Add workaround for frequent Travis build failures during Cython compilation.

[mdickinson]

We're seeing frequent Travis failures due to Cython build problems. An example is below (from this build).

This PR works around this problem in the manner suggested by Nathaniel Smith.

gcc -pthread -shared -L/opt/python/3.2.5/lib -Wl,-rpath=/opt/python/3.2.5/lib build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Plex/Scanners.o -L/opt/python/3.2.5/lib -lpython3.2mu -o build/lib.linux-x86_64-3.2/Cython/Plex/Scanners.cpython-32mu.so

skipping '/home/travis/virtualenv/python3.2.5/build/cython/Cython/Plex/Actions.c' Cython extension (up-to-date)

building 'Cython.Plex.Actions' extension

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/opt/python/3.2.5/include/python3.2mu -c /home/travis/virtualenv/python3.2.5/build/cython/Cython/Plex/Actions.c -o build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Plex/Actions.o

gcc -pthread -shared -L/opt/python/3.2.5/lib -Wl,-rpath=/opt/python/3.2.5/lib build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Plex/Actions.o -L/opt/python/3.2.5/lib -lpython3.2mu -o build/lib.linux-x86_64-3.2/Cython/Plex/Actions.cpython-32mu.so

skipping '/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Lexicon.c' Cython extension (up-to-date)

building 'Cython.Compiler.Lexicon' extension

creating build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/opt/python/3.2.5/include/python3.2mu -c /home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Lexicon.c -o build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Lexicon.o

gcc -pthread -shared -L/opt/python/3.2.5/lib -Wl,-rpath=/opt/python/3.2.5/lib build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Lexicon.o -L/opt/python/3.2.5/lib -lpython3.2mu -o build/lib.linux-x86_64-3.2/Cython/Compiler/Lexicon.cpython-32mu.so

skipping '/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Scanning.c' Cython extension (up-to-date)

building 'Cython.Compiler.Scanning' extension

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/opt/python/3.2.5/include/python3.2mu -c /home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Scanning.c -o build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Scanning.o

gcc -pthread -shared -L/opt/python/3.2.5/lib -Wl,-rpath=/opt/python/3.2.5/lib build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Scanning.o -L/opt/python/3.2.5/lib -lpython3.2mu -o build/lib.linux-x86_64-3.2/Cython/Compiler/Scanning.cpython-32mu.so

skipping '/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Parsing.c' Cython extension (up-to-date)

building 'Cython.Compiler.Parsing' extension

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/opt/python/3.2.5/include/python3.2mu -c /home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Parsing.c -o build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Parsing.o

gcc -pthread -shared -L/opt/python/3.2.5/lib -Wl,-rpath=/opt/python/3.2.5/lib build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Parsing.o -L/opt/python/3.2.5/lib -lpython3.2mu -o build/lib.linux-x86_64-3.2/Cython/Compiler/Parsing.cpython-32mu.so

skipping '/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Visitor.c' Cython extension (up-to-date)

building 'Cython.Compiler.Visitor' extension

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/opt/python/3.2.5/include/python3.2mu -c /home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Visitor.c -o build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Visitor.o

gcc -pthread -shared -L/opt/python/3.2.5/lib -Wl,-rpath=/opt/python/3.2.5/lib build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Visitor.o -L/opt/python/3.2.5/lib -lpython3.2mu -o build/lib.linux-x86_64-3.2/Cython/Compiler/Visitor.cpython-32mu.so

skipping '/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/FlowControl.c' Cython extension (up-to-date)

building 'Cython.Compiler.FlowControl' extension

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/opt/python/3.2.5/include/python3.2mu -c /home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/FlowControl.c -o build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/FlowControl.o

gcc -pthread -shared -L/opt/python/3.2.5/lib -Wl,-rpath=/opt/python/3.2.5/lib build/temp.linux-x86_64-3.2/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/FlowControl.o -L/opt/python/3.2.5/lib -lpython3.2mu -o build/lib.linux-x86_64-3.2/Cython/Compiler/FlowControl.cpython-32mu.so

cythoning /home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Code.py to /home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Code.c

Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/home/travis/virtualenv/python3.2.5/build/cython/setup.py", line 337, in <module>

    **setup_args

  File "/opt/python/3.2.5/lib/python3.2/distutils/core.py", line 148, in setup

    dist.run_commands()

  File "/opt/python/3.2.5/lib/python3.2/distutils/dist.py", line 917, in run_commands

    self.run_command(cmd)

  File "/opt/python/3.2.5/lib/python3.2/distutils/dist.py", line 936, in run_command

    cmd_obj.run()

  File "/home/travis/virtualenv/python3.2.5/lib/python3.2/site-packages/setuptools/command/install.py", line 54, in run

    return _install.run(self)

  File "/opt/python/3.2.5/lib/python3.2/distutils/command/install.py", line 569, in run

    self.run_command('build')

  File "/opt/python/3.2.5/lib/python3.2/distutils/cmd.py", line 313, in run_command

    self.distribution.run_command(command)

  File "/opt/python/3.2.5/lib/python3.2/distutils/dist.py", line 936, in run_command

    cmd_obj.run()

  File "/opt/python/3.2.5/lib/python3.2/distutils/command/build.py", line 126, in run

    self.run_command(cmd_name)

  File "/opt/python/3.2.5/lib/python3.2/distutils/cmd.py", line 313, in run_command

    self.distribution.run_command(command)

  File "/opt/python/3.2.5/lib/python3.2/distutils/dist.py", line 936, in run_command

    cmd_obj.run()

  File "Cython/Distutils/build_ext.py", line 163, in run

    _build_ext.build_ext.run(self)

  File "/opt/python/3.2.5/lib/python3.2/distutils/command/build_ext.py", line 344, in run

    self.build_extensions()

  File "/home/travis/virtualenv/python3.2.5/build/cython/setup.py", line 169, in build_extensions

    build_ext_orig.build_extensions(self)

  File "Cython/Distutils/build_ext.py", line 170, in build_extensions

    ext.sources = self.cython_sources(ext.sources, ext)

  File "Cython/Distutils/build_ext.py", line 319, in cython_sources

    full_module_name=module_name)

  File "/home/travis/virtualenv/python3.2.5/build/cython/build/lib.linux-x86_64-3.2/Cython/Compiler/Main.py", line 627, in compile

    return compile_single(source, options, full_module_name)

  File "/home/travis/virtualenv/python3.2.5/build/cython/build/lib.linux-x86_64-3.2/Cython/Compiler/Main.py", line 580, in compile_single

    return run_pipeline(source, options, full_module_name)

  File "/home/travis/virtualenv/python3.2.5/build/cython/build/lib.linux-x86_64-3.2/Cython/Compiler/Main.py", line 406, in run_pipeline

    context = options.create_context()

  File "/home/travis/virtualenv/python3.2.5/build/cython/build/lib.linux-x86_64-3.2/Cython/Compiler/Main.py", line 527, in create_context

    self.cplus, self.language_level, options=self)

  File "/home/travis/virtualenv/python3.2.5/build/cython/build/lib.linux-x86_64-3.2/Cython/Compiler/Main.py", line 69, in __init__

    from . import Builtin, CythonScope

  File "/home/travis/virtualenv/python3.2.5/build/cython/build/lib.linux-x86_64-3.2/Cython/Compiler/CythonScope.py", line 5, in <module>

    from .UtilityCode import CythonUtilityCode

  File "/home/travis/virtualenv/python3.2.5/build/cython/build/lib.linux-x86_64-3.2/Cython/Compiler/UtilityCode.py", line 3, in <module>

    from .TreeFragment import parse_from_strings, StringParseContext

  File "/home/travis/virtualenv/python3.2.5/build/cython/build/lib.linux-x86_64-3.2/Cython/Compiler/TreeFragment.py", line 20, in <module>

    from . import Parsing

  File "Cython/Plex/Actions.pxd", line 2, in init Cython.Compiler.Parsing (/home/travis/virtualenv/python3.2.5/build/cython/Cython/Compiler/Parsing.c:55686)

    cdef class Action:

ValueError: Cython.Plex.Actions.Action has the wrong size, try recompiling

[coveralls]

Coverage increased (+0.0%) when pulling d98ba5c on fix/travis-cython-failures into 676a69c on master.

[mdickinson]

Looks like this change also halved our Travis CI runtimes! Most of the recent runs have taken longer than 20 minutes; this one took less than 10.

[corranwebster]

We're trusting that the pure Python version of Cython produced output identical to the behaviour of the compiled version (when it doesn't crash!), which makes me a little bit twitchy, since we will almost always be using .c produced by the compiled version in production.

But from a practical standpoint, this seems like the right thing to do at the moment.

[mdickinson]

Agreed; it's a workaround, and should probably be reverted once the underlying Cython bug (or whatever it turns out to be) is fixed. Though it'll be hard to give up the 100% faster Travis CI runs...