[sfepy] 02/04: Remove patch, applied by upstream.
Anton Gladky
gladk at moszumanska.debian.org
Sat May 14 07:43:10 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 a7409bc0e926485a128a5c7a6c52434bc306ffa7
Author: Anton Gladky <gladk at debian.org>
Date: Sat May 14 08:04:15 2016 +0200
Remove patch, applied by upstream.
---
...Rename-extractor.py-to-extractor_sfepy.py.patch | 534 ---------------------
debian/patches/series | 1 -
2 files changed, 535 deletions(-)
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
deleted file mode 100644
index e71a0b8..0000000
--- a/debian/patches/0001-Rename-extractor.py-to-extractor_sfepy.py.patch
+++ /dev/null
@@ -1,534 +0,0 @@
-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 21ad2a9..b4e6505 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1 @@
01_remove_google_analytics.patch
-0001-Rename-extractor.py-to-extractor_sfepy.py.patch
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/sfepy.git
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