[sfepy] 03/06: Rename extractor to extractor_sfepy. (Closes: #822435)
Anton Gladky
gladk at moszumanska.debian.org
Tue May 3 20:00:48 UTC 2016
This is an automated email from the git hooks/post-receive script.
gladk pushed a commit to branch master
in repository sfepy.
commit 2649ad0e31f3d5f53de8497e40ab1e6059011ab9
Author: Anton Gladky <gladk at debian.org>
Date: Tue May 3 21:38:29 2016 +0200
Rename extractor to extractor_sfepy. (Closes: #822435)
---
...Rename-extractor.py-to-extractor_sfepy.py.patch | 534 +++++++++++++++++++++
debian/patches/series | 1 +
2 files changed, 535 insertions(+)
diff --git a/debian/patches/0001-Rename-extractor.py-to-extractor_sfepy.py.patch b/debian/patches/0001-Rename-extractor.py-to-extractor_sfepy.py.patch
new file mode 100644
index 0000000..e71a0b8
--- /dev/null
+++ b/debian/patches/0001-Rename-extractor.py-to-extractor_sfepy.py.patch
@@ -0,0 +1,534 @@
+From a2cdc8fde2c3da696589052eb2c18bdc2294e26b Mon Sep 17 00:00:00 2001
+From: Anton Gladky <gladk at debian.org>
+Date: Tue, 3 May 2016 21:09:24 +0200
+Subject: [PATCH] Rename extractor.py to extractor_sfepy.py
+
+---
+ doc/developer_guide.rst | 2 +-
+ doc/release_notes.rst | 14 +--
+ doc/src/extractor.rst | 2 +-
+ doc/users_guide.rst | 2 +-
+ examples/linear_elasticity/its2D_4.py | 2 +-
+ extractor.py | 178 ----------------------------------
+ extractor_sfepy.py | 178 ++++++++++++++++++++++++++++++++++
+ setup.py | 2 +-
+ test_install.py | 2 +-
+ 9 files changed, 191 insertions(+), 191 deletions(-)
+ delete mode 100755 extractor.py
+ create mode 100755 extractor_sfepy.py
+
+diff --git a/doc/developer_guide.rst b/doc/developer_guide.rst
+index 9035c8a..a24cbbe 100644
+--- a/doc/developer_guide.rst
++++ b/doc/developer_guide.rst
+@@ -844,7 +844,7 @@ Main scripts
+ .. toctree::
+ :maxdepth: 2
+
+- src/extractor
++ src/extractor_sfepy
+ src/homogen
+ src/phonon
+ src/postproc
+diff --git a/doc/release_notes.rst b/doc/release_notes.rst
+index 84ec9a9..692bdff 100644
+--- a/doc/release_notes.rst
++++ b/doc/release_notes.rst
+@@ -2112,7 +2112,7 @@ from 2013.4 to 2014.1
+ - fix typo in examples/piezo_elasticity/piezo.py
+ - fix docstring of examples/navier_stokes/stokes_slip_bc.py
+ - update test_install.py to test mesh generation/conversion scripts
+- - update test_install.py to test probe.py, extractor.py
++ - update test_install.py to test probe.py, extractor_sfepy.py
+
+ - general clean up:
+
+@@ -3527,7 +3527,7 @@ from 2012.1 to 2012.2
+
+ - change default value of omit_facets to False (Mesh.from_file() etc.)
+ - update HDF5MeshIO.read_times() to return also time steps
+- - update extract_times(), dump_to_vtk(), extractor.py for missing time steps
++ - update extract_times(), dump_to_vtk(), extractor_sfepy.py for missing time steps
+
+ - extraction now works with files where not all the time steps are saved
+
+@@ -3691,7 +3691,7 @@ from 2011.4 to 2012.1
+ - remove FieldVariable.extend_dofs(), .remove_extra_dofs(), .linearize()
+
+ - update recover_bones(), recover_paraflow()
+- - extractor.py: new --linearization option
++ - extractor_sfepy.py: new --linearization option
+
+ - support linearization when dumping to VTK
+ - new create_problem(), parse_linearization()
+@@ -4606,7 +4606,7 @@ from 2011.2 to 2011.3
+
+ - scripts:
+
+- - extractor.py: improve help message
++ - extractor_sfepy.py: improve help message
+ - remove sfepy_gui.py
+ - update test_install.py to report success/failure in log of times
+ - update test_install.py to test --config option
+@@ -4772,7 +4772,7 @@ from 2011.1 to 2011.2
+
+ - input-output:
+
+- - extractor.py: new --times option
++ - extractor_sfepy.py: new --times option
+ - support for variable time steps:
+
+ - new extract_times()
+@@ -5485,7 +5485,7 @@ from 2010.1 to 2010.2
+
+ - simple.py: new --log, --quiet options
+ - postproc.py: new --wireframe, --group-names options
+- - extractor.py: new --same-dir, --to, --step options
++ - extractor_sfepy.py: new --same-dir, --to, --step options
+ - split homogen.py:
+
+ - HomogenizationApp moved to sfepy/homogenization/homogen_app.py
+@@ -5597,7 +5597,7 @@ from 2009.4 to 2010.1
+ - miscellaneous updates:
+
+ - new --save-regions-as-groups option in simple.py
+- - move and update functions from extractor.py into time_history.py
++ - move and update functions from extractor_sfepy.py into time_history.py
+ - Oseen solver: leave setup of stabilization parameters to user
+ - allow also 'dq', 'de' call modes in InstantaneousBase._call()
+ - split termsHyperElasticity.py to base, TL and UL parts
+diff --git a/doc/src/extractor.rst b/doc/src/extractor.rst
+index fb6ca5d..a633d60 100644
+--- a/doc/src/extractor.rst
++++ b/doc/src/extractor.rst
+@@ -1,6 +1,6 @@
+ extractor.py script
+ ===================
+
+-.. automodule:: extractor
++.. automodule:: extractor_sfepy
+ :members:
+ :undoc-members:
+diff --git a/doc/users_guide.rst b/doc/users_guide.rst
+index 554cfdc..b8224a2 100644
+--- a/doc/users_guide.rst
++++ b/doc/users_guide.rst
+@@ -78,7 +78,7 @@ All top-level *SfePy* scripts (applications) can be run via single
+ Simple wrapper for main SfePy commands.
+
+ positional arguments:
+- {extractor,homogen,phonon,postproc,probe,run_tests,schroedinger,shaper,simple}
++ {extractor_sfepy,homogen,phonon,postproc,probe,run_tests,schroedinger,shaper,simple}
+ Available SfePy command(s).
+ options Additional options passed directly to selected
+ [command].
+diff --git a/examples/linear_elasticity/its2D_4.py b/examples/linear_elasticity/its2D_4.py
+index fd860f2..57c1cd1 100644
+--- a/examples/linear_elasticity/its2D_4.py
++++ b/examples/linear_elasticity/its2D_4.py
+@@ -15,7 +15,7 @@ may need to prefix all the commands with "python " and remove "./"):
+
+ 3. optionally, convert results to VTK, and view again::
+
+- ./extractor.py -d its2D.h5
++ ./extractor_sfepy.py -d its2D.h5
+ ./postproc.py its2D.vtk -b
+
+ 4. probe the data::
+diff --git a/extractor.py b/extractor.py
+deleted file mode 100755
+index d207129..0000000
+--- a/extractor.py
++++ /dev/null
+@@ -1,178 +0,0 @@
+-#!/usr/bin/env python
+-"""
+-Examples
+---------
+-
+-$ ./extractor.py -e "p e 0 1999" bone.h5
+-$ ./extractor.py -e "p e 0 1999" bone.h5 -a
+-$ ./extractor.py -e "p e 0 1999" bone.h5 -o extracted.h5
+-$ ./extractor.py -e "p e 0 1999" bone.h5 -o extracted.h5 -a
+-"""
+-import os
+-from optparse import OptionParser
+-
+-import sfepy
+-from sfepy.base.base import nm, dict_to_struct, get_default, Struct
+-from sfepy.base.ioutils import get_trunk
+-import sfepy.postprocess.time_history as th
+-
+-def create_problem(filename):
+- from sfepy.discrete import Problem
+-
+- problem = Problem.from_conf_file(filename,
+- init_equations=False, init_solvers=False)
+- return problem
+-
+-def parse_linearization(linearization):
+- out = {}
+- for item in linearization.split(','):
+- key, val = item.split(':')
+- if key == 'eps':
+- val = float(val)
+- elif key in ('min_level', 'max_level'):
+- val = int(val)
+- elif key == 'kind':
+- pass
+- else:
+- raise ValueError('wrong linearization option key! (%s)'
+- % key)
+- out[key] = val
+-
+- return dict_to_struct(out)
+-
+-usage = """%prog [options] [<input file>] <results file>
+-
+-Extract information from a SfePy multi-time-step results file (HDF5
+-format) and/or linearize results with stored higher order DOFs.
+-
+-For the linearization, the original input (problem description) file must
+-be specified as the first argument. Use the option --linearization below
+-to override linearization parameters defined in the input file. The
+-linearization forces --dump option, i.e., output to VTK files.
+-"""
+-
+-help = {
+- 'filename' :
+- 'basename of output file(s) [default: <basename of input file>]',
+- 'dump' :
+- 'dump to sequence of VTK files',
+- 'same_dir' :
+- 'store the dumped VTK files in the directory of filename_in',
+- 'linearization' :
+- 'linearization options. Default values apply if neither command'
+- ' line nor input file options are set.'
+- " [default: 'kind:adaptive,min_level:0,max_level:2,eps:1e-2']",
+- 'times' :
+- 'extract and print times of individual time steps',
+- 'from' :
+- 'start dumping from time step ii [default: %default]',
+- 'to' :
+- 'stop dumping at time step ii [default: <last step>]',
+- 'step' :
+- 'use every ii-th step for dumping [default: %default]',
+- 'extract' :
+- 'extract variables according to extraction list.'
+- " Example: 'u n 10 15, p e 0' means variable 'u' in nodes 10, 15"
+- " and variable 'p' in element 0",
+- 'average' :
+- 'average vertex variable into cells ("e" extraction mode)'
+-}
+-
+-def main():
+- parser = OptionParser(usage=usage, version="%prog " + sfepy.__version__)
+- parser.add_option('-o', '', metavar='filename',
+- action='store', dest='output_filename_trunk',
+- default=None, help=help['filename'])
+- parser.add_option('-d', '--dump', action='store_true', dest='dump',
+- default=False, help=help['dump'])
+- parser.add_option('', '--same-dir', action='store_true', dest='same_dir',
+- default=False, help=help['same_dir'])
+- parser.add_option('-l', '--linearization', metavar='options',
+- action='store', dest='linearization',
+- default=None, help=help['linearization'])
+- parser.add_option('', '--times', action='store_true', dest='times',
+- default=False, help=help['times'])
+- parser.add_option('-f', '--from', type=int, metavar='ii',
+- action='store', dest='step_from',
+- default=0, help=help['from'])
+- parser.add_option('-t', '--to', type=int, metavar='ii',
+- action='store', dest='step_to',
+- default=None, help=help['to'])
+- parser.add_option('-s', '--step', type=int, metavar='ii',
+- action='store', dest='step_by',
+- default=1, help=help['step'])
+- parser.add_option('-e', '--extract', metavar='list',
+- action='store', dest='extract',
+- default=None, help=help['extract'])
+- parser.add_option('-a', '--average', action='store_true', dest='average',
+- default=False, help=help['average'])
+-
+- (options, args) = parser.parse_args()
+-
+- nargs = len(args)
+- if nargs == 1:
+- filename_results = args[0]
+- linearize = False
+-
+- elif nargs == 2:
+- filename_in, filename_results = args
+- linearize = True
+- options.dump = True
+-
+- else:
+- parser.print_help()
+- return
+-
+- if options.times:
+- steps, times, nts, dts = th.extract_times(filename_results)
+- for ii, time in enumerate(times):
+- step = steps[ii]
+- print '%d %e %e %e' % (step, time, nts[ii], dts[ii])
+-
+- if options.dump:
+- trunk = get_default(options.output_filename_trunk,
+- get_trunk(filename_results))
+- if options.same_dir:
+- trunk = os.path.join(os.path.dirname(filename_results),
+- os.path.basename(trunk))
+-
+- args = {}
+- if linearize:
+- problem = create_problem(filename_in)
+-
+- linearization = Struct(kind='adaptive', min_level=0,
+- max_level=2, eps=1e-2)
+- aux = problem.conf.options.get('linearization', None)
+- linearization.update(aux)
+-
+- if options.linearization is not None:
+- aux = parse_linearization(options.linearization)
+- linearization.update(aux)
+-
+- args.update({'fields' : problem.fields,
+- 'linearization' : linearization})
+-
+- if options.step_to is None:
+- args.update({'step0' : options.step_from})
+-
+- else:
+- args.update({'steps' : nm.arange(options.step_from,
+- options.step_to + 1,
+- options.step_by, dtype=nm.int)})
+-
+- th.dump_to_vtk(filename_results, output_filename_trunk=trunk, **args)
+-
+- if options.extract:
+- ths, ts = th.extract_time_history(filename_results, options.extract)
+-
+- if options.average:
+- ths = th.average_vertex_var_in_cells(ths)
+-
+- if options.output_filename_trunk:
+- th.save_time_history(ths, ts, options.output_filename_trunk + '.h5')
+-
+- else:
+- print dict_to_struct(ths, flag=(1, 1, 1)).str_all()
+-
+-if __name__ == '__main__':
+- main()
+diff --git a/extractor_sfepy.py b/extractor_sfepy.py
+new file mode 100755
+index 0000000..cca13cb
+--- /dev/null
++++ b/extractor_sfepy.py
+@@ -0,0 +1,178 @@
++#!/usr/bin/env python
++"""
++Examples
++--------
++
++$ ./extractor_sfepy.py -e "p e 0 1999" bone.h5
++$ ./extractor_sfepy.py -e "p e 0 1999" bone.h5 -a
++$ ./extractor_sfepy.py -e "p e 0 1999" bone.h5 -o extracted.h5
++$ ./extractor_sfepy.py -e "p e 0 1999" bone.h5 -o extracted.h5 -a
++"""
++import os
++from optparse import OptionParser
++
++import sfepy
++from sfepy.base.base import nm, dict_to_struct, get_default, Struct
++from sfepy.base.ioutils import get_trunk
++import sfepy.postprocess.time_history as th
++
++def create_problem(filename):
++ from sfepy.discrete import Problem
++
++ problem = Problem.from_conf_file(filename,
++ init_equations=False, init_solvers=False)
++ return problem
++
++def parse_linearization(linearization):
++ out = {}
++ for item in linearization.split(','):
++ key, val = item.split(':')
++ if key == 'eps':
++ val = float(val)
++ elif key in ('min_level', 'max_level'):
++ val = int(val)
++ elif key == 'kind':
++ pass
++ else:
++ raise ValueError('wrong linearization option key! (%s)'
++ % key)
++ out[key] = val
++
++ return dict_to_struct(out)
++
++usage = """%prog [options] [<input file>] <results file>
++
++Extract information from a SfePy multi-time-step results file (HDF5
++format) and/or linearize results with stored higher order DOFs.
++
++For the linearization, the original input (problem description) file must
++be specified as the first argument. Use the option --linearization below
++to override linearization parameters defined in the input file. The
++linearization forces --dump option, i.e., output to VTK files.
++"""
++
++help = {
++ 'filename' :
++ 'basename of output file(s) [default: <basename of input file>]',
++ 'dump' :
++ 'dump to sequence of VTK files',
++ 'same_dir' :
++ 'store the dumped VTK files in the directory of filename_in',
++ 'linearization' :
++ 'linearization options. Default values apply if neither command'
++ ' line nor input file options are set.'
++ " [default: 'kind:adaptive,min_level:0,max_level:2,eps:1e-2']",
++ 'times' :
++ 'extract and print times of individual time steps',
++ 'from' :
++ 'start dumping from time step ii [default: %default]',
++ 'to' :
++ 'stop dumping at time step ii [default: <last step>]',
++ 'step' :
++ 'use every ii-th step for dumping [default: %default]',
++ 'extract' :
++ 'extract variables according to extraction list.'
++ " Example: 'u n 10 15, p e 0' means variable 'u' in nodes 10, 15"
++ " and variable 'p' in element 0",
++ 'average' :
++ 'average vertex variable into cells ("e" extraction mode)'
++}
++
++def main():
++ parser = OptionParser(usage=usage, version="%prog " + sfepy.__version__)
++ parser.add_option('-o', '', metavar='filename',
++ action='store', dest='output_filename_trunk',
++ default=None, help=help['filename'])
++ parser.add_option('-d', '--dump', action='store_true', dest='dump',
++ default=False, help=help['dump'])
++ parser.add_option('', '--same-dir', action='store_true', dest='same_dir',
++ default=False, help=help['same_dir'])
++ parser.add_option('-l', '--linearization', metavar='options',
++ action='store', dest='linearization',
++ default=None, help=help['linearization'])
++ parser.add_option('', '--times', action='store_true', dest='times',
++ default=False, help=help['times'])
++ parser.add_option('-f', '--from', type=int, metavar='ii',
++ action='store', dest='step_from',
++ default=0, help=help['from'])
++ parser.add_option('-t', '--to', type=int, metavar='ii',
++ action='store', dest='step_to',
++ default=None, help=help['to'])
++ parser.add_option('-s', '--step', type=int, metavar='ii',
++ action='store', dest='step_by',
++ default=1, help=help['step'])
++ parser.add_option('-e', '--extract', metavar='list',
++ action='store', dest='extract',
++ default=None, help=help['extract'])
++ parser.add_option('-a', '--average', action='store_true', dest='average',
++ default=False, help=help['average'])
++
++ (options, args) = parser.parse_args()
++
++ nargs = len(args)
++ if nargs == 1:
++ filename_results = args[0]
++ linearize = False
++
++ elif nargs == 2:
++ filename_in, filename_results = args
++ linearize = True
++ options.dump = True
++
++ else:
++ parser.print_help()
++ return
++
++ if options.times:
++ steps, times, nts, dts = th.extract_times(filename_results)
++ for ii, time in enumerate(times):
++ step = steps[ii]
++ print '%d %e %e %e' % (step, time, nts[ii], dts[ii])
++
++ if options.dump:
++ trunk = get_default(options.output_filename_trunk,
++ get_trunk(filename_results))
++ if options.same_dir:
++ trunk = os.path.join(os.path.dirname(filename_results),
++ os.path.basename(trunk))
++
++ args = {}
++ if linearize:
++ problem = create_problem(filename_in)
++
++ linearization = Struct(kind='adaptive', min_level=0,
++ max_level=2, eps=1e-2)
++ aux = problem.conf.options.get('linearization', None)
++ linearization.update(aux)
++
++ if options.linearization is not None:
++ aux = parse_linearization(options.linearization)
++ linearization.update(aux)
++
++ args.update({'fields' : problem.fields,
++ 'linearization' : linearization})
++
++ if options.step_to is None:
++ args.update({'step0' : options.step_from})
++
++ else:
++ args.update({'steps' : nm.arange(options.step_from,
++ options.step_to + 1,
++ options.step_by, dtype=nm.int)})
++
++ th.dump_to_vtk(filename_results, output_filename_trunk=trunk, **args)
++
++ if options.extract:
++ ths, ts = th.extract_time_history(filename_results, options.extract)
++
++ if options.average:
++ ths = th.average_vertex_var_in_cells(ths)
++
++ if options.output_filename_trunk:
++ th.save_time_history(ths, ts, options.output_filename_trunk + '.h5')
++
++ else:
++ print dict_to_struct(ths, flag=(1, 1, 1)).str_all()
++
++if __name__ == '__main__':
++ main()
+diff --git a/setup.py b/setup.py
+index 3c941d3..e646623 100644
+--- a/setup.py
++++ b/setup.py
+@@ -199,7 +199,7 @@ def setup_package():
+
+ data_files = main_scripts = [
+ 'phonon.py',
+- 'extractor.py',
++ 'extractor_sfepy.py',
+ 'homogen.py',
+ 'postproc.py',
+ 'probe.py',
+diff --git a/test_install.py b/test_install.py
+index 3ab0141..6b85ea9 100755
+--- a/test_install.py
++++ b/test_install.py
+@@ -130,7 +130,7 @@ def main():
+ out, err = check_output('python ./simple.py examples/linear_elasticity/linear_elastic.py --format h5')
+ eok += report(out, '...', -2, 5, '4.638192e-18', eps=1e-15)
+
+- out, err = check_output('python ./extractor.py -d cylinder.h5')
++ out, err = check_output('python ./extractor_sfepy.py -d cylinder.h5')
+ eok += report(out, '...', -2, 1, '...done')
+
+ out, err = check_output('python ./postproc.py -n --no-offscreen -o cylinder.png cylinder.h5')
+--
+2.8.1
+
diff --git a/debian/patches/series b/debian/patches/series
index b4e6505..21ad2a9 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
01_remove_google_analytics.patch
+0001-Rename-extractor.py-to-extractor_sfepy.py.patch
--
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