From ralf.gommers at gmail.com Sun Oct 2 03:36:28 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sun, 2 Oct 2016 20:36:28 +1300 Subject: [SciPy-Dev] Moving SciPy project organization forward In-Reply-To: References: Message-ID: On Fri, Sep 30, 2016 at 6:12 AM, Evgeni Burovski wrote: > > Now that the mailing list is alive again: how about I organize the first > one > > for say 2 weeks from now? Proposed topic: producing (a) paper(s). > > +1. > Looking at time zones, what will work best is evening in Europe, which is daytime in the US and early morning in Australasia. Here is a poll: http://whenisgood.net/bdkqjkr. I'll pick a time based on responses in 3 days; if there are more than fit in Google Hangout (10) I'll look for an alternative. Everyone who's interested welcome I'd say. I'll put the agenda and call details on a GitHub wiki page, then people can add proposed topics to the agenda. Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From tyler.je.reddy at gmail.com Sun Oct 2 14:26:35 2016 From: tyler.je.reddy at gmail.com (Tyler Reddy) Date: Sun, 2 Oct 2016 19:26:35 +0100 Subject: [SciPy-Dev] ENH: The directed Hausdorff distance Message-ID: Hello, Just thought I'd make everyone aware of my proposal to incorporate code for the directed Hausdorff distance into scipy -- the detailed PR is here: https://github.com/scipy/scipy/pull/6649 Best wishes, Tyler -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Mon Oct 3 22:15:24 2016 From: charlesr.harris at gmail.com (Charles R Harris) Date: Mon, 3 Oct 2016 20:15:24 -0600 Subject: [SciPy-Dev] NumPy 1.11.2 released Message-ID: *Hi All,* I'm pleased to announce the release of Numpy 1.11.2. This release supports Python 2.6 - 2.7, and 3.2 - 3.5 and fixes bugs and regressions found in Numpy 1.11.1. Wheels for Linux, Windows, and OSX can be found on PyPI. Sources are available on both PyPI and Sourceforge . Thanks to all who were involved in this release. Contributors and merged pull requests are listed below. *Contributors to v1.11.2* - Allan Haldane - Bertrand Lefebvre - Charles Harris - Julian Taylor - Lo?c Est?ve - Marshall Bockrath-Vandegrift + - Michael Seifert + - Pauli Virtanen - Ralf Gommers - Sebastian Berg - Shota Kawabuchi + - Thomas A Caswell - Valentin Valls + - Xavier Abellan Ecija + A total of 14 people contributed to this release. People with a "+" by their names contributed a patch for the first time. *Pull requests merged for v1.11.2* - #7736 : Backport 4619, BUG: many functions silently drop keepdims kwarg - #7738 : Backport 5706, ENH: add extra kwargs and update doc of many MA... - #7778 : DOC: Update Numpy 1.11.1 release notes. - #7793 : Backport 7515, BUG: MaskedArray.count treats negative axes incorrectly - #7816 : Backport 7463, BUG: fix array too big error for wide dtypes. - #7821 : Backport 7817, BUG: Make sure npy_mul_with_overflow_ detects... - #7824 : Backport 7820, MAINT: Allocate fewer bytes for empty arrays. - #7847 : Backport 7791, MAINT,DOC: Fix some imp module uses and update... - #7849 : Backport 7848, MAINT: Fix remaining uses of deprecated Python... - #7851 : Backport 7840, Fix ATLAS version detection - #7870 : Backport 7853, BUG: Raise RuntimeError when reloading numpy is... - #7896 : Backport 7894, BUG: construct ma.array from np.array which contains... - #7904 : Backport 7903, BUG: fix float16 type not being called due to... - #7917 : BUG: Production install of numpy should not require nose. - #7919 : Backport 7908, BLD: Fixed MKL detection for recent versions of... - #7920 : Backport #7911: BUG: fix for issue#7835 (ma.median of 1d) - #7932 : Backport 7925, Monkey-patch _msvccompile.gen_lib_option like... - #7939 : Backport 7931, BUG: Check for HAVE_LDOUBLE_DOUBLE_DOUBLE_LE in... - #7953 : Backport 7937, BUG: Guard against buggy comparisons in generic... - #7954 : Backport 7952, BUG: Use keyword arguments to initialize Extension... - #7955 : Backport 7941, BUG: Make sure numpy globals keep identity after... - #7972 : Backport 7963, BUG: MSVCCompiler grows 'lib' & 'include' env... - #7990 : Backport 7977, DOC: Create 1.11.2 release notes. - #8005 : Backport 7956, BLD: remove __NUMPY_SETUP__ from builtins at end... - #8007 : Backport 8006, DOC: Update 1.11.2 release notes. - #8010 : Backport 8008, MAINT: Remove leftover imp module imports. - #8012 : Backport 8011, DOC: Update 1.11.2 release notes. - #8020 : Backport 8018, BUG: Fixes return for np.ma.count if keepdims... - #8024 : Backport 8016, BUG: Fix numpy.ma.median. - #8031 : Backport 8030, BUG: fix np.ma.median with only one non-masked... - #8032 : Backport 8028, DOC: Update 1.11.2 release notes. - #8044 : Backport 8042, BUG: core: fix bug in NpyIter buffering with discontinuous... - #8046 : Backport 8045, DOC: Update 1.11.2 release notes. Enjoy, Chuck -------------- next part -------------- An HTML attachment was scrubbed... URL: From gustavo.scalet at eldorado.org.br Thu Oct 6 18:21:33 2016 From: gustavo.scalet at eldorado.org.br (Gustavo Serra Scalet) Date: Thu, 6 Oct 2016 22:21:33 +0000 Subject: [SciPy-Dev] Why does forcing Numpy to compile with "sizeof(long double) == 8" fails tests? Message-ID: Hi, I'm checking how Numpy performs on a POWER8 machine and I noticed that some tests related to machar.py are failing: ====================================================================== ERROR: test_singleton (test_getlimits.TestLongdouble) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy-1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/tests/test_getlimits.py", line 41, in test_singleton ftype = finfo(longdouble) File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy-1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/getlimits.py", line 124, in __new__ obj = object.__new__(cls)._init(dtype) File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy-1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/getlimits.py", line 154, in _init 'numpy %s precision floating point number' % precname) File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy-1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/machar.py", line 114, in __init__ self._do_init(float_conv, int_conv, float_to_float, float_to_str, title) File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy-1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/machar.py", line 127, in _do_init a = a + a RuntimeWarning: overflow encountered in add FAILED (KNOWNFAIL=4, SKIP=10, errors=4) That happened because native long double actually uses 2 doubles[1] (that method is called IBM Extended double[2]). To avoid that, I changed the compile flags to use -mlong-double-64 [3] and despite solving those errors, now I have some of these failures: ====================================================================== FAIL: test_in_from_2casttype (test_array_from_pyobj.test_LONGDOUBLE_gen) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/gut/python/venv3.5/lib/python3.4/site-packages/numpy-1.12.0.dev0+7a962d1-py3.4-linux-ppc64le.egg/numpy/f2py/tests/test_array_from_pyobj.py", line 319, in test_in_from_2casttype a = self.array([len(self.num2seq)], intent.in_, obj) File "", line 6, in File "/home/gut/python/venv3.5/lib/python3.4/site-packages/numpy-1.12.0.dev0+7a962d1-py3.4-linux-ppc64le.egg/numpy/f2py/tests/test_array_from_pyobj.py", line 275, in __init__ assert_(self.has_shared_memory()) File "/home/gut/python/venv3.5/lib/python3.4/site-packages/numpy-1.12.0.dev0+7a962d1-py3.4-linux-ppc64le.egg/numpy/testing/utils.py", line 90, in assert_ raise AssertionError(smsg) AssertionError FAILED (KNOWNFAIL=6, SKIP=16, failures=3) I wanted to know if there is a better approach to solve this issue. I guess it supports 'long double == double', right? Thanks in advance! Environment: Repository head at 33d850d522b3a1940c3ad06b63c79a466def11e9 (from git://github.com/numpy/numpy.git) + patch on [3] Python-3.5.2 [1] https://github.com/gcc-mirror/gcc/blob/3ff1ad36ed4ee3cc490e6178db87b1b8f2326c61/libgcc/config/rs6000/ibm-ldouble.c#L36-L43 [2] https://gcc.gnu.org/wiki/Ieee128PowerPC [3] https://github.com/PPC64/numpy/commit/be15f1073802ab127162c5dcdd995de7f6452c78 From dieter at werthmuller.org Thu Oct 6 22:20:40 2016 From: dieter at werthmuller.org (=?UTF-8?Q?Dieter_Werthm=c3=bcller?=) Date: Thu, 6 Oct 2016 21:20:40 -0500 Subject: [SciPy-Dev] FFTLog Message-ID: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> Dear SciPy-devs, I recently had the need for a logarithmic FFT routine, and did a quick f2py around Andrew Hamilton's FFTLog: http://casa.colorado.edu/~ajsh/FFTLog I put my f2py-setup and my pyf-file up on GitHub: https://github.com/prisae/fftlog I thought it might be a useful addition to the SciPy FFTPack. Specifically as three out of the five fortran-files, of which FFTLog consists, are already in scipy/fftpack. I have never contributed to SciPy and therefore do not know how much work it would involve to get it into SciPy. However, I thought I ask. If there is interest I expect that it would not take long for an experienced person, as it is a fairly small addition. Or someone could point me to the right direction on what to do to get it in. I append some comments on the involved files of FFTLog and some comments regarding their licenses. I believe it is compatible with SciPy. Thanks for all your good work! Dieter Files and Licenses/Permissions ------------------------------ Files of FFTLog [1] cdgamma.f [2] drfftb.f [3] drfftf.f [4] drffti.f [5] fftlog.f (plus a test routine, fftlogtest.f) -- [1] -- The original FFTLog states about this file: FFTLog uses [...] and a modified version of the complex Gamma function from the gamerf package at momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html. The original gamerf copyright statement states: Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp). You may use, copy, modify this code for any purpose and without fee. You may distribute this ORIGINAL package. Permission to distribute the modified gamma function code with the FFTLog package has been granted (email from Takuya Ooura to Andrew Hamilton dated 16 March 1999). Hence I think it is compatible with SciPy, or am I wrong? Alternatively it could be replaced with scipy.special.loggamma, I think, but I do not know if it is possible to mix Fortran and Python code with f2py. -- [2], [3], [4] -- They are from the NCAR suite of FFT routines (Swarztrauber 1979). As far as I can see they are already in SciPy, in scipy/fftpack/src/dfftpack/ (dfftb.f, dfftf.f, and dffti.f). So there is definitely not a licensing problem here. -- [5] -- This is the actual FFTLog routine from Hamilton. I asked Hamilton for permission before publishing his source code at github.com/prisae/fftlog. His email response was: -- start email from 28/09/2016 -- Dieter, You are welcome to use fftlog in any way you choose. Please note the credits commented in the code: c FFTLog uses the NCAR suite of FFT routines, c and a modified version of the complex Gamma function c from the gamerf package at c http://momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html . c The original gamerf copyright statement states: c Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp). c You may use, copy, modify this code for any purpose and c without fee. You may distribute this ORIGINAL package. c c Permission to distribute the modified gamma function code c with the FFTLog package has been granted c (email from Takuya Ooura to Andrew Hamilton dated 16 March 1999). Andrew -- end email from 28/09/2016 -- From sebastian at sipsolutions.net Fri Oct 7 03:04:05 2016 From: sebastian at sipsolutions.net (Sebastian Berg) Date: Fri, 07 Oct 2016 09:04:05 +0200 Subject: [SciPy-Dev] Why does forcing Numpy to compile with "sizeof(long double) == 8" fails tests? In-Reply-To: References: Message-ID: <1475823845.18249.2.camel@sipsolutions.net> On Do, 2016-10-06 at 22:21 +0000, Gustavo Serra Scalet wrote: > Hi, > > I'm checking how Numpy performs on a POWER8 machine and I noticed > that some tests related to machar.py are failing: > ===================================================================== > = > ERROR: test_singleton (test_getlimits.TestLongdouble) > ------------------------------------------------------------------- > --- > Traceback (most recent call last): > ? File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy- > 1.12.0.dev0+33d850d-py3.4-linux- > ppc64le.egg/numpy/core/tests/test_getlimits.py", line 41, in > test_singleton > ????ftype = finfo(longdouble) > ? File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy- > 1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/getlimits.py", > line 124, in __new__ > ????obj = object.__new__(cls)._init(dtype) > ? File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy- > 1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/getlimits.py", > line 154, in _init > ????'numpy %s precision floating point number' % precname) > ? File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy- > 1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/machar.py", > line 114, in __init__ > ????self._do_init(float_conv, int_conv, float_to_float, float_to_str, > title) > ? File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy- > 1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/machar.py", > line 127, in _do_init > ????a = a + a > RuntimeWarning: overflow encountered in add? > > FAILED (KNOWNFAIL=4, SKIP=10, errors=4) > > > That happened because native long double actually uses 2 doubles[1] > (that method is called IBM Extended double[2]). > > To avoid that, I changed the compile flags to use -mlong-double-64 > [3] and despite solving those errors, now I have some of these > failures: > ===================================================================== > = > FAIL: test_in_from_2casttype > (test_array_from_pyobj.test_LONGDOUBLE_gen) > ------------------------------------------------------------------- > --- > Traceback (most recent call last): > ? File "/home/gut/python/venv3.5/lib/python3.4/site-packages/numpy- > 1.12.0.dev0+7a962d1-py3.4-linux- > ppc64le.egg/numpy/f2py/tests/test_array_from_pyobj.py", line 319, in > test_in_from_2casttype > ????a = self.array([len(self.num2seq)], intent.in_, obj) > ? File "", line 6, in > ? File "/home/gut/python/venv3.5/lib/python3.4/site-packages/numpy- > 1.12.0.dev0+7a962d1-py3.4-linux- > ppc64le.egg/numpy/f2py/tests/test_array_from_pyobj.py", line 275, in > __init__ > ????assert_(self.has_shared_memory()) > ? File "/home/gut/python/venv3.5/lib/python3.4/site-packages/numpy- > 1.12.0.dev0+7a962d1-py3.4-linux-ppc64le.egg/numpy/testing/utils.py", > line 90, in assert_ > ????raise AssertionError(smsg) > AssertionError > > FAILED (KNOWNFAIL=6, SKIP=16, failures=3) > > > I wanted to know if there is a better approach to solve this issue. I > guess it supports 'long double == double', right? > I would have a first look at the test, it is completely plausible that the tests are skipped on windows or so, but the check to skip it does not actually look at the long double size. So, I would not rule out the tests are simply invalid in your setting and are run because nobody tried this before. - Sebastian > Thanks in advance! > > > Environment: > Repository head at 33d850d522b3a1940c3ad06b63c79a466def11e9 (from > git://github.com/numpy/numpy.git) + patch on [3] > Python-3.5.2? > > > [1] https://github.com/gcc-mirror/gcc/blob/3ff1ad36ed4ee3cc490e6178db > 87b1b8f2326c61/libgcc/config/rs6000/ibm-ldouble.c#L36-L43 > [2] https://gcc.gnu.org/wiki/Ieee128PowerPC > [3] https://github.com/PPC64/numpy/commit/be15f1073802ab127162c5dcdd9 > 95de7f6452c78 > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 819 bytes Desc: This is a digitally signed message part URL: From jakevdp at cs.washington.edu Fri Oct 7 13:53:45 2016 From: jakevdp at cs.washington.edu (Jacob Vanderplas) Date: Fri, 7 Oct 2016 10:53:45 -0700 Subject: [SciPy-Dev] FFTLog In-Reply-To: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> Message-ID: Hi Dieter, That's very cool! Before discussion of whether this fits into SciPy, there's one issue: I don't see any license on the Fortran code. This means, unfortunately, that it defaults to some form of "all-rights-reserved" and cannot be used in SciPy. Often it's enough to email the package author, link to some information like my post at [1], and request that they add a BSD-style license to their code (note that a GPL-style license would make it unusable by SciPy). Though we may want to see what others think about including this in SciPy before going too far down that route. For what it's worth, I'd suggest starting by making sure your Python wrapper is well-documented & well-tested; if it proves useful to many people, it would then be quite easy to pull into SciPy. Jake [1] http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows-of-licensing-scientific-code/ Jake VanderPlas Senior Data Science Fellow Director of Research in Physical Sciences University of Washington eScience Institute On Thu, Oct 6, 2016 at 7:20 PM, Dieter Werthm?ller wrote: > Dear SciPy-devs, > > I recently had the need for a logarithmic FFT routine, and did a quick > f2py around Andrew Hamilton's FFTLog: > http://casa.colorado.edu/~ajsh/FFTLog > > I put my f2py-setup and my pyf-file up on GitHub: > https://github.com/prisae/fftlog > > I thought it might be a useful addition to the SciPy FFTPack. Specifically > as three out of the five fortran-files, of which FFTLog consists, are > already in scipy/fftpack. > > I have never contributed to SciPy and therefore do not know how much work > it would involve to get it into SciPy. However, I thought I ask. If there > is interest I expect that it would not take long for an experienced person, > as it is a fairly small addition. Or someone could point me to the right > direction on what to do to get it in. > > > I append some comments on the involved files of FFTLog and some comments > regarding their licenses. I believe it is compatible with SciPy. > > Thanks for all your good work! > Dieter > > > Files and Licenses/Permissions > ------------------------------ > > Files of FFTLog > > [1] cdgamma.f > [2] drfftb.f > [3] drfftf.f > [4] drffti.f > [5] fftlog.f > > (plus a test routine, fftlogtest.f) > > -- [1] -- > The original FFTLog states about this file: > > FFTLog uses [...] and a modified version of the complex Gamma function > from the gamerf package at momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html. > The original gamerf copyright statement states: > > Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp). > You may use, copy, modify this code for any purpose and > without fee. You may distribute this ORIGINAL package. > > Permission to distribute the modified gamma function code with the FFTLog > package has been granted (email from Takuya Ooura to Andrew Hamilton dated > 16 March 1999). > > Hence I think it is compatible with SciPy, or am I wrong? > > Alternatively it could be replaced with scipy.special.loggamma, I think, > but I do not know if it is possible to mix Fortran and Python code with > f2py. > > -- [2], [3], [4] -- > They are from the NCAR suite of FFT routines (Swarztrauber 1979). > > As far as I can see they are already in SciPy, in > scipy/fftpack/src/dfftpack/ (dfftb.f, dfftf.f, and dffti.f). > > So there is definitely not a licensing problem here. > > -- [5] -- > This is the actual FFTLog routine from Hamilton. > > I asked Hamilton for permission before publishing his source code at > github.com/prisae/fftlog. > > His email response was: > > -- start email from 28/09/2016 -- > Dieter, > > You are welcome to use fftlog in any way you choose. Please note the > credits commented in the code: > > c FFTLog uses the NCAR suite of FFT routines, > c and a modified version of the complex Gamma function > c from the gamerf package at > c http://momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html . > c The original gamerf copyright statement states: > c Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp). > c You may use, copy, modify this code for any purpose and > c without fee. You may distribute this ORIGINAL package. > c > c Permission to distribute the modified gamma function code > c with the FFTLog package has been granted > c (email from Takuya Ooura to Andrew Hamilton dated 16 March 1999). > > Andrew > -- end email from 28/09/2016 -- > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dieter at werthmuller.org Fri Oct 7 14:24:32 2016 From: dieter at werthmuller.org (=?UTF-8?Q?Dieter_Werthm=c3=bcller?=) Date: Fri, 7 Oct 2016 13:24:32 -0500 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> Message-ID: <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> Jake, Thanks for your reply. Have you seen my whole section on "Files and Licences/Permissions"? (I put that info at the end of my original message, after my name.) Do you think it is not enough if Hamilton gave his written permission to 'use fftlog in any way you choose'? Dieter On 07/10/16 12:53, Jacob Vanderplas wrote: > Hi Dieter, > That's very cool! Before discussion of whether this fits into SciPy, > there's one issue: I don't see any license on the Fortran code. This > means, unfortunately, that it defaults to some form of > "all-rights-reserved" and cannot be used in SciPy. > > Often it's enough to email the package author, link to some information > like my post at [1], and request that they add a BSD-style license to > their code (note that a GPL-style license would make it unusable by SciPy). > > Though we may want to see what others think about including this in > SciPy before going too far down that route. For what it's worth, I'd > suggest starting by making sure your Python wrapper is well-documented & > well-tested; if it proves useful to many people, it would then be quite > easy to pull into SciPy. > > Jake > > [1] http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows-of-licensing-scientific-code/ > > Jake VanderPlas > Senior Data Science Fellow > Director of Research in Physical Sciences > University of Washington eScience Institute > > On Thu, Oct 6, 2016 at 7:20 PM, Dieter Werthm?ller > > wrote: > > Dear SciPy-devs, > > I recently had the need for a logarithmic FFT routine, and did a > quick f2py around Andrew Hamilton's FFTLog: > http://casa.colorado.edu/~ajsh/FFTLog > > > I put my f2py-setup and my pyf-file up on GitHub: > https://github.com/prisae/fftlog > > I thought it might be a useful addition to the SciPy FFTPack. > Specifically as three out of the five fortran-files, of which FFTLog > consists, are already in scipy/fftpack. > > I have never contributed to SciPy and therefore do not know how much > work it would involve to get it into SciPy. However, I thought I > ask. If there is interest I expect that it would not take long for > an experienced person, as it is a fairly small addition. Or someone > could point me to the right direction on what to do to get it in. > > > I append some comments on the involved files of FFTLog and some > comments regarding their licenses. I believe it is compatible with > SciPy. > > Thanks for all your good work! > Dieter > > > Files and Licenses/Permissions > ------------------------------ > > Files of FFTLog > > [1] cdgamma.f > [2] drfftb.f > [3] drfftf.f > [4] drffti.f > [5] fftlog.f > > (plus a test routine, fftlogtest.f) > > -- [1] -- > The original FFTLog states about this file: > > FFTLog uses [...] and a modified version of the complex Gamma > function from the gamerf package at > momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html > . The original > gamerf copyright statement states: > > Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp > ). > You may use, copy, modify this code for any purpose and > without fee. You may distribute this ORIGINAL package. > > Permission to distribute the modified gamma function code with the > FFTLog package has been granted (email from Takuya Ooura to Andrew > Hamilton dated 16 March 1999). > > Hence I think it is compatible with SciPy, or am I wrong? > > Alternatively it could be replaced with scipy.special.loggamma, I > think, but I do not know if it is possible to mix Fortran and Python > code with f2py. > > -- [2], [3], [4] -- > They are from the NCAR suite of FFT routines (Swarztrauber 1979). > > As far as I can see they are already in SciPy, in > scipy/fftpack/src/dfftpack/ (dfftb.f, dfftf.f, and dffti.f). > > So there is definitely not a licensing problem here. > > -- [5] -- > This is the actual FFTLog routine from Hamilton. > > I asked Hamilton for permission before publishing his source code at > github.com/prisae/fftlog . > > His email response was: > > -- start email from 28/09/2016 -- > Dieter, > > You are welcome to use fftlog in any way you choose. Please note the > credits commented in the code: > > c FFTLog uses the NCAR suite of FFT routines, > c and a modified version of the complex Gamma function > c from the gamerf package at > c http://momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html > . > c The original gamerf copyright statement states: > c Copyright(C) 1996 Takuya OOURA (email: > ooura at mmm.t.u-tokyo.ac.jp ). > c You may use, copy, modify this code for any purpose and > c without fee. You may distribute this ORIGINAL package. > c > c Permission to distribute the modified gamma function code > c with the FFTLog package has been granted > c (email from Takuya Ooura to Andrew Hamilton dated 16 March 1999). > > Andrew > -- end email from 28/09/2016 -- > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > From jakevdp at cs.washington.edu Fri Oct 7 15:16:40 2016 From: jakevdp at cs.washington.edu (Jacob Vanderplas) Date: Fri, 7 Oct 2016 12:16:40 -0700 Subject: [SciPy-Dev] FFTLog In-Reply-To: <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> Message-ID: Hi, Unfortunately I don't think those notes are particularly helpful in this regard: for example, does bundling the software with SciPy meet the requirement of "distributing the ORIGINAL package", or not? It's murky, and most of the devs would likely err on the side of safety and assume the answer is no. The benefit of using an established license like BSD, MIT, GPL, etc. is that the language is well-defined and the intent of the license is well-understood. Jake Jake VanderPlas Senior Data Science Fellow Director of Research in Physical Sciences University of Washington eScience Institute On Fri, Oct 7, 2016 at 11:24 AM, Dieter Werthm?ller wrote: > Jake, > > Thanks for your reply. > > Have you seen my whole section on "Files and Licences/Permissions"? (I > put that info at the end of my original message, after my name.) Do you > think it is not enough if Hamilton gave his written permission to 'use > fftlog in any way you choose'? > > Dieter > > > On 07/10/16 12:53, Jacob Vanderplas wrote: > > Hi Dieter, > > That's very cool! Before discussion of whether this fits into SciPy, > > there's one issue: I don't see any license on the Fortran code. This > > means, unfortunately, that it defaults to some form of > > "all-rights-reserved" and cannot be used in SciPy. > > > > Often it's enough to email the package author, link to some information > > like my post at [1], and request that they add a BSD-style license to > > their code (note that a GPL-style license would make it unusable by > SciPy). > > > > Though we may want to see what others think about including this in > > SciPy before going too far down that route. For what it's worth, I'd > > suggest starting by making sure your Python wrapper is well-documented & > > well-tested; if it proves useful to many people, it would then be quite > > easy to pull into SciPy. > > > > Jake > > > > [1] http://www.astrobetter.com/blog/2014/03/10/the-whys-and- > hows-of-licensing-scientific-code/ > > > > Jake VanderPlas > > Senior Data Science Fellow > > Director of Research in Physical Sciences > > University of Washington eScience Institute > > > > On Thu, Oct 6, 2016 at 7:20 PM, Dieter Werthm?ller > > > wrote: > > > > Dear SciPy-devs, > > > > I recently had the need for a logarithmic FFT routine, and did a > > quick f2py around Andrew Hamilton's FFTLog: > > http://casa.colorado.edu/~ajsh/FFTLog > > > > > > I put my f2py-setup and my pyf-file up on GitHub: > > https://github.com/prisae/fftlog > > > > > I thought it might be a useful addition to the SciPy FFTPack. > > Specifically as three out of the five fortran-files, of which FFTLog > > consists, are already in scipy/fftpack. > > > > I have never contributed to SciPy and therefore do not know how much > > work it would involve to get it into SciPy. However, I thought I > > ask. If there is interest I expect that it would not take long for > > an experienced person, as it is a fairly small addition. Or someone > > could point me to the right direction on what to do to get it in. > > > > > > I append some comments on the involved files of FFTLog and some > > comments regarding their licenses. I believe it is compatible with > > SciPy. > > > > Thanks for all your good work! > > Dieter > > > > > > Files and Licenses/Permissions > > ------------------------------ > > > > Files of FFTLog > > > > [1] cdgamma.f > > [2] drfftb.f > > [3] drfftf.f > > [4] drffti.f > > [5] fftlog.f > > > > (plus a test routine, fftlogtest.f) > > > > -- [1] -- > > The original FFTLog states about this file: > > > > FFTLog uses [...] and a modified version of the complex Gamma > > function from the gamerf package at > > momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html > > . The original > > gamerf copyright statement states: > > > > Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp > > ). > > You may use, copy, modify this code for any purpose and > > without fee. You may distribute this ORIGINAL package. > > > > Permission to distribute the modified gamma function code with the > > FFTLog package has been granted (email from Takuya Ooura to Andrew > > Hamilton dated 16 March 1999). > > > > Hence I think it is compatible with SciPy, or am I wrong? > > > > Alternatively it could be replaced with scipy.special.loggamma, I > > think, but I do not know if it is possible to mix Fortran and Python > > code with f2py. > > > > -- [2], [3], [4] -- > > They are from the NCAR suite of FFT routines (Swarztrauber 1979). > > > > As far as I can see they are already in SciPy, in > > scipy/fftpack/src/dfftpack/ (dfftb.f, dfftf.f, and dffti.f). > > > > So there is definitely not a licensing problem here. > > > > -- [5] -- > > This is the actual FFTLog routine from Hamilton. > > > > I asked Hamilton for permission before publishing his source code at > > github.com/prisae/fftlog . > > > > His email response was: > > > > -- start email from 28/09/2016 -- > > Dieter, > > > > You are welcome to use fftlog in any way you choose. Please note > the > > credits commented in the code: > > > > c FFTLog uses the NCAR suite of FFT routines, > > c and a modified version of the complex Gamma function > > c from the gamerf package at > > c http://momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html > > . > > c The original gamerf copyright statement states: > > c Copyright(C) 1996 Takuya OOURA (email: > > ooura at mmm.t.u-tokyo.ac.jp ). > > c You may use, copy, modify this code for any purpose and > > c without fee. You may distribute this ORIGINAL package. > > c > > c Permission to distribute the modified gamma function code > > c with the FFTLog package has been granted > > c (email from Takuya Ooura to Andrew Hamilton dated 16 March 1999). > > > > Andrew > > -- end email from 28/09/2016 -- > > > > _______________________________________________ > > SciPy-Dev mailing list > > SciPy-Dev at scipy.org > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > > > > > > > _______________________________________________ > > SciPy-Dev mailing list > > SciPy-Dev at scipy.org > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dieter at werthmuller.org Fri Oct 7 15:59:15 2016 From: dieter at werthmuller.org (=?UTF-8?Q?Dieter_Werthm=c3=bcller?=) Date: Fri, 7 Oct 2016 14:59:15 -0500 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> Message-ID: Jake, Thanks for the clarification. I will try to get the permissions from the authors. What is regarded as sufficient? Is an email from the author, granting me/SciPy to distribute their code with a specific, BSD-style license sufficient? Or do they necessarily have to change the websites where they host the code to include the license? Dieter On 07/10/16 14:16, Jacob Vanderplas wrote: > Hi, > Unfortunately I don't think those notes are particularly helpful in this > regard: for example, does bundling the software with SciPy meet the > requirement of "distributing the ORIGINAL package", or not? It's murky, > and most of the devs would likely err on the side of safety and assume > the answer is no. The benefit of using an established license like BSD, > MIT, GPL, etc. is that the language is well-defined and the intent of > the license is well-understood. > Jake > > Jake VanderPlas > Senior Data Science Fellow > Director of Research in Physical Sciences > University of Washington eScience Institute > > On Fri, Oct 7, 2016 at 11:24 AM, Dieter Werthm?ller > > wrote: > > Jake, > > Thanks for your reply. > > Have you seen my whole section on "Files and Licences/Permissions"? (I > put that info at the end of my original message, after my name.) Do you > think it is not enough if Hamilton gave his written permission to 'use > fftlog in any way you choose'? > > Dieter > > > On 07/10/16 12:53, Jacob Vanderplas wrote: > > Hi Dieter, > > That's very cool! Before discussion of whether this fits into SciPy, > > there's one issue: I don't see any license on the Fortran code. This > > means, unfortunately, that it defaults to some form of > > "all-rights-reserved" and cannot be used in SciPy. > > > > Often it's enough to email the package author, link to some information > > like my post at [1], and request that they add a BSD-style license to > > their code (note that a GPL-style license would make it unusable by SciPy). > > > > Though we may want to see what others think about including this in > > SciPy before going too far down that route. For what it's worth, I'd > > suggest starting by making sure your Python wrapper is well-documented & > > well-tested; if it proves useful to many people, it would then be quite > > easy to pull into SciPy. > > > > Jake > > > > [1] http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows-of-licensing-scientific-code/ > > > > > Jake VanderPlas > > Senior Data Science Fellow > > Director of Research in Physical Sciences > > University of Washington eScience Institute > > > > On Thu, Oct 6, 2016 at 7:20 PM, Dieter Werthm?ller > > > >> wrote: > > > > Dear SciPy-devs, > > > > I recently had the need for a logarithmic FFT routine, and did a > > quick f2py around Andrew Hamilton's FFTLog: > > http://casa.colorado.edu/~ajsh/FFTLog > > > > > > > > I put my f2py-setup and my pyf-file up on GitHub: > > https://github.com/prisae/fftlog > > > > > > I thought it might be a useful addition to the SciPy FFTPack. > > Specifically as three out of the five fortran-files, of which > FFTLog > > consists, are already in scipy/fftpack. > > > > I have never contributed to SciPy and therefore do not know > how much > > work it would involve to get it into SciPy. However, I thought I > > ask. If there is interest I expect that it would not take long for > > an experienced person, as it is a fairly small addition. Or > someone > > could point me to the right direction on what to do to get it in. > > > > > > I append some comments on the involved files of FFTLog and some > > comments regarding their licenses. I believe it is compatible with > > SciPy. > > > > Thanks for all your good work! > > Dieter > > > > > > Files and Licenses/Permissions > > ------------------------------ > > > > Files of FFTLog > > > > [1] cdgamma.f > > [2] drfftb.f > > [3] drfftf.f > > [4] drffti.f > > [5] fftlog.f > > > > (plus a test routine, fftlogtest.f) > > > > -- [1] -- > > The original FFTLog states about this file: > > > > FFTLog uses [...] and a modified version of the complex Gamma > > function from the gamerf package at > > momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html > > > >. The original > > gamerf copyright statement states: > > > > Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp > > >). > > You may use, copy, modify this code for any purpose and > > without fee. You may distribute this ORIGINAL package. > > > > Permission to distribute the modified gamma function code with the > > FFTLog package has been granted (email from Takuya Ooura to Andrew > > Hamilton dated 16 March 1999). > > > > Hence I think it is compatible with SciPy, or am I wrong? > > > > Alternatively it could be replaced with scipy.special.loggamma, I > > think, but I do not know if it is possible to mix Fortran and Python > > code with f2py. > > > > -- [2], [3], [4] -- > > They are from the NCAR suite of FFT routines (Swarztrauber 1979). > > > > As far as I can see they are already in SciPy, in > > scipy/fftpack/src/dfftpack/ (dfftb.f, dfftf.f, and dffti.f). > > > > So there is definitely not a licensing problem here. > > > > -- [5] -- > > This is the actual FFTLog routine from Hamilton. > > > > I asked Hamilton for permission before publishing his source code at > > github.com/prisae/fftlog > >. > > > > His email response was: > > > > -- start email from 28/09/2016 -- > > Dieter, > > > > You are welcome to use fftlog in any way you choose. Please note the > > credits commented in the code: > > > > c FFTLog uses the NCAR suite of FFT routines, > > c and a modified version of the complex Gamma function > > c from the gamerf package at > > c http://momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html > > > > . > > c The original gamerf copyright statement states: > > c Copyright(C) 1996 Takuya OOURA (email: > > ooura at mmm.t.u-tokyo.ac.jp > >). > > c You may use, copy, modify this code for any purpose and > > c without fee. You may distribute this ORIGINAL package. > > c > > c Permission to distribute the modified gamma function code > > c with the FFTLog package has been granted > > c (email from Takuya Ooura to Andrew Hamilton dated 16 March 1999). > > > > Andrew > > -- end email from 28/09/2016 -- > > > > _______________________________________________ > > SciPy-Dev mailing list > > SciPy-Dev at scipy.org > > > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > > > > > > > > > _______________________________________________ > > SciPy-Dev mailing list > > SciPy-Dev at scipy.org > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > From jakevdp at cs.washington.edu Fri Oct 7 16:01:44 2016 From: jakevdp at cs.washington.edu (Jacob Vanderplas) Date: Fri, 7 Oct 2016 13:01:44 -0700 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> Message-ID: wrote: > Jake, > > Thanks for the clarification. I will try to get the permissions from the > authors. > > What is regarded as sufficient? Is an email from the author, granting > me/SciPy to distribute their code with a specific, BSD-style license > sufficient? Or do they necessarily have to change the websites where > they host the code to include the license? > Best would be a license in the software repository/tarball itself. Jake > > Dieter > > > On 07/10/16 14:16, Jacob Vanderplas wrote: > > Hi, > > Unfortunately I don't think those notes are particularly helpful in this > > regard: for example, does bundling the software with SciPy meet the > > requirement of "distributing the ORIGINAL package", or not? It's murky, > > and most of the devs would likely err on the side of safety and assume > > the answer is no. The benefit of using an established license like BSD, > > MIT, GPL, etc. is that the language is well-defined and the intent of > > the license is well-understood. > > Jake > > > > Jake VanderPlas > > Senior Data Science Fellow > > Director of Research in Physical Sciences > > University of Washington eScience Institute > > > > On Fri, Oct 7, 2016 at 11:24 AM, Dieter Werthm?ller > > > wrote: > > > > Jake, > > > > Thanks for your reply. > > > > Have you seen my whole section on "Files and Licences/Permissions"? > (I > > put that info at the end of my original message, after my name.) Do > you > > think it is not enough if Hamilton gave his written permission to > 'use > > fftlog in any way you choose'? > > > > Dieter > > > > > > On 07/10/16 12:53, Jacob Vanderplas wrote: > > > Hi Dieter, > > > That's very cool! Before discussion of whether this fits into > SciPy, > > > there's one issue: I don't see any license on the Fortran code. > This > > > means, unfortunately, that it defaults to some form of > > > "all-rights-reserved" and cannot be used in SciPy. > > > > > > Often it's enough to email the package author, link to some > information > > > like my post at [1], and request that they add a BSD-style license > to > > > their code (note that a GPL-style license would make it unusable > by SciPy). > > > > > > Though we may want to see what others think about including this in > > > SciPy before going too far down that route. For what it's worth, > I'd > > > suggest starting by making sure your Python wrapper is > well-documented & > > > well-tested; if it proves useful to many people, it would then be > quite > > > easy to pull into SciPy. > > > > > > Jake > > > > > > [1] http://www.astrobetter.com/blog/2014/03/10/the-whys-and- > hows-of-licensing-scientific-code/ > > hows-of-licensing-scientific-code/> > > > > > > Jake VanderPlas > > > Senior Data Science Fellow > > > Director of Research in Physical Sciences > > > University of Washington eScience Institute > > > > > > On Thu, Oct 6, 2016 at 7:20 PM, Dieter Werthm?ller > > > > > >> > wrote: > > > > > > Dear SciPy-devs, > > > > > > I recently had the need for a logarithmic FFT routine, and did > a > > > quick f2py around Andrew Hamilton's FFTLog: > > > http://casa.colorado.edu/~ajsh/FFTLog > > > > > > > > > > > > > I put my f2py-setup and my pyf-file up on GitHub: > > > https://github.com/prisae/fftlog > > > > > > > > > > I thought it might be a useful addition to the SciPy FFTPack. > > > Specifically as three out of the five fortran-files, of which > > FFTLog > > > consists, are already in scipy/fftpack. > > > > > > I have never contributed to SciPy and therefore do not know > > how much > > > work it would involve to get it into SciPy. However, I thought > I > > > ask. If there is interest I expect that it would not take long > for > > > an experienced person, as it is a fairly small addition. Or > > someone > > > could point me to the right direction on what to do to get it > in. > > > > > > > > > I append some comments on the involved files of FFTLog and some > > > comments regarding their licenses. I believe it is compatible > with > > > SciPy. > > > > > > Thanks for all your good work! > > > Dieter > > > > > > > > > Files and Licenses/Permissions > > > ------------------------------ > > > > > > Files of FFTLog > > > > > > [1] cdgamma.f > > > [2] drfftb.f > > > [3] drfftf.f > > > [4] drffti.f > > > [5] fftlog.f > > > > > > (plus a test routine, fftlogtest.f) > > > > > > -- [1] -- > > > The original FFTLog states about this file: > > > > > > FFTLog uses [...] and a modified version of the complex Gamma > > > function from the gamerf package at > > > momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html > > > > > > >. The original > > > gamerf copyright statement states: > > > > > > Copyright(C) 1996 Takuya OOURA (email: > ooura at mmm.t.u-tokyo.ac.jp > > > > >). > > > You may use, copy, modify this code for any purpose and > > > without fee. You may distribute this ORIGINAL package. > > > > > > Permission to distribute the modified gamma function code with > the > > > FFTLog package has been granted (email from Takuya Ooura to > Andrew > > > Hamilton dated 16 March 1999). > > > > > > Hence I think it is compatible with SciPy, or am I wrong? > > > > > > Alternatively it could be replaced with > scipy.special.loggamma, I > > > think, but I do not know if it is possible to mix Fortran and > Python > > > code with f2py. > > > > > > -- [2], [3], [4] -- > > > They are from the NCAR suite of FFT routines (Swarztrauber > 1979). > > > > > > As far as I can see they are already in SciPy, in > > > scipy/fftpack/src/dfftpack/ (dfftb.f, dfftf.f, and dffti.f). > > > > > > So there is definitely not a licensing problem here. > > > > > > -- [5] -- > > > This is the actual FFTLog routine from Hamilton. > > > > > > I asked Hamilton for permission before publishing his source > code at > > > github.com/prisae/fftlog > > >. > > > > > > His email response was: > > > > > > -- start email from 28/09/2016 -- > > > Dieter, > > > > > > You are welcome to use fftlog in any way you choose. Please > note the > > > credits commented in the code: > > > > > > c FFTLog uses the NCAR suite of FFT routines, > > > c and a modified version of the complex Gamma function > > > c from the gamerf package at > > > c http://momonga.t.u-tokyo.ac.jp/~ooura/gamerf.html > > > > > > > . > > > c The original gamerf copyright statement states: > > > c Copyright(C) 1996 Takuya OOURA (email: > > > ooura at mmm.t.u-tokyo.ac.jp > > >>). > > > c You may use, copy, modify this code for any purpose and > > > c without fee. You may distribute this ORIGINAL package. > > > c > > > c Permission to distribute the modified gamma function code > > > c with the FFTLog package has been granted > > > c (email from Takuya Ooura to Andrew Hamilton dated 16 March > 1999). > > > > > > Andrew > > > -- end email from 28/09/2016 -- > > > > > > _______________________________________________ > > > SciPy-Dev mailing list > > > SciPy-Dev at scipy.org > > > > > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > SciPy-Dev mailing list > > > SciPy-Dev at scipy.org > > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > > _______________________________________________ > > SciPy-Dev mailing list > > SciPy-Dev at scipy.org > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > > > > > > > _______________________________________________ > > SciPy-Dev mailing list > > SciPy-Dev at scipy.org > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Fri Oct 7 16:11:23 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sat, 8 Oct 2016 09:11:23 +1300 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> Message-ID: On Sat, Oct 8, 2016 at 8:59 AM, Dieter Werthm?ller wrote: > Jake, > > Thanks for the clarification. I will try to get the permissions from the > authors. > > What is regarded as sufficient? Is an email from the author, granting > me/SciPy to distribute their code with a specific, BSD-style license > sufficient? Or do they necessarily have to change the websites where > they host the code to include the license? > An email stating that the code can be distributed under a BSD license (or MIT or other compatible license) is enough. Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Fri Oct 7 16:13:52 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sat, 8 Oct 2016 09:13:52 +1300 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> Message-ID: On Sat, Oct 8, 2016 at 9:11 AM, Ralf Gommers wrote: > > > On Sat, Oct 8, 2016 at 8:59 AM, Dieter Werthm?ller > wrote: > >> Jake, >> >> Thanks for the clarification. I will try to get the permissions from the >> authors. >> >> What is regarded as sufficient? Is an email from the author, granting >> me/SciPy to distribute their code with a specific, BSD-style license >> sufficient? Or do they necessarily have to change the websites where >> they host the code to include the license? >> > > An email stating that the code can be distributed under a BSD license (or > MIT or other compatible license) is enough. > Some delay on the line, missed Jake's answer. Email is enough, but a change in the repo would of course be even better. Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From dieter at werthmuller.org Fri Oct 7 20:58:38 2016 From: dieter at werthmuller.org (=?UTF-8?Q?Dieter_Werthm=c3=bcller?=) Date: Fri, 7 Oct 2016 19:58:38 -0500 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> Message-ID: <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> Evening, I wrote to Andrew Hamilton, and below is his answer. He has basically no problem with it at all, I just don't know if his response is explicit enough. I think my email was quite extensive, and I assume that is as much as we will get from him. I also do not expect him to change his on "13 Mar 1999, 21:17" from TeX translated website... What do you think, is this enough? I also wrote to Takuya Ooura, and will let you know of his response, if I get one. However, as there are other complex logarithmic double precision gamma functions around, one already in scipy, this piece is not mission critical. Regards, Dieter ========== START email correspondence with Andrew Hamilton ========== Subject: Re: FFTLog - license From: Andrew Hamilton Date: 07/10/16 18:22 To: Dieter Werthm?ller CC: Andrew.Hamilton at colorado.edu Dieter, I approve your adding the license language you suggest to FFTLog, and making available the resulting package for distribution. Andrew On 10/07/2016 03:42 PM, Dieter Werthm?ller wrote: > Dear Andrew, > > Please apologize me bothering you again. > > After I published the code to wrap your FFTLog for Python I thought that > it would be much better if your FFTLog would make it straight into the > scientific library of Python. This would make your FFTLog available to a > much wider audience. > > I contacted the developers of SciPy (http://scipy.org), and they are > interested in including your code. However, there is one issue: > licensing. Code that is published on the web without a license file is > copyrighted under law, and SciPy can for this reason not include your > code into their library. > > All I ask for is if you could confirm to us by email that we are allowed > to distribute your FFTLog under the BSD-3-Clause license: > https://opensource.org/licenses/BSD-3-Clause > > The license is just a suggestion, any other BSD or MIT compatible > license would be fine as well. (For the same, legal reasons we recommend > to publish a license file on your website too, but that is obviously > entirely up to you. It might, however, clarify things for future visitors.) > > It would only affect your fftlog.f file, and the changes you made to > cdgamma.f. I will write Takuya OOURA as well regarding the original > cdgamma.f-file, asking him the same favour. And the three drfft*.f are > already in the SciPy-library with the whole FFTPack. > > If you are interested why this issue arises, Jake Vanderplas, one of the > developers of SciPy, wrote an interesting article about the topic: > http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows-of-licensing-scientific-code/ > > Thank you again for your time and for making FFTLog available! > Best regards, > Dieter > ========== END email correspondence with Andrew Hamilton ========== On 07/10/16 15:13, Ralf Gommers wrote: > > > On Sat, Oct 8, 2016 at 9:11 AM, Ralf Gommers > wrote: > > > > On Sat, Oct 8, 2016 at 8:59 AM, Dieter Werthm?ller > > wrote: > > Jake, > > Thanks for the clarification. I will try to get the permissions > from the > authors. > > What is regarded as sufficient? Is an email from the author, > granting > me/SciPy to distribute their code with a specific, BSD-style license > sufficient? Or do they necessarily have to change the websites where > they host the code to include the license? > > > An email stating that the code can be distributed under a BSD > license (or MIT or other compatible license) is enough. > > > Some delay on the line, missed Jake's answer. Email is enough, but a > change in the repo would of course be even better. > > Ralf > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > From ralf.gommers at gmail.com Fri Oct 7 21:16:28 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sat, 8 Oct 2016 14:16:28 +1300 Subject: [SciPy-Dev] FFTLog In-Reply-To: <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> Message-ID: On Sat, Oct 8, 2016 at 1:58 PM, Dieter Werthm?ller wrote: > Evening, > > I wrote to Andrew Hamilton, and below is his answer. He has basically no > problem with it at all, I just don't know if his response is explicit > enough. > > I think my email was quite extensive, and I assume that is as much as we > will get from him. I also do not expect him to change his on "13 Mar 1999, > 21:17" from TeX translated website... > > What do you think, is this enough? > Yes, that's perfectly fine. Thanks for clarifying that Dieter. Cheers, Ralf > I also wrote to Takuya Ooura, and will let you know of his response, if I > get one. However, as there are other complex logarithmic double precision > gamma functions around, one already in scipy, this piece is not mission > critical. > > Regards, > Dieter > > ========== START email correspondence with Andrew Hamilton ========== > Subject: Re: FFTLog - license > From: Andrew Hamilton > Date: 07/10/16 18:22 > To: Dieter Werthm?ller > CC: Andrew.Hamilton at colorado.edu > > Dieter, > > I approve your adding the license language you suggest to FFTLog, and > making available the resulting package for distribution. > > Andrew > > On 10/07/2016 03:42 PM, Dieter Werthm?ller wrote: > > Dear Andrew, > > > > Please apologize me bothering you again. > > > > After I published the code to wrap your FFTLog for Python I thought that > > it would be much better if your FFTLog would make it straight into the > > scientific library of Python. This would make your FFTLog available to a > > much wider audience. > > > > I contacted the developers of SciPy (http://scipy.org), and they are > > interested in including your code. However, there is one issue: > > licensing. Code that is published on the web without a license file is > > copyrighted under law, and SciPy can for this reason not include your > > code into their library. > > > > All I ask for is if you could confirm to us by email that we are allowed > > to distribute your FFTLog under the BSD-3-Clause license: > > https://opensource.org/licenses/BSD-3-Clause > > > > The license is just a suggestion, any other BSD or MIT compatible > > license would be fine as well. (For the same, legal reasons we recommend > > to publish a license file on your website too, but that is obviously > > entirely up to you. It might, however, clarify things for future > visitors.) > > > > It would only affect your fftlog.f file, and the changes you made to > > cdgamma.f. I will write Takuya OOURA as well regarding the original > > cdgamma.f-file, asking him the same favour. And the three drfft*.f are > > already in the SciPy-library with the whole FFTPack. > > > > If you are interested why this issue arises, Jake Vanderplas, one of the > > developers of SciPy, wrote an interesting article about the topic: > > http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows > -of-licensing-scientific-code/ > > > > Thank you again for your time and for making FFTLog available! > > Best regards, > > Dieter > > > ========== END email correspondence with Andrew Hamilton ========== > > On 07/10/16 15:13, Ralf Gommers wrote: > >> >> >> On Sat, Oct 8, 2016 at 9:11 AM, Ralf Gommers > > wrote: >> >> >> >> On Sat, Oct 8, 2016 at 8:59 AM, Dieter Werthm?ller >> > wrote: >> >> Jake, >> >> Thanks for the clarification. I will try to get the permissions >> from the >> authors. >> >> What is regarded as sufficient? Is an email from the author, >> granting >> me/SciPy to distribute their code with a specific, BSD-style >> license >> sufficient? Or do they necessarily have to change the websites >> where >> they host the code to include the license? >> >> >> An email stating that the code can be distributed under a BSD >> license (or MIT or other compatible license) is enough. >> >> >> Some delay on the line, missed Jake's answer. Email is enough, but a >> change in the repo would of course be even better. >> >> Ralf >> >> >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> >> _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From josh.craig.wilson at gmail.com Fri Oct 7 22:18:19 2016 From: josh.craig.wilson at gmail.com (Joshua Wilson) Date: Fri, 7 Oct 2016 21:18:19 -0500 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> Message-ID: Re log gamma: under the hood the SciPy versions are in C (real version) and Cython (complex version), so linking them up with Fortran code is definitely doable. On Fri, Oct 7, 2016 at 8:16 PM, Ralf Gommers wrote: > > > On Sat, Oct 8, 2016 at 1:58 PM, Dieter Werthm?ller > wrote: > >> Evening, >> >> I wrote to Andrew Hamilton, and below is his answer. He has basically no >> problem with it at all, I just don't know if his response is explicit >> enough. >> >> I think my email was quite extensive, and I assume that is as much as we >> will get from him. I also do not expect him to change his on "13 Mar 1999, >> 21:17" from TeX translated website... >> >> What do you think, is this enough? >> > > Yes, that's perfectly fine. Thanks for clarifying that Dieter. > > Cheers, > Ralf > > >> I also wrote to Takuya Ooura, and will let you know of his response, if I >> get one. However, as there are other complex logarithmic double precision >> gamma functions around, one already in scipy, this piece is not mission >> critical. >> >> Regards, >> Dieter >> >> ========== START email correspondence with Andrew Hamilton ========== >> Subject: Re: FFTLog - license >> From: Andrew Hamilton >> Date: 07/10/16 18:22 >> To: Dieter Werthm?ller >> CC: Andrew.Hamilton at colorado.edu >> >> Dieter, >> >> I approve your adding the license language you suggest to FFTLog, and >> making available the resulting package for distribution. >> >> Andrew >> >> On 10/07/2016 03:42 PM, Dieter Werthm?ller wrote: >> > Dear Andrew, >> > >> > Please apologize me bothering you again. >> > >> > After I published the code to wrap your FFTLog for Python I thought that >> > it would be much better if your FFTLog would make it straight into the >> > scientific library of Python. This would make your FFTLog available to a >> > much wider audience. >> > >> > I contacted the developers of SciPy (http://scipy.org), and they are >> > interested in including your code. However, there is one issue: >> > licensing. Code that is published on the web without a license file is >> > copyrighted under law, and SciPy can for this reason not include your >> > code into their library. >> > >> > All I ask for is if you could confirm to us by email that we are allowed >> > to distribute your FFTLog under the BSD-3-Clause license: >> > https://opensource.org/licenses/BSD-3-Clause >> > >> > The license is just a suggestion, any other BSD or MIT compatible >> > license would be fine as well. (For the same, legal reasons we recommend >> > to publish a license file on your website too, but that is obviously >> > entirely up to you. It might, however, clarify things for future >> visitors.) >> > >> > It would only affect your fftlog.f file, and the changes you made to >> > cdgamma.f. I will write Takuya OOURA as well regarding the original >> > cdgamma.f-file, asking him the same favour. And the three drfft*.f are >> > already in the SciPy-library with the whole FFTPack. >> > >> > If you are interested why this issue arises, Jake Vanderplas, one of the >> > developers of SciPy, wrote an interesting article about the topic: >> > http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows >> -of-licensing-scientific-code/ >> > >> > Thank you again for your time and for making FFTLog available! >> > Best regards, >> > Dieter >> > >> ========== END email correspondence with Andrew Hamilton ========== >> >> On 07/10/16 15:13, Ralf Gommers wrote: >> >>> >>> >>> On Sat, Oct 8, 2016 at 9:11 AM, Ralf Gommers >> > wrote: >>> >>> >>> >>> On Sat, Oct 8, 2016 at 8:59 AM, Dieter Werthm?ller >>> > wrote: >>> >>> Jake, >>> >>> Thanks for the clarification. I will try to get the permissions >>> from the >>> authors. >>> >>> What is regarded as sufficient? Is an email from the author, >>> granting >>> me/SciPy to distribute their code with a specific, BSD-style >>> license >>> sufficient? Or do they necessarily have to change the websites >>> where >>> they host the code to include the license? >>> >>> >>> An email stating that the code can be distributed under a BSD >>> license (or MIT or other compatible license) is enough. >>> >>> >>> Some delay on the line, missed Jake's answer. Email is enough, but a >>> change in the repo would of course be even better. >>> >>> Ralf >>> >>> >>> >>> >>> _______________________________________________ >>> SciPy-Dev mailing list >>> SciPy-Dev at scipy.org >>> https://mail.scipy.org/mailman/listinfo/scipy-dev >>> >>> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Sat Oct 8 04:50:12 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sat, 8 Oct 2016 21:50:12 +1300 Subject: [SciPy-Dev] Moving SciPy project organization forward In-Reply-To: References: Message-ID: On Sun, Oct 2, 2016 at 8:36 PM, Ralf Gommers wrote: > > > On Fri, Sep 30, 2016 at 6:12 AM, Evgeni Burovski < > evgeny.burovskiy at gmail.com> wrote: > >> > Now that the mailing list is alive again: how about I organize the >> first one >> > for say 2 weeks from now? Proposed topic: producing (a) paper(s). >> >> +1. >> > > Looking at time zones, what will work best is evening in Europe, which is > daytime in the US and early morning in Australasia. Here is a poll: > http://whenisgood.net/bdkqjkr. I'll pick a time based on responses in 3 > days; if there are more than fit in Google Hangout (10) I'll look for an > alternative. Everyone who's interested welcome I'd say. > > I'll put the agenda and call details on a GitHub wiki page, then people > can add proposed topics to the agenda. > Okay, it'll be 6pm UTC on 14 Oct. Here are the details: https://github.com/scipy/scipy/wiki/SciPy-development-Hangouts. Response to the poll was a bit low; please add your name on the wiki page if you plan to join (I need a change of plans for 10+ people). Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From josh.craig.wilson at gmail.com Sat Oct 8 12:39:47 2016 From: josh.craig.wilson at gmail.com (Joshua Wilson) Date: Sat, 8 Oct 2016 11:39:47 -0500 Subject: [SciPy-Dev] TOMS licensing Message-ID: Hey all, Recently in https://github.com/scipy/scipy/issues/2851 we got permission to use an algorithm from ACM TOMS--something I didn't know was possible for things published before 2013 when they stopped requiring authors to transfer their copyright to the ACM. Looking here: http://authors.acm.org/main.html I see three options for ACM author rights: """ Authors have the option to choose the level of rights management they prefer. ACM offers three different options for authors to manage the publication rights to their work. (1) Authors who want ACM to manage the rights and permissions associated with their work, which includes defending against improper use by third parties, can use ACM?s traditional copyright transfer agreement. (2) Authors who prefer to retain copyright of their work can sign an exclusive licensing agreement, which gives ACM the right but not the obligation to defend the work against improper use by third parties. (3) Authors who wish to retain all rights to their work can choose ACM's author-pays option, which allows for perpetual open access through the ACM Digital Library. Authors choosing the author-pays option can give ACM non-exclusive permission to publish, sign ACM's exclusive licensing agreement or sign ACM's traditional copyright transfer agreement. Those choosing to grant ACM a non-exclusive permission to publish may also choose to display a Creative Commons License on their works. """ In terms of us being able to use TOMS stuff, option (1) is no good and option (3) is good. But I can't figure out (2)--the "exclusive license" seems to suggest that authors are prohibited from re-licensing so it's no good? Can anyone clarify? I'm interested because there are a couple of other TOMS algorithms for special functions (850 and 914) that it would be very nice to not have to implement ourselves if the authors give us permission to use them. - Apologies for the dry email, Josh -------------- next part -------------- An HTML attachment was scrubbed... URL: From njs at pobox.com Sat Oct 8 12:47:46 2016 From: njs at pobox.com (Nathaniel Smith) Date: Sat, 8 Oct 2016 09:47:46 -0700 Subject: [SciPy-Dev] TOMS licensing In-Reply-To: References: Message-ID: I think you'd have to look at the language in the actual contract/copyright transfer agreement the authors signed. (Which might or might not match anything listed on the website currently.) -n On Sat, Oct 8, 2016 at 9:39 AM, Joshua Wilson wrote: > Hey all, > > Recently in https://github.com/scipy/scipy/issues/2851 we got permission to > use an algorithm from ACM TOMS--something I didn't know was possible for > things published before 2013 when they stopped requiring authors to transfer > their copyright to the ACM. Looking here: > > http://authors.acm.org/main.html > > I see three options for ACM author rights: > > """ > > Authors have the option to choose the level of rights management they > prefer. ACM offers three different options for authors to manage the > publication rights to their work. > > (1) Authors who want ACM to manage the rights and permissions associated > with their work, which includes defending against improper use by third > parties, can use ACM?s traditional copyright transfer agreement. > (2) Authors who prefer to retain copyright of their work can sign an > exclusive licensing agreement, which gives ACM the right but not the > obligation to defend the work against improper use by third parties. > (3) Authors who wish to retain all rights to their work can choose ACM's > author-pays option, which allows for perpetual open access through the ACM > Digital Library. Authors choosing the author-pays option can give ACM > non-exclusive permission to publish, sign ACM's exclusive licensing > agreement or sign ACM's traditional copyright transfer agreement. Those > choosing to grant ACM a non-exclusive permission to publish may also choose > to display a Creative Commons License on their works. > > """ > > In terms of us being able to use TOMS stuff, option (1) is no good and > option (3) is good. But I can't figure out (2)--the "exclusive license" > seems to suggest that authors are prohibited from re-licensing so it's no > good? Can anyone clarify? > > I'm interested because there are a couple of other TOMS algorithms for > special functions (850 and 914) that it would be very nice to not have to > implement ourselves if the authors give us permission to use them. > > - Apologies for the dry email, > Josh > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > -- Nathaniel J. Smith -- https://vorpus.org From dieter at werthmuller.org Sat Oct 8 14:11:27 2016 From: dieter at werthmuller.org (=?UTF-8?Q?Dieter_Werthm=c3=bcller?=) Date: Sat, 8 Oct 2016 13:11:27 -0500 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> Message-ID: <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> Joshua Thanks for your input. How could I include the Cython loggamma function within my setup script, so that fftlog.f would pick it up? Adjusting fftlog.f to pick up dfft*.f from scipy/fftpack/src/dfftpack worked without problems. So if I could do the same for loggamma, then the only new file would be fftlog.f, for which we have the permission. Thanks, Dieter On 07/10/16 21:18, Joshua Wilson wrote: > Re log gamma: under the hood the SciPy versions are in C (real version) > and Cython (complex version), so linking them up with Fortran code is > definitely doable. > > On Fri, Oct 7, 2016 at 8:16 PM, Ralf Gommers > wrote: > > > > On Sat, Oct 8, 2016 at 1:58 PM, Dieter Werthm?ller > > wrote: > > Evening, > > I wrote to Andrew Hamilton, and below is his answer. He has > basically no problem with it at all, I just don't know if his > response is explicit enough. > > I think my email was quite extensive, and I assume that is as > much as we will get from him. I also do not expect him to change > his on "13 Mar 1999, 21:17" from TeX translated website... > > What do you think, is this enough? > > > Yes, that's perfectly fine. Thanks for clarifying that Dieter. > > Cheers, > Ralf > > > I also wrote to Takuya Ooura, and will let you know of his > response, if I get one. However, as there are other complex > logarithmic double precision gamma functions around, one already > in scipy, this piece is not mission critical. > > Regards, > Dieter > > ========== START email correspondence with Andrew Hamilton > ========== > Subject: Re: FFTLog - license > From: Andrew Hamilton > > Date: 07/10/16 18:22 > To: Dieter Werthm?ller > > CC: Andrew.Hamilton at colorado.edu > > > Dieter, > > I approve your adding the license language you suggest to > FFTLog, and making available the resulting package for distribution. > > Andrew > > On 10/07/2016 03:42 PM, Dieter Werthm?ller wrote: > > Dear Andrew, > > > > Please apologize me bothering you again. > > > > After I published the code to wrap your FFTLog for Python I > thought that > > it would be much better if your FFTLog would make it straight > into the > > scientific library of Python. This would make your FFTLog > available to a > > much wider audience. > > > > I contacted the developers of SciPy (http://scipy.org), and > they are > > interested in including your code. However, there is one issue: > > licensing. Code that is published on the web without a license > file is > > copyrighted under law, and SciPy can for this reason not > include your > > code into their library. > > > > All I ask for is if you could confirm to us by email that we > are allowed > > to distribute your FFTLog under the BSD-3-Clause license: > > https://opensource.org/licenses/BSD-3-Clause > > > > > The license is just a suggestion, any other BSD or MIT compatible > > license would be fine as well. (For the same, legal reasons we > recommend > > to publish a license file on your website too, but that is > obviously > > entirely up to you. It might, however, clarify things for > future visitors.) > > > > It would only affect your fftlog.f file, and the changes you > made to > > cdgamma.f. I will write Takuya OOURA as well regarding the > original > > cdgamma.f-file, asking him the same favour. And the three > drfft*.f are > > already in the SciPy-library with the whole FFTPack. > > > > If you are interested why this issue arises, Jake Vanderplas, > one of the > > developers of SciPy, wrote an interesting article about the topic: > > > http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows-of-licensing-scientific-code/ > > > > > Thank you again for your time and for making FFTLog available! > > Best regards, > > Dieter > > > ========== END email correspondence with Andrew Hamilton ========== > > On 07/10/16 15:13, Ralf Gommers wrote: > > > > On Sat, Oct 8, 2016 at 9:11 AM, Ralf Gommers > > >> wrote: > > > > On Sat, Oct 8, 2016 at 8:59 AM, Dieter Werthm?ller > > >> wrote: > > Jake, > > Thanks for the clarification. I will try to get the > permissions > from the > authors. > > What is regarded as sufficient? Is an email from the > author, > granting > me/SciPy to distribute their code with a specific, > BSD-style license > sufficient? Or do they necessarily have to change > the websites where > they host the code to include the license? > > > An email stating that the code can be distributed under > a BSD > license (or MIT or other compatible license) is enough. > > > Some delay on the line, missed Jake's answer. Email is > enough, but a > change in the repo would of course be even better. > > Ralf > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > From josh.craig.wilson at gmail.com Sat Oct 8 16:04:25 2016 From: josh.craig.wilson at gmail.com (Joshua Wilson) Date: Sat, 8 Oct 2016 15:04:25 -0500 Subject: [SciPy-Dev] FFTLog In-Reply-To: <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> Message-ID: Dieter, First, a warning: this is going to involve some fun. ;-) Before going too far you should probably check that the different versions of the complex Gamma functions use the same branch cuts, etc. Note that if you want this to work in your external git repo you'll need to build against scipy master. Steps should be roughly: -- Write a Cython script that wraps the Cython version of SciPy's loggamma. See https://scipy.github.io/devdocs/special.cython_special.html#module-scipy. special.cython_special for info on cimporting loggamma. -- Export the wrapper as a C function using these steps: http://docs.cython.org/en/latest/src/userguide/external_ C_code.html#using-cython-declarations-from-c -- Add the Cythonized C file to your setup and add an Interface block to your Fortran code letting it know how to call the C function. On Sat, Oct 8, 2016 at 1:11 PM, Dieter Werthm?ller wrote: > Joshua > > Thanks for your input. How could I include the Cython loggamma function > within my setup script, so that fftlog.f would pick it up? > > Adjusting fftlog.f to pick up dfft*.f from scipy/fftpack/src/dfftpack > worked without problems. So if I could do the same for loggamma, then the > only new file would be fftlog.f, for which we have the permission. > > Thanks, > Dieter > > > On 07/10/16 21:18, Joshua Wilson wrote: > >> Re log gamma: under the hood the SciPy versions are in C (real version) >> and Cython (complex version), so linking them up with Fortran code is >> definitely doable. >> >> On Fri, Oct 7, 2016 at 8:16 PM, Ralf Gommers > > wrote: >> >> >> >> On Sat, Oct 8, 2016 at 1:58 PM, Dieter Werthm?ller >> > wrote: >> >> Evening, >> >> I wrote to Andrew Hamilton, and below is his answer. He has >> basically no problem with it at all, I just don't know if his >> response is explicit enough. >> >> I think my email was quite extensive, and I assume that is as >> much as we will get from him. I also do not expect him to change >> his on "13 Mar 1999, 21:17" from TeX translated website... >> >> What do you think, is this enough? >> >> >> Yes, that's perfectly fine. Thanks for clarifying that Dieter. >> >> Cheers, >> Ralf >> >> >> I also wrote to Takuya Ooura, and will let you know of his >> response, if I get one. However, as there are other complex >> logarithmic double precision gamma functions around, one already >> in scipy, this piece is not mission critical. >> >> Regards, >> Dieter >> >> ========== START email correspondence with Andrew Hamilton >> ========== >> Subject: Re: FFTLog - license >> From: Andrew Hamilton > > >> Date: 07/10/16 18:22 >> To: Dieter Werthm?ller > > >> CC: Andrew.Hamilton at colorado.edu >> >> >> >> Dieter, >> >> I approve your adding the license language you suggest to >> FFTLog, and making available the resulting package for >> distribution. >> >> Andrew >> >> On 10/07/2016 03:42 PM, Dieter Werthm?ller wrote: >> > Dear Andrew, >> > >> > Please apologize me bothering you again. >> > >> > After I published the code to wrap your FFTLog for Python I >> thought that >> > it would be much better if your FFTLog would make it straight >> into the >> > scientific library of Python. This would make your FFTLog >> available to a >> > much wider audience. >> > >> > I contacted the developers of SciPy (http://scipy.org), and >> they are >> > interested in including your code. However, there is one issue: >> > licensing. Code that is published on the web without a license >> file is >> > copyrighted under law, and SciPy can for this reason not >> include your >> > code into their library. >> > >> > All I ask for is if you could confirm to us by email that we >> are allowed >> > to distribute your FFTLog under the BSD-3-Clause license: >> > https://opensource.org/licenses/BSD-3-Clause >> >> > >> > The license is just a suggestion, any other BSD or MIT >> compatible >> > license would be fine as well. (For the same, legal reasons we >> recommend >> > to publish a license file on your website too, but that is >> obviously >> > entirely up to you. It might, however, clarify things for >> future visitors.) >> > >> > It would only affect your fftlog.f file, and the changes you >> made to >> > cdgamma.f. I will write Takuya OOURA as well regarding the >> original >> > cdgamma.f-file, asking him the same favour. And the three >> drfft*.f are >> > already in the SciPy-library with the whole FFTPack. >> > >> > If you are interested why this issue arises, Jake Vanderplas, >> one of the >> > developers of SciPy, wrote an interesting article about the >> topic: >> > >> http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows >> -of-licensing-scientific-code/ >> > s-of-licensing-scientific-code/> >> > >> > Thank you again for your time and for making FFTLog available! >> > Best regards, >> > Dieter >> > >> ========== END email correspondence with Andrew Hamilton >> ========== >> >> On 07/10/16 15:13, Ralf Gommers wrote: >> >> >> >> On Sat, Oct 8, 2016 at 9:11 AM, Ralf Gommers >> >> > >> wrote: >> >> >> >> On Sat, Oct 8, 2016 at 8:59 AM, Dieter Werthm?ller >> >> > >> wrote: >> >> Jake, >> >> Thanks for the clarification. I will try to get the >> permissions >> from the >> authors. >> >> What is regarded as sufficient? Is an email from the >> author, >> granting >> me/SciPy to distribute their code with a specific, >> BSD-style license >> sufficient? Or do they necessarily have to change >> the websites where >> they host the code to include the license? >> >> >> An email stating that the code can be distributed under >> a BSD >> license (or MIT or other compatible license) is enough. >> >> >> Some delay on the line, missed Jake's answer. Email is >> enough, but a >> change in the repo would of course be even better. >> >> Ralf >> >> >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> >> >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> >> >> >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> >> _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Sun Oct 9 05:55:03 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sun, 9 Oct 2016 22:55:03 +1300 Subject: [SciPy-Dev] Moving SciPy project organization forward In-Reply-To: References: Message-ID: On Sat, Oct 8, 2016 at 9:50 PM, Ralf Gommers wrote: > > > On Sun, Oct 2, 2016 at 8:36 PM, Ralf Gommers > wrote: > >> >> >> On Fri, Sep 30, 2016 at 6:12 AM, Evgeni Burovski < >> evgeny.burovskiy at gmail.com> wrote: >> >>> > Now that the mailing list is alive again: how about I organize the >>> first one >>> > for say 2 weeks from now? Proposed topic: producing (a) paper(s). >>> >>> +1. >>> >> >> Looking at time zones, what will work best is evening in Europe, which is >> daytime in the US and early morning in Australasia. Here is a poll: >> http://whenisgood.net/bdkqjkr. I'll pick a time based on responses in 3 >> days; if there are more than fit in Google Hangout (10) I'll look for an >> alternative. Everyone who's interested welcome I'd say. >> >> I'll put the agenda and call details on a GitHub wiki page, then people >> can add proposed topics to the agenda. >> > > Okay, it'll be 6pm UTC on 14 Oct. Here are the details: > https://github.com/scipy/scipy/wiki/SciPy-development-Hangouts. Response > to the poll was a bit low; please add your name on the wiki page if you > plan to join (I need a change of plans for 10+ people). > Sorry, correction: 7pm UTC. That's 6am for Andrew, anything earlier is too cruel. And it's then 11pm in Moscow I believe, Evgeni indicated he could make that time. Still middle of the day in the US, so those with a conflict may be able to shift a meeting. Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From dieter at werthmuller.org Sun Oct 9 13:13:12 2016 From: dieter at werthmuller.org (=?UTF-8?Q?Dieter_Werthm=c3=bcller?=) Date: Sun, 9 Oct 2016 12:13:12 -0500 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> Message-ID: Joshua, Thanks for the additional instructions for the fun :D Cython is at the moment unfortunately slightly outside my knowledge zone. I will therefore wait a little while to see if I hear back from Takuya Ooura regarding license. If not I might give it a try, given I find the time to dive into Cython. The actual fftlog.f-routine is not that long, and most if not all of the heavy lifting is done by rfft/irfft. Another approach might therefore be to rewrite fftlog.f into (c)python, instead of wrapping it. Just thinking. I keep you informed on the status of cdgamma.f. Dieter On 08/10/16 15:04, Joshua Wilson wrote: > Dieter, > > First, a warning: this is going to involve some fun. ;-) Before going > too far you should probably check that the different versions of the > complex Gamma functions use the same branch cuts, etc. Note that if you > want this to work in your external git repo you'll need to build against > scipy master. > > Steps should be roughly: > -- Write a Cython script that wraps the Cython version of SciPy's > loggamma. See > > https://scipy.github.io/devdocs/special.cython_special.html#module-scipy.special.cython_special > > > for info on cimporting loggamma. > -- Export the wrapper as a C function using these steps: > > http://docs.cython.org/en/latest/src/userguide/external_C_code.html#using-cython-declarations-from-c > > > -- Add the Cythonized C file to your setup and add an Interface block to > your Fortran code letting it know how to call the C function. > > On Sat, Oct 8, 2016 at 1:11 PM, Dieter Werthm?ller > > wrote: > > Joshua > > Thanks for your input. How could I include the Cython loggamma > function within my setup script, so that fftlog.f would pick it up? > > Adjusting fftlog.f to pick up dfft*.f from > scipy/fftpack/src/dfftpack worked without problems. So if I could do > the same for loggamma, then the only new file would be fftlog.f, for > which we have the permission. > > Thanks, > Dieter > > > On 07/10/16 21:18, Joshua Wilson wrote: > > Re log gamma: under the hood the SciPy versions are in C (real > version) > and Cython (complex version), so linking them up with Fortran > code is > definitely doable. > > On Fri, Oct 7, 2016 at 8:16 PM, Ralf Gommers > > >> > wrote: > > > > On Sat, Oct 8, 2016 at 1:58 PM, Dieter Werthm?ller > > >> > wrote: > > Evening, > > I wrote to Andrew Hamilton, and below is his answer. He has > basically no problem with it at all, I just don't know > if his > response is explicit enough. > > I think my email was quite extensive, and I assume that > is as > much as we will get from him. I also do not expect him > to change > his on "13 Mar 1999, 21:17" from TeX translated website... > > What do you think, is this enough? > > > Yes, that's perfectly fine. Thanks for clarifying that Dieter. > > Cheers, > Ralf > > > I also wrote to Takuya Ooura, and will let you know of his > response, if I get one. However, as there are other complex > logarithmic double precision gamma functions around, one > already > in scipy, this piece is not mission critical. > > Regards, > Dieter > > ========== START email correspondence with Andrew Hamilton > ========== > Subject: Re: FFTLog - license > From: Andrew Hamilton > >> > Date: 07/10/16 18:22 > To: Dieter Werthm?ller > >> > CC: Andrew.Hamilton at colorado.edu > > > > > > Dieter, > > I approve your adding the license language you suggest to > FFTLog, and making available the resulting package for > distribution. > > Andrew > > On 10/07/2016 03:42 PM, Dieter Werthm?ller wrote: > > Dear Andrew, > > > > Please apologize me bothering you again. > > > > After I published the code to wrap your FFTLog for > Python I > thought that > > it would be much better if your FFTLog would make it > straight > into the > > scientific library of Python. This would make your FFTLog > available to a > > much wider audience. > > > > I contacted the developers of SciPy > (http://scipy.org), and > they are > > interested in including your code. However, there is > one issue: > > licensing. Code that is published on the web without a > license > file is > > copyrighted under law, and SciPy can for this reason not > include your > > code into their library. > > > > All I ask for is if you could confirm to us by email > that we > are allowed > > to distribute your FFTLog under the BSD-3-Clause license: > > https://opensource.org/licenses/BSD-3-Clause > > > > > > > The license is just a suggestion, any other BSD or MIT > compatible > > license would be fine as well. (For the same, legal > reasons we > recommend > > to publish a license file on your website too, but that is > obviously > > entirely up to you. It might, however, clarify things for > future visitors.) > > > > It would only affect your fftlog.f file, and the > changes you > made to > > cdgamma.f. I will write Takuya OOURA as well regarding the > original > > cdgamma.f-file, asking him the same favour. And the three > drfft*.f are > > already in the SciPy-library with the whole FFTPack. > > > > If you are interested why this issue arises, Jake > Vanderplas, > one of the > > developers of SciPy, wrote an interesting article > about the topic: > > > > http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows-of-licensing-scientific-code/ > > > > > > > > Thank you again for your time and for making FFTLog > available! > > Best regards, > > Dieter > > > ========== END email correspondence with Andrew Hamilton > ========== > > On 07/10/16 15:13, Ralf Gommers wrote: > > > > On Sat, Oct 8, 2016 at 9:11 AM, Ralf Gommers > > > > >>> wrote: > > > > On Sat, Oct 8, 2016 at 8:59 AM, Dieter Werthm?ller > > > > >>> wrote: > > Jake, > > Thanks for the clarification. I will try to > get the > permissions > from the > authors. > > What is regarded as sufficient? Is an email > from the > author, > granting > me/SciPy to distribute their code with a > specific, > BSD-style license > sufficient? Or do they necessarily have to > change > the websites where > they host the code to include the license? > > > An email stating that the code can be > distributed under > a BSD > license (or MIT or other compatible license) is > enough. > > > Some delay on the line, missed Jake's answer. Email is > enough, but a > change in the repo would of course be even better. > > Ralf > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > From gustavo.scalet at eldorado.org.br Mon Oct 10 15:50:23 2016 From: gustavo.scalet at eldorado.org.br (Gustavo Serra Scalet) Date: Mon, 10 Oct 2016 19:50:23 +0000 Subject: [SciPy-Dev] Why does forcing Numpy to compile with "sizeof(long double) == 8" fails tests? In-Reply-To: <1475823845.18249.2.camel@sipsolutions.net> References: <1475823845.18249.2.camel@sipsolutions.net> Message-ID: > -----Original Message----- > From: SciPy-Dev [mailto:scipy-dev-bounces at scipy.org] On Behalf Of > Sebastian Berg > Sent: sexta-feira, 7 de outubro de 2016 04:04 > To: scipy-dev at scipy.org > Subject: Re: [SciPy-Dev] Why does forcing Numpy to compile with > "sizeof(long double) == 8" fails tests? > > On Do, 2016-10-06 at 22:21 +0000, Gustavo Serra Scalet wrote: > > Hi, > > > > I'm checking how Numpy performs on a POWER8 machine and I noticed that > > some tests related to machar.py are failing: > > ===================================================================== > > = > > ERROR: test_singleton (test_getlimits.TestLongdouble) > > ------------------------------------------------------------------- > > --- > > Traceback (most recent call last): > > ? File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy- > > 1.12.0.dev0+33d850d-py3.4-linux- > > ppc64le.egg/numpy/core/tests/test_getlimits.py", line 41, in > > test_singleton > > ????ftype = finfo(longdouble) > > ? File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy- > > 1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/getlimits.py", > > line 124, in __new__ > > ????obj = object.__new__(cls)._init(dtype) > > ? File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy- > > 1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/getlimits.py", > > line 154, in _init > > ????'numpy %s precision floating point number' % precname) > > ? File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy- > > 1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/machar.py", > > line 114, in __init__ > > ????self._do_init(float_conv, int_conv, float_to_float, float_to_str, > > title) > > ? File "/home/gut/python/venv3.5-b/lib/python3.4/site-packages/numpy- > > 1.12.0.dev0+33d850d-py3.4-linux-ppc64le.egg/numpy/core/machar.py", > > line 127, in _do_init > > ????a = a + a > > RuntimeWarning: overflow encountered in add > > > > FAILED (KNOWNFAIL=4, SKIP=10, errors=4) > > > > > > That happened because native long double actually uses 2 doubles[1] > > (that method is called IBM Extended double[2]). > > > > To avoid that, I changed the compile flags to use -mlong-double-64 [3] > > and despite solving those errors, now I have some of these > > failures: > > ===================================================================== > > = > > FAIL: test_in_from_2casttype > > (test_array_from_pyobj.test_LONGDOUBLE_gen) > > ------------------------------------------------------------------- > > --- > > Traceback (most recent call last): > > ? File "/home/gut/python/venv3.5/lib/python3.4/site-packages/numpy- > > 1.12.0.dev0+7a962d1-py3.4-linux- > > ppc64le.egg/numpy/f2py/tests/test_array_from_pyobj.py", line 319, in > > test_in_from_2casttype > > ????a = self.array([len(self.num2seq)], intent.in_, obj) > > ? File "", line 6, in > > ? File "/home/gut/python/venv3.5/lib/python3.4/site-packages/numpy- > > 1.12.0.dev0+7a962d1-py3.4-linux- > > ppc64le.egg/numpy/f2py/tests/test_array_from_pyobj.py", line 275, in > > __init__ > > ????assert_(self.has_shared_memory()) > > ? File "/home/gut/python/venv3.5/lib/python3.4/site-packages/numpy- > > 1.12.0.dev0+7a962d1-py3.4-linux-ppc64le.egg/numpy/testing/utils.py", > > line 90, in assert_ > > ????raise AssertionError(smsg) > > AssertionError > > > > FAILED (KNOWNFAIL=6, SKIP=16, failures=3) > > > > > > I wanted to know if there is a better approach to solve this issue. I > > guess it supports 'long double == double', right? > > > > I would have a first look at the test, it is completely plausible that > the tests are skipped on windows or so, but the check to skip it does > not actually look at the long double size. So, I would not rule out the > tests are simply invalid in your setting and are run because nobody > tried this before. > > - Sebastian The tests were not being skipped by anybody but there was a condition to test longdoubles inside of the module that is not expecting it to be 8 bytes as double: https://github.com/PPC64/numpy/commit/f24d6278ca774524828fbd79a11089f3789c0916 The main reason might be due to how the architecture is handling alignment of longdouble. I don't know. I hope to have some review of it on this PR: https://github.com/numpy/numpy/pull/8134 Thanks for you feedback Sebastian. > > > > Thanks in advance! > > > > > > Environment: > > Repository head at 33d850d522b3a1940c3ad06b63c79a466def11e9 (from > > git://github.com/numpy/numpy.git) + patch on [3] > > Python-3.5.2 > > > > > > [1] https://github.com/gcc-mirror/gcc/blob/3ff1ad36ed4ee3cc490e6178db > > 87b1b8f2326c61/libgcc/config/rs6000/ibm-ldouble.c#L36-L43 > > [2] https://gcc.gnu.org/wiki/Ieee128PowerPC > > [3] https://github.com/PPC64/numpy/commit/be15f1073802ab127162c5dcdd9 > > 95de7f6452c78 > > _______________________________________________ > > SciPy-Dev mailing list > > SciPy-Dev at scipy.org > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > From gfyoung17 at gmail.com Mon Oct 10 19:54:23 2016 From: gfyoung17 at gmail.com (G Young) Date: Mon, 10 Oct 2016 19:54:23 -0400 Subject: [SciPy-Dev] Negative Data Points in Center of Mass Message-ID: Hello! I have a PR open (#6668 ) that issues a UserWarning if negative values for data inputs are passed in for "center_of_mass". While I cannot think of any applications of negative values, initial discussion suggested it would be prudent to double check with other developers in the community to see if there were any applications. Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From hodge at stsci.edu Tue Oct 11 08:41:22 2016 From: hodge at stsci.edu (Phil Hodge) Date: Tue, 11 Oct 2016 08:41:22 -0400 Subject: [SciPy-Dev] Negative Data Points in Center of Mass In-Reply-To: References: Message-ID: <7f0bd79a-6805-afc9-feb0-25b60878523f@stsci.edu> On 10/10/2016 07:54 PM, G Young wrote: > I have a PR open (#6668 ) > that issues a UserWarning if negative values for data inputs are > passed in for "center_of_mass". While I cannot think of any > applications of negative values, initial discussion suggested it would > be prudent to double check with other developers in the community to > see if there were any applications. > > Thanks! There will likely be negative values in measured data after subtracting a bias level or background, due to random noise. If you set those negative-valued elements to zero, that will bias the result. Consider the case of using center_of_mass to determine the location of a star image. There will be a background due to dark current in the sensor and sky brightness. If you don't subtract the background, the output of center_of_mass will be biased toward the center of the slice passed to center_of_mass. A common way to measure the background is to find the average value (excluding outliers) within an annular ring around the star. After subtracting the value, the average (again, excluding outliers) in that annular region will be zero, and if there's any noise at all (e.g. read noise, Poisson noise) there should be pixels with negative values. If there is a case where negative values should never be encountered, please just let the user check his/her own data. There can be other values (e.g. saturated) that would cause center_of_mass to give an incorrect result, and the user is responsible for checking for those, too. Phil From dieter at werthmuller.org Wed Oct 12 12:38:36 2016 From: dieter at werthmuller.org (=?UTF-8?Q?Dieter_Werthm=c3=bcller?=) Date: Wed, 12 Oct 2016 11:38:36 -0500 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> Message-ID: <489aa41c-7ad4-9dee-fa57-f644ef0cef33@werthmuller.org> Everyone, I have a response from Takuya Ooura, appended below. He has no problem with it either, I just don't know if his response is explicit enough (again). What do you think, is this enough? Regards, Dieter ========== START email correspondence with Takuya Ooura ========== Subject: Re: cdgamma - license From: Takuya Ooura Date: Wed, 12 Oct 2016 21:31:01 +0900 (JST) To: dieter at werthmuller.org Dear Dieter Werthm?ller, Please use the modified version of cdgamma.f. The license of my code is similar to the BSD-3-Clause license at present. -- Takuya Ooura Email : ooura at kurims.kyoto-u.ac.jp >Dear Takuya Ooura, > >Firstly thank you very much for making your code available on your website. > >I am writing to you regarding your cdgamma.f function. Andrew Hamilton >used a modified version of it for his FFTLog, and got your written >permission to distribute the modified version in his code. > >We would like to include FFTLog in the scientific library of the python >programming language, SciPy, and with it the modified version of cdgamma.f. > >The copyright statement distributed with your code states > > Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp). > You may use, copy, modify this code for any purpose and > without fee. You may distribute this ORIGINAL package. > >which makes it impossible for SciPy to include the modified version of >cdgamma.f in FFTLog into their library, as the version in FFTLog is a >MODIFIED version, and not the original version. > >Would it be possible that you could give SciPy the permission to >distribute cdgamma.f under a permissive license? My suggestion would be >the BSD-3-Clause license, >https://opensource.org/licenses/BSD-3-Clause >But any other BSD or MIT compatible license would be fine as well. > >Thank you for your time and for making cdgamma.f available on your website. > >Best regards, >Dieter Werthm?ller ========== END email correspondence with Takuya Ooura ========== On 08/10/16 15:04, Joshua Wilson wrote: > Dieter, > > First, a warning: this is going to involve some fun. ;-) Before going > too far you should probably check that the different versions of the > complex Gamma functions use the same branch cuts, etc. Note that if you > want this to work in your external git repo you'll need to build against > scipy master. > > Steps should be roughly: > -- Write a Cython script that wraps the Cython version of SciPy's > loggamma. See > > https://scipy.github.io/devdocs/special.cython_special.html#module-scipy.special.cython_special > > > for info on cimporting loggamma. > -- Export the wrapper as a C function using these steps: > > http://docs.cython.org/en/latest/src/userguide/external_C_code.html#using-cython-declarations-from-c > > > -- Add the Cythonized C file to your setup and add an Interface block to > your Fortran code letting it know how to call the C function. > > On Sat, Oct 8, 2016 at 1:11 PM, Dieter Werthm?ller > > wrote: > > Joshua > > Thanks for your input. How could I include the Cython loggamma > function within my setup script, so that fftlog.f would pick it up? > > Adjusting fftlog.f to pick up dfft*.f from > scipy/fftpack/src/dfftpack worked without problems. So if I could do > the same for loggamma, then the only new file would be fftlog.f, for > which we have the permission. > > Thanks, > Dieter > > > On 07/10/16 21:18, Joshua Wilson wrote: > > Re log gamma: under the hood the SciPy versions are in C (real > version) > and Cython (complex version), so linking them up with Fortran > code is > definitely doable. > > On Fri, Oct 7, 2016 at 8:16 PM, Ralf Gommers > > >> > wrote: > > > > On Sat, Oct 8, 2016 at 1:58 PM, Dieter Werthm?ller > > >> > wrote: > > Evening, > > I wrote to Andrew Hamilton, and below is his answer. He has > basically no problem with it at all, I just don't know > if his > response is explicit enough. > > I think my email was quite extensive, and I assume that > is as > much as we will get from him. I also do not expect him > to change > his on "13 Mar 1999, 21:17" from TeX translated website... > > What do you think, is this enough? > > > Yes, that's perfectly fine. Thanks for clarifying that Dieter. > > Cheers, > Ralf > > > I also wrote to Takuya Ooura, and will let you know of his > response, if I get one. However, as there are other complex > logarithmic double precision gamma functions around, one > already > in scipy, this piece is not mission critical. > > Regards, > Dieter > > ========== START email correspondence with Andrew Hamilton > ========== > Subject: Re: FFTLog - license > From: Andrew Hamilton > >> > Date: 07/10/16 18:22 > To: Dieter Werthm?ller > >> > CC: Andrew.Hamilton at colorado.edu > > > > > > Dieter, > > I approve your adding the license language you suggest to > FFTLog, and making available the resulting package for > distribution. > > Andrew > > On 10/07/2016 03:42 PM, Dieter Werthm?ller wrote: > > Dear Andrew, > > > > Please apologize me bothering you again. > > > > After I published the code to wrap your FFTLog for > Python I > thought that > > it would be much better if your FFTLog would make it > straight > into the > > scientific library of Python. This would make your FFTLog > available to a > > much wider audience. > > > > I contacted the developers of SciPy > (http://scipy.org), and > they are > > interested in including your code. However, there is > one issue: > > licensing. Code that is published on the web without a > license > file is > > copyrighted under law, and SciPy can for this reason not > include your > > code into their library. > > > > All I ask for is if you could confirm to us by email > that we > are allowed > > to distribute your FFTLog under the BSD-3-Clause license: > > https://opensource.org/licenses/BSD-3-Clause > > > > > > > The license is just a suggestion, any other BSD or MIT > compatible > > license would be fine as well. (For the same, legal > reasons we > recommend > > to publish a license file on your website too, but that is > obviously > > entirely up to you. It might, however, clarify things for > future visitors.) > > > > It would only affect your fftlog.f file, and the > changes you > made to > > cdgamma.f. I will write Takuya OOURA as well regarding the > original > > cdgamma.f-file, asking him the same favour. And the three > drfft*.f are > > already in the SciPy-library with the whole FFTPack. > > > > If you are interested why this issue arises, Jake > Vanderplas, > one of the > > developers of SciPy, wrote an interesting article > about the topic: > > > > http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows-of-licensing-scientific-code/ > > > > > > > > Thank you again for your time and for making FFTLog > available! > > Best regards, > > Dieter > > > ========== END email correspondence with Andrew Hamilton > ========== > > On 07/10/16 15:13, Ralf Gommers wrote: > > > > On Sat, Oct 8, 2016 at 9:11 AM, Ralf Gommers > > > > >>> wrote: > > > > On Sat, Oct 8, 2016 at 8:59 AM, Dieter Werthm?ller > > > > >>> wrote: > > Jake, > > Thanks for the clarification. I will try to > get the > permissions > from the > authors. > > What is regarded as sufficient? Is an email > from the > author, > granting > me/SciPy to distribute their code with a > specific, > BSD-style license > sufficient? Or do they necessarily have to > change > the websites where > they host the code to include the license? > > > An email stating that the code can be > distributed under > a BSD > license (or MIT or other compatible license) is > enough. > > > Some delay on the line, missed Jake's answer. Email is > enough, but a > change in the repo would of course be even better. > > Ralf > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > From nonhermitian at gmail.com Fri Oct 14 00:56:08 2016 From: nonhermitian at gmail.com (Paul Nation) Date: Thu, 13 Oct 2016 22:56:08 -0600 Subject: [SciPy-Dev] ENH: Add structural rank to sparse.csgraph Message-ID: <104B6E16-798C-4E1E-BBD0-A5356DB18458@gmail.com> Greetings, I was recently looking for a quick way to find out if a given sparse matrix is singular. As it turns out the solution is to calculate the structural rank (an upper bound on the numerical rank) of the sparsity pattern associated with the matrix: http://www.mathworks.com/help/matlab/ref/sprank.html http://www.cise.ufl.edu/research/sparse/matrices/legend.html Since this calculation is done via the maximum bipartite matching algorithm that I added to sparse.csgraph some time ago, I thought it would be a nice addition to include this straightforward structural rank calculation. The Pull for this feature is here: https://github.com/scipy/scipy/pull/6680 Best regards, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Fri Oct 14 14:50:41 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sat, 15 Oct 2016 07:50:41 +1300 Subject: [SciPy-Dev] Moving SciPy project organization forward In-Reply-To: References: Message-ID: On Sun, Oct 9, 2016 at 10:55 PM, Ralf Gommers wrote: > > > On Sat, Oct 8, 2016 at 9:50 PM, Ralf Gommers > wrote: > >> >> >> On Sun, Oct 2, 2016 at 8:36 PM, Ralf Gommers >> wrote: >> >>> >>> >>> On Fri, Sep 30, 2016 at 6:12 AM, Evgeni Burovski < >>> evgeny.burovskiy at gmail.com> wrote: >>> >>>> > Now that the mailing list is alive again: how about I organize the >>>> first one >>>> > for say 2 weeks from now? Proposed topic: producing (a) paper(s). >>>> >>>> +1. >>>> >>> >>> Looking at time zones, what will work best is evening in Europe, which >>> is daytime in the US and early morning in Australasia. Here is a poll: >>> http://whenisgood.net/bdkqjkr. I'll pick a time based on responses in 3 >>> days; if there are more than fit in Google Hangout (10) I'll look for an >>> alternative. Everyone who's interested welcome I'd say. >>> >>> I'll put the agenda and call details on a GitHub wiki page, then people >>> can add proposed topics to the agenda. >>> >> >> Okay, it'll be 6pm UTC on 14 Oct. Here are the details: >> https://github.com/scipy/scipy/wiki/SciPy-development-Hangouts. Response >> to the poll was a bit low; please add your name on the wiki page if you >> plan to join (I need a change of plans for 10+ people). >> > > Sorry, correction: 7pm UTC. > > That's 6am for Andrew, anything earlier is too cruel. And it's then 11pm > in Moscow I believe, Evgeni indicated he could make that time. Still middle > of the day in the US, so those with a conflict may be able to shift a > meeting. > Reminder just in case you didn't see these links on the wiki: - Link to connect: https://hangouts.google.com/call/3rb6vaez7bf63e6ih4qhxtsuaqe - Minutes: https://docs.google.com/document/d/1srVFUvxEUOKzJBuCI8oqn17D7TYLcLIwMJKFRRD4bB0/edit?usp=sharing Start in 10 minutes. Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From evgeny.burovskiy at gmail.com Fri Oct 14 17:45:01 2016 From: evgeny.burovskiy at gmail.com (Evgeni Burovski) Date: Sat, 15 Oct 2016 00:45:01 +0300 Subject: [SciPy-Dev] Moving SciPy project organization forward In-Reply-To: References: Message-ID: On Oct 14, 2016 9:51 PM, "Ralf Gommers" wrote: > > > > On Sun, Oct 9, 2016 at 10:55 PM, Ralf Gommers wrote: >> >> >> >> On Sat, Oct 8, 2016 at 9:50 PM, Ralf Gommers wrote: >>> >>> >>> >>> On Sun, Oct 2, 2016 at 8:36 PM, Ralf Gommers wrote: >>>> >>>> >>>> >>>> On Fri, Sep 30, 2016 at 6:12 AM, Evgeni Burovski < evgeny.burovskiy at gmail.com> wrote: >>>>> >>>>> > Now that the mailing list is alive again: how about I organize the first one >>>>> > for say 2 weeks from now? Proposed topic: producing (a) paper(s). >>>>> >>>>> +1. >>>> >>>> >>>> Looking at time zones, what will work best is evening in Europe, which is daytime in the US and early morning in Australasia. Here is a poll: http://whenisgood.net/bdkqjkr. I'll pick a time based on responses in 3 days; if there are more than fit in Google Hangout (10) I'll look for an alternative. Everyone who's interested welcome I'd say. >>>> >>>> I'll put the agenda and call details on a GitHub wiki page, then people can add proposed topics to the agenda. >>> >>> >>> Okay, it'll be 6pm UTC on 14 Oct. Here are the details: https://github.com/scipy/scipy/wiki/SciPy-development-Hangouts. Response to the poll was a bit low; please add your name on the wiki page if you plan to join (I need a change of plans for 10+ people). >> >> >> Sorry, correction: 7pm UTC. >> >> That's 6am for Andrew, anything earlier is too cruel. And it's then 11pm in Moscow I believe, Evgeni indicated he could make that time. Still middle of the day in the US, so those with a conflict may be able to shift a meeting. > > > Reminder just in case you didn't see these links on the wiki: > - Link to connect: https://hangouts.google.com/call/3rb6vaez7bf63e6ih4qhxtsuaqe > - Minutes: https://docs.google.com/document/d/1srVFUvxEUOKzJBuCI8oqn17D7TYLcLIwMJKFRRD4bB0/edit?usp=sharing > > Start in 10 minutes. > > Ralf > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > Thanks for organizing it Ralf! -------------- next part -------------- An HTML attachment was scrubbed... URL: From prabhu at aero.iitb.ac.in Mon Oct 17 02:19:36 2016 From: prabhu at aero.iitb.ac.in (Prabhu Ramachandran) Date: Mon, 17 Oct 2016 11:49:36 +0530 Subject: [SciPy-Dev] [ANN] SciPy India 2016: call for papers Message-ID: <54902ef9-7612-4c2a-ac77-7bb114fad057@aero.iitb.ac.in> Hello, We are pleased to announce the SciPy India conference 2016. SciPy India is an annual conference on using Python for research and education. The conference is currently in its eighth year and will be held at IIT Bombay on 10th and 11th December, 2016. The registration and call for papers are open. Please visit http://scipy.in to register and submit your proposals. Please spread the word! Call for Papers ============= We look forward to your submissions on the use of Python for scientific computing and education. This includes pedagogy, exploration, modeling, and analysis from both applied and developmental perspectives. We welcome contributions from academia as well as industry. For details on the paper submission please see here: http://scipy.in/2016/cfp/ Important Dates ================ - Call for proposals end: 20th November 2016 - List of accepted proposals will be published: 1st December 2016. We look forward to seeing you at SciPy India. Regards, Prabhu Ramachandran (For the SciPy organizing team) From jjstickel at gmail.com Mon Oct 17 12:04:34 2016 From: jjstickel at gmail.com (Jonathan Stickel) Date: Mon, 17 Oct 2016 10:04:34 -0600 Subject: [SciPy-Dev] pypi support Message-ID: <33be4eea-2fd4-c9ee-8d2a-3b2eb2021c9b@gmail.com> Probably a bit off topic, but I am at a loss. How does one go about getting help with a PyPI problem you can't fix by yourself? I submitted a ticket on the sourceforge site, but it looks like there isn't much activity there. Thanks, Jonathan From jfoxrabinovitz at gmail.com Mon Oct 17 13:05:23 2016 From: jfoxrabinovitz at gmail.com (Joseph Fox-Rabinovitz) Date: Mon, 17 Oct 2016 13:05:23 -0400 Subject: [SciPy-Dev] pypi support In-Reply-To: <33be4eea-2fd4-c9ee-8d2a-3b2eb2021c9b@gmail.com> References: <33be4eea-2fd4-c9ee-8d2a-3b2eb2021c9b@gmail.com> Message-ID: Seems that the GitHub issue tracker is pretty active: https://github.com/pypa/pypi-legacy/issues. -Joe On Mon, Oct 17, 2016 at 12:04 PM, Jonathan Stickel wrote: > Probably a bit off topic, but I am at a loss. How does one go about > getting help with a PyPI problem you can't fix by yourself? I submitted a > ticket on the sourceforge site, but it looks like there isn't much activity > there. > > Thanks, > Jonathan > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From njs at pobox.com Mon Oct 17 14:40:40 2016 From: njs at pobox.com (Nathaniel Smith) Date: Mon, 17 Oct 2016 11:40:40 -0700 Subject: [SciPy-Dev] pypi support In-Reply-To: <33be4eea-2fd4-c9ee-8d2a-3b2eb2021c9b@gmail.com> References: <33be4eea-2fd4-c9ee-8d2a-3b2eb2021c9b@gmail.com> Message-ID: Yeah, the sourceforge tracker isn't where I'd start. The github tracker is a good suggestion; other good places to try would be #pypa on irc.freenode.net, and the distutils-sig mailing list. -n On Mon, Oct 17, 2016 at 9:04 AM, Jonathan Stickel wrote: > Probably a bit off topic, but I am at a loss. How does one go about getting > help with a PyPI problem you can't fix by yourself? I submitted a ticket on > the sourceforge site, but it looks like there isn't much activity there. > > Thanks, > Jonathan > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev -- Nathaniel J. Smith -- https://vorpus.org From ralf.gommers at gmail.com Sun Oct 23 04:00:54 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sun, 23 Oct 2016 10:00:54 +0200 Subject: [SciPy-Dev] FFTLog In-Reply-To: <489aa41c-7ad4-9dee-fa57-f644ef0cef33@werthmuller.org> References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> <489aa41c-7ad4-9dee-fa57-f644ef0cef33@werthmuller.org> Message-ID: On Wed, Oct 12, 2016 at 6:38 PM, Dieter Werthm?ller wrote: > Everyone, > > I have a response from Takuya Ooura, appended below. He has no problem > with it either, I just don't know if his response is explicit enough > (again). > > What do you think, is this enough? > Hmm, it's slightly ambiguous. I would tend to say no, better to get a clear statement. It sounds like he's happy, so you just need to spell out exactly what you need him to say. Or you add a BSD-3 license and "Copyright Takuya Ooura" at the top of that file in your scipy fork, point him to it, and say "can you please agree to that exact text". Cheers, Ralf > > Regards, > Dieter > > ========== START email correspondence with Takuya Ooura ========== > Subject: Re: cdgamma - license > From: Takuya Ooura > Date: Wed, 12 Oct 2016 21:31:01 +0900 (JST) > To: dieter at werthmuller.org > > Dear Dieter Werthm ?ller, > > Please use the modified version of cdgamma.f. > The license of my code is similar to the BSD-3-Clause license at present. > > -- > Takuya Ooura > Email : ooura at kurims.kyoto-u.ac.jp > > >Dear Takuya Ooura, > > > >Firstly thank you very much for making your code available on your > website. > > > >I am writing to you regarding your cdgamma.f function. Andrew Hamilton > >used a modified version of it for his FFTLog, and got your written > >permission to distribute the modified version in his code. > > > >We would like to include FFTLog in the scientific library of the python > >programming language, SciPy, and with it the modified version of > cdgamma.f. > > > >The copyright statement distributed with your code states > > > > Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp). > > You may use, copy, modify this code for any purpose and > > without fee. You may distribute this ORIGINAL package. > > > >which makes it impossible for SciPy to include the modified version of > >cdgamma.f in FFTLog into their library, as the version in FFTLog is a > >MODIFIED version, and not the original version. > > > >Would it be possible that you could give SciPy the permission to > >distribute cdgamma.f under a permissive license? My suggestion would be > >the BSD-3-Clause license, > >https://opensource.org/licenses/BSD-3-Clause > >But any other BSD or MIT compatible license would be fine as well. > > > >Thank you for your time and for making cdgamma.f available on your > website. > > > >Best regards, > >Dieter Werthm ?ller > > ========== END email correspondence with Takuya Ooura ========== > > > On 08/10/16 15:04, Joshua Wilson wrote: > >> Dieter, >> >> First, a warning: this is going to involve some fun. ;-) Before going >> too far you should probably check that the different versions of the >> complex Gamma functions use the same branch cuts, etc. Note that if you >> want this to work in your external git repo you'll need to build against >> scipy master. >> >> Steps should be roughly: >> -- Write a Cython script that wraps the Cython version of SciPy's >> loggamma. See >> >> https://scipy.github.io/devdocs/special.cython_special.html# >> module-scipy.special.cython_special >> > html#module-scipy.special.cython_special> >> >> for info on cimporting loggamma. >> -- Export the wrapper as a C function using these steps: >> >> http://docs.cython.org/en/latest/src/userguide/external_C_ >> code.html#using-cython-declarations-from-c >> > code.html#using-cython-declarations-from-c> >> >> -- Add the Cythonized C file to your setup and add an Interface block to >> your Fortran code letting it know how to call the C function. >> >> On Sat, Oct 8, 2016 at 1:11 PM, Dieter Werthm?ller >> > wrote: >> >> Joshua >> >> Thanks for your input. How could I include the Cython loggamma >> function within my setup script, so that fftlog.f would pick it up? >> >> Adjusting fftlog.f to pick up dfft*.f from >> scipy/fftpack/src/dfftpack worked without problems. So if I could do >> the same for loggamma, then the only new file would be fftlog.f, for >> which we have the permission. >> >> Thanks, >> Dieter >> >> >> On 07/10/16 21:18, Joshua Wilson wrote: >> >> Re log gamma: under the hood the SciPy versions are in C (real >> version) >> and Cython (complex version), so linking them up with Fortran >> code is >> definitely doable. >> >> On Fri, Oct 7, 2016 at 8:16 PM, Ralf Gommers >> >> >> >> wrote: >> >> >> >> On Sat, Oct 8, 2016 at 1:58 PM, Dieter Werthm?ller >> >> >> >> wrote: >> >> Evening, >> >> I wrote to Andrew Hamilton, and below is his answer. He >> has >> basically no problem with it at all, I just don't know >> if his >> response is explicit enough. >> >> I think my email was quite extensive, and I assume that >> is as >> much as we will get from him. I also do not expect him >> to change >> his on "13 Mar 1999, 21:17" from TeX translated website... >> >> What do you think, is this enough? >> >> >> Yes, that's perfectly fine. Thanks for clarifying that Dieter. >> >> Cheers, >> Ralf >> >> >> I also wrote to Takuya Ooura, and will let you know of his >> response, if I get one. However, as there are other >> complex >> logarithmic double precision gamma functions around, one >> already >> in scipy, this piece is not mission critical. >> >> Regards, >> Dieter >> >> ========== START email correspondence with Andrew Hamilton >> ========== >> Subject: Re: FFTLog - license >> From: Andrew Hamilton > >> > >> >> Date: 07/10/16 18:22 >> To: Dieter Werthm?ller > >> > >> >> CC: Andrew.Hamilton at colorado.edu >> >> > >> > >> >> >> Dieter, >> >> I approve your adding the license language you suggest to >> FFTLog, and making available the resulting package for >> distribution. >> >> Andrew >> >> On 10/07/2016 03:42 PM, Dieter Werthm?ller wrote: >> > Dear Andrew, >> > >> > Please apologize me bothering you again. >> > >> > After I published the code to wrap your FFTLog for >> Python I >> thought that >> > it would be much better if your FFTLog would make it >> straight >> into the >> > scientific library of Python. This would make your >> FFTLog >> available to a >> > much wider audience. >> > >> > I contacted the developers of SciPy >> (http://scipy.org), and >> they are >> > interested in including your code. However, there is >> one issue: >> > licensing. Code that is published on the web without a >> license >> file is >> > copyrighted under law, and SciPy can for this reason not >> include your >> > code into their library. >> > >> > All I ask for is if you could confirm to us by email >> that we >> are allowed >> > to distribute your FFTLog under the BSD-3-Clause >> license: >> > https://opensource.org/licenses/BSD-3-Clause >> >> > > >> > >> > The license is just a suggestion, any other BSD or MIT >> compatible >> > license would be fine as well. (For the same, legal >> reasons we >> recommend >> > to publish a license file on your website too, but that >> is >> obviously >> > entirely up to you. It might, however, clarify things >> for >> future visitors.) >> > >> > It would only affect your fftlog.f file, and the >> changes you >> made to >> > cdgamma.f. I will write Takuya OOURA as well regarding >> the >> original >> > cdgamma.f-file, asking him the same favour. And the >> three >> drfft*.f are >> > already in the SciPy-library with the whole FFTPack. >> > >> > If you are interested why this issue arises, Jake >> Vanderplas, >> one of the >> > developers of SciPy, wrote an interesting article >> about the topic: >> > >> >> http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows >> -of-licensing-scientific-code/ >> > s-of-licensing-scientific-code/> >> >> > s-of-licensing-scientific-code/ >> > s-of-licensing-scientific-code/>> >> > >> > Thank you again for your time and for making FFTLog >> available! >> > Best regards, >> > Dieter >> > >> ========== END email correspondence with Andrew Hamilton >> ========== >> >> On 07/10/16 15:13, Ralf Gommers wrote: >> >> >> >> On Sat, Oct 8, 2016 at 9:11 AM, Ralf Gommers >> > > > >> > >> > >>> wrote: >> >> >> >> On Sat, Oct 8, 2016 at 8:59 AM, Dieter Werthm?ller >> > > > >> > >> > >>> wrote: >> >> Jake, >> >> Thanks for the clarification. I will try to >> get the >> permissions >> from the >> authors. >> >> What is regarded as sufficient? Is an email >> from the >> author, >> granting >> me/SciPy to distribute their code with a >> specific, >> BSD-style license >> sufficient? Or do they necessarily have to >> change >> the websites where >> they host the code to include the license? >> >> >> An email stating that the code can be >> distributed under >> a BSD >> license (or MIT or other compatible license) is >> enough. >> >> >> Some delay on the line, missed Jake's answer. Email is >> enough, but a >> change in the repo would of course be even better. >> >> Ralf >> >> >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> > >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> >> > > >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> > >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> >> > > >> >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> > >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> >> > > >> >> >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> >> >> >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> >> _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Sun Oct 23 05:33:54 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sun, 23 Oct 2016 11:33:54 +0200 Subject: [SciPy-Dev] ENH: Add structural rank to sparse.csgraph In-Reply-To: <104B6E16-798C-4E1E-BBD0-A5356DB18458@gmail.com> References: <104B6E16-798C-4E1E-BBD0-A5356DB18458@gmail.com> Message-ID: On Fri, Oct 14, 2016 at 6:56 AM, Paul Nation wrote: > Greetings, > > I was recently looking for a quick way to find out if a given sparse > matrix is singular. As it turns out the solution is to calculate the > structural rank (an upper bound on the numerical rank) of the sparsity > pattern associated with the matrix: > > http://www.mathworks.com/help/matlab/ref/sprank.html > > http://www.cise.ufl.edu/research/sparse/matrices/legend.html > > > Since this calculation is done via the maximum bipartite matching > algorithm that I added to sparse.csgraph some time ago, I thought it would > be a nice addition to include this straightforward structural rank > calculation. > > The Pull for this feature is here: https://github.com/ > scipy/scipy/pull/6680 > Thanks Paul. It looks like a nice addition. There's a reasonable amount of use in the literature, and the implementation is straightforward. So +1 from me. Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From josh.craig.wilson at gmail.com Sun Oct 23 23:32:50 2016 From: josh.craig.wilson at gmail.com (Joshua Wilson) Date: Sun, 23 Oct 2016 22:32:50 -0500 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> <489aa41c-7ad4-9dee-fa57-f644ef0cef33@werthmuller.org> Message-ID: TBH I'd rather we try to use SciPy's version anyway rather than have an implementation of unknown quality sitting around in the wrong module. It people want this feature (I don't know enough about it to have an opinion), then I can send a PR to your fork with necessary changes to special. I *think* this can be done in a portable way even though we can't use ISO_C_BINDING. (Or can we? It's from the 2003 standard but gfortran and ifort support it.) On Sun, Oct 23, 2016 at 3:00 AM, Ralf Gommers wrote: > > > On Wed, Oct 12, 2016 at 6:38 PM, Dieter Werthm?ller < > dieter at werthmuller.org> wrote: > >> Everyone, >> >> I have a response from Takuya Ooura, appended below. He has no problem >> with it either, I just don't know if his response is explicit enough >> (again). >> >> What do you think, is this enough? >> > > Hmm, it's slightly ambiguous. I would tend to say no, better to get a > clear statement. It sounds like he's happy, so you just need to spell out > exactly what you need him to say. Or you add a BSD-3 license and "Copyright > Takuya Ooura" at the top of that file in your scipy fork, point him to it, > and say "can you please agree to that exact text". > > Cheers, > Ralf > > > > >> >> Regards, >> Dieter >> >> ========== START email correspondence with Takuya Ooura ========== >> Subject: Re: cdgamma - license >> From: Takuya Ooura >> Date: Wed, 12 Oct 2016 21:31:01 +0900 (JST) >> To: dieter at werthmuller.org >> >> Dear Dieter Werthm ?ller, >> >> Please use the modified version of cdgamma.f. >> The license of my code is similar to the BSD-3-Clause license at present. >> >> -- >> Takuya Ooura >> Email : ooura at kurims.kyoto-u.ac.jp >> >> >Dear Takuya Ooura, >> > >> >Firstly thank you very much for making your code available on your >> website. >> > >> >I am writing to you regarding your cdgamma.f function. Andrew Hamilton >> >used a modified version of it for his FFTLog, and got your written >> >permission to distribute the modified version in his code. >> > >> >We would like to include FFTLog in the scientific library of the python >> >programming language, SciPy, and with it the modified version of >> cdgamma.f. >> > >> >The copyright statement distributed with your code states >> > >> > Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp). >> > You may use, copy, modify this code for any purpose and >> > without fee. You may distribute this ORIGINAL package. >> > >> >which makes it impossible for SciPy to include the modified version of >> >cdgamma.f in FFTLog into their library, as the version in FFTLog is a >> >MODIFIED version, and not the original version. >> > >> >Would it be possible that you could give SciPy the permission to >> >distribute cdgamma.f under a permissive license? My suggestion would be >> >the BSD-3-Clause license, >> >https://opensource.org/licenses/BSD-3-Clause >> >But any other BSD or MIT compatible license would be fine as well. >> > >> >Thank you for your time and for making cdgamma.f available on your >> website. >> > >> >Best regards, >> >Dieter Werthm ?ller >> >> ========== END email correspondence with Takuya Ooura ========== >> >> >> On 08/10/16 15:04, Joshua Wilson wrote: >> >>> Dieter, >>> >>> First, a warning: this is going to involve some fun. ;-) Before going >>> too far you should probably check that the different versions of the >>> complex Gamma functions use the same branch cuts, etc. Note that if you >>> want this to work in your external git repo you'll need to build against >>> scipy master. >>> >>> Steps should be roughly: >>> -- Write a Cython script that wraps the Cython version of SciPy's >>> loggamma. See >>> >>> https://scipy.github.io/devdocs/special.cython_special.html# >>> module-scipy.special.cython_special >>> >> #module-scipy.special.cython_special> >>> >>> for info on cimporting loggamma. >>> -- Export the wrapper as a C function using these steps: >>> >>> http://docs.cython.org/en/latest/src/userguide/external_C_co >>> de.html#using-cython-declarations-from-c >>> >> ode.html#using-cython-declarations-from-c> >>> >>> -- Add the Cythonized C file to your setup and add an Interface block to >>> your Fortran code letting it know how to call the C function. >>> >>> On Sat, Oct 8, 2016 at 1:11 PM, Dieter Werthm?ller >>> > wrote: >>> >>> Joshua >>> >>> Thanks for your input. How could I include the Cython loggamma >>> function within my setup script, so that fftlog.f would pick it up? >>> >>> Adjusting fftlog.f to pick up dfft*.f from >>> scipy/fftpack/src/dfftpack worked without problems. So if I could do >>> the same for loggamma, then the only new file would be fftlog.f, for >>> which we have the permission. >>> >>> Thanks, >>> Dieter >>> >>> >>> On 07/10/16 21:18, Joshua Wilson wrote: >>> >>> Re log gamma: under the hood the SciPy versions are in C (real >>> version) >>> and Cython (complex version), so linking them up with Fortran >>> code is >>> definitely doable. >>> >>> On Fri, Oct 7, 2016 at 8:16 PM, Ralf Gommers >>> >>> >> >>> wrote: >>> >>> >>> >>> On Sat, Oct 8, 2016 at 1:58 PM, Dieter Werthm?ller >>> >>> >> >>> wrote: >>> >>> Evening, >>> >>> I wrote to Andrew Hamilton, and below is his answer. He >>> has >>> basically no problem with it at all, I just don't know >>> if his >>> response is explicit enough. >>> >>> I think my email was quite extensive, and I assume that >>> is as >>> much as we will get from him. I also do not expect him >>> to change >>> his on "13 Mar 1999, 21:17" from TeX translated >>> website... >>> >>> What do you think, is this enough? >>> >>> >>> Yes, that's perfectly fine. Thanks for clarifying that >>> Dieter. >>> >>> Cheers, >>> Ralf >>> >>> >>> I also wrote to Takuya Ooura, and will let you know of >>> his >>> response, if I get one. However, as there are other >>> complex >>> logarithmic double precision gamma functions around, one >>> already >>> in scipy, this piece is not mission critical. >>> >>> Regards, >>> Dieter >>> >>> ========== START email correspondence with Andrew >>> Hamilton >>> ========== >>> Subject: Re: FFTLog - license >>> From: Andrew Hamilton >> >>> >> >> >>> Date: 07/10/16 18:22 >>> To: Dieter Werthm?ller >> >>> >> >> >>> CC: Andrew.Hamilton at colorado.edu >>> >>> >> >>> > >>> >>> >>> Dieter, >>> >>> I approve your adding the license language you suggest to >>> FFTLog, and making available the resulting package for >>> distribution. >>> >>> Andrew >>> >>> On 10/07/2016 03:42 PM, Dieter Werthm?ller wrote: >>> > Dear Andrew, >>> > >>> > Please apologize me bothering you again. >>> > >>> > After I published the code to wrap your FFTLog for >>> Python I >>> thought that >>> > it would be much better if your FFTLog would make it >>> straight >>> into the >>> > scientific library of Python. This would make your >>> FFTLog >>> available to a >>> > much wider audience. >>> > >>> > I contacted the developers of SciPy >>> (http://scipy.org), and >>> they are >>> > interested in including your code. However, there is >>> one issue: >>> > licensing. Code that is published on the web without a >>> license >>> file is >>> > copyrighted under law, and SciPy can for this reason >>> not >>> include your >>> > code into their library. >>> > >>> > All I ask for is if you could confirm to us by email >>> that we >>> are allowed >>> > to distribute your FFTLog under the BSD-3-Clause >>> license: >>> > https://opensource.org/licenses/BSD-3-Clause >>> >>> >> > >>> > >>> > The license is just a suggestion, any other BSD or MIT >>> compatible >>> > license would be fine as well. (For the same, legal >>> reasons we >>> recommend >>> > to publish a license file on your website too, but >>> that is >>> obviously >>> > entirely up to you. It might, however, clarify things >>> for >>> future visitors.) >>> > >>> > It would only affect your fftlog.f file, and the >>> changes you >>> made to >>> > cdgamma.f. I will write Takuya OOURA as well regarding >>> the >>> original >>> > cdgamma.f-file, asking him the same favour. And the >>> three >>> drfft*.f are >>> > already in the SciPy-library with the whole FFTPack. >>> > >>> > If you are interested why this issue arises, Jake >>> Vanderplas, >>> one of the >>> > developers of SciPy, wrote an interesting article >>> about the topic: >>> > >>> >>> http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows >>> -of-licensing-scientific-code/ >>> >> s-of-licensing-scientific-code/> >>> >>> >> s-of-licensing-scientific-code/ >>> >> s-of-licensing-scientific-code/>> >>> > >>> > Thank you again for your time and for making FFTLog >>> available! >>> > Best regards, >>> > Dieter >>> > >>> ========== END email correspondence with Andrew Hamilton >>> ========== >>> >>> On 07/10/16 15:13, Ralf Gommers wrote: >>> >>> >>> >>> On Sat, Oct 8, 2016 at 9:11 AM, Ralf Gommers >>> >> >> > >>> >> >>> >> >>> wrote: >>> >>> >>> >>> On Sat, Oct 8, 2016 at 8:59 AM, Dieter >>> Werthm?ller >>> >> >> > >>> >> >>> >> >>> wrote: >>> >>> Jake, >>> >>> Thanks for the clarification. I will try to >>> get the >>> permissions >>> from the >>> authors. >>> >>> What is regarded as sufficient? Is an email >>> from the >>> author, >>> granting >>> me/SciPy to distribute their code with a >>> specific, >>> BSD-style license >>> sufficient? Or do they necessarily have to >>> change >>> the websites where >>> they host the code to include the license? >>> >>> >>> An email stating that the code can be >>> distributed under >>> a BSD >>> license (or MIT or other compatible license) is >>> enough. >>> >>> >>> Some delay on the line, missed Jake's answer. Email >>> is >>> enough, but a >>> change in the repo would of course be even better. >>> >>> Ralf >>> >>> >>> >>> >>> _______________________________________________ >>> SciPy-Dev mailing list >>> SciPy-Dev at scipy.org >>> > >>> https://mail.scipy.org/mailman/listinfo/scipy-dev >>> >>> >> > >>> >>> _______________________________________________ >>> SciPy-Dev mailing list >>> SciPy-Dev at scipy.org >>> > >>> https://mail.scipy.org/mailman/listinfo/scipy-dev >>> >>> >> > >>> >>> >>> >>> _______________________________________________ >>> SciPy-Dev mailing list >>> SciPy-Dev at scipy.org >>> > >>> https://mail.scipy.org/mailman/listinfo/scipy-dev >>> >>> >> > >>> >>> >>> >>> >>> _______________________________________________ >>> SciPy-Dev mailing list >>> SciPy-Dev at scipy.org >>> https://mail.scipy.org/mailman/listinfo/scipy-dev >>> >>> >>> _______________________________________________ >>> SciPy-Dev mailing list >>> SciPy-Dev at scipy.org >>> https://mail.scipy.org/mailman/listinfo/scipy-dev >>> >>> >>> >>> >>> >>> _______________________________________________ >>> SciPy-Dev mailing list >>> SciPy-Dev at scipy.org >>> https://mail.scipy.org/mailman/listinfo/scipy-dev >>> >>> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at scipy.org >> https://mail.scipy.org/mailman/listinfo/scipy-dev >> > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dieter at werthmuller.org Mon Oct 24 10:25:08 2016 From: dieter at werthmuller.org (=?UTF-8?Q?Dieter_Werthm=c3=bcller?=) Date: Mon, 24 Oct 2016 09:25:08 -0500 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> <489aa41c-7ad4-9dee-fa57-f644ef0cef33@werthmuller.org> Message-ID: <24f91419-833e-5194-5d74-48c064b2ff95@werthmuller.org> I agree, probably the best would be to use the already existing FFTPACK and the already existing complex gamma function, which would mean only one file, fftlog.f, has to be added. In this regard, it might be best to first ask if there is sufficient interest for a logarithmic FFT, as you point out Joshua, before investing more time. Any opinions? For anyone interested I list the website of the original FFTLog again: http://casa.colorado.edu/~ajsh/FFTLog Ralf, one question out of interest and to learn something about licenses: Takuya's license has 3 sentences: 1. Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp). 2. You may use, copy, modify this code for any purpose and without fee. 3. You may distribute this ORIGINAL package. In the second sentence, it basically states that you can do whatever you want with it. Then as far as I understand the third sentence, it just gives additionally and specifically the permission to even distribute the unchanged package. Or does the absence of the word 'distribute' in the second sentence cause a problem? Thank you both for your continued inputs, Dieter On 23/10/16 22:32, Joshua Wilson wrote: > TBH I'd rather we try to use SciPy's version anyway rather than have an > implementation of unknown quality sitting around in the wrong module. It > people want this feature (I don't know enough about it to have an > opinion), then I can send a PR to your fork with necessary changes to > special. I *think* this can be done in a portable way even though we > can't use ISO_C_BINDING. (Or can we? It's from the 2003 standard but > gfortran and ifort support it.) > > On Sun, Oct 23, 2016 at 3:00 AM, Ralf Gommers > wrote: > > > > On Wed, Oct 12, 2016 at 6:38 PM, Dieter Werthm?ller > > wrote: > > Everyone, > > I have a response from Takuya Ooura, appended below. He has no > problem with it either, I just don't know if his response is > explicit enough (again). > > What do you think, is this enough? > > > Hmm, it's slightly ambiguous. I would tend to say no, better to get > a clear statement. It sounds like he's happy, so you just need to > spell out exactly what you need him to say. Or you add a BSD-3 > license and "Copyright Takuya Ooura" at the top of that file in your > scipy fork, point him to it, and say "can you please agree to that > exact text". > > Cheers, > Ralf > > > > > > Regards, > Dieter > > ========== START email correspondence with Takuya Ooura ========== > Subject: Re: cdgamma - license > From: Takuya Ooura > > Date: Wed, 12 Oct 2016 21:31:01 +0900 (JST) > To: dieter at werthmuller.org > > Dear Dieter Werthm ?ller, > > Please use the modified version of cdgamma.f. > The license of my code is similar to the BSD-3-Clause license at > present. > > -- > Takuya Ooura > Email : ooura at kurims.kyoto-u.ac.jp > > > >Dear Takuya Ooura, > > > >Firstly thank you very much for making your code available on > your website. > > > >I am writing to you regarding your cdgamma.f function. Andrew > Hamilton > >used a modified version of it for his FFTLog, and got your written > >permission to distribute the modified version in his code. > > > >We would like to include FFTLog in the scientific library of > the python > >programming language, SciPy, and with it the modified version > of cdgamma.f. > > > >The copyright statement distributed with your code states > > > > Copyright(C) 1996 Takuya OOURA (email: > ooura at mmm.t.u-tokyo.ac.jp ). > > You may use, copy, modify this code for any purpose and > > without fee. You may distribute this ORIGINAL package. > > > >which makes it impossible for SciPy to include the modified > version of > >cdgamma.f in FFTLog into their library, as the version in > FFTLog is a > >MODIFIED version, and not the original version. > > > >Would it be possible that you could give SciPy the permission to > >distribute cdgamma.f under a permissive license? My suggestion > would be > >the BSD-3-Clause license, > >https://opensource.org/licenses/BSD-3-Clause > > >But any other BSD or MIT compatible license would be fine as well. > > > >Thank you for your time and for making cdgamma.f available on > your website. > > > >Best regards, > >Dieter Werthm ?ller > > ========== END email correspondence with Takuya Ooura ========== > > > On 08/10/16 15:04, Joshua Wilson wrote: > > Dieter, > > First, a warning: this is going to involve some fun. ;-) > Before going > too far you should probably check that the different > versions of the > complex Gamma functions use the same branch cuts, etc. Note > that if you > want this to work in your external git repo you'll need to > build against > scipy master. > > Steps should be roughly: > -- Write a Cython script that wraps the Cython version of > SciPy's > loggamma. See > > https://scipy.github.io/devdocs/special.cython_special.html#module-scipy.special.cython_special > > > > > for info on cimporting loggamma. > -- Export the wrapper as a C function using these steps: > > http://docs.cython.org/en/latest/src/userguide/external_C_code.html#using-cython-declarations-from-c > > > > > -- Add the Cythonized C file to your setup and add an > Interface block to > your Fortran code letting it know how to call the C function. > > On Sat, Oct 8, 2016 at 1:11 PM, Dieter Werthm?ller > > >> wrote: > > Joshua > > Thanks for your input. How could I include the Cython > loggamma > function within my setup script, so that fftlog.f would > pick it up? > > Adjusting fftlog.f to pick up dfft*.f from > scipy/fftpack/src/dfftpack worked without problems. So > if I could do > the same for loggamma, then the only new file would be > fftlog.f, for > which we have the permission. > > Thanks, > Dieter > > > On 07/10/16 21:18, Joshua Wilson wrote: > > Re log gamma: under the hood the SciPy versions are > in C (real > version) > and Cython (complex version), so linking them up > with Fortran > code is > definitely doable. > > On Fri, Oct 7, 2016 at 8:16 PM, Ralf Gommers > > > > > >>> > wrote: > > > > On Sat, Oct 8, 2016 at 1:58 PM, Dieter Werthm?ller > > > > > >>> > wrote: > > Evening, > > I wrote to Andrew Hamilton, and below is his > answer. He has > basically no problem with it at all, I just > don't know > if his > response is explicit enough. > > I think my email was quite extensive, and I > assume that > is as > much as we will get from him. I also do not > expect him > to change > his on "13 Mar 1999, 21:17" from TeX > translated website... > > What do you think, is this enough? > > > Yes, that's perfectly fine. Thanks for > clarifying that Dieter. > > Cheers, > Ralf > > > I also wrote to Takuya Ooura, and will let > you know of his > response, if I get one. However, as there > are other complex > logarithmic double precision gamma functions > around, one > already > in scipy, this piece is not mission critical. > > Regards, > Dieter > > ========== START email correspondence with > Andrew Hamilton > ========== > Subject: Re: FFTLog - license > From: Andrew Hamilton > > > > > >>> > Date: 07/10/16 18:22 > To: Dieter Werthm?ller > > > > > >>> > CC: Andrew.Hamilton at colorado.edu > > > > > > >> > > > Dieter, > > I approve your adding the license language > you suggest to > FFTLog, and making available the resulting > package for > distribution. > > Andrew > > On 10/07/2016 03:42 PM, Dieter Werthm?ller > wrote: > > Dear Andrew, > > > > Please apologize me bothering you again. > > > > After I published the code to wrap your > FFTLog for > Python I > thought that > > it would be much better if your FFTLog > would make it > straight > into the > > scientific library of Python. This would > make your FFTLog > available to a > > much wider audience. > > > > I contacted the developers of SciPy > (http://scipy.org), and > they are > > interested in including your code. > However, there is > one issue: > > licensing. Code that is published on the > web without a > license > file is > > copyrighted under law, and SciPy can for > this reason not > include your > > code into their library. > > > > All I ask for is if you could confirm to > us by email > that we > are allowed > > to distribute your FFTLog under the > BSD-3-Clause license: > > > https://opensource.org/licenses/BSD-3-Clause > > > > > > >> > > > > The license is just a suggestion, any > other BSD or MIT > compatible > > license would be fine as well. (For the > same, legal > reasons we > recommend > > to publish a license file on your website > too, but that is > obviously > > entirely up to you. It might, however, > clarify things for > future visitors.) > > > > It would only affect your fftlog.f file, > and the > changes you > made to > > cdgamma.f. I will write Takuya OOURA as > well regarding the > original > > cdgamma.f-file, asking him the same > favour. And the three > drfft*.f are > > already in the SciPy-library with the > whole FFTPack. > > > > If you are interested why this issue > arises, Jake > Vanderplas, > one of the > > developers of SciPy, wrote an interesting > article > about the topic: > > > > > http://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows-of-licensing-scientific-code/ > > > > > > > > > >> > > > > Thank you again for your time and for > making FFTLog > available! > > Best regards, > > Dieter > > > ========== END email correspondence with > Andrew Hamilton > ========== > > On 07/10/16 15:13, Ralf Gommers wrote: > > > > On Sat, Oct 8, 2016 at 9:11 AM, Ralf Gommers > > > > > >> > > > > > >>>> wrote: > > > > On Sat, Oct 8, 2016 at 8:59 AM, > Dieter Werthm?ller > > > > > >> > > > > > >>>> wrote: > > Jake, > > Thanks for the clarification. I > will try to > get the > permissions > from the > authors. > > What is regarded as sufficient? > Is an email > from the > author, > granting > me/SciPy to distribute their > code with a > specific, > BSD-style license > sufficient? Or do they > necessarily have to > change > the websites where > they host the code to include > the license? > > > An email stating that the code can be > distributed under > a BSD > license (or MIT or other compatible > license) is > enough. > > > Some delay on the line, missed Jake's > answer. Email is > enough, but a > change in the repo would of course be > even better. > > Ralf > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > > > >> > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > >> > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > > > >> > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > >> > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > > > >> > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > >> > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > > > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > From davidmenhur at gmail.com Mon Oct 24 10:57:05 2016 From: davidmenhur at gmail.com (=?UTF-8?B?RGHPgGlk?=) Date: Mon, 24 Oct 2016 16:57:05 +0200 Subject: [SciPy-Dev] FFTLog In-Reply-To: <24f91419-833e-5194-5d74-48c064b2ff95@werthmuller.org> References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> <489aa41c-7ad4-9dee-fa57-f644ef0cef33@werthmuller.org> <24f91419-833e-5194-5d74-48c064b2ff95@werthmuller.org> Message-ID: On 24 October 2016 at 16:25, Dieter Werthm?ller wrote: > > 1. Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp). > 2. You may use, copy, modify this code for any purpose and without fee. > 3. You may distribute this ORIGINAL package. > In the second sentence, it basically states that you can do whatever you > want with it. Then as far as I understand the third sentence, it just > gives additionally and specifically the permission to even distribute > the unchanged package. Or does the absence of the word 'distribute' in > the second sentence cause a problem? With my scientist hat on, I think that he intended to let you do whatever you want with it, but with my not-really-a-lawyer hat, it can be interpreted both ways, so an actual lawyer may get squeamish without a more explicit agreement. /David. From sanchezgnzlz.alvaro at gmail.com Thu Oct 27 09:43:09 2016 From: sanchezgnzlz.alvaro at gmail.com (Alvaro Sanchez) Date: Thu, 27 Oct 2016 14:43:09 +0100 Subject: [SciPy-Dev] inversefunc: a method to obtain the numerical inverse of a callable Message-ID: Hi everyone! I have been lately working on a user-friendly tool to calculate the numerical inverse of a function, in the shape of a callable that is returned by the function and that lets the user evaluate the inverse function for any given value/array of values. There is an open PR (https://github.com/scipy/scipy/pull/6725), where there is a full description and some examples of usage. At this point I am quite happy with how the function is performing, however there is an ongoing discussion on whether it actually should be part of scipy or not. I would appreciate if you could take a look at the description (including a summary of the ongoing discussion at the end of the first comment), and give some feedback on this line as I would like to know whether I should invest more time on this or not. Thank you in advance :) A From ralf.gommers at gmail.com Mon Oct 31 05:48:51 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Mon, 31 Oct 2016 22:48:51 +1300 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> <489aa41c-7ad4-9dee-fa57-f644ef0cef33@werthmuller.org> <24f91419-833e-5194-5d74-48c064b2ff95@werthmuller.org> Message-ID: On Tue, Oct 25, 2016 at 3:57 AM, Da?id wrote: > On 24 October 2016 at 16:25, Dieter Werthm?ller > wrote: > > > > 1. Copyright(C) 1996 Takuya OOURA (email: ooura at mmm.t.u-tokyo.ac.jp). > > 2. You may use, copy, modify this code for any purpose and without fee. > > 3. You may distribute this ORIGINAL package. > > In the second sentence, it basically states that you can do whatever you > > want with it. Then as far as I understand the third sentence, it just > > gives additionally and specifically the permission to even distribute > > the unchanged package. Or does the absence of the word 'distribute' in > > the second sentence cause a problem? > > > With my scientist hat on, I think that he intended to let you do > whatever you want with it, but with my not-really-a-lawyer hat, it can > be interpreted both ways, so an actual lawyer may get squeamish > without a more explicit agreement. > Agreed. With common sense it's clearly fine to reuse his code, but legal stuff isn't common sense - it could also be read as giving permission to redistribute only the original code and not a modified version. Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Mon Oct 31 05:59:08 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Mon, 31 Oct 2016 22:59:08 +1300 Subject: [SciPy-Dev] FFTLog In-Reply-To: <24f91419-833e-5194-5d74-48c064b2ff95@werthmuller.org> References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <59b17c91-fab7-46b7-1495-868a44156ec9@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> <489aa41c-7ad4-9dee-fa57-f644ef0cef33@werthmuller.org> <24f91419-833e-5194-5d74-48c064b2ff95@werthmuller.org> Message-ID: On Tue, Oct 25, 2016 at 3:25 AM, Dieter Werthm?ller wrote: > I agree, probably the best would be to use the already existing FFTPACK > and the already existing complex gamma function, which would mean only > one file, fftlog.f, has to be added. > > In this regard, it might be best to first ask if there is sufficient > interest for a logarithmic FFT, as you point out Joshua, before > investing more time. Any opinions? For anyone interested I list the > website of the original FFTLog again: > http://casa.colorado.edu/~ajsh/FFTLog > I haven't come across a use case for this myself, but the original paper [1] is highly cited and the citation come from a range of fields. The one fftlog.f file doesn't look worse than the average Fortran file, so this will likely be okay to maintain. So I'm fine with adding this feature. Ralf [1] http://www.sciencedirect.com/science/article/pii/0021999178901079 -------------- next part -------------- An HTML attachment was scrubbed... URL: From dieter at werthmuller.org Mon Oct 31 20:12:49 2016 From: dieter at werthmuller.org (=?UTF-8?Q?Dieter_Werthm=c3=bcller?=) Date: Mon, 31 Oct 2016 18:12:49 -0600 Subject: [SciPy-Dev] FFTLog In-Reply-To: References: <723489e6-c783-aefc-3472-00d42fe472d8@werthmuller.org> <8641887f-3c5c-6605-1806-169ebd90ca1c@werthmuller.org> <1997ab61-0688-2d6f-6974-24118cf33924@werthmuller.org> <489aa41c-7ad4-9dee-fa57-f644ef0cef33@werthmuller.org> <24f91419-833e-5194-5d74-48c064b2ff95@werthmuller.org> Message-ID: Great. I am out of the office most of November. I will pick it up latest in December again and see how far I get with my knowledge, and come back for help if I am lost. Dieter On 31/10/16 03:59, Ralf Gommers wrote: > > > On Tue, Oct 25, 2016 at 3:25 AM, Dieter Werthm?ller > > wrote: > > I agree, probably the best would be to use the already existing FFTPACK > and the already existing complex gamma function, which would mean only > one file, fftlog.f, has to be added. > > In this regard, it might be best to first ask if there is sufficient > interest for a logarithmic FFT, as you point out Joshua, before > investing more time. Any opinions? For anyone interested I list the > website of the original FFTLog again: > http://casa.colorado.edu/~ajsh/FFTLog > > > > I haven't come across a use case for this myself, but the original paper > [1] is highly cited and the citation come from a range of fields. The > one fftlog.f file doesn't look worse than the average Fortran file, so > this will likely be okay to maintain. So I'm fine with adding this feature. > > Ralf > > [1] http://www.sciencedirect.com/science/article/pii/0021999178901079 > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-dev > From warren.weckesser at gmail.com Mon Oct 31 22:45:10 2016 From: warren.weckesser at gmail.com (Warren Weckesser) Date: Mon, 31 Oct 2016 22:45:10 -0400 Subject: [SciPy-Dev] www.scipy.org down Message-ID: I was getting the following error when I tried to go to https://www.scipy.org: Secure Connection Failed An error occurred during a connection to www.scipy.org. SSL received a record that exceeded the maximum permissible length. Error code: SSL_ERROR_RX_RECORD_TOO_LONG The page you are trying to view cannot be shown because the authenticity of the received data could not be verified. Please contact the website owners to inform them of this problem. Now I'm getting: Unable to connect Firefox can?t establish a connection to the server at www.scipy.org. The site could be temporarily unavailable or too busy. Try again in a few moments. If you are unable to load any pages, check your computer?s network connection. If your computer or network is protected by a firewall or proxy, make sure that Firefox is permitted to access the Web. Warren -------------- next part -------------- An HTML attachment was scrubbed... URL: