Making single setup.py (#1773)

AMSC is now in different location.
Removing crow/setup.py
Since directories were moved, changing in readme.
fixed library_report to find framework directory.

README.md

@@ -116,7 +116,7 @@ This project is supported by [Idaho National Laboratory](https://www.inl.gov/).
 
 ### License
 
-Files in /crow/contrib and /framework/contrib are third party libraries that are not part of Raven and are provided here for covenience. These are under their own, seperate licensing which is described in those directories.
+Files in crow/contrib, src/contrib and framework/contrib are third party libraries that are not part of Raven and are provided here for covenience. These are under their own, seperate licensing which is described in those directories.
 
 Raven itself is licensed as follows:
 

build_raven

@@ -105,9 +105,7 @@ if test `uname` = Darwin; then
 fi
 
 PIP_COMMAND=pip3
-(cd $CROW_DIR && ${PIP_COMMAND} --verbose install . --upgrade --target ./install)
-
-(cd $RAVEN_BUILD_DIR && ${PIP_COMMAND} --verbose install . --upgrade --target ./framework/contrib/AMSC)
+(cd $RAVEN_BUILD_DIR && ${PIP_COMMAND} --verbose install . --upgrade --target ./install)
 
 (cd $PYTHON_FMU_DIR && ./build_pythonfmu || echo PythonFMU build failed)
 

clean_raven

@@ -10,9 +10,10 @@ rm -f ${RAVEN_DIR}/framework/contrib/AMSC/_amsc*.so \
     ${RAVEN_DIR}/src/contrib/amsc_wrap.cxx \
     ${RAVEN_DIR}/src/contrib/amsc_wrap.cpp \
     ${RAVEN_DIR}/src/contrib/amsc.py \
-    ${RAVEN_DIR}/src/contrib/amsc.pyc \
-    ${RAVE_DIR}/cow/install/
-rm -Rf ${RAVEN_DIR}/build
+    ${RAVEN_DIR}/src/contrib/amsc.pyc
+rm -Rf ${RAVEN_DIR}/build  \
+   ${RAVEN_DIR}/crow/install/ \
+   ${RAVEN_DIR}/install/
 find ${RAVEN_DIR}/framework  -name '*.pyc' -exec rm '{}' \;
 find ${RAVEN_DIR}/scripts  -name '*.pyc' -exec rm '{}' \;
 find ${RAVEN_DIR}/rook  -name '*.pyc' -exec rm '{}' \;

framework/CustomDrivers/DriverUtils.py

@@ -100,7 +100,6 @@ def setupCpp():
   frameworkDir = findFramework()
   from utils import utils
   utils.find_crow(frameworkDir)
-  utils.add_path(os.path.join(frameworkDir,'contrib','AMSC'))
   utils.add_path(os.path.join(frameworkDir,'contrib'))
   ##TODO REMOVE PP3 WHEN RAY IS AVAILABLE FOR WINDOWS
   utils.add_path_recursively(os.path.join(frameworkDir,'contrib','pp'))

framework/Models/PostProcessors/TopologicalDecomposition.py

@@ -309,7 +309,7 @@ def run(self, inputIn):
 
     ## Possibly load this here in case people have trouble building it, so it
     ## only errors if they try to use it?
-    from AMSC_Object import AMSC_Object
+    from AMSC.AMSC_Object import AMSC_Object
 
     if self.__amsc is None:
       self.__amsc = AMSC_Object(X=self.inputData, Y=self.outputData,

framework/Samplers/LimitSurfaceSearch.py

@@ -27,7 +27,7 @@
 from math import ceil
 
 import Distributions
-from AMSC_Object import AMSC_Object
+from AMSC.AMSC_Object import AMSC_Object
 from utils import randomUtils
 from utils import InputData, InputTypes
 from .AdaptiveSampler import AdaptiveSampler

framework/SupervisedLearning/MSR.py

@@ -313,7 +313,7 @@ def __trainLocal__(self,featureVals,targetVals):
 
     # # Possibly load this here in case people have trouble building it, so it
     # # only errors if they try to use it?
-    from AMSC_Object import AMSC_Object
+    from AMSC.AMSC_Object import AMSC_Object
 
     self.X = featureVals[:][:]
     self.Y = targetVals

framework/UI/TopologyWindow.py

@@ -31,7 +31,7 @@
 
 from sys import path
 
-from AMSC_Object import QAMSC_Object
+from AMSC.AMSC_Object import QAMSC_Object
 from .BaseTopologicalView import BaseTopologicalView
 from .TopologyMapView import TopologyMapView
 from .SensitivityView import SensitivityView

framework/utils/utils.py

@@ -651,7 +651,8 @@ def find_crow(framework_dir):
     ravenDir = os.path.dirname(framework_dir)
     #Add the module directory to the search path.
     crowDirs = [os.path.join(ravenDir,"crow"),
-                os.path.join(os.path.dirname(ravenDir),"crow")]
+                os.path.join(os.path.dirname(ravenDir),"crow"),
+                ravenDir]
     if "CROW_DIR" in os.environ:
       crowDirs.insert(0,os.path.join(os.environ["CROW_DIR"]))
     for crowDir in crowDirs:

scripts/TestHarness/testers/RavenFramework.py

@@ -37,7 +37,7 @@
 RAVENDIR = os.path.abspath(os.path.join(myDir, '..', '..', '..', 'framework'))
 
 #Need to add the directory for AMSC for doing module checks.
-os.environ["PYTHONPATH"] = os.path.join(RAVENDIR, 'contrib') +\
+os.environ["PYTHONPATH"] = os.path.join(RAVENDIR, '..', 'install') +\
   os.pathsep + os.environ.get("PYTHONPATH", "")
 
 scriptDir = os.path.abspath(os.path.join(RAVENDIR, '..', 'scripts'))

scripts/library_report

@@ -54,7 +54,7 @@ for module, found, message, version in report_list:
     print(module,version,"\n",message,"\n")
   else:
     print(module+' not found\n')
-framework_dir = os.path.abspath(os.path.join(os.path.dirname(sys.argv[0]),"framework"))
+framework_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(sys.argv[0])),"framework"))
 utils.find_crow(framework_dir)
 try:
   distribution1D = utils.findCrowModule('distribution1D')

setup.py

@@ -25,6 +25,8 @@
 
 BOOST_INCLUDE_DIR = os.path.join(CROW_DIR,'contrib','include')
 RAVEN_INCLUDE_DIR = os.path.join('include','contrib')
+DIST_INCLUDE_DIR = os.path.join(CROW_DIR,'include', 'distributions')
+UTIL_INCLUDE_DIR = os.path.join(CROW_DIR,'include', 'utilities')
 
 # We need a custom build order in order to ensure that amsc.py is available
 # before we try to copy it to the target location
@@ -34,19 +36,44 @@ class CustomBuild(build):
                     ('build_clib', build.has_c_libraries),
                     ('build_scripts', build.has_scripts)]
 
-include_dirs=[RAVEN_INCLUDE_DIR,BOOST_INCLUDE_DIR]
-if sys.version_info.major > 2:
-  swig_opts=['-c++','-I'+RAVEN_INCLUDE_DIR, '-I'+BOOST_INCLUDE_DIR,'-py3']
-else:
-  swig_opts=['-c++','-I'+RAVEN_INCLUDE_DIR, '-I'+BOOST_INCLUDE_DIR]
+
+include_dirs=[RAVEN_INCLUDE_DIR,BOOST_INCLUDE_DIR, DIST_INCLUDE_DIR, UTIL_INCLUDE_DIR]
+swig_opts=['-c++','-I'+RAVEN_INCLUDE_DIR, '-I'+BOOST_INCLUDE_DIR,'-I'+DIST_INCLUDE_DIR, '-I'+UTIL_INCLUDE_DIR, '-py3']
 extra_compile_args=['-std=c++11']
-setup(name='amsc',
-      version='0.0',
-      description='A library for computing the Approximate Morse-Smale Complex (AMSC)',
-      ext_modules=[Extension('_amsc',['src/contrib/amsc.i',
-                                      'src/contrib/UnionFind.cpp',
-                                      'src/contrib/AMSC.cpp'],
-                             include_dirs=include_dirs, swig_opts=swig_opts,extra_compile_args=extra_compile_args)],
-      package_dir={'':'src/contrib'},
-      py_modules=['amsc'],
+try:
+    eigen_flags = subprocess.check_output(["./scripts/find_eigen.py"]).decode("ascii")
+except:
+  eigen_flags = ""
+if eigen_flags.startswith("-I"):
+  include_dirs.append(eigen_flags[2:].rstrip())
+setup(name='raven_cxx',
+      version='2.1',
+      description='RAVEN c++ dependenciences including A library for computing the Approximate Morse-Smale Complex (AMSC) and Crow probability tools',
+      package_dir={'AMSC': 'src/contrib/AMSC', 'crow_modules': 'src/crow_modules'},
+      ext_modules=[
+          Extension('crow_modules._distribution1D',
+                  ['src/crow_modules/distribution1D.i',
+                   'src/distributions/distribution.cxx',
+                   'src/utilities/MDreader.cxx',
+                   'src/utilities/inverseDistanceWeigthing.cxx',
+                   'src/utilities/microSphere.cxx',
+                   'src/utilities/NDspline.cxx',
+                   'src/utilities/ND_Interpolation_Functions.cxx',
+                   'src/distributions/distributionNDBase.cxx',
+                   'src/distributions/distributionNDNormal.cxx',
+                   'src/distributions/distributionFunctions.cxx',
+                   'src/distributions/DistributionContainer.cxx',
+                   'src/distributions/distribution_1D.cxx',
+                   'src/distributions/randomClass.cxx',
+                   'src/distributions/distributionNDCartesianSpline.cxx'],
+                include_dirs=include_dirs,
+                swig_opts=swig_opts,
+                extra_compile_args=extra_compile_args),
+          Extension('crow_modules._randomENG',['src/crow_modules/randomENG.i','src/distributions/randomClass.cxx'],include_dirs=include_dirs,swig_opts=swig_opts,extra_compile_args=extra_compile_args),
+          Extension('crow_modules._interpolationND',['src/crow_modules/interpolationND.i','src/utilities/ND_Interpolation_Functions.cxx','src/utilities/NDspline.cxx','src/utilities/microSphere.cxx','src/utilities/inverseDistanceWeigthing.cxx','src/utilities/MDreader.cxx','src/distributions/randomClass.cxx'],include_dirs=include_dirs,swig_opts=swig_opts,extra_compile_args=extra_compile_args),
+          Extension('AMSC._amsc',['src/contrib/AMSC/amsc.i',
+                             'src/contrib/AMSC/UnionFind.cpp',
+                             'src/contrib/AMSC/AMSC.cpp'],
+                    include_dirs=include_dirs, swig_opts=swig_opts,extra_compile_args=extra_compile_args)],
+      py_modules=['AMSC.amsc','crow_modules.distribution1D','crow_modules.randomENG','crow_modules.interpolationND', 'AMSC.AMSC_Object'],#+setuptools.find_packages('framework'),
       cmdclass={'build': CustomBuild})