fixed some dependency calls with new layout

CMakeLists.txt

@@ -81,7 +81,7 @@ ELSE()
 ENDIF()
 
 SET(PYTHONPATH ${PYTHON_LOCAL_SITE_PACKAGE})
-configure_exec(${CMAKE_SOURCE_DIR}/python_source/pipeline/vide_prepare_simulation
+configure_exec(${CMAKE_SOURCE_DIR}/python_source/vide_pipeline/vide_prepare_simulation.py
 ${CMAKE_BINARY_DIR}/pipeline vide_prepare_simulation)
 #configure_exec(${CMAKE_SOURCE_DIR}/python_tools/pipeline_source/applyMaskToMock.in.py
 #${CMAKE_BINARY_DIR}/pipeline applyMaskToMock.py)
@@ -96,7 +96,7 @@ if (INSTALL_CTOOLS_IN_PYTHON)
 else()
   SET(VIDE_BIN ${CMAKE_INSTALL_PREFIX}/bin)
 endif()
-message(STATUS "Vide binary directory: ${VIDE_BIN}")
+message(STATUS "VIDE binary directory: ${VIDE_BIN}")
 
 #add_custom_target(python_pipeline ALL
 #  COMMAND ${python_build_environment} ${CMAKE_SOURCE_DIR}/external/python_build.cmake

examples/example_observation/example_observation.py

@@ -21,7 +21,7 @@
 
 import os
 import numpy as np
-from vide.backend.classes import *
+from backend.classes import *
 
 # if True, will scan log files for last known completed state and run from there
 continueRun = False

python_source/backend/cosmologyTools.py

@@ -24,7 +24,7 @@ import numpy as np
 import scipy.integrate as integrate
 import healpy as healpy
 import os
-from vide.backend import *
+from backend import *
 
 __all__=['expansion', 'angularDiameter', 'aveExpansion', 'getSurveyProps']
 

python_source/backend/launchers.py

@@ -34,8 +34,8 @@ import subprocess
 import sys
 from   pylab import figure
 from   netCDF4 import Dataset
-from vide.backend.classes import *
+from backend.classes import *
-from vide.backend.cosmologyTools import *
+from backend.cosmologyTools import *
 import pickle
 import scipy.interpolate as interpolate
 

python_source/setup.py

@@ -30,5 +30,5 @@ setup(
     version='3.0',
     include_dirs = [np.get_include()],
     packages=
-       ['vide','vide.backend','vide.voidUtil'],
+       ['backend','voidUtil'],
 )

python_source/vide/__init__.py

@@ -1,21 +0,0 @@
-#+
-#   VIDE -- Void IDentification and Examination -- ./python_tools/vide/__init__.py
-#   Copyright (C) 2010-2014 Guilhem Lavaux
-#   Copyright (C) 2011-2014 P. M. Sutter
-#
-#   This program is free software; you can redistribute it and/or modify
-#   it under the terms of the GNU General Public License as published by
-#   the Free Software Foundation; version 2 of the License.
-# 
-#
-#   This program is distributed in the hope that it will be useful,
-#   but WITHOUT ANY WARRANTY; without even the implied warranty of
-#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#   GNU General Public License for more details.
-#
-#   You should have received a copy of the GNU General Public License along
-#   with this program; if not, write to the Free Software Foundation, Inc.,
-#   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#+
-from .backend  import *
-from .voidUtil import *

python_source/vide_pipeline/__main__.py

@@ -23,8 +23,8 @@
 # Stage 2 : find voids
 # Stage 3 : prune catalog
 
-from vide.backend import *
+from backend import *
-import vide
+import voidUtil
 import imp
 import os
 import pickle
@@ -44,10 +44,10 @@ if (len(sys.argv) > 1):
   parms = imp.load_source("name", filename)
   regenerateFlag = False
   globals().update(vars(parms))
-  void_path = os.path.split(vide.__file__)[0]
+  void_path = os.path.split(voidUtil.__file__)[0]
-  ZOBOV_PATH=f'{void_path}/bin/'
+  ZOBOV_PATH=f'{void_path}/../vide/bin/' # this needs to be cleaned up
   CTOOLS_PATH=ZOBOV_PATH
-  print(f"ZOBOV_PATH is  {ZOBOV_PATH}")
+  #print(f"ZOBOV_PATH is  {ZOBOV_PATH}")
 else:
   print(" Using default parameters")
 
@@ -105,7 +105,8 @@ for sample in dataSampleList:
 
     launchZobov(sample, ZOBOV_PATH, zobovDir=zobovDir, logDir=logDir, 
                 continueRun=continueRun, numZobovDivisions=numZobovDivisions,
-                 numZobovThreads=numZobovThreads, mergingThreshold=mergingThreshold)
+                 numZobovThreads=numZobovThreads,
+                 mergingThreshold=mergingThreshold)
 
   # -------------------------------------------------------------------------
   if (startCatalogStage <= 3) and (endCatalogStage >= 3) and not sample.isCombo:
@@ -119,7 +120,8 @@ for sample in dataSampleList:
 
     launchPrune(sample, PRUNE_PATH, 
                 logFile=logFile, zobovDir=zobovDir, 
-                useComoving=sample.useComoving, continueRun=continueRun, mergingThreshold=mergingThreshold)
+                useComoving=sample.useComoving, continueRun=continueRun,
+                mergingThreshold=mergingThreshold)
 
 # -------------------------------------------------------------------------
 if (startCatalogStage <= 4) and (endCatalogStage >= 4):

python_source/vide_pipeline/vide_prepare_simulation.py

@@ -22,7 +22,7 @@
 import numpy as np
 import os
 import sys
-import vide as vp
+import backend as vp
 import argparse
 import imp
 import subprocess
@@ -53,7 +53,7 @@ parser.add_argument('--parm', dest='parm',
 args = parser.parse_args()
 
 
-defaultsFile = "@CMAKE_SOURCE_DIR@/python_tools/pipeline_source/defaults.py"
+defaultsFile = "@CMAKE_SOURCE_DIR@/python_source/pipeline/defaults.py"
 parms = imp.load_source("name", defaultsFile)
 globals().update(vars(parms))
 
@@ -162,7 +162,7 @@ def writeScript(setName, dataFileNameBase, dataFormat,
 
   header = """#!/usr/bin/env/python
 import os
-from vide.backend.classes import *
+from backend.classes import *
 
 continueRun = {continueRun} # set to True to enable restarting aborted jobs
 startCatalogStage = {startCatalogStage}
@@ -345,7 +345,7 @@ for iSubSample in range(len(subSamples)):
     else:
       partFileList.append(particleFileBase.replace(particleFileDummy, 
                                                    fileNums[iRedshift]))
-
+  
   if args.script or args.all:
     print(" Doing subsample", thisSubSample, "scripts")
     sys.stdout.flush()

python_source/voidUtil/catalogUtil.py

@@ -23,7 +23,7 @@
 import numpy as np
 from netCDF4 import Dataset
 import sys
-from vide.backend import *
+from backend import *
 import pickle
 from .periodic_kdtree import PeriodicCKDTree
 import os
@@ -542,7 +542,7 @@ def filterVoidsOnCoreDen(catalog, maxCoreDen):
 # -----------------------------------------------------------------------------
 def filterVoidsOnDenCon(catalog, minDenCon):
   catalog.voids = [v for v in catalog.voids if v.densCon >= minDenCon]
-
+  catalog.numVoids = len(catalog.voids)
   return catalog
 
 

python_source/voidUtil/matchUtil.py

@@ -20,7 +20,7 @@
 #+
 __all__=['compareCatalogs',]
 
-from vide.backend import *
+from backend import *
 import imp
 import pickle
 import os

python_source/voidUtil/plotUtil.py

@@ -19,13 +19,13 @@
 #+
 __all__=['plotNumberFunction','plotEllipDist','plotVoidCells']
 
-from vide.backend.classes import *
+from backend.classes import *
 from .plotDefs import *
 import numpy as np
 import os
 import pylab as plt
-import vide.backend.cosmologyTools as vp
+import backend.cosmologyTools as vp
-from vide.voidUtil import getArray, shiftPart, getVoidPart
+from voidUtil import getArray, shiftPart, getVoidPart
 
 def fill_between(x, y1, y2=0, ax=None, **kwargs):
     """Plot filled region between `y1` and `y2`.

python_source/voidUtil/profileUtil.py

@@ -19,8 +19,8 @@
 #+
 __all__=['buildProfile','fitHSWProfile','getHSWProfile',]
 
-from vide.backend.classes import *
+from backend.classes import *
-from vide.voidUtil import *
+from voidUtil import *
 from .plotDefs import *
 import numpy as np
 import os

python_source/voidUtil/xcorUtil.py

@@ -23,7 +23,7 @@ import matplotlib.pyplot as plt
 import matplotlib.cm as cm
 from matplotlib import rc
 from . import xcorlib
-from vide.voidUtil import getArray
+from voidUtil import getArray
 
 def computeXcor(catalog,
                 figDir="./",

setup.py

@@ -213,7 +213,7 @@ setup(name='vide',
       setup_requires=['cython','setuptools','healpy','argparse','scipy','astropy','extension-helpers','netCDF4'],
       install_requires=['argparse','scipy','astropy','extension-helpers','netCDF4','healpy'],
       ext_modules=[vide_extension],
-      description='The VIDE pipeline analysis for Cosmic Voids',
+      description='The VIDE pipeline for Cosmic Voids',
       long_description=open("./README.md", 'r').read(),
       long_description_content_type="text/markdown",
       keywords="cosmology, interpolation, cmake, extension",
@@ -236,3 +236,5 @@ setup(name='vide',
           'install_scripts': install_scripts,
           }
 )
+
+print("Installation finished. VIDE is ready to run!")