[SCM] Yet Another Dynamic Engine. Platform for discrete element modeling. branch, master, updated. debian/0.70.0-5-7-g5550290
Anton Gladky
gladky.anton at gmail.com
Wed May 2 21:23:09 UTC 2012
The following commit has been merged in the master branch:
commit f5fe5b42e45763a4274d1b46d2f418f919e78774
Author: Anton Gladky <gladky.anton at gmail.com>
Date: Sun Apr 29 21:55:38 2012 +0200
Remove patches, applied by upstream.
diff --git a/debian/patches/fix_FTBFS_on_KFreeBSD.patch b/debian/patches/fix_FTBFS_on_KFreeBSD.patch
deleted file mode 100644
index 16c7a8c..0000000
--- a/debian/patches/fix_FTBFS_on_KFreeBSD.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Description: fix FTBFS on KFreeBSD and hopefully on other platforms, where was a problem with compiling qglviewer. Adding additional pathes for finding necessary header-files.
-Author: Anton Gladky <gladky.anton at gmail.com>
-Bug-Debian: http://bugs.debian.org/628376
-Last-Update: 2011-10-24
---- a/SConstruct
-+++ b/SConstruct
-@@ -100,7 +100,7 @@
- ('chunkSize','Maximum files to compile in one translation unit when building plugins. (unlimited if <= 0, per-file linkage is used if 1)',7,None,int),
- ('version','Yade version (if not specified, guess will be attempted)',None),
- ('realVersion','Revision (usually bzr revision); guessed automatically unless specified',None),
-- ('CPPPATH', 'Additional paths for the C preprocessor (colon-separated)','/usr/include/vtk-5.0:/usr/include/vtk-5.2:/usr/include/vtk-5.4:/usr/include/vtk-5.6:/usr/include/vtk'), # hardy has vtk-5.0
-+ ('CPPPATH', 'Additional paths for the C preprocessor (colon-separated)','/usr/include/vtk-5.0:/usr/include/vtk-5.2:/usr/include/vtk-5.4:/usr/include/vtk-5.6:/usr/include/vtk:/usr/include/qt4/QtCore/:/usr/include/qt4/:/usr/include/qt4/QtXml:/usr/include/qt4/QtOpenGL:/usr/include/qt4/QtGui'), # hardy has vtk-5.0
- ('LIBPATH','Additional paths for the linker (colon-separated)',None),
- ('libstdcxx','Specify libstdc++ location by hand (opened dynamically at startup), usually not needed',None),
- ('QT4CXX','Specify a different compiler for files including qt4; this is necessary for older qt version (<=4.7) which don\'t compile with clang',None),
diff --git a/debian/patches/fix_boost_1.48_compilation.patch b/debian/patches/fix_boost_1.48_compilation.patch
deleted file mode 100644
index e6f26b5..0000000
--- a/debian/patches/fix_boost_1.48_compilation.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-Description: fix FTBFS on with boost >=1.47.
-Author: Anton Gladky <gladky.anton at gmail.com>
-Applied-Upstream: http://bazaar.launchpad.net/~yade-dev/yade/trunk/revision/2987
-Last-Update: 2011-12-19
-
---- a/lib/serialization/ObjectIO.hpp
-+++ b/lib/serialization/ObjectIO.hpp
-@@ -9,8 +9,12 @@
- #include<boost/iostreams/filter/gzip.hpp>
- #include<boost/iostreams/device/file.hpp>
- #include<boost/algorithm/string.hpp>
--// local copy
--#include<boost/math/nonfinite_num_facets.hpp>
-+
-+#if BOOST_VERSION>=104700
-+ #include<boost/math/special_functions/nonfinite_num_facets.hpp>
-+#else
-+ #include<boost/math/nonfinite_num_facets.hpp>
-+#endif
-
- namespace yade{
- /* Utility template functions for (de)serializing objects using boost::serialization from/to streams or files.
---- a/py/wrapper/yadeWrapper.cpp
-+++ b/py/wrapper/yadeWrapper.cpp
-@@ -47,8 +47,11 @@
- // #include<yade/pkg/dem/Shop.hpp>
- #include<yade/pkg/dem/Clump.hpp>
-
--// local copy
--#include<boost/math/nonfinite_num_facets.hpp>
-+#if BOOST_VERSION>=104700
-+ #include<boost/math/special_functions/nonfinite_num_facets.hpp>
-+#else
-+ #include<boost/math/nonfinite_num_facets.hpp>
-+#endif
-
- #include<locale>
- #include<boost/archive/codecvt_null.hpp>
diff --git a/debian/patches/fix_ipython_0.12.patch b/debian/patches/fix_ipython_0.12.patch
deleted file mode 100644
index 6aceb28..0000000
--- a/debian/patches/fix_ipython_0.12.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-Description: small fixes due to ipython 0.12
-Author: Anton Gladky <gladky.anton at gmail.com>
-Applied-Upstream: https://github.com/yade/trunk/commit/307beb3c39da3e29dbd88d0b114adf05233e4e85
-Last-Update: 2012-04-03
-
---- a/core/main/main.py.in
-+++ b/core/main/main.py.in
-@@ -217,15 +217,13 @@
- # http://lists.ipython.scipy.org/pipermail/ipython-user/2008-September/005839.html
- import IPython.ipapi
- IPython.ipapi.get().IP.atexit_operations()
-- elif yade.runtime.ipython_version==11:
-+ elif yade.runtime.ipython_version>=11:
- from IPython.frontend.terminal.embed import InteractiveShellEmbed
- # use the dict to set attributes
- for k in ipconfig: setattr(InteractiveShellEmbed,k,ipconfig[k])
-- InteractiveShellEmbed.banner1=banner # called banner1 here, not banner anymore
-+ InteractiveShellEmbed.banner1=banner+'\n' # called banner1 here, not banner anymore
- ipshell=InteractiveShellEmbed()
- ipshell()
-- # similar to the workaround, as for 0.10 (perhaps not needed?)
-- ipshell.atexit_operations()
-
- ## run userSession in a way corresponding to the features we use:
- gui=None
-@@ -262,6 +260,3 @@
- import yade.qt # this yade.qt is different from the one that comes with qt3
- qapp=QtGui.QApplication(sys.argv)
- userSession(qt4=True,qapp=qapp)
--
--#O.exitNoBacktrace()
--
---- a/py/runtime.py
-+++ b/py/runtime.py
-@@ -11,7 +11,7 @@
- except ValueError:
- print 'WARN: unable to extract IPython version from %s, defaulting to 10'%(IPython.__version__)
- ipython_version=10
--if ipython_version not in (10,11): # versions that we are able to handle, round up or down correspondingly
-+if ipython_version not in (10,11,12): # versions that we are able to handle, round up or down correspondingly
- newipver=10 if ipython_version<10 else 11
- print 'WARN: unhandled IPython version 0.%d, assuming 0.%d instead.'%(ipython_version,newipver)
- ipython_version=newipver
diff --git a/debian/patches/fix_vtk-5.8_compilation.patch b/debian/patches/fix_vtk-5.8_compilation.patch
deleted file mode 100644
index fdee683..0000000
--- a/debian/patches/fix_vtk-5.8_compilation.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Description: fix FTBFS with vtk-5.8.
-Author: Anton Gladky <gladky.anton at gmail.com>
-Applied-Upstream: http://bazaar.launchpad.net/~yade-dev/yade/trunk/revision/2967
- http://bazaar.launchpad.net/~yade-dev/yade/trunk/revision/2970
-Last-Update: 2011-11-24
-
---- a/SConstruct
-+++ b/SConstruct
-@@ -100,7 +100,7 @@
- ('chunkSize','Maximum files to compile in one translation unit when building plugins. (unlimited if <= 0, per-file linkage is used if 1)',7,None,int),
- ('version','Yade version (if not specified, guess will be attempted)',None),
- ('realVersion','Revision (usually bzr revision); guessed automatically unless specified',None),
-- ('CPPPATH', 'Additional paths for the C preprocessor (colon-separated)','/usr/include/vtk-5.0:/usr/include/vtk-5.2:/usr/include/vtk-5.4:/usr/include/vtk-5.6:/usr/include/vtk:/usr/include/qt4/QtCore/:/usr/include/qt4/:/usr/include/qt4/QtXml:/usr/include/qt4/QtOpenGL:/usr/include/qt4/QtGui'), # hardy has vtk-5.0
-+ ('CPPPATH', 'Additional paths for the C preprocessor (colon-separated)','/usr/include/vtk-5.0:/usr/include/vtk-5.2:/usr/include/vtk-5.4:/usr/include/vtk-5.6:/usr/include/vtk-5.8:/usr/include/vtk:/usr/include/qt4/QtCore/:/usr/include/qt4/:/usr/include/qt4/QtXml:/usr/include/qt4/QtOpenGL:/usr/include/qt4/QtGui'), # hardy has vtk-5.0
- ('LIBPATH','Additional paths for the linker (colon-separated)',None),
- ('libstdcxx','Specify libstdc++ location by hand (opened dynamically at startup), usually not needed',None),
- ('QT4CXX','Specify a different compiler for files including qt4; this is necessary for older qt version (<=4.7) which don\'t compile with clang',None),
-@@ -355,7 +355,7 @@
- else: featureNotOK('qt4','Building with Qt4 implies the QGLViewer library installed (package libqglviewer-qt4-dev package in debian/ubuntu, libQGLViewer in RPM-based distributions)')
- if 'vtk' in env['features']:
- ok=conf.CheckLibWithHeader(['vtkCommon'],'vtkInstantiator.h','c++','vtkInstantiator::New();',autoadd=1)
-- env.Append(LIBS=['vtkHybrid','vtkFiltering','vtkRendering','vtkIO','vtkexoIIc','vtkParallel','vtkGraphics','vtkverdict','vtkImaging','vtkftgl','vtkDICOMParser','vtkmetaio','vtksqlite'])
-+ env.Append(LIBS=['vtkHybrid','vtkFiltering','vtkRendering','vtkIO','vtkexoIIc','vtkParallel','vtkGraphics','vtkverdict','vtkImaging','vtkftgl','vtkDICOMParser','vtkmetaio'])
- if not ok: featureNotOK('vtk',note="Installer can`t find vtk-library. Be sure you have it installed (usually, libvtk5-dev package). Or you might have to add VTK header directory (e.g. /usr/include/vtk-5.4) to CPPPATH.")
- if 'gts' in env['features']:
- env.ParseConfig('pkg-config gts --cflags --libs');
diff --git a/debian/patches/get_rid_off_suffix.patch b/debian/patches/get_rid_off_suffix.patch
deleted file mode 100644
index 49a5440..0000000
--- a/debian/patches/get_rid_off_suffix.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Description: Delete the suffix
-Author: Anton Gladky <gladky.anton at gmail.com>
-Last-Update: 2011-10-24
---- a/SConstruct
-+++ b/SConstruct
-@@ -186,7 +186,7 @@
- if not env.has_key('realVersion') or not env['realVersion']: env['realVersion']=yadeSCons.getRealVersion() or 'unknown' # unknown if nothing returned
- if not env.has_key('version'): env['version']=env['realVersion']
-
--env['SUFFIX']=('-'+env['version'] if len(env['version'])>0 else '')+env['variant']
-+env['SUFFIX']=''
- env['SUFFIX_DBG']=env['SUFFIX']+('' if not env['debug'] else '/dbg')
- env['LIBDIR']='$PREFIX/lib/yade$SUFFIX_DBG'
- print "Yade version is `%s' (%s), installed files will be suffixed with `%s'."%(env['version'],env['realVersion'],env['SUFFIX'])
diff --git a/debian/patches/ipython-0.11-migration.patch b/debian/patches/ipython-0.11-migration.patch
deleted file mode 100644
index 9b7151e..0000000
--- a/debian/patches/ipython-0.11-migration.patch
+++ /dev/null
@@ -1,865 +0,0 @@
-Description: provide ipython-0.11 compatibility
-Author: Anton Gladky <gladky.anton at gmail.com>
-Bug: http://bugs.debian.org/636475
-Last-Update: 2011-11-25
-
---- a/core/main/main.py.in
-+++ b/core/main/main.py.in
-@@ -218,7 +218,7 @@
- import IPython.ipapi
- IPython.ipapi.get().IP.atexit_operations()
- elif yade.runtime.ipython_version==11:
-- from IPython.core.embed import InteractiveShellEmbed
-+ from IPython.frontend.terminal.embed import InteractiveShellEmbed
- # use the dict to set attributes
- for k in ipconfig: setattr(InteractiveShellEmbed,k,ipconfig[k])
- InteractiveShellEmbed.banner1=banner # called banner1 here, not banner anymore
-@@ -263,5 +263,5 @@
- qapp=QtGui.QApplication(sys.argv)
- userSession(qt4=True,qapp=qapp)
-
--O.exitNoBacktrace()
-+#O.exitNoBacktrace()
-
---- a/doc/sphinx/conf.py
-+++ b/doc/sphinx/conf.py
-@@ -366,7 +366,7 @@
- id.fmtout =' -> [%d]: ' # for some reason, out and cont must have the trailing space
- id.fmtcont=' .\D.: '
- id.rc_override=dict(prompt_in1="Yade [\#]:",prompt_in2=" .\D.:",prompt_out=r" -> [\#]: ")
-- id.reconfig_shell()
-+ #id.reconfig_shell()
-
- import ipython_console_highlighting as ich
- ich.IPythonConsoleLexer.input_prompt = re.compile("(Yade \[[0-9]+\]: )")
---- a/doc/sphinx/ipython_console_highlighting.py
-+++ b/doc/sphinx/ipython_console_highlighting.py
-@@ -13,7 +13,7 @@
-
- # Third party
- from pygments.lexer import Lexer, do_insertions
--from pygments.lexers.agile import (PythonConsoleLexer, PythonLexer,
-+from pygments.lexers.agile import (PythonConsoleLexer, PythonLexer,
- PythonTracebackLexer)
- from pygments.token import Comment, Generic
-
-@@ -48,7 +48,7 @@
-
- - It assumes the default IPython prompts, not customized ones.
- """
--
-+
- name = 'IPython console session'
- aliases = ['ipython']
- mimetypes = ['text/x-ipython-console']
---- a/doc/sphinx/ipython_directive.py
-+++ b/doc/sphinx/ipython_directive.py
-@@ -3,37 +3,38 @@
-
- This directive allows pasting of entire interactive IPython sessions, prompts
- and all, and their code will actually get re-executed at doc build time, with
--all prompts renumbered sequentially.
-+all prompts renumbered sequentially. It also allows you to input code as a pure
-+python input by giving the argument python to the directive. The output looks
-+like an interactive ipython section.
-
- To enable this directive, simply list it in your Sphinx ``conf.py`` file
- (making sure the directory where you placed it is visible to sphinx, as is
- needed for all Sphinx directives).
-
- By default this directive assumes that your prompts are unchanged IPython ones,
--but this can be customized. For example, the following code in your Sphinx
--config file will configure this directive for the following input/output
--prompts ``Yade [1]:`` and ``-> [1]:``::
--
-- import ipython_directive as id
-- id.rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
-- id.rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*')
-- id.fmtin ='Yade [%d]:'
-- id.fmtout=' -> [%d]:'
--
-- id.rc_override=dict(
-- prompt_in1="Yade [\#]:",
-- prompt_in2=" .\D..",
-- prompt_out=" -> [\#]:"
-- )
-- id.reconfig_shell()
--
-- import ipython_console_highlighting as ich
-- ich.IPythonConsoleLexer.input_prompt=
-- re.compile("(Yade \[[0-9]+\]: )|( \.\.\.+:)")
-- ich.IPythonConsoleLexer.output_prompt=
-- re.compile("(( -> )|(Out)\[[0-9]+\]: )|( \.\.\.+:)")
-- ich.IPythonConsoleLexer.continue_prompt=re.compile(" \.\.\.+:")
-+but this can be customized. The configurable options that can be placed in
-+conf.py are
-
-+ipython_savefig_dir:
-+ The directory in which to save the figures. This is relative to the
-+ Sphinx source directory. The default is `html_static_path`.
-+ipython_rgxin:
-+ The compiled regular expression to denote the start of IPython input
-+ lines. The default is re.compile('In \[(\d+)\]:\s?(.*)\s*'). You
-+ shouldn't need to change this.
-+ipython_rgxout:
-+ The compiled regular expression to denote the start of IPython output
-+ lines. The default is re.compile('Out\[(\d+)\]:\s?(.*)\s*'). You
-+ shouldn't need to change this.
-+ipython_promptin:
-+ The string to represent the IPython input prompt in the generated ReST.
-+ The default is 'In [%d]:'. This expects that the line numbers are used
-+ in the prompt.
-+ipython_promptout:
-+
-+ The string to represent the IPython prompt in the generated ReST. The
-+ default is 'Out [%d]:'. This expects that the line numbers are used
-+ in the prompt.
-
- ToDo
- ----
-@@ -41,15 +42,14 @@
- - Turn the ad-hoc test() function into a real test suite.
- - Break up ipython-specific functionality from matplotlib stuff into better
- separated code.
--- Make sure %bookmarks used internally are removed on exit.
--
-
- Authors
- -------
-
- - John D Hunter: orignal author.
--- Fernando Perez: refactoring, documentation, cleanups.
--- VáclavŠmilauer <eudoxos-AT-arcig.cz>: Prompt generatlizations.
-+- Fernando Perez: refactoring, documentation, cleanups, port to 0.11.
-+- VáclavŠmilauer <eudoxos-AT-arcig.cz>: Prompt generalizations.
-+- Skipper Seabold, refactoring, cleanups, pure python addition
- """
-
- #-----------------------------------------------------------------------------
-@@ -58,12 +58,10 @@
-
- # Stdlib
- import cStringIO
--import imp
- import os
- import re
--import shutil
- import sys
--import warnings
-+import tempfile
-
- # To keep compatibility with various python versions
- try:
-@@ -75,36 +73,26 @@
- import matplotlib
- import sphinx
- from docutils.parsers.rst import directives
-+from docutils import nodes
-+from sphinx.util.compat import Directive
-
- matplotlib.use('Agg')
-
- # Our own
--import IPython
--from IPython.Shell import MatplotlibShell
-+from IPython import Config, InteractiveShell
-+from IPython.core.profiledir import ProfileDir
-+from IPython.utils import io
-
- #-----------------------------------------------------------------------------
- # Globals
- #-----------------------------------------------------------------------------
--
--sphinx_version = sphinx.__version__.split(".")
--# The split is necessary for sphinx beta versions where the string is
--# '6b1'
--sphinx_version = tuple([int(re.split('[a-z]', x)[0])
-- for x in sphinx_version[:2]])
--
-+# for tokenizing blocks
- COMMENT, INPUT, OUTPUT = range(3)
--rc_override = {}
--rgxin = re.compile('In \[(\d+)\]:\s?(.*)\s*')
--rgxcont = re.compile(' \.+:\s?(.*)\s*')
--rgxout = re.compile('Out\[(\d+)\]:\s?(.*)\s*')
--fmtin = 'In [%d]:'
--fmtout = 'Out[%d]:'
--fmtcont = ' .\D.:'
-
- #-----------------------------------------------------------------------------
- # Functions and class declarations
- #-----------------------------------------------------------------------------
--def block_parser(part):
-+def block_parser(part, rgxin, rgxout, fmtin, fmtout):
- """
- part is a string of ipython text, comprised of at most one
- input, one ouput, comments, and blank lines. The block parser
-@@ -156,8 +144,8 @@
- lineno, inputline = int(matchin.group(1)), matchin.group(2)
-
- # the ....: continuation string
-- #continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2))
-- #Nc = len(continuation)
-+ continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2))
-+ Nc = len(continuation)
- # input lines can continue on for more than one line, if
- # we have a '\' line continuation char or a function call
- # echo line 'print'. The input line can only be
-@@ -173,12 +161,11 @@
-
- nextline = lines[i]
- matchout = rgxout.match(nextline)
-- matchcont = rgxcont.match(nextline)
- #print "nextline=%s, continuation=%s, starts=%s"%(nextline, continuation, nextline.startswith(continuation))
- if matchout or nextline.startswith('#'):
- break
-- elif matchcont: #nextline.startswith(continuation):
-- inputline += '\n' + matchcont.group(1) #nextline[Nc:]
-+ elif nextline.startswith(continuation):
-+ inputline += '\n' + nextline[Nc:]
- else:
- rest.append(nextline)
- i+= 1
-@@ -199,7 +186,6 @@
-
- return block
-
--
- class EmbeddedSphinxShell(object):
- """An embedded IPython instance to run inside Sphinx"""
-
-@@ -207,17 +193,38 @@
-
- self.cout = cStringIO.StringIO()
-
-- IPython.Shell.Term.cout = self.cout
-- IPython.Shell.Term.cerr = self.cout
-- argv = ['-autocall', '0']
-- self.user_ns = {}
-- self.user_glocal_ns = {}
--
-- self.IP = IPython.ipmaker.make_IPython(
-- argv, self.user_ns, self.user_glocal_ns, embedded=True,
-- #shell_class=IPython.Shell.InteractiveShell,
-- shell_class=MatplotlibShell,
-- rc_override = dict(colors = 'NoColor', **rc_override))
-+
-+ # Create config object for IPython
-+ config = Config()
-+ config.Global.display_banner = False
-+ config.Global.exec_lines = ['import numpy as np',
-+ 'from pylab import *'
-+ ]
-+ config.InteractiveShell.autocall = False
-+ config.InteractiveShell.autoindent = False
-+ config.InteractiveShell.colors = 'NoColor'
-+
-+ # create a profile so instance history isn't saved
-+ tmp_profile_dir = tempfile.mkdtemp(prefix='profile_')
-+ profname = 'auto_profile_sphinx_build'
-+ pdir = os.path.join(tmp_profile_dir,profname)
-+ profile = ProfileDir.create_profile_dir(pdir)
-+
-+ # Create and initialize ipython, but don't start its mainloop
-+ IP = InteractiveShell.instance(config=config, profile_dir=profile)
-+ # io.stdout redirect must be done *after* instantiating InteractiveShell
-+ io.stdout = self.cout
-+ io.stderr = self.cout
-+
-+ # For debugging, so we can see normal output, use this:
-+ #from IPython.utils.io import Tee
-+ #io.stdout = Tee(self.cout, channel='stdout') # dbg
-+ #io.stderr = Tee(self.cout, channel='stderr') # dbg
-+
-+ # Store a few parts of IPython we'll need.
-+ self.IP = IP
-+ self.user_ns = self.IP.user_ns
-+ self.user_global_ns = self.IP.user_global_ns
-
- self.input = ''
- self.output = ''
-@@ -230,28 +237,62 @@
- # pyplot as plt so we can make a call to the plt.gcf().savefig
- self._pyplot_imported = False
-
-- # we need bookmark the current dir first so we can save
-- # relative to it
-- self.process_input_line('bookmark ipy_basedir')
-+ def clear_cout(self):
- self.cout.seek(0)
- self.cout.truncate(0)
-
-- def process_input_line(self, line):
-+ def process_input_line(self, line, store_history=True):
- """process the input, capturing stdout"""
- #print "input='%s'"%self.input
- stdout = sys.stdout
-- sys.stdout = self.cout
-- #self.IP.resetbuffer()
-- self.IP.push(self.IP.prefilter(line, 0))
-- #self.IP.runlines(line)
-- sys.stdout = stdout
-+ splitter = self.IP.input_splitter
-+ try:
-+ sys.stdout = self.cout
-+ splitter.push(line)
-+ more = splitter.push_accepts_more()
-+ if not more:
-+ source_raw = splitter.source_raw_reset()[1]
-+ self.IP.run_cell(source_raw, store_history=store_history)
-+ finally:
-+ sys.stdout = stdout
-+
-+ def process_image(self, decorator):
-+ """
-+ # build out an image directive like
-+ # .. image:: somefile.png
-+ # :width 4in
-+ #
-+ # from an input like
-+ # savefig somefile.png width=4in
-+ """
-+ savefig_dir = self.savefig_dir
-+ source_dir = self.source_dir
-+ saveargs = decorator.split(' ')
-+ filename = saveargs[1]
-+ # insert relative path to image file in source
-+ outfile = os.path.relpath(os.path.join(savefig_dir,filename),
-+ source_dir)
-+
-+ imagerows = ['.. image:: %s'%outfile]
-+
-+ for kwarg in saveargs[2:]:
-+ arg, val = kwarg.split('=')
-+ arg = arg.strip()
-+ val = val.strip()
-+ imagerows.append(' :%s: %s'%(arg, val))
-+
-+ image_file = os.path.basename(outfile) # only return file name
-+ image_directive = '\n'.join(imagerows)
-+ return image_file, image_directive
-+
-
- # Callbacks for each type of token
- def process_input(self, data, input_prompt, lineno):
- """Process data block for INPUT token."""
- decorator, input, rest = data
- image_file = None
-- #print 'INPUT:', data
-+ image_directive = None
-+ #print 'INPUT:', data # dbg
- is_verbatim = decorator=='@verbatim' or self.is_verbatim
- is_doctest = decorator=='@doctest' or self.is_doctest
- is_suppress = decorator=='@suppress' or self.is_suppress
-@@ -260,54 +301,37 @@
-
- input_lines = input.split('\n')
-
-- #continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2))
-- #Nc = len(continuation)
-+ continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2))
-+ Nc = len(continuation)
-
- if is_savefig:
-- saveargs = decorator.split(' ')
-- filename = saveargs[1]
-- outfile = os.path.join('_static/%s'%filename)
-- # build out an image directive like
-- # .. image:: somefile.png
-- # :width 4in
-- #
-- # from an input like
-- # savefig somefile.png width=4in
-- imagerows = ['.. image:: %s'%outfile]
--
-- for kwarg in saveargs[2:]:
-- arg, val = kwarg.split('=')
-- arg = arg.strip()
-- val = val.strip()
-- imagerows.append(' :%s: %s'%(arg, val))
--
-- image_file = outfile
-- image_directive = '\n'.join(imagerows)
--
-- # TODO: can we get "rest" from ipython
-- #self.process_input_line('\n'.join(input_lines))
-+ image_file, image_directive = self.process_image(decorator)
-
- ret = []
- is_semicolon = False
-+ store_history = True
-
- for i, line in enumerate(input_lines):
- if line.endswith(';'):
- is_semicolon = True
-+ if is_semicolon or is_suppress:
-+ store_history = False
-
- if i==0:
- # process the first input line
- if is_verbatim:
- self.process_input_line('')
-+ self.IP.execution_count += 1 # increment it anyway
- else:
- # only submit the line in non-verbatim mode
-- self.process_input_line(line)
-+ self.process_input_line(line, store_history=store_history)
- formatted_line = '%s %s'%(input_prompt, line)
- else:
- # process a continuation line
- if not is_verbatim:
-- self.process_input_line(line)
-+ self.process_input_line(line, store_history=store_history)
-
-- formatted_line = fmtcont.replace('\D','.'*len(str(lineno)))+line #'%s %s'%(continuation, line)
-+ formatted_line = '%s %s'%(continuation, line)
-
- if not is_suppress:
- ret.append(formatted_line)
-@@ -326,7 +350,8 @@
- ret.append(output)
-
- self.cout.truncate(0)
-- return ret, input_lines, output, is_doctest, image_file
-+ return (ret, input_lines, output, is_doctest, image_file,
-+ image_directive)
- #print 'OUTPUT', output # dbg
-
- def process_output(self, data, output_prompt,
-@@ -336,46 +361,68 @@
- submitted = data.strip()
- found = output
- if found is not None:
-+ found = found.strip()
-+
-+ # XXX - fperez: in 0.11, 'output' never comes with the prompt
-+ # in it, just the actual output text. So I think all this code
-+ # can be nuked...
-+
-+ # the above comment does not appear to be accurate... (minrk)
-+
- ind = found.find(output_prompt)
- if ind<0:
-- raise RuntimeError('output prompt="%s" does not match out line=%s'%(output_prompt, found))
-+ e='output prompt="%s" does not match out line=%s' % \
-+ (output_prompt, found)
-+ raise RuntimeError(e)
- found = found[len(output_prompt):].strip()
-
- if found!=submitted:
-- raise RuntimeError('doctest failure for input_lines="%s" with found_output="%s" and submitted output="%s"'%(input_lines, found, submitted))
-+ e = ('doctest failure for input_lines="%s" with '
-+ 'found_output="%s" and submitted output="%s"' %
-+ (input_lines, found, submitted) )
-+ raise RuntimeError(e)
- #print 'doctest PASSED for input_lines="%s" with found_output="%s" and submitted output="%s"'%(input_lines, found, submitted)
-
- def process_comment(self, data):
-- """Process data block for COMMENT token."""
-+ """Process data fPblock for COMMENT token."""
- if not self.is_suppress:
- return [data]
-
-+ def save_image(self, image_file):
-+ """
-+ Saves the image file to disk.
-+ """
-+ self.ensure_pyplot()
-+ command = 'plt.gcf().savefig("%s")'%image_file
-+ #print 'SAVEFIG', command # dbg
-+ self.process_input_line('bookmark ipy_thisdir', store_history=False)
-+ self.process_input_line('cd -b ipy_savedir', store_history=False)
-+ self.process_input_line(command, store_history=False)
-+ self.process_input_line('cd -b ipy_thisdir', store_history=False)
-+ self.process_input_line('bookmark -d ipy_thisdir', store_history=False)
-+ self.clear_cout()
-+
-+
- def process_block(self, block):
- """
- process block from the block_parser and return a list of processed lines
- """
--
- ret = []
- output = None
- input_lines = None
-+ lineno = self.IP.execution_count
-
-- m = rgxin.match(str(self.IP.outputcache.prompt1).strip())
-- lineno = int(m.group(1))
--
-- input_prompt = fmtin%lineno
-- output_prompt = fmtout%lineno
-+ input_prompt = self.promptin%lineno
-+ output_prompt = self.promptout%lineno
- image_file = None
- image_directive = None
-- # XXX - This needs a second refactor. There's too much state being
-- # held globally, which makes for a very awkward interface and large,
-- # hard to test functions. I've already broken this up at least into
-- # three separate processors to isolate the logic better, but this only
-- # serves to highlight the coupling. Next we need to clean it up...
-+
- for token, data in block:
- if token==COMMENT:
- out_data = self.process_comment(data)
- elif token==INPUT:
-- out_data, input_lines, output, is_doctest, image_file= \
-+ (out_data, input_lines, output, is_doctest, image_file,
-+ image_directive) = \
- self.process_input(data, input_prompt, lineno)
- elif token==OUTPUT:
- out_data = \
-@@ -385,87 +432,235 @@
- if out_data:
- ret.extend(out_data)
-
-+ # save the image files
- if image_file is not None:
-- self.ensure_pyplot()
-- command = 'plt.gcf().savefig("%s")'%image_file
-- #print 'SAVEFIG', command # dbg
-- self.process_input_line('bookmark ipy_thisdir')
-- self.process_input_line('cd -b ipy_basedir')
-- self.process_input_line(command)
-- self.process_input_line('cd -b ipy_thisdir')
-- self.cout.seek(0)
-- self.cout.truncate(0)
-+ self.save_image(image_file)
-+
- return ret, image_directive
-
- def ensure_pyplot(self):
- if self._pyplot_imported:
- return
-- self.process_input_line('import matplotlib.pyplot as plt')
-+ self.process_input_line('import matplotlib.pyplot as plt',
-+ store_history=False)
-
--# A global instance used below. XXX: not sure why this can't be created inside
--# ipython_directive itself.
--shell = EmbeddedSphinxShell()
--
--def reconfig_shell():
-- """Called after setting module-level variables to re-instantiate
-- with the set values (since shell is instantiated first at import-time
-- when module variables have default values)"""
-- global shell
-- shell = EmbeddedSphinxShell()
-+ def process_pure_python(self, content):
-+ """
-+ content is a list of strings. it is unedited directive conent
-
-+ This runs it line by line in the InteractiveShell, prepends
-+ prompts as needed capturing stderr and stdout, then returns
-+ the content as a list as if it were ipython code
-+ """
-+ output = []
-+ savefig = False # keep up with this to clear figure
-+ multiline = False # to handle line continuation
-+ fmtin = self.promptin
-+
-+ for lineno, line in enumerate(content):
-+
-+ line_stripped = line.strip()
-+
-+ if not len(line):
-+ output.append(line) # preserve empty lines in output
-+ continue
-+
-+ # handle decorators
-+ if line_stripped.startswith('@'):
-+ output.extend([line])
-+ if 'savefig' in line:
-+ savefig = True # and need to clear figure
-+ continue
-+
-+ # handle comments
-+ if line_stripped.startswith('#'):
-+ output.extend([line])
-+ continue
-+
-+ # deal with multilines
-+ if not multiline: # not currently on a multiline
-+
-+ if line_stripped.endswith('\\'): # now we are
-+ multiline = True
-+ cont_len = len(str(lineno)) + 2
-+ line_to_process = line.strip('\\')
-+ output.extend([u"%s %s" % (fmtin%lineno,line)])
-+ continue
-+ else: # no we're still not
-+ line_to_process = line.strip('\\')
-+ else: # we are currently on a multiline
-+ line_to_process += line.strip('\\')
-+ if line_stripped.endswith('\\'): # and we still are
-+ continuation = '.' * cont_len
-+ output.extend([(u' %s: '+line_stripped) % continuation])
-+ continue
-+ # else go ahead and run this multiline then carry on
-+
-+ # get output of line
-+ self.process_input_line(unicode(line_to_process.strip()),
-+ store_history=False)
-+ out_line = self.cout.getvalue()
-+ self.clear_cout()
-+
-+ # clear current figure if plotted
-+ if savefig:
-+ self.ensure_pyplot()
-+ self.process_input_line('plt.clf()', store_history=False)
-+ self.clear_cout()
-+ savefig = False
-+
-+ # line numbers don't actually matter, they're replaced later
-+ if not multiline:
-+ in_line = u"%s %s" % (fmtin%lineno,line)
-
--def ipython_directive(name, arguments, options, content, lineno,
-- content_offset, block_text, state, state_machine,
-- ):
--
-- debug = ipython_directive.DEBUG
-- shell.is_suppress = options.has_key('suppress')
-- shell.is_doctest = options.has_key('doctest')
-- shell.is_verbatim = options.has_key('verbatim')
--
-- #print 'ipy', shell.is_suppress, options
-- parts = '\n'.join(content).split('\n\n')
-- lines = ['.. sourcecode:: ipython', '']
--
-- figures = []
-- for part in parts:
-- block = block_parser(part)
--
-- if len(block):
-- rows, figure = shell.process_block(block)
-- for row in rows:
-- lines.extend([' %s'%line for line in row.split('\n')])
--
-- if figure is not None:
-- figures.append(figure)
--
-- for figure in figures:
-- lines.append('')
-- lines.extend(figure.split('\n'))
-- lines.append('')
--
-- #print lines
-- if len(lines)>2:
-- if debug:
-- print '\n'.join(lines)
-- else:
-- #print 'INSERTING %d lines'%len(lines)
-- state_machine.insert_input(
-- lines, state_machine.input_lines.source(0))
-+ output.extend([in_line])
-+ else:
-+ output.extend([(u' %s: '+line_stripped) % continuation])
-+ multiline = False
-+ if len(out_line):
-+ output.extend([out_line])
-+ output.extend([u''])
-+
-+ return output
-+
-+class IpythonDirective(Directive):
-+
-+ has_content = True
-+ required_arguments = 0
-+ optional_arguments = 4 # python, suppress, verbatim, doctest
-+ final_argumuent_whitespace = True
-+ option_spec = { 'python': directives.unchanged,
-+ 'suppress' : directives.flag,
-+ 'verbatim' : directives.flag,
-+ 'doctest' : directives.flag,
-+ }
-+
-+ shell = EmbeddedSphinxShell()
-+
-+ def get_config_options(self):
-+ # contains sphinx configuration variables
-+ config = self.state.document.settings.env.config
-+
-+ # get config variables to set figure output directory
-+ confdir = self.state.document.settings.env.app.confdir
-+ savefig_dir = config.ipython_savefig_dir
-+ source_dir = os.path.dirname(self.state.document.current_source)
-+ if savefig_dir is None:
-+ savefig_dir = config.html_static_path
-+ if isinstance(savefig_dir, list):
-+ savefig_dir = savefig_dir[0] # safe to assume only one path?
-+ savefig_dir = os.path.join(confdir, savefig_dir)
-+
-+ # get regex and prompt stuff
-+ rgxin = config.ipython_rgxin
-+ rgxout = config.ipython_rgxout
-+ promptin = config.ipython_promptin
-+ promptout = config.ipython_promptout
-+
-+ return savefig_dir, source_dir, rgxin, rgxout, promptin, promptout
-+
-+ def setup(self):
-+ # get config values
-+ (savefig_dir, source_dir, rgxin,
-+ rgxout, promptin, promptout) = self.get_config_options()
-+
-+ # and attach to shell so we don't have to pass them around
-+ self.shell.rgxin = rgxin
-+ self.shell.rgxout = rgxout
-+ self.shell.promptin = promptin
-+ self.shell.promptout = promptout
-+ self.shell.savefig_dir = savefig_dir
-+ self.shell.source_dir = source_dir
-+
-+ # setup bookmark for saving figures directory
-+
-+ self.shell.process_input_line('bookmark ipy_savedir %s'%savefig_dir,
-+ store_history=False)
-+ self.shell.clear_cout()
-+
-+ return rgxin, rgxout, promptin, promptout
-+
-+
-+ def teardown(self):
-+ # delete last bookmark
-+ self.shell.process_input_line('bookmark -d ipy_savedir',
-+ store_history=False)
-+ self.shell.clear_cout()
-+
-+ def run(self):
-+ debug = False
-+
-+ #TODO, any reason block_parser can't be a method of embeddable shell
-+ # then we wouldn't have to carry these around
-+ rgxin, rgxout, promptin, promptout = self.setup()
-+
-+ options = self.options
-+ self.shell.is_suppress = 'suppress' in options
-+ self.shell.is_doctest = 'doctest' in options
-+ self.shell.is_verbatim = 'verbatim' in options
-+
-+
-+ # handle pure python code
-+ if 'python' in self.arguments:
-+ content = self.content
-+ self.content = self.shell.process_pure_python(content)
-+
-+ parts = '\n'.join(self.content).split('\n\n')
-+
-+ lines = ['.. code-block:: ipython','']
-+ figures = []
-+
-+ for part in parts:
-+
-+ block = block_parser(part, rgxin, rgxout, promptin, promptout)
-+
-+ if len(block):
-+ rows, figure = self.shell.process_block(block)
-+ for row in rows:
-+ lines.extend([' %s'%line for line in row.split('\n')])
-+
-+ if figure is not None:
-+ figures.append(figure)
-+
-+ #text = '\n'.join(lines)
-+ #figs = '\n'.join(figures)
-+
-+ for figure in figures:
-+ lines.append('')
-+ lines.extend(figure.split('\n'))
-+ lines.append('')
-+
-+ #print lines
-+ if len(lines)>2:
-+ if debug:
-+ print '\n'.join(lines)
-+ else: #NOTE: this raises some errors, what's it for?
-+ #print 'INSERTING %d lines'%len(lines)
-+ self.state_machine.insert_input(
-+ lines, self.state_machine.input_lines.source(0))
-+
-+ text = '\n'.join(lines)
-+ txtnode = nodes.literal_block(text, text)
-+ txtnode['language'] = 'ipython'
-+ #imgnode = nodes.image(figs)
-
-- return []
-+ # cleanup
-+ self.teardown()
-
--ipython_directive.DEBUG = False
-+ return []#, imgnode]
-
- # Enable as a proper Sphinx directive
- def setup(app):
- setup.app = app
-- options = {'suppress': directives.flag,
-- 'doctest': directives.flag,
-- 'verbatim': directives.flag,
-- }
-
-- app.add_directive('ipython', ipython_directive, True, (0, 2, 0), **options)
-+ app.add_directive('ipython', IpythonDirective)
-+ app.add_config_value('ipython_savefig_dir', None, True)
-+ app.add_config_value('ipython_rgxin',
-+ re.compile('In \[(\d+)\]:\s?(.*)\s*'), True)
-+ app.add_config_value('ipython_rgxout',
-+ re.compile('Out\[(\d+)\]:\s?(.*)\s*'), True)
-+ app.add_config_value('ipython_promptin', 'In [%d]:', True)
-+ app.add_config_value('ipython_promptout', 'Out[%d]:', True)
-
-
- # Simple smoke test, needs to be converted to a proper automatic test.
-@@ -488,7 +683,7 @@
- @savefig mystinkbug.png width=4in
- In [4]: imshow(im)
- Out[4]: <matplotlib.image.AxesImage object at 0x39ea850>
--
-+
- """,
- r"""
-
-@@ -523,7 +718,7 @@
- In [134]: numpy.random.seed(2358)
-
- @doctest
--In [135]: np.random.rand(10,2)
-+In [135]: numpy.random.rand(10,2)
- Out[135]:
- array([[ 0.64524308, 0.59943846],
- [ 0.47102322, 0.8715456 ],
-@@ -556,8 +751,6 @@
- 7
- 8
- 9
--
--
- """,
-
- r"""
-@@ -597,11 +790,12 @@
- In [153]: grid(True)
-
- """,
-- ]
--
-+ ]
-+ # skip local-file depending first example:
-+ examples = examples[1:]
-
-- ipython_directive.DEBUG = True
-- #options = dict(suppress=True)
-+ #ipython_directive.DEBUG = True # dbg
-+ #options = dict(suppress=True) # dbg
- options = dict()
- for example in examples:
- content = example.split('\n')
-@@ -613,4 +807,7 @@
-
- # Run test suite as a script
- if __name__=='__main__':
-+ if not os.path.isdir('_static'):
-+ os.mkdir('_static')
- test()
-+ print 'All OK? Check figures in _static/'
diff --git a/debian/patches/series b/debian/patches/series
index 0e9758f..fead62e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,7 +1 @@
-fix_FTBFS_on_KFreeBSD.patch
get_rid_off_suffix.patch
-fix_vtk-5.8_compilation.patch
-ipython-0.11-migration.patch
-disable_tex_creation.patch
-fix_boost_1.48_compilation.patch
-fix_ipython_0.12.patch
--
Yet Another Dynamic Engine. Platform for discrete element modeling.
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