diff --git a/.gitignore b/.gitignore index 9e01266..2567731 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,10 @@ .mydepend ./pipeline/miscTools/*.out +build/ +cmake-build-debug +examples/example_observation/* +examples/examplesimulation/* output_* pipeline/ramses_simulation.py external/libsdf/libsw/Malloc.c diff --git a/CMakeLists.txt b/CMakeLists.txt index 874a889..6538256 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -81,7 +81,7 @@ ELSE() ENDIF() SET(PYTHONPATH ${PYTHON_LOCAL_SITE_PACKAGE}) -configure_exec(${CMAKE_SOURCE_DIR}/python_tools/pipeline_source/prepareInputs.in.py +configure_exec(${CMAKE_SOURCE_DIR}/python_src/pipeline_source/prepareInputs.in.py ${CMAKE_BINARY_DIR}/pipeline prepareInputs.py) #configure_exec(${CMAKE_SOURCE_DIR}/python_tools/pipeline_source/applyMaskToMock.in.py #${CMAKE_BINARY_DIR}/pipeline applyMaskToMock.py) diff --git a/c_src/CMakeLists.txt b/c_source/CMakeLists.txt similarity index 100% rename from c_src/CMakeLists.txt rename to c_source/CMakeLists.txt diff --git a/c_src/jozov2/CMakeLists.txt b/c_source/jozov2/CMakeLists.txt similarity index 100% rename from c_src/jozov2/CMakeLists.txt rename to c_source/jozov2/CMakeLists.txt diff --git a/c_src/jozov2/findrtop.c b/c_source/jozov2/findrtop.c similarity index 100% rename from c_src/jozov2/findrtop.c rename to c_source/jozov2/findrtop.c diff --git a/c_src/jozov2/jozov2.cpp b/c_source/jozov2/jozov2.cpp similarity index 100% rename from c_src/jozov2/jozov2.cpp rename to c_source/jozov2/jozov2.cpp diff --git a/c_src/jozov2/jozov2.hpp b/c_source/jozov2/jozov2.hpp similarity index 100% rename from c_src/jozov2/jozov2.hpp rename to c_source/jozov2/jozov2.hpp diff --git a/c_src/jozov2/jozov2_io.cpp b/c_source/jozov2/jozov2_io.cpp similarity index 100% rename from c_src/jozov2/jozov2_io.cpp rename to c_source/jozov2/jozov2_io.cpp diff --git a/c_src/jozov2/jozov2_watershed.cpp b/c_source/jozov2/jozov2_watershed.cpp similarity index 100% rename from c_src/jozov2/jozov2_watershed.cpp rename to c_source/jozov2/jozov2_watershed.cpp diff --git a/c_src/jozov2/jozov2_zones.cpp b/c_source/jozov2/jozov2_zones.cpp similarity index 100% rename from c_src/jozov2/jozov2_zones.cpp rename to c_source/jozov2/jozov2_zones.cpp diff --git a/c_src/jozov2/zobov.hpp b/c_source/jozov2/zobov.hpp similarity index 100% rename from c_src/jozov2/zobov.hpp rename to c_source/jozov2/zobov.hpp diff --git a/c_src/prep/CMakeLists.txt b/c_source/prep/CMakeLists.txt similarity index 100% rename from c_src/prep/CMakeLists.txt rename to c_source/prep/CMakeLists.txt diff --git a/c_src/prep/generateMock.cpp b/c_source/prep/generateMock.cpp similarity index 100% rename from c_src/prep/generateMock.cpp rename to c_source/prep/generateMock.cpp diff --git a/c_src/prep/loaders/CMakeLists.txt b/c_source/prep/loaders/CMakeLists.txt similarity index 100% rename from c_src/prep/loaders/CMakeLists.txt rename to c_source/prep/loaders/CMakeLists.txt diff --git a/c_src/prep/loaders/basic_loader.cpp b/c_source/prep/loaders/basic_loader.cpp similarity index 100% rename from c_src/prep/loaders/basic_loader.cpp rename to c_source/prep/loaders/basic_loader.cpp diff --git a/c_src/prep/loaders/flash_loader.cpp b/c_source/prep/loaders/flash_loader.cpp similarity index 100% rename from c_src/prep/loaders/flash_loader.cpp rename to c_source/prep/loaders/flash_loader.cpp diff --git a/c_src/prep/loaders/gadget_loader.cpp b/c_source/prep/loaders/gadget_loader.cpp similarity index 100% rename from c_src/prep/loaders/gadget_loader.cpp rename to c_source/prep/loaders/gadget_loader.cpp diff --git a/c_src/prep/loaders/multidark_loader.cpp b/c_source/prep/loaders/multidark_loader.cpp similarity index 100% rename from c_src/prep/loaders/multidark_loader.cpp rename to c_source/prep/loaders/multidark_loader.cpp diff --git a/c_src/prep/loaders/ramses_loader.cpp b/c_source/prep/loaders/ramses_loader.cpp similarity index 100% rename from c_src/prep/loaders/ramses_loader.cpp rename to c_source/prep/loaders/ramses_loader.cpp diff --git a/c_src/prep/loaders/sdf_loader.cpp b/c_source/prep/loaders/sdf_loader.cpp similarity index 100% rename from c_src/prep/loaders/sdf_loader.cpp rename to c_source/prep/loaders/sdf_loader.cpp diff --git a/c_src/prep/loaders/sdfloader_internal.hpp b/c_source/prep/loaders/sdfloader_internal.hpp similarity index 100% rename from c_src/prep/loaders/sdfloader_internal.hpp rename to c_source/prep/loaders/sdfloader_internal.hpp diff --git a/c_src/prep/loaders/simulation_loader.cpp b/c_source/prep/loaders/simulation_loader.cpp similarity index 100% rename from c_src/prep/loaders/simulation_loader.cpp rename to c_source/prep/loaders/simulation_loader.cpp diff --git a/c_src/prep/loaders/simulation_loader.hpp b/c_source/prep/loaders/simulation_loader.hpp similarity index 100% rename from c_src/prep/loaders/simulation_loader.hpp rename to c_source/prep/loaders/simulation_loader.hpp diff --git a/c_src/prep/prepObservation.cpp b/c_source/prep/prepObservation.cpp similarity index 100% rename from c_src/prep/prepObservation.cpp rename to c_source/prep/prepObservation.cpp diff --git a/c_src/prep/prepObservation.ggo b/c_source/prep/prepObservation.ggo similarity index 100% rename from c_src/prep/prepObservation.ggo rename to c_source/prep/prepObservation.ggo diff --git a/c_src/prep/prepSimulation.cpp b/c_source/prep/prepSimulation.cpp similarity index 100% rename from c_src/prep/prepSimulation.cpp rename to c_source/prep/prepSimulation.cpp diff --git a/c_src/prep/prepSimulation.ggo b/c_source/prep/prepSimulation.ggo similarity index 100% rename from c_src/prep/prepSimulation.ggo rename to c_source/prep/prepSimulation.ggo diff --git a/c_src/pruning/CMakeLists.txt b/c_source/pruning/CMakeLists.txt similarity index 100% rename from c_src/pruning/CMakeLists.txt rename to c_source/pruning/CMakeLists.txt diff --git a/c_src/pruning/pruneVoids.cpp b/c_source/pruning/pruneVoids.cpp similarity index 100% rename from c_src/pruning/pruneVoids.cpp rename to c_source/pruning/pruneVoids.cpp diff --git a/c_src/pruning/pruneVoids.ggo b/c_source/pruning/pruneVoids.ggo similarity index 100% rename from c_src/pruning/pruneVoids.ggo rename to c_source/pruning/pruneVoids.ggo diff --git a/c_src/util/CMakeLists.txt b/c_source/util/CMakeLists.txt similarity index 100% rename from c_src/util/CMakeLists.txt rename to c_source/util/CMakeLists.txt diff --git a/c_src/util/contour_pixels.cpp b/c_source/util/contour_pixels.cpp similarity index 100% rename from c_src/util/contour_pixels.cpp rename to c_source/util/contour_pixels.cpp diff --git a/c_src/util/contour_pixels.hpp b/c_source/util/contour_pixels.hpp similarity index 100% rename from c_src/util/contour_pixels.hpp rename to c_source/util/contour_pixels.hpp diff --git a/c_src/util/gslIntegrate.hpp b/c_source/util/gslIntegrate.hpp similarity index 100% rename from c_src/util/gslIntegrate.hpp rename to c_source/util/gslIntegrate.hpp diff --git a/c_src/util/loadZobov.cpp b/c_source/util/loadZobov.cpp similarity index 100% rename from c_src/util/loadZobov.cpp rename to c_source/util/loadZobov.cpp diff --git a/c_src/util/loadZobov.hpp b/c_source/util/loadZobov.hpp similarity index 100% rename from c_src/util/loadZobov.hpp rename to c_source/util/loadZobov.hpp diff --git a/c_src/util/particleInfo.cpp b/c_source/util/particleInfo.cpp similarity index 100% rename from c_src/util/particleInfo.cpp rename to c_source/util/particleInfo.cpp diff --git a/c_src/util/particleInfo.hpp b/c_source/util/particleInfo.hpp similarity index 100% rename from c_src/util/particleInfo.hpp rename to c_source/util/particleInfo.hpp diff --git a/c_src/util/voidTree.hpp b/c_source/util/voidTree.hpp similarity index 100% rename from c_src/util/voidTree.hpp rename to c_source/util/voidTree.hpp diff --git a/c_src/zobov/CMakeLists.txt b/c_source/zobov/CMakeLists.txt similarity index 100% rename from c_src/zobov/CMakeLists.txt rename to c_source/zobov/CMakeLists.txt diff --git a/c_src/zobov/findrtop.c b/c_source/zobov/findrtop.c similarity index 100% rename from c_src/zobov/findrtop.c rename to c_source/zobov/findrtop.c diff --git a/c_src/zobov/jozov.c b/c_source/zobov/jozov.c similarity index 100% rename from c_src/zobov/jozov.c rename to c_source/zobov/jozov.c diff --git a/c_src/zobov/readfiles.c b/c_source/zobov/readfiles.c similarity index 100% rename from c_src/zobov/readfiles.c rename to c_source/zobov/readfiles.c diff --git a/c_src/zobov/voz.h b/c_source/zobov/voz.h similarity index 100% rename from c_src/zobov/voz.h rename to c_source/zobov/voz.h diff --git a/c_src/zobov/voz1b1.c b/c_source/zobov/voz1b1.c similarity index 100% rename from c_src/zobov/voz1b1.c rename to c_source/zobov/voz1b1.c diff --git a/c_src/zobov/vozinit.c b/c_source/zobov/vozinit.c similarity index 100% rename from c_src/zobov/vozinit.c rename to c_source/zobov/vozinit.c diff --git a/c_src/zobov/voztie.c b/c_source/zobov/voztie.c similarity index 100% rename from c_src/zobov/voztie.c rename to c_source/zobov/voztie.c diff --git a/c_src/zobov/vozutil.c b/c_source/zobov/vozutil.c similarity index 100% rename from c_src/zobov/vozutil.c rename to c_source/zobov/vozutil.c diff --git a/c_src/zobov/zobov_readme.txt b/c_source/zobov/zobov_readme.txt similarity index 100% rename from c_src/zobov/zobov_readme.txt rename to c_source/zobov/zobov_readme.txt diff --git a/python_src/misc_util/figureOutMask.py b/python_source/misc_util/figureOutMask.py similarity index 100% rename from python_src/misc_util/figureOutMask.py rename to python_source/misc_util/figureOutMask.py diff --git a/python_src/misc_util/gather_sources.py b/python_source/misc_util/gather_sources.py similarity index 100% rename from python_src/misc_util/gather_sources.py rename to python_source/misc_util/gather_sources.py diff --git a/python_src/pipeline_source/defaults.py b/python_source/pipeline_source/defaults.py similarity index 100% rename from python_src/pipeline_source/defaults.py rename to python_source/pipeline_source/defaults.py diff --git a/python_src/pipeline_source/prepareInputs.in.py b/python_source/pipeline_source/prepareInputs.in.py similarity index 100% rename from python_src/pipeline_source/prepareInputs.in.py rename to python_source/pipeline_source/prepareInputs.in.py diff --git a/python_src/setup.py b/python_source/setup.py similarity index 100% rename from python_src/setup.py rename to python_source/setup.py diff --git a/python_src/vide/__init__.py b/python_source/vide/__init__.py similarity index 100% rename from python_src/vide/__init__.py rename to python_source/vide/__init__.py diff --git a/python_src/vide/backend/__init__.py b/python_source/vide/backend/__init__.py similarity index 100% rename from python_src/vide/backend/__init__.py rename to python_source/vide/backend/__init__.py diff --git a/python_src/vide/backend/classes.py b/python_source/vide/backend/classes.py similarity index 100% rename from python_src/vide/backend/classes.py rename to python_source/vide/backend/classes.py diff --git a/python_src/vide/backend/cosmologyTools.py b/python_source/vide/backend/cosmologyTools.py similarity index 100% rename from python_src/vide/backend/cosmologyTools.py rename to python_source/vide/backend/cosmologyTools.py diff --git a/python_src/vide/backend/launchers.py b/python_source/vide/backend/launchers.py similarity index 100% rename from python_src/vide/backend/launchers.py rename to python_source/vide/backend/launchers.py diff --git a/python_src/vide/voidUtil/__init__.py b/python_source/vide/voidUtil/__init__.py similarity index 100% rename from python_src/vide/voidUtil/__init__.py rename to python_source/vide/voidUtil/__init__.py diff --git a/python_src/vide/voidUtil/catalogUtil.py b/python_source/vide/voidUtil/catalogUtil.py similarity index 100% rename from python_src/vide/voidUtil/catalogUtil.py rename to python_source/vide/voidUtil/catalogUtil.py diff --git a/python_src/vide/voidUtil/matchUtil.py b/python_source/vide/voidUtil/matchUtil.py similarity index 100% rename from python_src/vide/voidUtil/matchUtil.py rename to python_source/vide/voidUtil/matchUtil.py diff --git a/python_src/vide/voidUtil/periodic_kdtree.py b/python_source/vide/voidUtil/periodic_kdtree.py similarity index 100% rename from python_src/vide/voidUtil/periodic_kdtree.py rename to python_source/vide/voidUtil/periodic_kdtree.py diff --git a/python_src/vide/voidUtil/plotDefs.py b/python_source/vide/voidUtil/plotDefs.py similarity index 100% rename from python_src/vide/voidUtil/plotDefs.py rename to python_source/vide/voidUtil/plotDefs.py diff --git a/python_src/vide/voidUtil/plotUtil.py b/python_source/vide/voidUtil/plotUtil.py similarity index 100% rename from python_src/vide/voidUtil/plotUtil.py rename to python_source/vide/voidUtil/plotUtil.py diff --git a/python_src/vide/voidUtil/profileUtil.py b/python_source/vide/voidUtil/profileUtil.py similarity index 100% rename from python_src/vide/voidUtil/profileUtil.py rename to python_source/vide/voidUtil/profileUtil.py diff --git a/python_src/vide/voidUtil/xcorUtil.py b/python_source/vide/voidUtil/xcorUtil.py similarity index 100% rename from python_src/vide/voidUtil/xcorUtil.py rename to python_source/vide/voidUtil/xcorUtil.py diff --git a/python_src/vide/voidUtil/xcorlib.py b/python_source/vide/voidUtil/xcorlib.py similarity index 100% rename from python_src/vide/voidUtil/xcorlib.py rename to python_source/vide/voidUtil/xcorlib.py diff --git a/python_src/void_pipeline/__init__.py b/python_source/void_pipeline/__init__.py similarity index 100% rename from python_src/void_pipeline/__init__.py rename to python_source/void_pipeline/__init__.py diff --git a/python_src/void_pipeline/__main__.py b/python_source/void_pipeline/__main__.py similarity index 100% rename from python_src/void_pipeline/__main__.py rename to python_source/void_pipeline/__main__.py diff --git a/setup.py b/setup.py index 03e0a1b..0afebfd 100644 --- a/setup.py +++ b/setup.py @@ -208,8 +208,8 @@ vide_extension = CMakeExtension(name="vide") setup(name='vide', version='2.0', - packages=find_packages('python_tools'), - package_dir={'': 'python_tools'}, + packages=find_packages('python_src'), + package_dir={'': 'python_src'}, setup_requires=['cython','setuptools','healpy','argparse','scipy','astropy','extension-helpers','netCDF4'], install_requires=['argparse','scipy','astropy','extension-helpers','netCDF4','healpy'], ext_modules=[vide_extension],