Mailman 3 June 2016 - cython-devel

cygdb: no debug files were found
by Nathan Goldbaum Sept. 14, 2016

Sept. 14, 2016

Hi all, I'm following the directions in the link below to debug some cython code using cygdb: http://docs.cython.org/src/userguide/debugging.html Unfortunately, when I try to actually debug my program using cygdb, I get a "no debug files were found" error. It looks like the error is getting raised here: https://github.com/cython/cython/blob/master/Cython/Debugger/Cygdb.py#L33 So for some reason the "cython_debug" folder isn't being generated at build time. I tried to follow the directions closely, you can see the notes I put together during the installation process here: https://bpaste.net/show/6b11f815d449 Unfortunately the library I'm trying to debug (yt: bitbucket.org/yt_analysis/yt) uses a somewhat nonstandard build setup based on numpy distutils, and I suspect that is breaking some of the assumptions that went into the cygdb instructions in the cython docs. Does anyone have any idea what went wrong here? For now I'm going to fall back to regular gdb, and debug the autogenerated cython sources. Thanks for your help, Nathan Goldbaum

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Minor issue with running tests and -Wlong-long
by Erik Bray Sept. 5, 2016

Sept. 5, 2016

Hello, As some of you already know I've been doing some work on Cython on Cygwin [in the process I I'm constantly mixing the two up in speech, but maybe in writing I'll do better :)]. There are several issues with the tests on Cygwin, and that's one thing I'll work on. But a major annoyance I've encountered when running any tests is a huge number of warnings from gcc such as: embray@PC-pret-47 ~/src/cython $ CFLAGS="-O0" ./runtests.py -vv --no-cpp addloop Python 2.7.10 (default, Jun 1 2015, 18:05:38) [GCC 4.9.2] Running tests against Cython 0.24 f68b5bd0fa620d0dc26166bffe5fe42d94068720 Backends: c runTest (__main__.CythonRunTestCase) compiling (c) and running addloop ... === C/C++ compiler error output: === In file included from /usr/include/python2.7/Python.h:58:0, from addloop.c:4: /usr/include/python2.7/pyport.h:69:27: warning: ISO C90 does not support ‘long long’ [-Wlong-long] #define PY_LONG_LONG long long ^ /usr/include/python2.7/pyport.h:793:34: note: in definition of macro ‘PyAPI_FUNC’ # define PyAPI_FUNC(RTYPE) RTYPE ^ /usr/include/python2.7/intobject.h:46:21: note: in expansion of macro ‘PY_LONG_LONG’ PyAPI_FUNC(unsigned PY_LONG_LONG) PyInt_AsUnsignedLongLongMask(PyObject *); ^ In file included from /usr/include/python2.7/Python.h:58:0, from addloop.c:4: ... And so on. For now an easy workaround is to add -Wno-long-long to the compiler flags. But I was curious why I was seeing this in Cygwin but not on my Ubuntu system, and here's why: In runtests.py there is a check https://github.com/cython/cython/blob/master/runtests.py#L829 if self.language=='c' and compiler='gcc': ext_compile_flags.extend(['-std=c89', '-pedantic']) where in this case `compiler` is assigned `sysconfig.get_config_var('CC')`. On my Linux system this expands to "x86_64-linux-gnu-gcc -pthread". Whereas on Cygwin (and probably many other systems) it expands simply to "gcc". I'm guessing that to do what it intended the above line should read "and 'gcc' in compiler". But this also raises the question: Why are the tests run with these flags? If Python was configured with HAVE_LONG_LONG, then these warnings will be inevitable. Thanks, Erik

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cython.org
by William Stein July 16, 2016

July 16, 2016

Hi Cython devs, Unfortunately, cython.org is down, since it was hosted at UW, and pretty much all UW math computing infrastructure I have is dead. I don't know why, though I suspect an attack of some sort. I don't know whether there are any backups of cython.org as it was hosted on hardware that I didn't manage at all. Sorry. There is no ETA for recovery. -- William -- William (http://wstein.org)

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Virtual cpdef methods
by Jeroen Demeyer June 21, 2016

June 21, 2016

Hello, I would like to have a "virtual" cpdef method: something which allows a fast Cython call *when implemented* but without a default implementation. The most simple implementation would be a "cpdef" method but without an entry for the method in the Python method table. Of course, the "cdef" part needs to be implemented by the user (you need to put something in the vtab). For my purposes, something like "raise AttributeError" would be sufficient. 1. Can this be accomplished currently in Cython? 2. Is this something that makes sense to add to Cython? 3. What do you think of the following syntax? cdef class MyClass(object): cpdef virtual_method(self): # implementation of "cdef" part ... del virtual_method # don't put virtual_method in the method table

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Static checker for cython extension dependencies?
by Nathan Goldbaum June 11, 2016

June 11, 2016

Hi all, I'm working on a pretty large python/cython codebase (yt) that has many interdependent C extensions written in cython. I've found it to be pretty hit or miss to depend on contributors to manually update cython dependency information in our setup.py file. The dependency information seems to only be used by setuptools to trigger recompilation, but critically setuptools will happily compile a C extension for the first time if the depends information is incomplete. This means that during development, if I update a cython routine, there's no way to ensure that other cython routines that cimport the one I modified will be recompiled unless I manually ensure the depends information is updated whenever cython code gains or loses a cimport. To make that more concrete, here's a pull request I just made to yt that adds missing dependencies for a cython header. Without this pull request, setuptools fails to recompile these routines when selection_routines.pxd changes, causing a build failure. https://bitbucket.org/yt_analysis/yt/pull-requests/2220 I think it should be possible to write a test for this by defining the dependency information outside of setup.py and parsing grep and looking for all cython files that cimport other cython files defined inside yt. However, before I do that, I'm curious whether anyone has done something similar, or if there is some other way of forcing the dependency information to be complete on the first compilation, rather than just for subsequent incremental recompilations during development. Thanks for your help! -Nathan

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Suggested action for "Python.h not found"
by Abdeali Kothari June 9, 2016

June 9, 2016

Hi, Currently, when a user installs cython, if the Python headers are not found, an error message saying "Python.h: no such file or directory" is shown (Example: https://justpaste.it/v0gz). Would it be possible to suggest an action to install the headers ? I found http://trac.cython.org/ticket/247 which is quite old, and makes the error message easier to find, but doesn't recommend a solution. `sys.platform`, `platform.linux_distribution` or `distro`[1] can be used to find which OS, platform, etc is and use that to suggest a command like: if sys.version_info < (3, ) and sys.platform.startswith("linux") and platform.linux_distribution()[0] in ("ubuntu", "debian"): print("Python headers were not found. On Debian/Ubuntu, `sudo apt-get install python-dev` should install the Python headers.") elif sys.version_info < (3, ) and sys.platform.startswith("linux") and platform.linux_distribution()[0] in ("ubuntu", "debian"): print("Python headers were not found. On Debian/Ubuntu, `sudo apt-get install python3-dev` should install the Python3 headers.") This would help so that non-developers can use cython based packages easily as it provides helpful instructions on what to do. Currently, you essentially search for the error message and go to one of the forums/blogs explaining what can be done. Or maybe by default it can just point the user to an Installation Page which explains in detail what needs to be done to get those headers for various systems ? [1] - https://pypi.python.org/pypi/distro

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Cygwin: Handling missing C99 long double functions
by Erik Bray June 7, 2016

June 7, 2016

Hi again, Sorry if I'm spamming the list too much, but I've encountered another pretty serious and unfortunate issue with Cython on Cygwin. The problem now is that many of libm long double functions like sqrtl, tanl, etc. are missing on Cygwin (missing from newlib to be specific). I think this is a previously known issue, but nothing's ever really been done about it. Well, to be clear, sometimes they're present, but only when sizeof(double) == sizeof(long double). However on 64-bit Cygwin sizeof(long double) == 16, so the functions are simply not defined. This seems to be due to lack of interest / effort: https://www.cygwin.com/ml/cygwin/2011-04/msg00231.html That post is 5 years old, but I can't find any evidence that this has changed. There are quite a few tests in Cygwin's test suite that test long double support. I guess what I'm asking is what would be the best thing to do about it. I could just skip those tests on Cygwin, though I'm not sure the best way to go about skipping an entire test for a given platform. More generally though, outside the context of testing, this means Cygwin will sometimes generate code that cannot be compiled on this platform, and a question arises as to what to do about that. I have some thoughts, but am not sure if it's worth discussing any further or not. Thanks, Erik

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Supporting cython.operator in C
by Jeroen Demeyer June 2, 2016

June 2, 2016

The following code cimport cython.operator cdef long foo(long x, long y): return cython.operator.comma(x, y) gives AttributeError: 'CBinopNode' object has no attribute 'analyse_c_operation' Is there any fundamental reason why such operators are only implemented for C++ and not pure C? What would be needed to support such operators in C? Jeroen.

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