[cig-commits] r19793 - in short/3D/PyLith/trunk/applications: . utilities
brad at geodynamics.org
brad at geodynamics.org
Thu Mar 15 15:57:56 PDT 2012
Author: brad
Date: 2012-03-15 15:57:55 -0700 (Thu, 15 Mar 2012)
New Revision: 19793
Added:
short/3D/PyLith/trunk/applications/utilities/pylith_genxdmf.in
short/3D/PyLith/trunk/applications/utilities/pylithinfo.in
Removed:
short/3D/PyLith/trunk/applications/utilities/pylith_genxdmf
short/3D/PyLith/trunk/applications/utilities/pylithinfo
Modified:
short/3D/PyLith/trunk/applications/pylith.in
short/3D/PyLith/trunk/applications/pylith_prepmesh.in
short/3D/PyLith/trunk/applications/utilities/Makefile.am
Log:
Merge from stable.
Modified: short/3D/PyLith/trunk/applications/pylith.in
===================================================================
--- short/3D/PyLith/trunk/applications/pylith.in 2012-03-15 22:55:32 UTC (rev 19792)
+++ short/3D/PyLith/trunk/applications/pylith.in 2012-03-15 22:57:55 UTC (rev 19793)
@@ -10,7 +10,7 @@
# This code was developed as part of the Computational Infrastructure
# for Geodynamics (http://geodynamics.org).
#
-# Copyright (c) 2010-2011 University of California, Davis
+# Copyright (c) 2010-2012 University of California, Davis
#
# See COPYING for license information.
#
Modified: short/3D/PyLith/trunk/applications/pylith_prepmesh.in
===================================================================
--- short/3D/PyLith/trunk/applications/pylith_prepmesh.in 2012-03-15 22:55:32 UTC (rev 19792)
+++ short/3D/PyLith/trunk/applications/pylith_prepmesh.in 2012-03-15 22:57:55 UTC (rev 19793)
@@ -10,7 +10,7 @@
# This code was developed as part of the Computational Infrastructure
# for Geodynamics (http://geodynamics.org).
#
-# Copyright (c) 2010-2011 University of California, Davis
+# Copyright (c) 2010-2012 University of California, Davis
#
# See COPYING for license information.
#
Modified: short/3D/PyLith/trunk/applications/utilities/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/applications/utilities/Makefile.am 2012-03-15 22:55:32 UTC (rev 19792)
+++ short/3D/PyLith/trunk/applications/utilities/Makefile.am 2012-03-15 22:57:55 UTC (rev 19793)
@@ -16,10 +16,50 @@
# ----------------------------------------------------------------------
#
-dist_bin_SCRIPTS = \
+bin_SCRIPTS = \
pylithinfo \
pylith_genxdmf \
powerlaw_gendb.py
+INTERPRETER = $(PYTHON)
+noinstINTERPRETER = $(PYTHON)
+
+do_build = sed -e s%[@]INTERPRETER[@]%$(noinstINTERPRETER)%g -e s%[@]PYTHONPATH[@]%$(noinstPYTHONPATH)%g
+do_install = sed -e s%[@]INTERPRETER[@]%$(INTERPRETER)%g -e s%[@]PYTHONPATH[@]%$(PYTHONPATH)%g
+
+pylithinfo: $(srcdir)/pylithinfo.in Makefile
+ $(do_build) < $(srcdir)/pylithinfo.in > $@ || (rm -f $@ && exit 1)
+ chmod +x $@
+
+pylith_genxdmf: $(srcdir)/pylith_genxdmf.in Makefile
+ $(do_build) < $(srcdir)/pylith_genxdmf.in > $@ || (rm -f $@ && exit 1)
+ chmod +x $@
+
+install-binSCRIPTS: $(bin_SCRIPTS)
+ @$(NORMAL_INSTALL)
+ test -z "$(bindir)" || $(mkdir_p) "$(DESTDIR)$(bindir)"
+ @list='$(bin_SCRIPTS)'; for p in $$list; do \
+ if test -f "$$p.in"; then d=; else d="$(srcdir)/"; fi; \
+ if test -f $$d$$p.in; then \
+ f=`echo "$$p" | sed 's|^.*/||;$(transform)'`; \
+ echo " $(do_install) '$$d$$p.in' > '$(DESTDIR)$(bindir)/$$f'"; \
+ $(do_install) "$$d$$p.in" > "$(DESTDIR)$(bindir)/$$f"; \
+ echo " chmod +x '$(DESTDIR)$(bindir)/$$f'"; \
+ chmod +x "$(DESTDIR)$(bindir)/$$f"; \
+ else :; fi; \
+ done
+
+EXTRA_DIST = \
+ pylithinfo.in \
+ pylith_genxdmf.in
+
+CLEANFILES = $(bin_SCRIPTS)
+
+
# End of file
+
+
+
+
+# End of file
Deleted: short/3D/PyLith/trunk/applications/utilities/pylith_genxdmf
===================================================================
--- short/3D/PyLith/trunk/applications/utilities/pylith_genxdmf 2012-03-15 22:55:32 UTC (rev 19792)
+++ short/3D/PyLith/trunk/applications/utilities/pylith_genxdmf 2012-03-15 22:57:55 UTC (rev 19793)
@@ -1,74 +0,0 @@
-#!/usr/bin/env nemesis
-#
-# ======================================================================
-#
-# Brad T. Aagaard, U.S. Geological Survey
-# Charles A. Williams, GNS Science
-# Matthew G. Knepley, University of Chicago
-#
-# This code was developed as part of the Computational Infrastructure
-# for Geodynamics (http://geodynamics.org).
-#
-# Copyright (c) 2010-2011 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ======================================================================
-#
-
-# This script creates a metadata file (.xmf) from an HDF5 file written
-# by PyLith permitting the data to be viewed in VTK visualization
-# software, such as ParaView and Visit.
-#
-# Usage: pylith_genxdmf --file=FILE
-
-__requires__ = "PyLith"
-
-
-# ======================================================================
-class GenXdmfApp(object):
- """
- Application for generating an Xdmf file for an HDF5 file.
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="pylith_genxdmf"):
- """
- Constructor.
- """
- self.filename = "output.h5"
- return
-
-
- def main(self, *args, **kwds):
- """
- Main entry point for application.
- """
- from pylith.meshio.Xdmf import Xdmf
- writer = Xdmf()
- filenameHDF5 = self.filename
- filenameXdmf = filenameHDF5.replace(".h5", ".xmf")
- writer.write(filenameXdmf, filenameHDF5)
- return
-
-
-# ----------------------------------------------------------------------
-if __name__ == "__main__":
-
- usage = "%prog --file=FILE"
- from optparse import OptionParser
- parser = OptionParser(usage=usage)
- parser.add_option("-f", "--file",
- dest="filename",
- type="string", metavar="FILE",
- help="Create Xdmf file for HDF5 file FILE. [output.h5]",
- default="output.h5")
- (options, args) = parser.parse_args()
-
- app = GenXdmfApp()
- app.filename = options.filename
- app.main()
-
-
-# End of file
Copied: short/3D/PyLith/trunk/applications/utilities/pylith_genxdmf.in (from rev 19792, short/3D/PyLith/branches/v1.6-stable/applications/utilities/pylith_genxdmf.in)
===================================================================
--- short/3D/PyLith/trunk/applications/utilities/pylith_genxdmf.in (rev 0)
+++ short/3D/PyLith/trunk/applications/utilities/pylith_genxdmf.in 2012-03-15 22:57:55 UTC (rev 19793)
@@ -0,0 +1,74 @@
+#!/usr/bin/env nemesis
+#
+# ======================================================================
+#
+# Brad T. Aagaard, U.S. Geological Survey
+# Charles A. Williams, GNS Science
+# Matthew G. Knepley, University of Chicago
+#
+# This code was developed as part of the Computational Infrastructure
+# for Geodynamics (http://geodynamics.org).
+#
+# Copyright (c) 2010-2012 University of California, Davis
+#
+# See COPYING for license information.
+#
+# ======================================================================
+#
+
+# This script creates a metadata file (.xmf) from an HDF5 file written
+# by PyLith permitting the data to be viewed in VTK visualization
+# software, such as ParaView and Visit.
+#
+# Usage: pylith_genxdmf --file=FILE
+
+__requires__ = "PyLith"
+
+
+# ======================================================================
+class GenXdmfApp(object):
+ """
+ Application for generating an Xdmf file for an HDF5 file.
+ """
+
+ # PUBLIC METHODS /////////////////////////////////////////////////////
+
+ def __init__(self, name="pylith_genxdmf"):
+ """
+ Constructor.
+ """
+ self.filename = "output.h5"
+ return
+
+
+ def main(self, *args, **kwds):
+ """
+ Main entry point for application.
+ """
+ from pylith.meshio.Xdmf import Xdmf
+ writer = Xdmf()
+ filenameHDF5 = self.filename
+ filenameXdmf = filenameHDF5.replace(".h5", ".xmf")
+ writer.write(filenameXdmf, filenameHDF5)
+ return
+
+
+# ----------------------------------------------------------------------
+if __name__ == "__main__":
+
+ usage = "%prog --file=FILE"
+ from optparse import OptionParser
+ parser = OptionParser(usage=usage)
+ parser.add_option("-f", "--file",
+ dest="filename",
+ type="string", metavar="FILE",
+ help="Create Xdmf file for HDF5 file FILE. [output.h5]",
+ default="output.h5")
+ (options, args) = parser.parse_args()
+
+ app = GenXdmfApp()
+ app.filename = options.filename
+ app.main()
+
+
+# End of file
Deleted: short/3D/PyLith/trunk/applications/utilities/pylithinfo
===================================================================
--- short/3D/PyLith/trunk/applications/utilities/pylithinfo 2012-03-15 22:55:32 UTC (rev 19792)
+++ short/3D/PyLith/trunk/applications/utilities/pylithinfo 2012-03-15 22:57:55 UTC (rev 19793)
@@ -1,193 +0,0 @@
-#!/usr/bin/env nemesis
-#
-# ======================================================================
-#
-# Brad T. Aagaard, U.S. Geological Survey
-# Charles A. Williams, GNS Science
-# Matthew G. Knepley, University of Chicago
-#
-# This code was developed as part of the Computational Infrastructure
-# for Geodynamics (http://geodynamics.org).
-#
-# Copyright (c) 2010-2011 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ======================================================================
-#
-
-# This script dumps all PyLith parameters (defaults plus those
-# specified by the user to a text file. The default name of the output
-# file is 'pylith_parameters.txt'. Verbose output includes a
-# description of the parameter along with where it's current value was
-# set.
-#
-# Usage: pylithinfo.py [--verbose] [--fileout=FILE] [PyLith args]
-
-__requires__ = "PyLith"
-
-
-# ======================================================================
-class ParametersApp(object):
- """
- Application for printing current PyLith parameters to a text file.
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="pylithinfo"):
- """
- Constructor.
- """
- self.verbose = False
- self.filename = "pylith_parameters.txt"
- self.pylith_args = ""
- self._tab = " "
- self._printPropertyFn = self._printPropertyBasic
- self._printFacilityFn = self._printFacilityBasic
- return
-
-
- def main(self, *args, **kwds):
- """
- Main entry point for application.
- """
- from pylith.apps.PyLithApp import InfoApp
- targetapp = InfoApp(self.pylith_args)
- targetapp.run(*args, **kwds)
-
- if self.verbose:
- self._printPropertyFn = self._printPropertyVerbose
- self._printFacilityFn = self._printFacilityVerbose
- else:
- self._printPropertyFn = self._printPropertyBasic
- self._printFacilityFn = self._printFacilityBasic
-
- depth = 0
- fout = open(self.filename, "w")
- fout.write("Application: %s %s\n" % (targetapp.name, targetapp))
- self._printParams(fout, targetapp, depth+1)
- fout.close()
- return
-
-
- # PRIVATE METHODS ////////////////////////////////////////////////////
-
- def _printParams(self, fout, obj, depth):
- """
- Print objects parameters to fout.
- """
- propertyNames = obj.inventory.propertyNames()
- facilityNames = obj.inventory.facilityNames()
-
- propertiesOmit = ["help",
- "help-components",
- "help-persistence",
- "help-properties",
- "typos",
- ]
- facilitiesOmit = ["weaver",
- ]
-
- propertyNames.sort()
- facilityNames.sort()
-
- for name in propertyNames:
- if name in facilityNames or name in propertiesOmit:
- continue
- trait = obj.inventory.getTrait(name)
- descriptor = obj.inventory.getTraitDescriptor(name)
- self._printPropertyFn(fout, name, trait, descriptor, depth)
- for name in facilityNames:
- if name in facilitiesOmit:
- continue
- trait = obj.inventory.getTrait(name)
- descriptor = obj.inventory.getTraitDescriptor(name)
- self._printFacilityFn(fout, name, trait, descriptor, depth)
- return
-
-
- def _printPropertyBasic(self, fout, name, trait, descriptor, depth):
- """
- Print property name, type, and value.
- """
- indent = self._tab*depth
- fout.write("%s%s (%s) = %s\n" % \
- (indent, name, trait.type, descriptor.value))
- return
-
-
- def _printFacilityBasic(self, fout, name, trait, descriptor, depth):
- """
- Print facility name, type, and value.
- """
- indent = self._tab*depth
- fout.write("%s%s = %s (%s)\n" % \
- (indent, name, descriptor.value.name, descriptor.value))
- self._printParams(fout, descriptor.value, depth+1)
- return
-
-
- def _printPropertyVerbose(self, fout, name, trait, descriptor, depth):
- """
- Print property, name, type, value, description, and location set.
- """
- indent = self._tab*depth
- fout.write("\n%s%s (%s) = %s\n" % \
- (indent, name, trait.type, descriptor.value))
-
- indent += self._tab
- try:
- description = trait.meta['tip']
- except KeyError:
- description = "No description available."
- fout.write("%sDescription: %s\n" % (indent, description))
- fout.write("%sSet from: %s\n" % (indent, descriptor.locator))
- return
-
-
- def _printFacilityVerbose(self, fout, name, trait, descriptor, depth):
- """
- Print facility name, type, value, description, and location set.
- """
- indent = self._tab*depth
- fout.write("\n%s%s = %s (%s)\n" % \
- (indent, name, descriptor.value.name, descriptor.value))
-
- indent += self._tab
- try:
- description = trait.meta['tip']
- except KeyError:
- description = "No description available."
- fout.write("%sDescription: %s\n" % (indent, description))
- fout.write("%sSet from: %s\n" % (indent, descriptor.locator))
- fout.write("%sConfigurable as: %s\n" % \
- (indent, ", ".join(descriptor.value.aliases)))
-
- self._printParams(fout, descriptor.value, depth+1)
- return
-
-
-# ----------------------------------------------------------------------
-if __name__ == "__main__":
-
- usage = "%prog [options] [PyLith args]"
- from optparse import OptionParser
- parser = OptionParser(usage=usage)
- parser.add_option("-v", "--verbose", dest="verbose",
- action="store_true", default=False,
- help="Print verbose output.")
- parser.add_option("-o", "--fileout", dest="filename",
- type="string", metavar="FILE",
- help="Write to FILE. [pylith_parameters.txt]",
- default="pylith_parameters.txt")
- (options, args) = parser.parse_args()
-
- app = ParametersApp()
- app.verbose = options.verbose
- app.filename = options.filename
- app.pylith_args = args
- app.main()
-
-
-# End of file
Copied: short/3D/PyLith/trunk/applications/utilities/pylithinfo.in (from rev 19792, short/3D/PyLith/branches/v1.6-stable/applications/utilities/pylithinfo.in)
===================================================================
--- short/3D/PyLith/trunk/applications/utilities/pylithinfo.in (rev 0)
+++ short/3D/PyLith/trunk/applications/utilities/pylithinfo.in 2012-03-15 22:57:55 UTC (rev 19793)
@@ -0,0 +1,193 @@
+#!/usr/bin/env nemesis
+#
+# ======================================================================
+#
+# Brad T. Aagaard, U.S. Geological Survey
+# Charles A. Williams, GNS Science
+# Matthew G. Knepley, University of Chicago
+#
+# This code was developed as part of the Computational Infrastructure
+# for Geodynamics (http://geodynamics.org).
+#
+# Copyright (c) 2010-2012 University of California, Davis
+#
+# See COPYING for license information.
+#
+# ======================================================================
+#
+
+# This script dumps all PyLith parameters (defaults plus those
+# specified by the user to a text file. The default name of the output
+# file is 'pylith_parameters.txt'. Verbose output includes a
+# description of the parameter along with where it's current value was
+# set.
+#
+# Usage: pylithinfo.py [--verbose] [--fileout=FILE] [PyLith args]
+
+__requires__ = "PyLith"
+
+
+# ======================================================================
+class ParametersApp(object):
+ """
+ Application for printing current PyLith parameters to a text file.
+ """
+
+ # PUBLIC METHODS /////////////////////////////////////////////////////
+
+ def __init__(self, name="pylithinfo"):
+ """
+ Constructor.
+ """
+ self.verbose = False
+ self.filename = "pylith_parameters.txt"
+ self.pylith_args = ""
+ self._tab = " "
+ self._printPropertyFn = self._printPropertyBasic
+ self._printFacilityFn = self._printFacilityBasic
+ return
+
+
+ def main(self, *args, **kwds):
+ """
+ Main entry point for application.
+ """
+ from pylith.apps.PyLithApp import InfoApp
+ targetapp = InfoApp(self.pylith_args)
+ targetapp.run(*args, **kwds)
+
+ if self.verbose:
+ self._printPropertyFn = self._printPropertyVerbose
+ self._printFacilityFn = self._printFacilityVerbose
+ else:
+ self._printPropertyFn = self._printPropertyBasic
+ self._printFacilityFn = self._printFacilityBasic
+
+ depth = 0
+ fout = open(self.filename, "w")
+ fout.write("Application: %s %s\n" % (targetapp.name, targetapp))
+ self._printParams(fout, targetapp, depth+1)
+ fout.close()
+ return
+
+
+ # PRIVATE METHODS ////////////////////////////////////////////////////
+
+ def _printParams(self, fout, obj, depth):
+ """
+ Print objects parameters to fout.
+ """
+ propertyNames = obj.inventory.propertyNames()
+ facilityNames = obj.inventory.facilityNames()
+
+ propertiesOmit = ["help",
+ "help-components",
+ "help-persistence",
+ "help-properties",
+ "typos",
+ ]
+ facilitiesOmit = ["weaver",
+ ]
+
+ propertyNames.sort()
+ facilityNames.sort()
+
+ for name in propertyNames:
+ if name in facilityNames or name in propertiesOmit:
+ continue
+ trait = obj.inventory.getTrait(name)
+ descriptor = obj.inventory.getTraitDescriptor(name)
+ self._printPropertyFn(fout, name, trait, descriptor, depth)
+ for name in facilityNames:
+ if name in facilitiesOmit:
+ continue
+ trait = obj.inventory.getTrait(name)
+ descriptor = obj.inventory.getTraitDescriptor(name)
+ self._printFacilityFn(fout, name, trait, descriptor, depth)
+ return
+
+
+ def _printPropertyBasic(self, fout, name, trait, descriptor, depth):
+ """
+ Print property name, type, and value.
+ """
+ indent = self._tab*depth
+ fout.write("%s%s (%s) = %s\n" % \
+ (indent, name, trait.type, descriptor.value))
+ return
+
+
+ def _printFacilityBasic(self, fout, name, trait, descriptor, depth):
+ """
+ Print facility name, type, and value.
+ """
+ indent = self._tab*depth
+ fout.write("%s%s = %s (%s)\n" % \
+ (indent, name, descriptor.value.name, descriptor.value))
+ self._printParams(fout, descriptor.value, depth+1)
+ return
+
+
+ def _printPropertyVerbose(self, fout, name, trait, descriptor, depth):
+ """
+ Print property, name, type, value, description, and location set.
+ """
+ indent = self._tab*depth
+ fout.write("\n%s%s (%s) = %s\n" % \
+ (indent, name, trait.type, descriptor.value))
+
+ indent += self._tab
+ try:
+ description = trait.meta['tip']
+ except KeyError:
+ description = "No description available."
+ fout.write("%sDescription: %s\n" % (indent, description))
+ fout.write("%sSet from: %s\n" % (indent, descriptor.locator))
+ return
+
+
+ def _printFacilityVerbose(self, fout, name, trait, descriptor, depth):
+ """
+ Print facility name, type, value, description, and location set.
+ """
+ indent = self._tab*depth
+ fout.write("\n%s%s = %s (%s)\n" % \
+ (indent, name, descriptor.value.name, descriptor.value))
+
+ indent += self._tab
+ try:
+ description = trait.meta['tip']
+ except KeyError:
+ description = "No description available."
+ fout.write("%sDescription: %s\n" % (indent, description))
+ fout.write("%sSet from: %s\n" % (indent, descriptor.locator))
+ fout.write("%sConfigurable as: %s\n" % \
+ (indent, ", ".join(descriptor.value.aliases)))
+
+ self._printParams(fout, descriptor.value, depth+1)
+ return
+
+
+# ----------------------------------------------------------------------
+if __name__ == "__main__":
+
+ usage = "%prog [options] [PyLith args]"
+ from optparse import OptionParser
+ parser = OptionParser(usage=usage)
+ parser.add_option("-v", "--verbose", dest="verbose",
+ action="store_true", default=False,
+ help="Print verbose output.")
+ parser.add_option("-o", "--fileout", dest="filename",
+ type="string", metavar="FILE",
+ help="Write to FILE. [pylith_parameters.txt]",
+ default="pylith_parameters.txt")
+ (options, args) = parser.parse_args()
+
+ app = ParametersApp()
+ app.verbose = options.verbose
+ app.filename = options.filename
+ app.pylith_args = args
+ app.main()
+
+
+# End of file
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