { c_echo 'Check code quality
Examples:
./run check -f # run coding style and static type checking.
./run check --autofix # run automatic code formatting using "isort" and "black".
Code style check options:
--black : perform "black" code format checks
--autofix : format code using "isort" and "black"
--isort : perform "isort" import sort checks
--flake8 : perform "flake8" code format checks
Python type check options:
--pytype : perform "pytype" static type checks
--mypy : perform "mypy" static type checks
-j, --jobs : number of parallel jobs to run "pytype" (default: ' $(nproc) ')
Misc. options:
--dryrun : display the commands to the screen without running
-f, --codeformat : shorthand to run all code style and static analysis tests
--------------------------------------------------------------------------------
For bug reports and feature requests, please file an issue at:
https://github.com/Project-MONAI/monai-deploy-app-sdk/issues/new/choose
To choose an alternative python executable, set the environmental variable, "MONAI_PY_EXE".
'
}
check() {
local do_black_format="false"
local do_black_fix="false"
local do_isort_format="false"
local do_isort_fix="false"
local do_flake8_format="false"
local do_pytype_format="false"
local do_mypy_format="false"
local num_workers=$(nproc)
local arg
# parse arguments
while [ $# -gt 0 ]; do
arg="$1"
case ${arg} in
--dryrun)
DO_DRY_RUN="true" # set to true to print commands to screen without running
;;
-f|--codeformat)
do_black_format="true"
do_isort_format="true"
do_flake8_format="true"
do_pytype_format="true"
do_mypy_format="true"
;;
--black)
do_black_format="true"
;;
--autofix)
do_isort_fix="true"
do_black_fix="true"
do_isort_format="true"
do_black_format="true"
;;
--isort)
do_isort_format="true"
;;
--flake8)
do_flake8_format="true"
;;
--pytype)
do_pytype_format="true"
;;
--mypy)
do_mypy_format="true"
;;
-j|--jobs)
num_workers=$2
shift
;;
*)
c_echo_err R "Incorrect command is provided (invalid arg: " B "${arg}" R ")."
print_cmd_help_messages check
;;
esac
shift
done
c_echo B "DO_DRY_RUN:" W " ${DO_DRY_RUN}"
c_echo B "do_black_format:" W " ${do_black_format}"
c_echo B "do_black_fix:" W " ${do_black_fix}"
c_echo B "do_isort_format:" W " ${do_isort_format}"
c_echo B "do_isort_fix:" W " ${do_isort_fix}"
c_echo B "do_flake8_format:" W " ${do_flake8_format}"
c_echo B "do_pytype_format:" W " ${do_pytype_format}"
c_echo B "do_mypy_format:" W " ${do_mypy_format}"
check_import "monai.deploy"
if [ "${do_isort_format}" = "true" ]; then
if [ "${do_isort_fix}" = "true" ]; then
isort_format "fix"
else
isort_format "check"
fi
fi
if [ "${do_black_format}" = "true" ]; then
if [ "${do_black_fix}" = "true" ]; then
black_format "fix"
else
black_format "check"
fi
fi
if [ "${do_flake8_format}" = "true" ]; then
flake8_format
fi
if [ "${do_pytype_format}" = "true" ]; then
pytype_format "${num_workers}"
fi
if [ "${do_mypy_format}" = "true" ]; then
mypy_format
fi
}
pytest_desc() { c_echo 'Run tests with pytest
It executes the following command:
' "${MONAI_PY_EXE}"' -m py.test --cache-clear -vv \
--cov=monai \
--junitxml="'"$TOP/junit-monai-deploy-app-sdk.xml"'" \
--cov-config="'"$TOP/.coveragerc"'" \
--cov-report=xml:"'"$TOP/monai-deploy-app-sdk-coverage.xml"'" \
--cov-report term \
"$@"
Examples:
./run pytest tests/unit
Arguments:
$@ - arguments to pass to pytest
'
}
pytest() {
local result=0
pushd $TOP > /dev/null
run_command ${MONAI_PY_EXE} -m py.test --cache-clear -vv \
--cov=monai \
--junitxml="$TOP/junit-monai-deploy-app-sdk.xml" \
--cov-config="$TOP/.coveragerc" \
--cov-report=xml:"$TOP/monai-deploy-app-sdk-coverage.xml" \
--cov-report term \
"$@"
result=$?
popd > /dev/null
return ${result}
}
test_desc() { c_echo 'Execute test cases
Arguments:
$1 - subcommand [all] (default: all)
$2 - test_type [all|unit|integration|system|performance] (default: all)
$3 - test_component [all] (default: all)
'
}
test() {
local subcommand="${1:-all}"
local test_type="${2:-all}"
shift;
if [ "$subcommand" = "all" ] || [ "$subcommand" = "python" ]; then
test_python "$@"
fi
}
test_python() {
local test_type="${1:-all}"
local test_component="${2:-all}"
local result=0
local testsuite=""
local testsuite_unit="tests/unit"
local testsuite_integration="tests/integration"
local testsuite_performance="tests/performance"
local testsuite_system="tests/system"
install_python_dev_deps
if [ "$test_type" = "all" ] || [ "$test_type" = "unit" ]; then
local testsuite="${testsuite_unit}"
fi
if [ "$test_type" = "all" ] || [ "$test_type" = "integration" ]; then
local testsuite="${testsuite} ${testsuite_integration}"
fi
if [ "$test_type" = "all" ] || [ "$test_type" = "performance" ]; then
testsuite="${testsuite} ${testsuite_performance}"
fi
if [ "$test_type" = "all" ] || [ "$test_type" = "system" ]; then
testsuite="${testsuite} ${testsuite_system}"
fi
pytest ${testsuite}
result=$?
return $result
}
#==================================================================================
# Section: Example
#==================================================================================
#==================================================================================
# Section: Documentation
#==================================================================================
install_doc_requirements() {
if [ -n "${VIRTUAL_ENV}" ] || [ -n "${CONDA_PREFIX}" ]; then
run_command ${MONAI_PY_EXE} -m pip install -q -U setuptools pip wheel build
run_command ${MONAI_PY_EXE} -m pip install -q -r ${TOP}/docs/requirements.txt
install_edit_mode
hash -r # reload hash for sphinx-build command
else
c_echo_err R "You must be in a virtual environment to install dependencies."
if [ ! -e "$TOP/.venv/dev/bin/python3" ]; then
c_echo_err W "Installing a virtual environment at " G "$TOP/.venv/dev" W " ..."
run_command ${MONAI_PY_EXE} -m venv "$TOP/.venv/dev"
fi
c_echo_err W "Please activate the virtual environment at " G "$TOP/.venv/dev" W " and execute the command again."
c_echo_err
c_echo_err G " source $TOP/.venv/dev/bin/activate"
c_echo_err G " $0 $CMD $ARGS"
exit 1
fi
}
setup_gen_docs() {
local output_folder=${1:-${TOP}/dist/docs}
# Remove existing files in dist/docs
run_command rm -rf ${output_folder}/*
# Remove existing _autosummary folder
run_command rm -rf ${TOP}/docs/source/modules/_autosummary
# Symbolic link notebooks folder from 'docs/source/notebooks' to 'notebooks'
run_command rm -rf ${TOP}/docs/source/notebooks
run_command ln -sfn ${TOP}/notebooks ${TOP}/docs/source/notebooks
# Symbolic link notebooks folder from 'docs/source/notebooks' to '_static/notebooks'
run_command rm -rf ${TOP}/docs/_static/notebooks
run_command ln -sfn ${TOP}/notebooks ${TOP}/docs/_static/notebooks
}
gen_docs_desc() { c_echo 'Generate documents
Generated docs would be avaialable at ${TOP}/dist/docs.
Arguments:
$1 - output folder path (html docs)
Returns:
None
Exit code:
exit code returned from generating document
'
}
gen_docs() {
local output_folder=${1:-${TOP}/dist/docs}
local ret=0
# Install prerequisites
install_doc_requirements
setup_gen_docs ${output_folder}
c_echo W "Sphinx build html..."
sphinx-build -E -b html $TOP/docs/source ${output_folder}
ret=$?
if [ $ret -eq 0 ]; then
c_echo W "Sphinx linkcheck..."
sphinx-build -b linkcheck $TOP/docs/source ${output_folder}
ret=$?
fi
# Remove jupyter_execute folder explicitly until the issue is solved
# https://github.com/executablebooks/MyST-NB/issues/129
rm -rf $(dirname ${output_folder})/jupyter_execute
return $ret
}
gen_docs_dev_desc() { c_echo 'Generate documents (with dev-server)
Launch dev-server for sphinx.
Generated docs would be avaialable at ${TOP}/dist/docs.
Arguments:
-p <port> - port number
-h <host> - hostname to serve documentation on (default: 0.0.0.0)
-o <path> - output folder path (html docs)
Returns:
None
Exit code:
exit code returned from generating document
'
}
gen_docs_dev() {
local ret=0
local OPTIND
local output_folder=${TOP}/dist/docs