-
Notifications
You must be signed in to change notification settings - Fork 44
/
run
executable file
·1266 lines (1049 loc) · 37.6 KB
/
run
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
#!/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}"
local is_read_the_docs="false"
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
is_read_the_docs="true"
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
# Adding temp fix to address the issue of holoscan sdk dragging in low level dependencies, e.g. libcuda.so
# fix_holoscan_import
install_edit_mode
# Install packages overridden by Holoscan package if readthedocs is enabled
if [ ${is_read_the_docs} = "true" ]; then
# Upgrade pip overridden by Holoscan
run_command ${MONAI_PY_EXE} -m pip install -q -U pip wheel build
# Upgrade PyYAML to avoid the issue with the version installed by Holoscan
run_command ${MONAI_PY_EXE} -m pip install -U PyYAML
# Install cuda runtime dependency
run_command ${MONAI_PY_EXE} -m pip install nvidia-cuda-runtime-cu12
# Copy the cuda runtime library to the fixed location (workaround for readthedocs) so that
# we can leverage the existing LD_LIBRARY_PATH (configured by the readthedocs UI) to locate the cuda runtime library.
# (LD_LIBRARY_PATH is set to /home/docs/ for that purpose)
# Note that 'python3.8' is hard-coded here, it should be updated if the Python version changes by
# .readthedocs.yml or other configurations.
run_command ls -al /home/docs/checkouts/readthedocs.org/user_builds/${READTHEDOCS_PROJECT}/envs/${READTHEDOCS_VERSION}/lib/python3.8/site-packages/nvidia/cuda_runtime/lib/
run_command cp /home/docs/checkouts/readthedocs.org/user_builds/${READTHEDOCS_PROJECT}/envs/${READTHEDOCS_VERSION}/lib/python3.8/site-packages/nvidia/cuda_runtime/lib/*.so* /home/docs/
run_command ls -al /home/docs/
fi
}
fix_holoscan_import() {
local holoscan_package_path=$(${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py dist_module_path holoscan)
c_echo b "holoscan_package_path : " Z "${holoscan_package_path}"
init_file_path=$(${MONAI_PY_EXE} $TOP/monai/deploy/utils/importutil.py fix_holoscan_import)
c_echo b "done fixing file: " Z "${init_file_path}"
}
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
run_command ${MONAI_PY_EXE} -m pip uninstall holoscan
fi
local monai_package_path=$(${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 pytest --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 ${MONAI_PY_EXE} -m pytest --cache-clear -vv \
--cov=monai \
--junitxml="$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}