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#!/bin/bash
#
# Copyright (c) 2020-2021, NVIDIA CORPORATION.
# 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 [ "$0" != "/bin/bash" ]; then
RUN_SCRIPT_FILE="$(readlink -f "$0")"
SCRIPT_DIR=$(dirname "${RUN_SCRIPT_FILE}")
export RUN_SCRIPT_FILE
else
RUN_SCRIPT_FILE="$(readlink -f "${BASH_SOURCE[0]}")"
export RUN_SCRIPT_FILE
fi
TOP=$(git rev-parse --show-toplevel || dirname "${RUN_SCRIPT_FILE}")
export TOP
}
################################################################################
# Utility functions
################################################################################
#######################################
# Get list of available commands from a given input file.
#
# Available commands and command summary are extracted by checking a pattern
# "_desc() { 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() { 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() {
if [ ! -e "$1" ]; then
echo "$1 doesn't exist!"
fi
local line_str='--------------------------------'
local IFS
local cmd_lines
cmd_lines="$(IFS= grep -E -e "^(([[:alpha:]_[:digit:]]+)_desc\(\)|# Section: )" "$1" | sed "s/_desc() *{ *echo '/ : /")"
local line
while IFS= read -r line; do
local cmd
local desc
cmd=$(echo "$line" | cut -d":" -f1)
desc=$(echo "$line" | cut -d":" -f2-)
if [ "$cmd" = "# Section" ]; then
c_echo B "${desc}"
else
# there is no substring operation in 'sh' so use 'cut'
local dash_line
dash_line="$(echo "${line_str}" | cut -c ${#cmd}-)" # = "${line_str:${#cmd}}"
c_echo 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}${line}" # -e option doesn't work in 'sh' so disallow escaped characters
done <&0
}
c_str() {
local old_color=39
local old_attr=0
local color=39
local attr=0
local text=""
#local no_change=0
for i in "$@"; 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 [ ${old_color} -ne ${color} ] || [ ${old_attr} -ne ${attr} ]; then
text="${text}\033[${attr};${color}m"
old_color=$color
old_attr=$attr
fi
done
/bin/echo -en "$text"
}
c_echo() {
# shellcheck disable=SC2155
local old_opt="$(shopt -op xtrace)" # save old xtrace option
set +x # unset xtrace
local text
text="$(c_str "$@")"
/bin/echo -e "$text\033[0m"
eval "${old_opt}" # restore old xtrace option
}
echo_err() {
>&2 echo "$@"
}
c_echo_err() {
>&2 c_echo "$@"
}
printf_err() {
>&2 printf '%s' "$@"
}
get_item_ranges() {
local indexes="$1"
local list="$2"
echo -n "$(echo "${list}" | xargs | cut -d " " -f "${indexes}")"
}
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 $4}' | while read -r line; do echo "${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="$*"
c_echo B "$(date -u '+%Y-%m-%d %H:%M:%S') " W "\$ " G "${cmd}"
[ "$(echo -n "$@")" = "" ] && return 1 # return 1 if there is no command available
"$@"
status=$?
unset IFS
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=$exit, no more retries left."
return 1
fi
done
return 0
}
get_arch() {
local platform
platform="$(uname -p)"
local platform_str
case "${platform}" in
amd64|x86_64|x86|linux/amd64)
platform_str="x86_64"
;;
arm64|aarch64|arm|linux/arm64)
platform_str="aarch64"
;;
esac
echo -n "${platform_str}"
}
is_aarch64() {
get_arch | grep -q "aarch64" && return 0 || return 1
}
is_x86_64() {
get_arch | grep -q "x86_64" && return 0 || return 1
}
#==================================================================================
# Section: Build
#==================================================================================
build_local_libcucim_() {
local source_folder=${1:-${TOP}}
local build_type=${2:-debug}
local build_type_str=${3:-Debug}
local prefix=${4:-}
local build_folder=${source_folder}/build-${build_type}
local CMAKE_CMD=${CMAKE_CMD:-cmake}
pushd "${source_folder}" > /dev/null
${CMAKE_CMD} -S "${source_folder}" -B "${build_folder}" -G "Unix Makefiles" \
-DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE \
-DCMAKE_PREFIX_PATH="${prefix}" \
-DCMAKE_BUILD_TYPE="${build_type_str}" \
-DCMAKE_INSTALL_PREFIX="${source_folder}/install"
${CMAKE_CMD} --build "${build_folder}" --config "${build_type_str}" --target cucim -- -j "$(nproc)"
${CMAKE_CMD} --build "${build_folder}" --config "${build_type_str}" --target install -- -j "$(nproc)"
popd
}
build_local_cuslide_() {
local source_folder=${1:-${TOP}/cpp/plugins/cucim.kit.cuslide}
local build_type=${2:-debug}
local build_type_str=${3:-Debug}
local prefix=${4:-}
local build_folder=${source_folder}/build-${build_type}
local CMAKE_CMD=${CMAKE_CMD:-cmake}
pushd "${source_folder}" > /dev/null
${CMAKE_CMD} -S "${source_folder}" -B "${build_folder}" -G "Unix Makefiles" \
-DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE \
-DCMAKE_BUILD_TYPE="${build_type_str}" \
-DCMAKE_PREFIX_PATH="${prefix}" \
-DCMAKE_INSTALL_PREFIX="${source_folder}/install"
${CMAKE_CMD} --build "${build_folder}" --config "${build_type_str}" --target cucim.kit.cuslide -- -j "$(nproc)"
${CMAKE_CMD} --build "${build_folder}" --config "${build_type_str}" --target install -- -j "$(nproc)"
popd
}
build_local_cuslide2_() {
local source_folder=${1:-${TOP}/cpp/plugins/cucim.kit.cuslide2}
local build_type=${2:-debug}
local build_type_str=${3:-Debug}
local prefix=${4:-}
local build_folder=${source_folder}/build-${build_type}
local CMAKE_CMD=${CMAKE_CMD:-cmake}
pushd "${source_folder}" > /dev/null
${CMAKE_CMD} -S "${source_folder}" -B "${build_folder}" -G "Unix Makefiles" \
-DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE \
-DCMAKE_BUILD_TYPE="${build_type_str}" \
-DCMAKE_PREFIX_PATH="${prefix}" \
-DCMAKE_INSTALL_PREFIX="${source_folder}/install"
${CMAKE_CMD} --build "${build_folder}" --config "${build_type_str}" --target cucim.kit.cuslide2 -- -j "$(nproc)"
${CMAKE_CMD} --build "${build_folder}" --config "${build_type_str}" --target install -- -j "$(nproc)"
popd
}
build_local_cumed_() {
local source_folder=${1:-${TOP}/cpp/plugins/cucim.kit.cumed}
local build_type=${2:-debug}
local build_type_str=${3:-Debug}
local prefix=${4:-}
local build_folder=${source_folder}/build-${build_type}
local CMAKE_CMD=${CMAKE_CMD:-cmake}
pushd "${source_folder}" > /dev/null
${CMAKE_CMD} -S "${source_folder}" -B "${build_folder}" -G "Unix Makefiles" \
-DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE \
-DCMAKE_BUILD_TYPE="${build_type_str}" \
-DCMAKE_PREFIX_PATH="${prefix}" \
-DCMAKE_INSTALL_PREFIX="${source_folder}/install"
${CMAKE_CMD} --build "${build_folder}" --config "${build_type_str}" --target cucim.kit.cumed -- -j "$(nproc)"
${CMAKE_CMD} --build "${build_folder}" --config "${build_type_str}" --target install -- -j "$(nproc)"
popd
}
build_local_cucim_() {
local source_folder=${1:-${TOP}/python}
local build_type=${2:-debug}
local build_type_str=${3:-Debug}
local prefix=${4:-}
local build_folder=${source_folder}/build-${build_type}
local CMAKE_CMD=${CMAKE_CMD:-cmake}
pushd "${source_folder}" > /dev/null
local python_library
python_library=$(python3 -c "import sysconfig, os; print(os.path.join(sysconfig.get_config_var('LIBDIR'), sysconfig.get_config_var('LDLIBRARY')))")
local python_include_dir
python_include_dir=$(python3 -c "import sysconfig; print(sysconfig.get_path('include'))")
${CMAKE_CMD} -S "${source_folder}" -B "${build_folder}" -G "Unix Makefiles" \
-DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE \
-DCMAKE_BUILD_TYPE="${build_type_str}" \
-DCMAKE_PREFIX_PATH="${prefix}" \
-DCMAKE_INSTALL_PREFIX="${source_folder}/install" \
-DPYTHON_EXECUTABLE="$(which python3)" \
-DPYTHON_LIBRARY="${python_library}" \
-DPYTHON_INCLUDE_DIR="${python_include_dir}"
${CMAKE_CMD} --build "${build_folder}" --config "${build_type_str}" --target cucim -- -j "$(nproc)"
${CMAKE_CMD} --build "${build_folder}" --config "${build_type_str}" --target install -- -j "$(nproc)"
popd
}
# shellcheck disable=SC2016
build_local_desc() { echo 'Build locally
Compile binaries locally
Arguments:
$1 - subcommand [all|clean_cache|clean|libcucim|cuslide|cumed|cucim] (default: all)
$2 - build type [debug|release|rel-debug] (default: debug)
'
}
build_local() {
local subcommand="${1:-all}"
local build_type="${2:-debug}"
local build_type_str="Debug"
local prefix=${3:-}
local major_version
major_version="$(cut -d. -f1 "${TOP}/VERSION")" # major version number
[ "${build_type}" = "debug" ] && build_type_str="Debug"
[ "${build_type}" = "release" ] && build_type_str="Release"
[ "${build_type}" = "rel-debug" ] && build_type_str="RelWithDebInfo"
local old_opt
old_opt="$(shopt -op errexit);$(shopt -op nounset)" # save old shopts
set -eu
if [ "$subcommand" = "clean_cache" ]; then
rm -f "${TOP}"/build-*/CMakeCache.txt
rm -f "${TOP}"/cpp/plugins/cucim.kit.cuslide/build-*/CMakeCache.txt
rm -f "${TOP}"/cpp/plugins/cucim.kit.cumed/build-*/CMakeCache.txt
rm -f "${TOP}"/cpp/plugins/cucim.kit.cuslide2/build-*/CMakeCache.txt
rm -f "${TOP}"/python/build-*/CMakeCache.txt
fi
if [ "$subcommand" = "clean" ]; then
rm -rf "${TOP}"/build-*
rm -rf "${TOP}"/install
rm -rf "${TOP}"/cpp/plugins/cucim.kit.cuslide/build-*/
rm -rf "${TOP}"/cpp/plugins/cucim.kit.cuslide/install
rm -rf "${TOP}"/cpp/plugins/cucim.kit.cumed/build-*/
rm -rf "${TOP}"/cpp/plugins/cucim.kit.cumed/install
rm -rf "${TOP}"/cpp/plugins/cucim.kit.cuslide2/build-*/
rm -rf "${TOP}"/cpp/plugins/cucim.kit.cuslide2/install
rm -rf "${TOP}"/python/build-*
rm -rf "${TOP}"/python/install
fi
if [ "$subcommand" = "all" ] || [ "$subcommand" = "libcucim" ]; then
build_local_libcucim_ "${TOP}" "${build_type}" ${build_type_str} "${prefix}"
fi
if [ "$subcommand" = "all" ] || [ "$subcommand" = "cuslide" ]; then
build_local_cuslide_ "${TOP}"/cpp/plugins/cucim.kit.cuslide "${build_type}" ${build_type_str} "${prefix}"
fi
if [ "$subcommand" = "all" ] || [ "$subcommand" = "cuslide2" ]; then
build_local_cuslide2_ "${TOP}"/cpp/plugins/cucim.kit.cuslide2 "${build_type}" ${build_type_str} "${prefix}"
fi
if [ "$subcommand" = "all" ] || [ "$subcommand" = "cumed" ]; then
build_local_cumed_ "${TOP}"/cpp/plugins/cucim.kit.cumed "${build_type}" ${build_type_str} "${prefix}"
fi
if [ "$subcommand" = "all" ] || [ "$subcommand" = "cucim" ]; then
build_local_cucim_ "${TOP}"/python "${build_type}" ${build_type_str} "${prefix}"
fi
# Remove existing library files at python/cucim/src/cucim/clara
rm -f "${TOP}"/python/cucim/src/cucim/clara/*.so*
if [ "$subcommand" = "all" ] || [ "$subcommand" = "cucim" ]; then
# We don't need to copy binary if executed by conda-build
if [ "${CONDA_BUILD:-}" != "1" ]; then
# Copy .so files from libcucim & cuslide/cumed's build folders to cuCIM's Python source folder
# Since wheel file doesn't support symbolic link (https://github.com/pypa/wheel/issues/203),
# we don't need to copy symbolic links. Instead copy only libcucim.so.${major_version} (without symbolic link)
cp "${TOP}"/build-"${build_type}"/lib*/libcucim.so."${major_version}" "${TOP}"/python/cucim/src/cucim/clara/
cp -P "${TOP}"/cpp/plugins/cucim.kit.cuslide/build-"${build_type}"/lib*/cucim* "${TOP}"/python/cucim/src/cucim/clara/
cp -P "${TOP}"/cpp/plugins/cucim.kit.cumed/build-"${build_type}"/lib*/cucim* "${TOP}"/python/cucim/src/cucim/clara/
# Only copy cuslide2 if it exists (infrastructure-only mode has no .so file)
if ls "${TOP}"/cpp/plugins/cucim.kit.cuslide2/build-"${build_type}"/lib*/cucim* 1> /dev/null 2>&1; then
cp -P "${TOP}"/cpp/plugins/cucim.kit.cuslide2/build-"${build_type}"/lib*/cucim* "${TOP}"/python/cucim/src/cucim/clara/
fi
# Copy .so files from pybind's build folder to cuCIM's Python source folder
cp "${TOP}"/python/build-"${build_type}"/lib/cucim/_cucim.*.so "${TOP}"/python/cucim/src/cucim/clara/
fi
fi
eval "${old_opt}" # restore old shopts
}
get_arch_name_() {
architecture="unknown"
case $(uname -m) in
x86_64) architecture="x86_64" ;;
arm|aarch64) lscpu | awk '/Architecture:/{print $2}' | grep -i -q "aarch64" && architecture="sbsa";;
esac
echo "${architecture}"
}
#==================================================================================
# Section: Test
#==================================================================================
# shellcheck disable=SC2016
test_desc() { echo 'Execute test cases
Arguments:
$1 - subcommand [all|python|c++] (default: all)
$2 - test_type [all|unit|integration|system|performance] (default: all)
$3 - test_component [all|clara|skimage] (default: all)
'
}
test() {
local subcommand="${1:-all}"
local test_type="${2:-all}"
shift;
if [ "$subcommand" = "all" ] || [ "$subcommand" = "python" ]; then
test_python "$@"
fi
}
install_python_test_deps_() {
if [ -n "${CONDA_PREFIX}" ]; then
# Install test dependencies from pip because conda does not have all the dependencies (e.g., opencv-python).
# (https://github.com/rapidsai/cucim/pull/433)
run_command pip install -r "${TOP}"/python/cucim/requirements-test.txt
else
pushd "${TOP}/python/cucim"
if [ -n "${VIRTUAL_ENV}" ]; then
run_command pip3 install -e ".[test]"
else
run_command pip3 install --user -e ".[test]"
fi
popd
fi
hash -r
}
# shellcheck disable=SC2016
test_python_desc() { echo 'Execute Python test cases
Arguments:
$1 - test_type [all|unit|integration|system|performance] (default: all)
$2 - test_component [all|clara|skimage] (default: all)
'
}
test_python() {
local test_type="${1:-all}"
local test_component="${2:-all}"
local result=0
local testsuite=()
local testsuite_unit_skimage="src"
local testsuite_unit_clara="tests/unit"
local testsuite_performance="tests/performance"
install_python_test_deps_
if [ "$test_type" = "all" ] || [ "$test_type" = "unit" ]; then
if [ "$test_component" = "skimage" ]; then
testsuite+=("${testsuite_unit_skimage}")
elif [ "$test_component" = "clara" ]; then
testsuite+=("${testsuite_unit_clara}")
else
testsuite+=("${testsuite_unit_skimage}" "${testsuite_unit_clara}")
fi
fi
if [ "$test_type" = "all" ] || [ "$test_type" = "performance" ]; then
testsuite+=("${testsuite_performance}")
fi
pushd "$TOP"/python/cucim
# Set CUDA environment for CuPy JIT compilation
if [ -n "${CONDA_PREFIX}" ]; then
export CUDA_PATH="${CONDA_PREFIX}"
export CUDA_HOME="${CONDA_PREFIX}"
# CuPy NVRTC needs to find CUDA headers in targets subdirectory
# Detect platform architecture for correct CUDA include path
CUDA_ARCH=$(uname -m)
if [ "${CUDA_ARCH}" = "aarch64" ]; then
export CUDA_INCLUDE_PATH="${CONDA_PREFIX}/targets/sbsa-linux/include"
else
export CUDA_INCLUDE_PATH="${CONDA_PREFIX}/targets/x86_64-linux/include"
fi
echo "🔧 Set CUDA_HOME=${CUDA_HOME} CUDA_INCLUDE_PATH=${CUDA_INCLUDE_PATH}"
fi
run_command py.test --cache-clear -vv \
--cov=cucim \
--junitxml="$TOP/junit-cucim.xml" \
--cov-config="$TOP/python/cucim/.coveragerc" \
--cov-report=xml:"$TOP/cucim-coverage.xml" \
--cov-report term \
"${testsuite[@]}"
result=$?
popd
return $result
}
#==================================================================================
# Section: Example
#==================================================================================
download_testdata_desc() { echo 'Download test data from Docker Hub
'
}
download_testdata() {
c_echo W "Downloading test data..."
run_command mkdir -p "${TOP}/notebooks/input"
if [ ! -e "${TOP}/notebooks/input/image.tif" ]; then
run_command rm -rf "${TOP}/notebooks/input"
id=$(docker create gigony/svs-testdata:little-big)
run_command docker cp "$id":/input "${TOP}/notebooks"
run_command docker rm -v "$id"
c_echo G "Test data is downloaded to '${TOP}/notebooks/input'!"
else
c_echo G "Test data already exists at '${TOP}/notebooks/input'!"
fi
}
#==================================================================================
# Section: Release
#==================================================================================
update_version_desc() { echo 'Update version
Executes ci/release/update-version.sh which updates some version-related
files based on VERSION file.
Returns:
Outputs executed by update-version.sh
Exit code:
exit code returned from update-version.sh
'
}
update_version() {
local new_version=${1:-}
local ret=0
[ -z "${new_version}" ] && c_echo_err R "Please specify '[new version]' (e.g., '21.06.00')!" && return 1
"$TOP"/ci/release/update-version.sh "$@"
ret=$?
return $ret
}
parse_args() {
local OPTIND
while getopts 'yh' option;
do
case "${option}" in
h)
print_usage
exit 1
;;
*)
;;
esac
done
shift $((OPTIND-1))
CMD="$1"
shift
ARGS=("$@")
}
print_usage() {
set +x
echo_err
echo_err "USAGE: $0 [command] [arguments]..."
echo_err ""
c_echo_err W "Global Arguments"
echo_err
c_echo_err W "Command List"
c_echo_err Y " help " w "---------------------------- Print detailed description for a given argument (command name)"
echo_err "$(get_list_of_available_commands "${RUN_SCRIPT_FILE}" | my_cat_prefix " ")"
echo_err
}
print_cmd_help_messages() {
local cmd="$1"
if [ -n "${cmd}" ]; then
if type "${cmd}"_desc > /dev/null 2>&1; then
"${cmd}"_desc
exit 0
else
c_echo_err R "Command '${cmd}' doesn't exist!"
exit 1
fi
fi
print_usage
return 0
}
main() {
local ret=0
parse_args "$@"
case "$CMD" in
help)
print_cmd_help_messages "${ARGS[@]}"
exit 0
;;
''|main)
print_usage
;;
*)
if type "${CMD}" > /dev/null 2>&1; then
"$CMD" "${ARGS[@]}"
else
print_usage
exit 1
fi
;;
esac
ret=$?
if [ -n "${SCRIPT_DIR}" ]; then
exit $ret
fi
}
init_globals
if [ -n "${SCRIPT_DIR}" ]; then
main "$@"
fi
# Description template
# Globals:
# CS_OS
# CS_TARGET
# CS_USER (used if CS_OS is "l4t")
# CS_HOST (used if CS_OS is "l4t")
# CS_OBSCURA_MODE (used in Obscura server)
# Arguments:
# Command line to execute
# Returns:
# Outputs print messages during the execution (stdout->stdout, stderr->stderr).
# Note:
# This command removes "\r" characters from stdout.
# Exit code:
# exit code returned from executing a given command