From d48d740b78f456787e73c180d2b62a27b9ed914d Mon Sep 17 00:00:00 2001 From: "Paul M. Sutter" Date: Tue, 4 Jun 2024 08:57:09 +0200 Subject: [PATCH] fixed some dependency calls with new layout --- CMakeLists.txt | 4 ++-- .../example_observation.py | 2 +- python_source/{vide => }/backend/__init__.py | 0 python_source/{vide => }/backend/classes.py | 0 .../{vide => }/backend/cosmologyTools.py | 2 +- python_source/{vide => }/backend/launchers.py | 4 ++-- python_source/setup.py | 2 +- python_source/vide/__init__.py | 21 ------------------- .../{pipeline => vide_pipeline}/__init__.py | 0 .../{pipeline => vide_pipeline}/__main__.py | 16 +++++++------- .../{pipeline => vide_pipeline}/defaults.py | 0 .../vide_prepare_simulation.py} | 8 +++---- python_source/{vide => }/voidUtil/__init__.py | 0 .../{vide => }/voidUtil/catalogUtil.py | 4 ++-- .../{vide => }/voidUtil/matchUtil.py | 2 +- .../{vide => }/voidUtil/periodic_kdtree.py | 0 python_source/{vide => }/voidUtil/plotDefs.py | 0 python_source/{vide => }/voidUtil/plotUtil.py | 6 +++--- .../{vide => }/voidUtil/profileUtil.py | 4 ++-- python_source/{vide => }/voidUtil/xcorUtil.py | 2 +- python_source/{vide => }/voidUtil/xcorlib.py | 0 setup.py | 4 +++- 22 files changed, 32 insertions(+), 49 deletions(-) rename python_source/{vide => }/backend/__init__.py (100%) rename python_source/{vide => }/backend/classes.py (100%) rename python_source/{vide => }/backend/cosmologyTools.py (99%) rename python_source/{vide => }/backend/launchers.py (99%) delete mode 100644 python_source/vide/__init__.py rename python_source/{pipeline => vide_pipeline}/__init__.py (100%) rename python_source/{pipeline => vide_pipeline}/__main__.py (93%) rename python_source/{pipeline => vide_pipeline}/defaults.py (100%) rename python_source/{pipeline/vide_prepare_simulation => vide_pipeline/vide_prepare_simulation.py} (99%) rename python_source/{vide => }/voidUtil/__init__.py (100%) rename python_source/{vide => }/voidUtil/catalogUtil.py (99%) rename python_source/{vide => }/voidUtil/matchUtil.py (99%) rename python_source/{vide => }/voidUtil/periodic_kdtree.py (100%) rename python_source/{vide => }/voidUtil/plotDefs.py (100%) rename python_source/{vide => }/voidUtil/plotUtil.py (98%) rename python_source/{vide => }/voidUtil/profileUtil.py (99%) rename python_source/{vide => }/voidUtil/xcorUtil.py (99%) rename python_source/{vide => }/voidUtil/xcorlib.py (100%) diff --git a/CMakeLists.txt b/CMakeLists.txt index 5f166bb..8eaa656 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_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 diff --git a/examples/example_observation/example_observation.py b/examples/example_observation/example_observation.py index eb2c5f4..5f93b89 100644 --- a/examples/example_observation/example_observation.py +++ b/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 diff --git a/python_source/vide/backend/__init__.py b/python_source/backend/__init__.py similarity index 100% rename from python_source/vide/backend/__init__.py rename to python_source/backend/__init__.py diff --git a/python_source/vide/backend/classes.py b/python_source/backend/classes.py similarity index 100% rename from python_source/vide/backend/classes.py rename to python_source/backend/classes.py diff --git a/python_source/vide/backend/cosmologyTools.py b/python_source/backend/cosmologyTools.py similarity index 99% rename from python_source/vide/backend/cosmologyTools.py rename to python_source/backend/cosmologyTools.py index c6edd24..326dbac 100644 --- a/python_source/vide/backend/cosmologyTools.py +++ b/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'] diff --git a/python_source/vide/backend/launchers.py b/python_source/backend/launchers.py similarity index 99% rename from python_source/vide/backend/launchers.py rename to python_source/backend/launchers.py index cd7c86c..29ce9c1 100644 --- a/python_source/vide/backend/launchers.py +++ b/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 vide.backend.cosmologyTools import * +from backend.classes import * +from backend.cosmologyTools import * import pickle import scipy.interpolate as interpolate diff --git a/python_source/setup.py b/python_source/setup.py index 502b2b6..092328f 100644 --- a/python_source/setup.py +++ b/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'], ) diff --git a/python_source/vide/__init__.py b/python_source/vide/__init__.py deleted file mode 100644 index 2e41082..0000000 --- a/python_source/vide/__init__.py +++ /dev/null @@ -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 * diff --git a/python_source/pipeline/__init__.py b/python_source/vide_pipeline/__init__.py similarity index 100% rename from python_source/pipeline/__init__.py rename to python_source/vide_pipeline/__init__.py diff --git a/python_source/pipeline/__main__.py b/python_source/vide_pipeline/__main__.py similarity index 93% rename from python_source/pipeline/__main__.py rename to python_source/vide_pipeline/__main__.py index a14bf9b..cce451b 100644 --- a/python_source/pipeline/__main__.py +++ b/python_source/vide_pipeline/__main__.py @@ -23,8 +23,8 @@ # Stage 2 : find voids # Stage 3 : prune catalog -from vide.backend import * -import vide +from backend import * +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] - ZOBOV_PATH=f'{void_path}/bin/' + void_path = os.path.split(voidUtil.__file__)[0] + 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): diff --git a/python_source/pipeline/defaults.py b/python_source/vide_pipeline/defaults.py similarity index 100% rename from python_source/pipeline/defaults.py rename to python_source/vide_pipeline/defaults.py diff --git a/python_source/pipeline/vide_prepare_simulation b/python_source/vide_pipeline/vide_prepare_simulation.py similarity index 99% rename from python_source/pipeline/vide_prepare_simulation rename to python_source/vide_pipeline/vide_prepare_simulation.py index 4fbd5a8..02499ee 100644 --- a/python_source/pipeline/vide_prepare_simulation +++ b/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() diff --git a/python_source/vide/voidUtil/__init__.py b/python_source/voidUtil/__init__.py similarity index 100% rename from python_source/vide/voidUtil/__init__.py rename to python_source/voidUtil/__init__.py diff --git a/python_source/vide/voidUtil/catalogUtil.py b/python_source/voidUtil/catalogUtil.py similarity index 99% rename from python_source/vide/voidUtil/catalogUtil.py rename to python_source/voidUtil/catalogUtil.py index dbae453..d7e31dd 100644 --- a/python_source/vide/voidUtil/catalogUtil.py +++ b/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 diff --git a/python_source/vide/voidUtil/matchUtil.py b/python_source/voidUtil/matchUtil.py similarity index 99% rename from python_source/vide/voidUtil/matchUtil.py rename to python_source/voidUtil/matchUtil.py index 6856880..d365098 100644 --- a/python_source/vide/voidUtil/matchUtil.py +++ b/python_source/voidUtil/matchUtil.py @@ -20,7 +20,7 @@ #+ __all__=['compareCatalogs',] -from vide.backend import * +from backend import * import imp import pickle import os diff --git a/python_source/vide/voidUtil/periodic_kdtree.py b/python_source/voidUtil/periodic_kdtree.py similarity index 100% rename from python_source/vide/voidUtil/periodic_kdtree.py rename to python_source/voidUtil/periodic_kdtree.py diff --git a/python_source/vide/voidUtil/plotDefs.py b/python_source/voidUtil/plotDefs.py similarity index 100% rename from python_source/vide/voidUtil/plotDefs.py rename to python_source/voidUtil/plotDefs.py diff --git a/python_source/vide/voidUtil/plotUtil.py b/python_source/voidUtil/plotUtil.py similarity index 98% rename from python_source/vide/voidUtil/plotUtil.py rename to python_source/voidUtil/plotUtil.py index b835019..bdba618 100644 --- a/python_source/vide/voidUtil/plotUtil.py +++ b/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 -from vide.voidUtil import getArray, shiftPart, getVoidPart +import backend.cosmologyTools as vp +from voidUtil import getArray, shiftPart, getVoidPart def fill_between(x, y1, y2=0, ax=None, **kwargs): """Plot filled region between `y1` and `y2`. diff --git a/python_source/vide/voidUtil/profileUtil.py b/python_source/voidUtil/profileUtil.py similarity index 99% rename from python_source/vide/voidUtil/profileUtil.py rename to python_source/voidUtil/profileUtil.py index 0577680..b5ba21d 100644 --- a/python_source/vide/voidUtil/profileUtil.py +++ b/python_source/voidUtil/profileUtil.py @@ -19,8 +19,8 @@ #+ __all__=['buildProfile','fitHSWProfile','getHSWProfile',] -from vide.backend.classes import * -from vide.voidUtil import * +from backend.classes import * +from voidUtil import * from .plotDefs import * import numpy as np import os diff --git a/python_source/vide/voidUtil/xcorUtil.py b/python_source/voidUtil/xcorUtil.py similarity index 99% rename from python_source/vide/voidUtil/xcorUtil.py rename to python_source/voidUtil/xcorUtil.py index 5fe4109..6b92850 100644 --- a/python_source/vide/voidUtil/xcorUtil.py +++ b/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="./", diff --git a/python_source/vide/voidUtil/xcorlib.py b/python_source/voidUtil/xcorlib.py similarity index 100% rename from python_source/vide/voidUtil/xcorlib.py rename to python_source/voidUtil/xcorlib.py diff --git a/setup.py b/setup.py index 966a570..25e568a 100644 --- a/setup.py +++ b/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!")