forked from CBICA/CaPTk
/
azure-pipelines.yml
899 lines (702 loc) · 34 KB
/
azure-pipelines.yml
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
# Schedule a build for every midnight Eastern time. This is visible to the pipeline as Build.Reason
schedules:
- cron: "0 4 * * *"
displayName: Daily midnight build
branches:
include:
- master
trigger:
batch: true
branches:
include: ['master']
# 20200312: apparently this is now explicitly required for azure
pr:
branches:
include: ['master']
jobs:
- job: 'WindowsBuild'
displayName: "End-to-end Windows build & package"
timeoutInMinutes: 0
cancelTimeoutInMinutes: 300
pool:
vmImage: 'vs2017-win2016'
steps:
- checkout: self # self represents the repo where the initial Pipelines YAML file was found
# fetchDepth: 1 # the depth of commits to ask Git to fetch; defaults to no limit
# submodule
- bash: |
git submodule update --init --recursive
# ls -lt
# ls ./src/applications/Preprocessing/greedy
displayName: 'Git Submodule Init and Update'
- script: |
choco install doxygen.install nsis.install wget cmake git
displayName: 'Install dependencies'
# # Pull LFS
# - bash: |
# export GIT_LFS_SKIP_SMUDGE=1
# # git lfs pull --include "binaries/precompiledApps/windows.zip"
# # git lfs pull --include "binaries/qt_5.12.1/windows.zip"
# #echo "Not doing this until quota is improved on GitHub"
# displayName: 'Pull LFS'
# condition: ne(variables.CACHE_RESTORED_WINDOWS, 'true')
# - powershell: |
# wmic logicaldisk get size,freespace,caption
# displayName: 'Disk space check'
- powershell: |
wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/windows.zip -O binaries_windows.zip
wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/windows.zip -O qt.zip
displayName: 'Downloading via wget'
# Moving LFS Files
- bash: |
mkdir -p bin
cd bin
mv ../binaries_windows.zip .
mv ../qt.zip .
# wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/windows.zip -O binaries_windows.zip
# wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/windows.zip -O qt.zip
rm -rf ../binaries/*
rm -rf ../data/georgetown
rm -rf ../data/georgetown
rm -rf ../docs
rm -rf ../.git
ls -lt
displayName: 'Moving LFS files to the appropriate location under bin and freeing up some space'
- script: |
cd bin
call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./installLibs" -DCMAKE_CONFIGURATION_TYPES="Release" ..
# freeing up space
rm -rf ../src/applications/individualApps/libra_source/doc
rm -rf ../src/applications/individualApps/libra_source/LIBRA_Software_Manual.pdf
# freeing up space
setx PATH "%PATH%;$(Build.SourcesDirectory)/bin/qt/5.12.1/bin"
cmake --build . --target ALL_BUILD --config Release
rm -rf installLibs
rm -rf qt.zip
rm -rf install
displayName: 'Configure and compile Superbuild'
- bash: |
git pull origin master
git log -1
cat CMakeLists.txt | grep -i "PROJECT_VERSION"
displayName: 'Testing git pull and version'
# - powershell: |
# wmic logicaldisk get size,freespace,caption
# displayName: 'Disk space check'
- script: |
cd bin
call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./install" -DCMAKE_CONFIGURATION_TYPES="Release" -DCAPTK_DISABLE_CWL=ON -DITK_DIR="$(Build.SourcesDirectory)/bin/ITK-build" -DDCMTK_DIR="$(Build.SourcesDirectory)/bin/DCMTK-build" -DBUILD_TESTING=OFF ..
setx PATH "%PATH%;$(Build.SourcesDirectory)/bin/qt/5.12.1/bin"
setx CMAKE_PREFIX_PATH "%CMAKE_PREFIX_PATH%;$(Build.SourcesDirectory)/bin/ITK-build;$(Build.SourcesDirectory)/bin/DCMTK-build;$(Build.SourcesDirectory)/bin/qt/5.12.1/lib/cmake/Qt5"
rm -rf binaries_windows.zip
rm -rf externalApps/binaries_windows/libra
cmake --build . --target ALL_BUILD --config Release
rm -rf externalApps
displayName: 'Configure and compile CaPTk'
# - powershell: |
# get-psdrive | Where Free*
# cd bin
# # Remove-Item install_manifest.txt
# pwd
# switch((ls -r|measure -s Length).Sum) {
# {$_ -gt 1GB} {
# '{0:0.0} GiB' -f ($_/1GB)
# break
# }
# {$_ -gt 1MB} {
# '{0:0.0} MiB' -f ($_/1MB)
# break
# }
# {$_ -gt 1KB} {
# '{0:0.0} KiB' -f ($_/1KB)
# break
# }
# default { "$_ bytes" }
# }
# displayName: 'Disk space check'
- job: 'MacOSBuild'
displayName: "End-to-end MacOS build & package"
timeoutInMinutes: 0
cancelTimeoutInMinutes: 300
pool:
vmImage: 'MacOS-10.14'
steps:
- checkout: self # self represents the repo where the initial Pipelines YAML file was found
# fetchDepth: 1 # the depth of commits to ask Git to fetch; defaults to no limit
# submodule
- bash: |
git submodule update --init --recursive
# ls -lt
# ls ./src/applications/Preprocessing/greedy
displayName: 'Git Submodule Init and Update'
- bash: |
brew install make doxygen libomp openmpi glfw
#brew install caskroom/cask/mactex # latex is not used for documentation right now
export GIT_LFS_SKIP_SMUDGE=1
displayName: 'Brew dependencies'
# - bash: |
# brew install git-lfs
# git lfs install
# displayName: 'Brew dependency install LFS'
# condition: ne(variables['CACHE_RESTORED_MAC'], 'true')
# # Pull LFS
# - bash: |
# export GIT_LFS_SKIP_SMUDGE=1
# git lfs pull --include "binaries/precompiledApps/macos.zip"
# git lfs pull --include "binaries/qt_5.12.1/macos.zip"
# #echo "Not doing this until quota is improved on GitHub"
# displayName: 'Pull LFS'
# condition: ne(variables['CACHE_RESTORED_MAC'], 'true')
# Moving LFS Files
- bash: |
mkdir -p bin
cd bin
wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/macos.zip -O binaries_macos.zip
wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/macos.zip -O qt.zip
# mv ../binaries/precompiledApps/macos.zip ./binaries_macos.zip
# mv ../binaries/qt_5.12.1/macos.zip ./qt.zip
ls -lt
displayName: 'Downloading & Moving LFS files to the appropriate location under bin'
# condition: ne(variables['CACHE_RESTORED_MAC'], 'true')
- bash: |
cd bin
export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
export CMAKE_PREFIX_PATH="/Library/TeX/texbin"
cmake ../ -DCMAKE_INSTALL_PREFIX="./install"
make -j 2
rm -rf install
displayName: 'Configure and compile Superbuild'
# condition: ne(variables['CACHE_RESTORED_MAC'], 'true')
# Check qt
- bash: |
cd bin
ls -a
ls ./qt/
displayName: 'Check qt'
# - bash: |
# tar cvfz bin_macos_20200212.tar.gz bin
# displayName: 'Zipping Superbuild'
- bash: |
git pull origin master
git log -1
cat CMakeLists.txt | grep -i "PROJECT_VERSION"
displayName: 'Testing git pull and version'
- bash: |
cd bin
sudo rm -rf CaPTk_*
cmake ../
rm CMakeCache.txt
export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
export CMAKE_PREFIX_PATH="/Library/TeX/texbin"
export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/bin/ITK-build:$(Build.SourcesDirectory)/bin/DCMTK-build:$(Build.SourcesDirectory)/bin/qt/5.12.1/clang_64/lib/cmake/Qt5:$(Build.SourcesDirectory)/bin/qt/5.12.1/clang_64/lib/cmake/Qt5Core:$CMAKE_PREFIX_PATH
cmake -DITK_DIR=./ITK-build -DDCMTK_DIR=./DCMTK-build ../
rm -rf binaries_*.zip
make -j 2
displayName: 'Configure and compile CaPTk'
# - script: |
# cd bin
# sudo rm -rf CaPTk_*
# cmake ../
# rm CMakeCache.txt
# export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
# export CMAKE_PREFIX_PATH="/Library/TeX/texbin"
# export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/bin/ITK-build:$(Build.SourcesDirectory)/bin/DCMTK-build:$(Build.SourcesDirectory)/bin/qt/5.12.1/clang_64/lib/cmake/Qt5:$(Build.SourcesDirectory)/bin/qt/5.12.1/clang_64/lib/cmake/Qt5Core:$CMAKE_PREFIX_PATH
# cmake -DITK_DIR=./ITK-build -DDCMTK_DIR=./DCMTK-build -DBUILD_TESTING=ON ../
# make -j 2
# make test
# rm -rf testing
# displayName: 'Performing the Tests'
- job: 'Windows_SelfHost_Windows_7'
displayName: "Self-hosted agent on Windows 7"
timeoutInMinutes: 0
cancelTimeoutInMinutes: 300
pool: 'Windows'
steps:
- checkout: self
# submodule
- powershell: |
git submodule update --init --recursive
displayName: 'Git Submodule Init and Update'
- powershell: |
Remove-Item -Recurse -Force -ErrorAction Ignore bin
mkdir bin
displayName: 'Reset bin'
# Moving LFS Files
- powershell: |
cd bin
[Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12
wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/windows.zip -OutFile binaries_windows.zip
displayName: 'Moving LFS files to the appropriate location under bin and freeing up some space'
# - script: |
# cd bin
# call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvarsall.bat" x64
# cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./installLibs" -DCMAKE_CONFIGURATION_TYPES="Release" ..
# setx PATH "$(Build.SourcesDirectory)/bin/qt/5.12.1/bin;%PATH%"
# cmake --build . --target ALL_BUILD --config Release
# displayName: 'Configure and compile Superbuild'
# - powershell: |
# # Copy-Item -Recurse ../../../superbuild/ ./bin
# # cd bin
# # ls
# cd bin
# Copy-Item -Recurse ./ ../../../../superbuild
# displayName: 'Move superbuild and qt and compiled apps'
- powershell: |
$env:GIT_REDIRECT_STDERR = '2>&1'
git pull origin master
git log -1
# cat CMakeLists.txt | grep -i "PROJECT_VERSION"
displayName: 'Testing git pull and version'
- script: |
cd bin
call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"
cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./install" -DCMAKE_CONFIGURATION_TYPES="Release" -DCAPTK_DISABLE_CWL=ON -DITK_DIR="E:/LibsCaPTk/ITK-build" -DDCMTK_DIR="E:/LibsCaPTk/DCMTK-build" -DQt5_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5" -DQt5Core_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core" -DBUILD_TESTING=OFF ..
setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"
rm -rf externalApps/binaries_windows/libra
cmake --build . --target ALL_BUILD --config Release
displayName: 'Configure and compile CaPTk'
# - script: |
# cd bin
# export GIT_LFS_SKIP_SMUDGE=1
# git lfs pull --include "data/TestData.zip"
# call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
# setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
# setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"
# cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./install" -DCMAKE_CONFIGURATION_TYPES="Release" -DCAPTK_DISABLE_CWL=ON -DITK_DIR="E:/LibsCaPTk/ITK-build" -DDCMTK_DIR="E:/LibsCaPTk/DCMTK-build" -DQt5_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5" -DQt5Core_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core" -DBUILD_TESTING=ON ..
# setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
# setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"
# cmake --build . --target RUN_TESTS --config Release
# displayName: 'Performing the Tests'
- script: |
cd bin
call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"
cmake -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX="./install" -DCMAKE_CONFIGURATION_TYPES="Release" -DCAPTK_DISABLE_CWL=ON -DITK_DIR="E:/LibsCaPTk/ITK-build" -DDCMTK_DIR="E:/LibsCaPTk/DCMTK-build" -DQt5_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5" -DQt5Core_DIR="E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core" -DBUILD_TESTING=OFF ..
setx PATH "E:/LibsCaPTk/bin/qt/5.12.1/bin;%PATH%"
setx CMAKE_PREFIX_PATH "E:/LibsCaPTk/ITK-build;E:/LibsCaPTk/DCMTK-build;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5Core;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebView;E:/LibsCaPTk/qt/5.12.1/lib/cmake/Qt5WebEngineCore;%CMAKE_PREFIX_PATH%"
cmake --build . --target PACKAGE --config Release
displayName: 'Build & Package CaPTk'
- powershell: |
cd bin
mv *_Installer.* $(Build.ArtifactStagingDirectory)
displayName: 'Move installer to staging directory'
- task: PublishBuildArtifacts@1
inputs:
pathtoPublish: '$(Build.ArtifactStagingDirectory)'
artifactName: '$(Build.DefinitionName)_installer_Windows'
- task: DownloadBuildArtifacts@0
inputs:
buildType: 'current'
downloadType: 'single'
artifactName: '$(Build.DefinitionName)_installer_Windows'
downloadPath: '$(System.ArtifactsDirectory)'
- task: CopyFilesOverSSH@0
inputs:
sshEndpoint: cbicaNITRC
sourceFolder: $(Build.ArtifactStagingDirectory)
contents: '*_Installer.*'
targetFolder: /var/home/groups/captk/htdocs # previously /mnt/gforge-data/gforge/home/groups/captk/downloads
cleanTargetFolder: false
overwrite: true
continueOnError: true
displayName: Uploading to NITRC
condition: and( eq(variables['Build.DefinitionName'], 'CBICA.CaPTk'), or( eq(variables['Build.Reason'], 'Manual'), eq(variables['Build.Reason'], 'Schedule')) )
- job: 'Linux_SelfHost_Ubuntu_1604'
displayName: "Self-hosted agent on Ubuntu 16.04"
timeoutInMinutes: 0
cancelTimeoutInMinutes: 300
pool: 'Ubuntu_16.04'
steps:
- checkout: self # self represents the repo where the initial Pipelines YAML file was found
# submodule
- bash: |
git submodule update --init --recursive
rm -rf bin
ls
displayName: 'Git Submodule Init and Update'
# Moving LFS Files
- bash: |
rm -rf binaries
mkdir -p bin
cd bin
wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/linux.zip -O binaries_linux.zip
# wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/linux.zip -O qt.zip
ls -lt
displayName: 'Downloading & Moving LFS files to the appropriate location under bin'
# Configure and build superbuild
# - bash: |
# cd bin
# cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" ..
# make -j2
# rm -rf install
# displayName: 'Configure and compile Superbuild'
# - bash: |
# # mkdir $(Build.SourcesDirectory)/../superbuild
# # cd bin
# # mv ./* $(Build.SourcesDirectory)/../superbuild
# # cd $(Build.SourcesDirectory)/..
# # ls
# # echo "Done cd"
# # tar cvfz superbuild.tar.gz superbuild
# # ls
# # echo "done tar"
# # rm -rf superbuild
# # ls
# # cd $(Build.SourcesDirectory)
# pwd
# rm -rf bin
# mkdir bin
# cd bin
# cp -r $(Build.SourcesDirectory)/../superbuild.tar.gz ./
# ls
# echo "Done cp"
# tar xvfz superbuild.tar.gz
# rm -rf superbuild.tar.gz
# ls
# echo "Done tar"
# mv superbuild/* ./
# ls
# displayName: 'Move superbuild and qt and compiled apps'
- bash: |
git pull origin master
git log -1
cat CMakeLists.txt | grep -i "PROJECT_VERSION"
displayName: 'Testing git pull and version'
- bash: |
rm -rf bin/qt.zip
rm -rf bin/5.12.1
df -k .
displayName: 'Disk space check'
# # Configure and build CaPTk
# - bash: |
# cd bin
# export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/../../superbuild/bin/ITK-build:$(Build.SourcesDirectory)/../../superbuild/bin/DCMTK-build:$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH
# cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" -DITK_DIR=./ITK-build -DDCMTK_DIR=./DCMTK-build -DBUILD_TESTING=ON ..
# make -j2
# displayName: 'Configure and compile CaPTk with Testing enabled'
# - script: |
# cd bin
# make test
# rm -rf testing
# displayName: 'Performing the Tests'
# Configure and build CaPTk
- bash: |
pwd
cd bin
ls $(Build.SourcesDirectory)/../../superbuild/bin
export PATH=$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/bin:$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/libexec:$PATH
export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/../../superbuild/bin/ITK-build:$(Build.SourcesDirectory)/../../superbuild/bin/DCMTK-build:$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH
cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" -DITK_DIR="$(Build.SourcesDirectory)/../../superbuild/bin/ITK-build" -DDCMTK_DIR="$(Build.SourcesDirectory)/../../superbuild/bin/DCMTK-build" -DBUILD_TESTING=OFF ..
rm -rf binaries_linux.zip
rm -rf qt.zip
rm -rf 5.12.1
rm -rf externalApps/binaries_linux/libra
make -j2
make install/strip
displayName: 'Configure and compile CaPTk'
- bash: |
rm -rf bin/qt.zip
rm -rf bin/5.12.1
rm -rf regression
rm -rf binaries
rm -rf bin_linux_*.tar.gz
df -k .
displayName: 'Disk space check'
# Build a package
- bash: |
export PATH=$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/bin:$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/libexec:$PATH
export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/../../superbuild/bin/ITK-build:$(Build.SourcesDirectory)/../../superbuild/bin/DCMTK-build:$(Build.SourcesDirectory)/../../superbuild/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH
rm -rf regression
rm -rf binaries
export PKG_FAST_MODE=1
export ARCH=x86_64 appimagetool
# export PKG_COPY_QT_LIBS=1
./scripts/captk-pkg
mv *_Installer.* $(Build.ArtifactStagingDirectory)
rm -rf bin
df -k .
displayName: 'Set up environment variables for packager and build a package'
- task: PublishBuildArtifacts@1
inputs:
pathtoPublish: '$(Build.ArtifactStagingDirectory)'
artifactName: '$(Build.DefinitionName)_installer_Linux_ubuntu1604'
continueOnError: true
- task: DownloadBuildArtifacts@0
inputs:
buildType: 'current'
downloadType: 'single'
artifactName: '$(Build.DefinitionName)_installer_Linux_ubuntu1604'
downloadPath: '$(System.ArtifactsDirectory)'
continueOnError: true
- task: CopyFilesOverSSH@0
inputs:
sshEndpoint: cbicaNITRC
sourceFolder: $(Build.ArtifactStagingDirectory)
contents: '*_Installer.*'
targetFolder: /var/home/groups/captk/htdocs # previously /mnt/gforge-data/gforge/home/groups/captk/downloads
cleanTargetFolder: false
overwrite: true
continueOnError: true
displayName: Uploading to NITRC
condition: and( eq(variables['Build.DefinitionName'], 'CBICA.CaPTk'), or( eq(variables['Build.Reason'], 'Manual'), eq(variables['Build.Reason'], 'Schedule')) )
# - job: 'macOS_SelfHost_1014'
# displayName: "Self-hosted agent on macOS 10.14"
# timeoutInMinutes: 0
# cancelTimeoutInMinutes: 300
# pool: 'macOS_10.14_alt' # Change to alt pool to try running this outside of Phuc's account -- possible permissions problems
# steps:
# - checkout: self # self represents the repo where the initial Pipelines YAML file was found
# # submodule
# - bash: |
# export GIT_LFS_SKIP_SMUDGE=1
# git submodule update --init --recursive
# displayName: 'Git Submodule Init and Update'
# # Moving LFS Files
# - bash: |
# rm -rf bin
# mkdir -p bin
# cd bin
# wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/macos.zip -O binaries_macos.zip
# wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/macos.zip -O qt.zip
# # mv ../binaries/precompiledApps/macos.zip ./binaries_macos.zip
# # mv ../binaries/qt_5.12.1/macos.zip ./qt.zip
# ls -lt
# displayName: 'Downloading & Moving LFS files to the appropriate location under bin'
# # - bash: |
# # cd bin
# # export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
# # export CMAKE_PREFIX_PATH="/Library/TeX/texbin"
# # cmake ../ -DCMAKE_INSTALL_PREFIX="./install"
# # make -j 2
# # displayName: 'Configure and compile Superbuild'
# # - bash: |
# # # mkdir $(Build.SourcesDirectory)/../superbuild
# # # cd bin
# # # mv ./* $(Build.SourcesDirectory)/../superbuild
# # # cd $(Build.SourcesDirectory)/..
# # # ls
# # # echo "Done cd"
# # # tar cvfz superbuild.tar.gz superbuild
# # # ls
# # # echo "done tar"
# # # rm -rf superbuild
# # # ls
# # # cd $(Build.SourcesDirectory)
# # pwd
# # cd $(Build.SourcesDirectory)/../../
# # ls
# # tar xvfz superbuild.tar.gz
# # rm -rf superbuild.tar.gz
# # cd $(Build.SourcesDirectory)/../../superbuild/bin
# # ls
# # echo "Done tar"
# # displayName: 'Move superbuild and qt and compiled apps'
# - bash: |
# git pull origin master
# git log -1
# cat CMakeLists.txt | grep -i "PROJECT_VERSION"
# displayName: 'Testing git pull and version'
# - bash: |
# cd bin
# pwd
# rm -rf CaPTk_*
# export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
# export CMAKE_PREFIX_PATH=/Users/Shared/superbuild/ITK-build:/Users/Shared/superbuild/DCMTK-build:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5Core:$(pwd)/qt/5.12.1/clang_64/lib/cmake/Qt5:$(pwd)/qt/5.12.1/clang_64/lib/cmake/Qt5Core:$CMAKE_PREFIX_PATH
# echo "[DEBUG] CMAKE_PREFIX_PATH: " $CMAKE_PREFIX_PATH
# #cmake ../
# #rm -f CMakeCache.txt
# cmake -DITK_DIR="/Users/Shared/superbuild/ITK-build" -DDCMTK_DIR="/Users/Shared/superbuild/DCMTK-build" -DVTK_DIR="/Users/Shared/superbuild/VTK-build" -DCMAKE_INSTALL_PREFIX="./install" -DQt5_DIR=/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5 -DQt5Core_DIR=/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5Core ../
# # Debug using vsts' cache
# cp CMakeCache.txt /Users/Shared/debug-vsts-getkaa-cmakecache.txt
# make -j 2
# displayName: 'Configure and compile CaPTk'
# - bash: |
# cd bin
# version=$(grep -i -e "project_version:*" CMakeCache.txt | cut -c24-)
# rm -rf CaPTk_$version.app/Contents/Resources/bin/ITK-SNAP.app
# rm -rf CaPTk*.app
# cmake ../
# rm -f CMakeCache.txt
# export CMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE
# export CMAKE_PREFIX_PATH=/Users/Shared/superbuild/ITK-build:/Users/Shared/superbuild/DCMTK-build:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5Core:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5:/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5Core:$CMAKE_PREFIX_PATH
# cmake -DITK_DIR="/Users/Shared/superbuild/ITK-build" -DDCMTK_DIR="/Users/Shared/superbuild/DCMTK-build" -DCMAKE_INSTALL_PREFIX="./install" -DQt5_DIR=/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5 -DQt5Core_DIR=/Users/Shared/superbuild/qt/5.12.1/clang_64/lib/cmake/Qt5Core ../
# make -j 2
# displayName: 'Ensure documentation is picked up properly'
# - bash: |
# cd bin
# version=$(grep -i -e "project_version:*" CMakeCache.txt | cut -c24-)
# pkgname="_Installer"
# pkgname="$version$pkgname"
# rm -rf *.pkg
# rm -rf install_manifest.txt
# make package
# # print dir tree for debug
# ls -R _CPack_Packages
# pkgpath=""
# if [ -d "$(Build.SourcesDirectory)/bin/_CPack_Packages/OSX/DragNDrop/CaPTk_$version/ALL_IN_ONE/CaPTk_$version.app/" ]; then pkgpath="$(Build.SourcesDirectory)/bin/_CPack_Packages/OSX/DragNDrop/CaPTk_$version/ALL_IN_ONE/CaPTk_$version.app/"; else pkgpath="$(Build.SourcesDirectory)/bin/_CPack_Packages/OSX/DragNDrop/CaPTk_$version/CaPTk_$version.app/"; fi
# # Try patching Utilities as late as possible. Seems to be necessary for Utilities specifically.
# install_name_tool -change /usr/local/opt/libomp/lib/libomp.dylib @rpath/libomp.dylib $pkgpath/Contents/Resources/bin/Utilities
# pkgbuild --version $version --identifier com.cbica.captk --install-location /Applications --component $pkgpath ./CaPTk_$version.pkg
# productbuild --synthesize --package CaPTk_$version.pkg ./distribution.xml
# xml='<?xml version="1.0" encoding="utf-8"?>
# <installer-gui-script minSpecVersion="1">
# <title>CaPTk_'"$version"'</title>
# <license file="Combined.txt"></license>
# <pkg-ref id="com.cbica.captk"/>
# <options customize="never" require-scripts="false"/>
# <choices-outline>
# <line choice="default">
# <line choice="com.cbica.captk"/>
# </line>
# </choices-outline>
# <choice id="default"/>
# <choice id="com.cbica.captk" visible="false">
# <pkg-ref id="com.cbica.captk"/>
# </choice>
# <pkg-ref id="com.cbica.captk" version="$version" onConclusion="none">CaPTk_'"$version"'.pkg</pkg-ref>
# </installer-gui-script>'
# echo $xml > "./distribution.xml"
# productbuild --distribution ./distribution.xml --resources $(Build.SourcesDirectory)/bin/_CPack_Packages/OSX/DragNDrop/CaPTk_$version/ALL_IN_ONE/CaPTk_$version.app/Contents/Resources/license/ --package-path . ./CaPTk_$pkgname.pkg
# mv *_Installer* $(Build.ArtifactStagingDirectory)
# displayName: 'Package CaPTk (.dmg and .pkg)'
# - task: PublishBuildArtifacts@1
# inputs:
# pathtoPublish: '$(Build.ArtifactStagingDirectory)'
# artifactName: '$(Build.DefinitionName)_installer_macOS'
# - task: DownloadBuildArtifacts@0
# inputs:
# buildType: 'current'
# downloadType: 'single'
# artifactName: '$(Build.DefinitionName)_installer_macOS'
# downloadPath: '$(System.ArtifactsDirectory)'
# - task: CopyFilesOverSSH@0
# inputs:
# sshEndpoint: cbicaNITRC
# sourceFolder: $(Build.ArtifactStagingDirectory)
# contents: '*_Installer.*'
# targetFolder: /var/home/groups/captk/htdocs # previously /mnt/gforge-data/gforge/home/groups/captk/downloads
# cleanTargetFolder: false
# overwrite: true
# continueOnError: true
# displayName: Uploading to NITRC
# condition: and( eq(variables['Build.DefinitionName'], 'CBICA.CaPTk'), or( eq(variables['Build.Reason'], 'Manual'), eq(variables['Build.Reason'], 'Schedule')) )
# - job: 'Linux_SelfHost_CentOS7'
# displayName: "Self-hosted agent on CentOS 7"
# timeoutInMinutes: 0
# cancelTimeoutInMinutes: 300
# pool: 'CentOS7'
# steps:
# - checkout: self # self represents the repo where the initial Pipelines YAML file was found
# # submodule
# - bash: |
# git submodule update --init --recursive
# rm -rf bin
# ls
# displayName: 'Git Submodule Init and Update'
# # Moving LFS Files
# - bash: |
# rm -rf binaries
# mkdir -p bin
# cd bin
# wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/linux.zip -O binaries_linux.zip
# # wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/linux.zip -O qt.zip
# ls -lt
# displayName: 'Downloading & Moving LFS files to the appropriate location under bin'
# # Configure and build superbuild
# # - bash: |
# # cd bin
# # cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" ..
# # make -j2
# # rm -rf install
# # displayName: 'Configure and compile Superbuild'
# # - bash: |
# # displayName: 'Move superbuild and qt and compiled apps'
# - bash: |
# git pull origin master
# git log -1
# cat CMakeLists.txt | grep -i "PROJECT_VERSION"
# displayName: 'Testing git pull and version'
# # - bash: |
# # rm -rf bin/qt.zip
# # rm -rf bin/5.12.1
# # df -k .
# # displayName: 'Disk space check'
# # # Configure and build CaPTk
# # - bash: |
# # cd bin
# # export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/bin/ITK-build:$(Build.SourcesDirectory)/bin/DCMTK-build:$(Build.SourcesDirectory)/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH
# # cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" -DITK_DIR=./ITK-build -DDCMTK_DIR=./DCMTK-build -DBUILD_TESTING=ON ..
# # make -j2
# # displayName: 'Configure and compile CaPTk with Testing enabled'
# # - script: |
# # cd bin
# # make test
# # rm -rf testing
# # displayName: 'Performing the Tests'
# # Configure and build CaPTk
# - bash: |
# cd bin
# # export PATH=$(Build.SourcesDirectory)/bin/qt/5.12.1/bin:$(Build.SourcesDirectory)/bin/qt/5.12.1/libexec:$PATH
# # export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/bin/ITK-build:$(Build.SourcesDirectory)/bin/DCMTK-build:$(Build.SourcesDirectory)/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH
# cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" -DBUILD_TESTING=OFF ..
# rm -rf binaries_linux.zip
# rm -rf qt.zip
# rm -rf 5.12.1
# rm -rf externalApps/binaries_linux/libra
# make -j2
# make install/strip
# displayName: 'Configure and compile CaPTk'
# # - bash: |
# # rm -rf bin/qt.zip
# # rm -rf bin/5.12.1
# # rm -rf regression
# # rm -rf binaries
# # rm -rf bin_linux_*.tar.gz
# # df -k .
# # displayName: 'Disk space check'
# # Build a package
# - bash: |
# # export PATH=$(Build.SourcesDirectory)/bin/qt/5.12.1/bin:$(Build.SourcesDirectory)/bin/qt/5.12.1/libexec:$PATH
# # export CMAKE_PREFIX_PATH=$(Build.SourcesDirectory)/bin/ITK-build:$(Build.SourcesDirectory)/bin/DCMTK-build:$(Build.SourcesDirectory)/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH
# # rm -rf regression
# # rm -rf binaries
# export PKG_FAST_MODE=1
# export ARCH=x86_64 appimagetool
# # export PKG_COPY_QT_LIBS=1
# ./scripts/captk-pkg
# rm -rf src
# rm -rf docs*
# rm -rf scripts
# mv *_Installer.* $(Build.ArtifactStagingDirectory)
# rm -rf bin
# df -k .
# displayName: 'Set up environment variables for packager and build a package'
# - task: PublishBuildArtifacts@1
# inputs:
# pathtoPublish: '$(Build.ArtifactStagingDirectory)'
# artifactName: '$(Build.DefinitionName)_installer_Linux_centos7'
# continueOnError: true
# - task: DownloadBuildArtifacts@0
# inputs:
# buildType: 'current'
# downloadType: 'single'
# artifactName: '$(Build.DefinitionName)_installer_Linux_centos7'
# downloadPath: '$(System.ArtifactsDirectory)'
# continueOnError: true
# - task: CopyFilesOverSSH@0
# inputs:
# sshEndpoint: cbicaNITRC
# sourceFolder: $(Build.ArtifactStagingDirectory)
# contents: '*_Installer.*'
# targetFolder: /mnt/gforge-data/gforge/home/groups/captk/downloads
# cleanTargetFolder: false
# overwrite: true
# continueOnError: true
# displayName: Uploading to NITRC
# condition: eq(variables['Build.DefinitionName'], 'CBICA.CaPTk')