Mailman 3 April 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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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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Re: [Cython] Fwd: Question about how best require compiler options for C sources
by Nathaniel Smith April 26, 2016

April 26, 2016

On Apr 11, 2016 04:18, "Erik Bray" <erik.m.bray(a)gmail.com> wrote: > > On Fri, Apr 8, 2016 at 5:49 PM, Nathaniel Smith <njs(a)vorpus.org> wrote: > > Can you give a tiny concrete example? My questions are basic enough that I > > feel like I'm missing something fundamental :-) > > Yes, I think you might be missing something, but I'm not sure exactly > where. In the issue I provided a tiny example which you can see here: > > https://gist.github.com/embray/12a67edb82b213217e31f408007898e6 > > The C code generated by this example currently does not compile on > Windows, because of how Cython uses DL_IMPORT incorrectly. Regardless > of what it *does* do, Cython should not be using the DL_IMPORT macro > at all actually since that no longer even exists in Python. Sure. For that example, the correct thing to do is to *not* export the function. Backing up, to make sure we're on the same page: There are three levels of symbol visibility in C: file-internal, shared library internal (different .c files that make up the library can see it, but users of the shared library can't see it), and shared library exported (everyone can see it; can also carry other consequences, e.g. on Linux then internal calls will become noticeably slower, and it becomes possible for weird symbol interposition issues to occur). So the rule of thumb is to make everything as private as you can get away with. Making this more interesting: - vanilla C only includes 2 ways to mark symbol visibility, which is not enough to make a 3-way distinction. Hence the need for an extra attribute thingummy. - everyone agrees that symbols marked 'static' should be file-internal, but different platforms disagree about what should happen if the extra attribute thingummy is missing. So on Windows, the convention is: 'static' -> file internal no marking -> shared library internal 'dllexport' -> public And on Linux it's: 'static' -> file internal 'visibility (hidden)' -> shared library internal no marking -> public It's generally agreed that Linux got this wrong and that you should always use '-fvisibility=hidden' to switch it to the windows style, but cython doesn't control compiler options and thus should probably generate code that works correctly regardless of such compiler settings. Fortunately, Linux does provide some markings to explicitly make things public: you can mark a symbol 'visibility (default)' (which means public), or you can use the dllexport syntax, just like Windows, because gcc is helpful like that. OTOH, windows is annoying because of this dllimport thing that started this whole thread: on other systems just marking symbols as extern is enough to handle both shared-object-internal and shared-library-exported symbols, and the linker will sort it out. On Windows, you have to explicitly distinguish between these. (And annoyingly, if you accidentally leave out the dllimport making on functions then it will use some fallback hack that works but silently degrades performance; on other symbols it just doesn't work, and ditto for if you use it when it isn't needed.) So final conclusion: for non-static symbols, cython should first decide whether they are supposed to be shared-library-internal or actually exported from the shared library. For shared-library-internal symbols: their definition should be marked 'visibility(hidden)' on Linux, and unmarked on Windows. This is easy using some preprocessor gunk. (Or maybe simplest is: marked that everywhere except if using msvc, because I think everyone else will understand 'visibility (hidden)' even if it's a no op.) Their declaration in the header file should just be 'extern' everywhere. For shared-library-exported symbols: I am dubious about whether cython should even support these at all. But if it does, then the definitions should be marked 'dllexport' (no macro trickery needed, because everyone understands this syntax), and their declaration in the header file needs some extra hack that is the subject of this thread. Now, back to your example: Here the caller and callee are both compiled into the same shared library, so you don't want dllexport/dllimport at all, you just want a shared-library-internal symbol, which as we see is much easier. NumPy also ran into some problems with this in our experiments with using cython internally. Our temporary solution was to use the preprocessor to monkeypatch DL_IMPORT into expanding to the appropriate shared-library-internal thing :-). > > My first question is why you even need this, since AFAIK there are no cases > > where it is correct to have a cython module dllexporting symbols that appear > > in header files. This is what cimport is for, right? > > I don't think this has anything to do with cimport. Could you explain > what you mean? We only need to solve the dllimport issue if we want to support shared-library-exported symbols from cython extensions. This is only useful if you have different extensions that are directly linking to each other using the platform linker. But this simply doesn't work in almost any cases, because platform linkers have all kinds of quirks that don't play well with python packages -- to start with, your runtime linker probably does not follow Python's rules for which directories to search to find a shared library... To solve these problems, the Cython devs invented the cimport mechanism, which is basically a portable, python-centric way of doing shared-library-exports while avoiding all the problems caused by using the platform linker. So my question was, what's your use case that's better served by linking directly against an extension module and using the platform's shared-library-export functionality, instead of cython's? > > My second question is why you would want to do this via the command line, > > when compiling the dll means that you are compiling some cython-generated > > .c, which means that you can put the #define directly in the source code, > > no? > > Not necessarily. As you can see in my example the file fooutil.c is > hand-written C code that was not generated by Cython, but which uses a > function in the Cython-generated code. It includes "foo.h". In > principle you're right--the hand-written C code could set the proper > #defines but it would have to do so *before* including "foo.h". It's > not very obvious that this would be needed. Most other code I've seen > that addresses this issue--including cpython itself--do so by passing > an appropriate define to the compiler via the command-line, and that > seems the clearest to me. I see, right. I guess my suggestion would be that if a symbol really does need to be marked for shared-library-export *and simultaneously* used by different files within the same shared library -- which is the only case where this arises -- then possibly the simplest and most robust thing is to set up the header file so that external users just do #include "foo.h", and the internal users do #define FOO_INTERNAL #include "foo.h" (This is how numpy's include files work, actually, though for reasons unrelated to symbol visibility.) -- bottom line -- I think the obvious thing is that cython should provide a natural way to mark a function as being shared-library-internal; that covers 99% of real use cases *and* just works without any further macros needed. Probably the existing "public" annotation should be changed to mean this. (Obviously it wasn't quite fully thought through in the first place and has few if any users, since it got this very wrong without anyone noticing. So fixing it seems viable to me.) And then *maybe* there should also be a way to make a symbol shared-library-exported, if that really is useful, but as a non-default experts-only kind of thing, and as such it would be OK to require these rare expert users to be a bit more careful about how they #include the resulting header within their own project. -n

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bug report on cython-mode.el: freezes when using which-function-mode
by Nathaniel Smith April 24, 2016

April 24, 2016

Hi all, Bug report here -- trying to edit some cython code in emacs just now, emacs was repeatedly freezing until I'd hit C-g repeatedly. Made things literally unusable -- I couldn't type characters into the buffer. M-x toggle-debug-on-quit gives the backtrace: Debugger entered--Lisp error: (quit) syntax-ppss() python-nav-beginning-of-statement() cython-beginning-of-block() cython-current-defun() run-hook-with-args-until-success(cython-current-defun) which-function() which-func-update-1(#<window 3 on _http_parser.pyx>) which-func-update() apply(which-func-update nil) timer-event-handler([t 0 0 500000 t which-func-update nil idle 0]) Which strongly suggests that the problem has something to do with my having which-function-mode enabled, and likely that something is wrong with cython-current-defun. (which-function-mode is a minor mode built into emacs.) Toggling which-function-mode off seems tentatively to have fixed the problem. So there's a workaround, but really cython-mode + which-function-mode shouldn't cause freezes :-). Possible contributing factor: this emacs is built from a git snapshot of master ("GNU Emacs 25.1.50.1 (x86_64-pc-linux-gnu, GTK+ Version 3.18.9) of 2016-04-22"), so it has the git versions of python-mode and which-function-mode. (I'm just using the python.el that ships with emacs, + elpy. But toggling elpy off didn't seem to affect the hangs.) I don't know whether the same thing happens with released versions of emacs. -n -- Nathaniel J. Smith -- https://vorpus.org

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Cython compiler crash in 0.24
by Isuru Fernando April 23, 2016

April 23, 2016

Hi, When cythonizing a .pyx I get an error in Cython 0.24 which was not there in Cython 0.23.3 After printing the stacktrace, this seems to be because of this line https://github.com/cython/cython/commit/6d55fd189f6ee9d4374d00b8c9c320bd043… where a None object is passed and the following line calls the None object. https://github.com/cython/cython/blob/6d55fd189f6ee9d4374d00b8c9c320bd04332… Let me know if you need more information. Thanks, Isuru Fernando [ 33%] Cythonizing symengine_wrapper.pyx Error compiling Cython file: ------------------------------------------------------------ ... cdef double complex[::1] cmplx_view if real: try: real_view = iterable except (ValueError, TypeError): real_view = cython.view.array(shape=(_size(iterable),), ^ ------------------------------------------------------------ symengine_wrapper.pyx:2464:54: Compiler crash in TransformBuiltinMethods ModuleNode.body = StatListNode(symengine_wrapper.pyx:1:0) StatListNode.stats[163] = StatListNode(symengine_wrapper.pyx:2455:0) StatListNode.stats[0] = DefNode(symengine_wrapper.pyx:2455:0, doc = ' if iterable supports the buffer interface: return iterable,\n if not, return a cython.view.array object (which does) ', modifiers = [...]/0, name = 'with_buffer', num_required_args = 1, py_wrapper_required = True, reqd_kw_flags_cname = '0') DefNode.body = StatListNode(symengine_wrapper.pyx:2456:4) StatListNode.stats[0] = IfStatNode(symengine_wrapper.pyx:2460:4) IfStatNode.if_clauses[0] = IfClauseNode(symengine_wrapper.pyx:2460:7) IfClauseNode.body = StatListNode(symengine_wrapper.pyx:2461:8) StatListNode.stats[0] = TryExceptStatNode(symengine_wrapper.pyx:2461:8) TryExceptStatNode.except_clauses[0] = ExceptClauseNode(symengine_wrapper.pyx:2463:8) ExceptClauseNode.body = StatListNode(symengine_wrapper.pyx:2464:12, is_terminator = True) StatListNode.stats[0] = SingleAssignmentNode(symengine_wrapper.pyx:2464:41) SingleAssignmentNode.rhs = GeneralCallNode(symengine_wrapper.pyx:2464:41, result_is_used = True, use_managed_ref = True) File 'ExprNodes.py', line 8035, in compile_time_value: DictNode(symengine_wrapper.pyx:2464:47, is_dict_literal = True, is_temp = 1, obj_conversion_errors = [...]/0, reject_duplicates = True, result_is_used = True, use_managed_ref = True) File 'ExprNodes.py', line 7334, in compile_time_value: TupleNode(symengine_wrapper.pyx:2464:49, is_sequence_constructor = 1, result_is_used = True, use_managed_ref = True) File 'ExprNodes.py', line 6730, in compile_time_value_list: TupleNode(symengine_wrapper.pyx:2464:49, is_sequence_constructor = 1, result_is_used = True, use_managed_ref = True) File 'ExprNodes.py', line 4981, in compile_time_value: SimpleCallNode(symengine_wrapper.pyx:2464:54, result_is_used = True, use_managed_ref = True) File 'ExprNodes.py', line 1783, in compile_time_value: NameNode(symengine_wrapper.pyx:2464:54, cf_maybe_null = True, is_name = True, name = '_size', result_is_used = True, use_managed_ref = True) Compiler crash traceback from this point on: File "/home/isuru/miniconda3/envs/test-cython/lib/python3.5/site-packages/Cython/Compiler/ExprNodes.py", line 1781, in compile_time_value return denv.lookup(self.name) AttributeError: 'NoneType' object has no attribute 'lookup'

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Manylinux wheels for Cython
by Matthew Brett April 22, 2016

April 22, 2016

Hi, I don't know whether y'all have been following over at distutils-sig, but there's a new distutils PEP that defines a `manylinux` format for Linux wheels that work on many different x86 Linux distributions: https://www.python.org/dev/peps/pep-0513/ https://github.com/pypa/manylinux The latest version of pip will install these, if the client Linux system is compatible with the manylinux spec: https://pip.pypa.io/en/stable/news/ I've already built and used manylinux Cython wheels, which y'all are welcome to test with: pip install -f https://nipy.bic.berkeley.edu/manylinux cython (The wheels there don't have the right manylinux filenames yet, but they have the same contents as the ones that would go up to pypi). I've already had good use from these wheels in speeding up project builds into docker containers and virtualenvs, and I'd love to upload these to pypi. I have permissions on pypi to do this, but I wanted to check in with y'all first... Cheers, Matthew

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unsupported meta-programming-related features
by Xuancong Wang April 21, 2016

April 21, 2016

Dear Cython developers, Python supports meta-programming, in which a variable with name specified in a string can be created at run-time. One built-in library which make use of this is argparse. For example: parser.add_argument('-N', '--max_threads', help='maximum number of concurrent decoding threads', type=int, default=16) in this case, the variable max_threads is created from the string argument. And then Cython will generate an incorrect C program with the following error: smt.py:78:88: undeclared name not builtin: headtail smt.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation. In comparison, I found that nuitka can convert this kind of Python programs sucessfully. I hope Cython can be improved. Thanks! Cheers, Xuancong

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Cannot cythonize subclasses of setuptools.extension._Extension
by Manuel Nuno Melo April 19, 2016

April 19, 2016

Hello devs, I'm developing the setup.py for a scientific package, MDAnalysis <https://github.com/MDAnalysis/mdanalysis/> (see PR #799 <https://github.com/MDAnalysis/mdanalysis/pull/799>). We depend on distutils and setuptool. Namely, we use setuptools.extension.Extension class for our extensions. Some older versions of setuptools (<18.0) do filename cythonization themselves upon initialization of the Extension object. Because we want to control name cythonization ourselves I try to directly use distutils.extension.Extension, which has none of setuptools' cythonization. However, this doesn't work because setuptools patches distutils, so that distutils.extension.Extension effectively becomes setuptools.extension.Extension. setuptools does provide a copy of the unpatched Extension class, via setuptools.extension._Extension. Yet, if I attempt to pass instances of this class to Cython.cythonize it fails because my extension parent no longer conforms to one of the expected classes: File "./setup.py", line 283, in cythonize new_ext_modules = Cython.cythonize(self.ext_modules) File "/scratch/virtualenv/lib/python2.7/site-packages/Cython-0.24-py2.7-linux-x86_64.egg/Cython/Build/Dependencies.py", line 796, in cythonize aliases=aliases) File "/scratch/virtualenv/lib/python2.7/site-packages/Cython-0.24-py2.7-linux-x86_64.egg/Cython/Build/Dependencies.py", line 686, in create_extension_list raise TypeError(msg) TypeError: pattern is not of type str nor subclass of Extension (<class setuptools.extension.Extension at 0x7f66be4e2a78>) but of type <type 'instance'> and class distutils.extension.Extension I believe cythonize should be more permissive with the extension parent classes it accepts, or at least have the setuptools _Extension one in the whitelist, since it's the only way to access the original distutils class. What do you think? In the meantime I'll solve this by subclassing setuptools.extension.Extension and making sure it doesn't cythonize anything. Cheers, Manuel

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PEP 509: detect dict modification by version tag
by Stefan Behnel April 14, 2016

April 14, 2016

Hi! This new PEP seems interesting for Cython optimisations, too: https://www.python.org/dev/peps/pep-0509/ Essentially, it adds a 64 bit modification counter to dicts that allows detecting unmodified dicts, e.g. during lookups of methods or globals. It's currently proposed for Py3.6. Stefan

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