Elx 34 remove testing external dependencies (#39)

* CI: Use the shutil equivalent of os.rename() and is.replace() which is available in Python 2.7 #33

* COMP: making sure python move operations work

Also with python 2.7.

* BUG: check for file existence

* COMP: copy paste error

* CI: Compile all components on AppVeyor

* CI: Touching appveyor.yml to trigger rebuild

* CI: Build ITK and elastix separately on AppVeyor to avoid build time limit

* CI: Fix AppVeyor script

* CI: Fix AppVeyor cache stamp

Testing/elx_compare_landmarks.py

@@ -78,7 +78,7 @@ def main():
   for line in f1 :
     f2.write( line.strip().split(';')[4].strip().strip( "OutputPoint = [ " ).rstrip( " ]" ) + "\n" );
   f1.close(); f2.close();
-  os.rename( landmarkstemp, landmarks1full ); # for later inspection
+  shutil.move( landmarkstemp, landmarks1full ); # for later inspection
 
   #
   # Transform the fixed image landmarks by the baseline result
@@ -95,7 +95,7 @@ def main():
   for line in f1 :
     f2.write( line.strip().split(';')[4].strip().strip( "OutputPoint = [ " ).rstrip( " ]" ) + "\n" );
   f1.close(); f2.close();
-  os.rename( landmarkstemp, landmarks2full ); # for later inspection
+  shutil.move( landmarkstemp, landmarks2full ); # for later inspection
 
   # Compute the distance between all transformed landmarks
   f1 = open( landmarks1, 'r' ); f2 = open( landmarks2, 'r' );

Testing/elx_compare_overlap.py

@@ -1,6 +1,7 @@
 import sys, subprocess
 import os
 import os.path
+import shutil
 import re
 import glob
 from optparse import OptionParser
@@ -71,7 +72,8 @@ def main():
   seg_defm = os.path.join( options.directory, "segmentation_deformed.mha" );
   subprocess.call( [ "transformix", "-in", options.mseg, "-out", options.directory, "-tp", tpFileName ],
     stdout=subprocess.PIPE );
-  os.replace( seg, seg_defm );
+  if( os.path.exists( seg_defm ) ) : os.remove( seg_defm );
+  shutil.move( seg, seg_defm );
 
   #
   # Deform the moving image segmentation by the baseline result
@@ -92,7 +94,8 @@ def main():
   seg_defb = os.path.join( options.directory, "segmentation_baseline.mha" );
   subprocess.call( [ "transformix", "-in", options.mseg, "-out", options.directory, "-tp", tpFileName_b ],
     stdout=subprocess.PIPE );
-  os.replace( seg, seg_defb );
+  if( os.path.exists( seg_defb ) ) : os.remove( seg_defb );
+  shutil.move( seg, seg_defb );
 
   # Compute the overlap between baseline segmentation and deformed moving segmentation
   try :

appveyor.yml

@@ -16,10 +16,12 @@ environment:
   ITK_URL: https://github.com/InsightSoftwareConsortium/ITK
   ITK_SOURCE_DIR: c:\ITK-source
   ITK_BUILD_DIR: c:\ITK-build
+  ITK_BUILD_CACHE_STAMP: c:\BUILT_ITK
 cache:
   - '%ITK_SOURCE_DIR%'
   - '%ITK_BUILD_DIR%'
 build_script:
   - cmd: if not exist %ITK_SOURCE_DIR% git clone %ITK_URL% %ITK_SOURCE_DIR% && cd %ITK_SOURCE_DIR% && git checkout v4.11.1
-  - cmd: if not exist %ITK_BUILD_DIR% mkdir -p %ITK_BUILD_DIR% && cd %ITK_BUILD_DIR% && cmake -DBUILD_EXAMPLES=OFF -DBUILD_TESTING:BOOL=OFF -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DITKGroup_IO:BOOL=ON -DModule_ITKDistanceMap:BOOL=ON -DModule_ITKImageFusion:BOOL=ON -DModule_ITKLabelMap:BOOL:=ON -DModule_ITKMathematicalMorphology:BOOL=ON -DModule_ITKOptimizers:BOOL=ON -DModule_ITKOptimizersv4:BOOL=ON -DModule_ITKRegistrationCommon:BOOL=ON -DModule_ITKVideoIO:BOOL=ON-DCMAKE_BUILD_TYPE=Release %ITK_SOURCE_DIR% && cmake --build . --config Release -- /m
-  - cmd: mkdir -p %ELASTIX_BUILD_DIR% && cd %ELASTIX_BUILD_DIR% && cmake -DITK_DIR=%ITK_BUILD_DIR% -DCMAKE_BUILD_TYPE=Release %ELASTIX_SOURCE_DIR% && cmake --build . --config Release -- /m && ctest -j4 -VV -C Release || true
+  - cmd: if not exist %ITK_BUILD_DIR% mkdir -p %ITK_BUILD_DIR% && cd %ITK_BUILD_DIR% && cmake -DBUILD_EXAMPLES=OFF -DBUILD_TESTING:BOOL=OFF -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DITKGroup_IO:BOOL=ON -DModule_ITKDistanceMap:BOOL=ON -DModule_ITKImageFusion:BOOL=ON -DModule_ITKLabelMap:BOOL:=ON -DModule_ITKMathematicalMorphology:BOOL=ON -DModule_ITKOptimizers:BOOL=ON -DModule_ITKOptimizersv4:BOOL=ON -DModule_ITKRegistrationCommon:BOOL=ON -DModule_ITKVideoIO:BOOL=ON-DCMAKE_BUILD_TYPE=Release %ITK_SOURCE_DIR% && cmake --build . --config Release -- /m && @echo BUILT_ITK > %ITK_BUILD_CACHE_STAMP%
+  - cmd: if not exist %ITK_BUILD_CACHE_STAMP% mkdir -p %ELASTIX_BUILD_DIR% && cd %ELASTIX_BUILD_DIR% && cmake -DUSE_ALL_COMPONENTS=ON -DITK_DIR=%ITK_BUILD_DIR% -DCMAKE_BUILD_TYPE=Release %ELASTIX_SOURCE_DIR% && cmake --build . --config Release -- /m && ctest -j4 -VV -C Release || true
+