From rlucente at pipeline.com Thu Feb 1 10:26:06 2018 From: rlucente at pipeline.com (Robert Lucente) Date: Thu, 1 Feb 2018 10:26:06 -0500 (GMT-05:00) Subject: [SciPy-Dev] email client is misconfigured - replies are breaking the threading Message-ID: <1971069526.3115.1517498766567@wamui-cinderella.atl.sa.earthlink.net> It has been many days since I checked "Off" for "Set Digest Mode". However, I am still getting email in digest mode. Any suggestions on what else to try would be appreciated. In the meantime, I will be very careful w/ the "Subject" so as not to break the thread. From rlucente at pipeline.com Thu Feb 1 11:15:49 2018 From: rlucente at pipeline.com (Robert Lucente) Date: Thu, 1 Feb 2018 11:15:49 -0500 (GMT-05:00) Subject: [SciPy-Dev] What we do struggle with is lack of progress on Message-ID: <993729943.3990.1517501749770@wamui-cinderella.atl.sa.earthlink.net> I realize that the subject line is truncated. However, I did not want to break the threading. I have lurked on the mailing list and this is my first time posting anything of substance. If I break tribal norms, please let me know and I will change. >The other open issue is for clarifying the build/install docs on >Windows: https://github.com/scipy/scipy/issues/7140 >start at the top with explaining that the only currently non-experimental >build is MSVC + MKL, and that you need an MKL license. >Then point to https://software.intel.com/en-us/articles/numpyscipy-with-intel-mkl When I went to the above intel link, it states Please note: The application notes is outdated, but keep here for reference. Instead of build Numpy/Scipy with Intel? MKL manually as below, we strongly recommend developer to use Intel? Distribution for Python* (https://software.intel.com/en-us/distribution-for-python), which has prebuild Numpy/Scipy based on Intel? Math Kernel Library (Intel? MKL) and more. Please refer to Intel? Distribution for Python* mainpage: https://software.intel.com/en-us/distribution-for-python Installing Intel? Distribution for Python* and Intel? Performance Libraries with Anaconda* by : https://software.intel.com/en-us/articles/using-intel-distribution-for-python-with-anaconda Q1: Do we really want to spend time doing something which Intel and Anaconda have already done? Q2: If Intel "application notes is outdated" and they "strongly recommend" to use their precompiled stuff, do we want to deviate? Q3: The above two things combined w/ needing an MKL license seems like a really high hurdle? What am I missing? I went to http://mingwpy.github.io/ which lead me to https://groups.google.com/forum/#!topic/mingwpy/1k_BLFPLmBI where it states that the mingwpy project is now abandoned. However, the LAPACK / CLAPACK / ScaLAPACK for Windows at utk.edu still makes references to Mingw http://icl.cs.utk.edu/lapack-for-windows/lapack/index.html#lapacke http://icl.cs.utk.edu/lapack-for-windows/ Hummm. Also, as I started digging and self educating, it became clear that I have a steep learning curve. There is a fine line between doing things yourself and asking questions. I would end up asking too many questions and making a nuisance of myself. Consequently, I will gladly support someone in this or other activities. However, as a newbie, it would be inappropriate for me to attempt this project as the lead. From deak.andris at gmail.com Thu Feb 1 12:33:56 2018 From: deak.andris at gmail.com (Andras Deak) Date: Thu, 1 Feb 2018 18:33:56 +0100 Subject: [SciPy-Dev] email client is misconfigured - replies are breaking the threading In-Reply-To: <1971069526.3115.1517498766567@wamui-cinderella.atl.sa.earthlink.net> References: <1971069526.3115.1517498766567@wamui-cinderella.atl.sa.earthlink.net> Message-ID: You are still listed as a digest member on the subscriber list: https://mail.python.org/mailman/roster/scipy-dev Your change of settings might not have been applied. I suggest that you try again. I changed my e-mail address a few days ago and it was instantaneous (and I also got confirmation emails). Andr?s On Thu, Feb 1, 2018 at 4:26 PM, Robert Lucente wrote: > It has been many days since I checked "Off" for "Set Digest Mode". However, I am still getting email in digest mode. Any suggestions on what else to try would be appreciated. > > In the meantime, I will be very careful w/ the "Subject" so as not to break the thread. > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev From rlucente at pipeline.com Thu Feb 1 13:01:33 2018 From: rlucente at pipeline.com (Robert Lucente) Date: Thu, 1 Feb 2018 13:01:33 -0500 (GMT-05:00) Subject: [SciPy-Dev] email client is misconfigured - replies are breaking the threading Message-ID: <1430881972.6193.1517508093648@wamui-cinderella.atl.sa.earthlink.net> >From: Andras Deak >Sent: Feb 1, 2018 12:33 PM >To: Robert Lucente , SciPy Developers List >Subject: Re: [SciPy-Dev] email client is misconfigured - replies are breaking the threading > >You are still listed as a digest member on the subscriber list: >https://mail.python.org/mailman/roster/scipy-dev >Your change of settings might not have been applied. I suggest that >you try again. I changed my e-mail address a few days ago and it was >instantaneous (and I also got confirmation emails). > >Andr?s > >On Thu, Feb 1, 2018 at 4:26 PM, Robert Lucente wrote: >> It has been many days since I checked "Off" for "Set Digest Mode". However, I am still getting email in digest mode. Any suggestions on what else to try would be appreciated. >> >> In the meantime, I will be very careful w/ the "Subject" so as not to break the thread. >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev I just tried again and now I show up under the "657 Non-digested Members of SciPy-Dev:". Thanks for the help. From haberland at ucla.edu Thu Feb 1 14:27:03 2018 From: haberland at ucla.edu (Matt Haberland) Date: Thu, 1 Feb 2018 11:27:03 -0800 Subject: [SciPy-Dev] What we do struggle with is lack of progress on big-ticket items In-Reply-To: <20180123232935.mr5sg4r2e63t4pil@fastmail.com> References: <1075549019.8362.1516663539259@wamui-cinderella.atl.sa.earthlink.net> <14f101d39430$84b127e0$8e1377a0$@pipeline.com> <20180123192038.mgenugikitd2x4wy@fastmail.com> <20180123232935.mr5sg4r2e63t4pil@fastmail.com> Message-ID: To help push the idea of updating install/workflow notes and making videos, I drafted a video for a Mac development install. I don't believe it's complete and perhaps we will decide to go in a totally different direction; just thought that having an example to work from would help stir the conversation. Please see https://github.com/scipy/scipy/issues/8353 if you're interested. On Tue, Jan 23, 2018 at 3:29 PM, Stefan van der Walt wrote: > On Tue, 23 Jan 2018 14:49:48 -0800, Matt Haberland wrote: > > Funny, I was just writing about this to suggest videos, too. > > > > I looked on YouTube but didn't find anything useful when searching for > > numpy/scipy development environment/workflow. > > Here is the scikit-image contributor guide: > > http://scikit-image.org/docs/dev/contribute.html > > It can do with some love, but it's probably quite similar to what we use > in SciPy. Perhaps it's worth collectively updating such a set of notes > first, that we can then turn into a series of small video snippets? > > > Besides the day-to-day workflow, I also had a hard time getting my > > development environment set up initially. A video on that would be really > > helpful, too. > > For that, I suggest we make one opinionated choice of environment for > illustrative purposes. We can probably come up with a set of 5 or 10 > things that a workable editing environment needs to have (spaces not > tabs, PEP8 checker, etc.). > > St?fan > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > -- Matt Haberland Assistant Adjunct Professor in the Program in Computing Department of Mathematics 6617A Math Sciences Building, UCLA -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Thu Feb 1 23:15:38 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Fri, 2 Feb 2018 15:15:38 +1100 Subject: [SciPy-Dev] stats.hypsecant2 Message-ID: Does anyone have any objections to adding a secant-squared distribution to stats? The CDF of this distribution (hyperbolic tangent) is frequently used for modelling scattering data (see appendix A in https://doi.org/10.1107/S1600576717013632, eqns 25 and 26). CDF = 0.5 * {1 + tanh(pi * (x - loc) / 2 / sqrt(3) / scale)} PDF = (pi / 4 / sqrt(3) / scale) * (cosh(pi * (x - loc) / 2 / sqrt(3) / scale))**-2 I'm guessing the name should be hypsecant2 Andrew. -------------- next part -------------- An HTML attachment was scrubbed... URL: From josef.pktd at gmail.com Fri Feb 2 11:04:37 2018 From: josef.pktd at gmail.com (josef.pktd at gmail.com) Date: Fri, 2 Feb 2018 11:04:37 -0500 Subject: [SciPy-Dev] stats.hypsecant2 In-Reply-To: References: Message-ID: On Thu, Feb 1, 2018 at 11:15 PM, Andrew Nelson wrote: > Does anyone have any objections to adding a secant-squared distribution to > stats? > The CDF of this distribution (hyperbolic tangent) is frequently used for > modelling scattering data (see appendix A in https://doi.org/10.1107/ > S1600576717013632, eqns 25 and 26). > > CDF = 0.5 * {1 + tanh(pi * (x - loc) / 2 / sqrt(3) / scale)} > PDF = (pi / 4 / sqrt(3) / scale) * (cosh(pi * (x - loc) / 2 / sqrt(3) / > scale))**-2 > > I'm guessing the name should be hypsecant2 > wikipedia redirects me to logistic distribution https://en.wikipedia.org/wiki/Logistic_distribution Can you check if it's the same? That seems to be the case based on the cdf Josef > > Andrew. > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bwana.marko at yahoo.com Sat Feb 3 17:41:08 2018 From: bwana.marko at yahoo.com (Mark Mikofski) Date: Sat, 3 Feb 2018 22:41:08 +0000 (UTC) Subject: [SciPy-Dev] "vectorize" scipy.optimize.newton In-Reply-To: References: Message-ID: <1223223219.2704429.1517697668365@mail.yahoo.com> I've submitted a pull request to allow arrays to be used in scipy.optimize.newton:BUG: ENH: vectorize scalar zero-search-functions by mikofski ? Pull Request #8357 ? scipy/scipy I would love to hear your comments. Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Sun Feb 4 04:42:28 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sun, 4 Feb 2018 09:42:28 +0000 Subject: [SciPy-Dev] SciPy 1.0 paper writing proposal In-Reply-To: References: <20180126074429.3csbkpsg7hbme22g@fastmail.com> <20180130195725.GC20306@lakota> Message-ID: On Tue, Jan 30, 2018 at 8:10 PM, Ilhan Polat wrote: > Same as Eric also if you need some TeX stuff, I have a very broad and > useless TeX experience. > Thanks Eric & Ilhan. I just sent the follow-up email to the coordinating volunteers. Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From serge.guelton at telecom-bretagne.eu Mon Feb 5 06:47:12 2018 From: serge.guelton at telecom-bretagne.eu (Serge Guelton) Date: Mon, 5 Feb 2018 12:47:12 +0100 Subject: [SciPy-Dev] Pythran 0.8.4 Message-ID: <20180205114712.GA28412@lakota> Hi there, A new minor version of Pythran was just released! Although it's a minor version, it still includes a lot of bugfixes and enhancement, including the topics covered by the recent blogposts on http://serge-sans-paille.github.io/pythran-stories/ The release is available on PyPI and on Github through the 0.8.4 tag. https://pypi.python.org/pypi/pythran https://github.com/serge-sans-paille/pythran We received a lot of issues over the past 4 months, that's much appreciated, thank you guys! -- (changelog below) 2018-02-05 Serge Guelton * Slimmer generated binaries * Preliminary native Windows support for Python3 * Several numpy-related function improvements * @ operator support * Better negative index support and range detection * Glimpses of OpenMP4 support, min/max support in OpenMP reductions * Python Capsule support * Work around GCC-7 parsing bug From sylvain.corlay at gmail.com Tue Feb 6 11:59:53 2018 From: sylvain.corlay at gmail.com (Sylvain Corlay) Date: Tue, 6 Feb 2018 17:59:53 +0100 Subject: [SciPy-Dev] Using Pythran to compile some of the scipy internals In-Reply-To: References: <20180120101034.GA3707@lakota> <20180122142840.GA22566@lakota> <20180129113402.GA2065@lakota> <20180131114223.GA20197@lakota> <20180131164925.GA28870@lakota> Message-ID: It is actually possible to compiler Windows Python 2.7 extension with more modern compilers than VS2008, and it works well. On Wed, Jan 31, 2018 at 5:55 PM, Olivier Grisel wrote: > 2018-01-31 17:49 GMT+01:00 Serge Guelton bretagne.eu>: > >> On Wed, Jan 31, 2018 at 03:33:29PM +0100, Olivier Grisel wrote: >> > msvc is the only supported toolchain to generate wheels that are >> compatible >> > with the official binary distribution of Python from python.org and >> therefore >> > the only compiler that can generate wheels suitable for distribution >> PyPI. >> >> OK. I have no trouble using the VS2017 toolchain fro python3, I hope I'm >> not bound to VS2008 (say for Python 2.7)? > > > Unfortunately yes. But I guess Python 2.7 support for new feature > releases of scipy will be phased out in 2019 or so, so maybe it's not that > a big problem to not provide pythran-based acceleration for Python 2. Beter > not waste too much time on Python 2 ;) > > -- > Olivier > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bwana.marko at yahoo.com Tue Feb 6 23:10:28 2018 From: bwana.marko at yahoo.com (Mark Mikofski) Date: Wed, 7 Feb 2018 04:10:28 +0000 (UTC) Subject: [SciPy-Dev] "vectorize" scipy.optimize.newton In-Reply-To: <1223223219.2704429.1517697668365@mail.yahoo.com> References: <1223223219.2704429.1517697668365@mail.yahoo.com> Message-ID: <727293084.64465.1517976628058@mail.yahoo.com> I am still looking for reviewers for PR #8357.?https://github.com/scipy/scipy/pull/8357 This PR proposes making few minor changes to make scipy.optimize.newton take and return numpy arrays so that users can quickly analyze very large datasets. There are at least two issues regarding this proposal #8354 and? #7242 The pvlib-python package on pypi is using newton to solve the the implicit solar cell model for millions of time intervals and to do Monte Carlo analysis. Looping over newton or using multi-processing is too slow, and a turn off to users, but the vectorised newton method is very fast. My colleagues and I have also looked at using cython, but the performance of typed native cython functions have not been as fast as using numpy, are more challenging, and more restrictive. Nevertheless we are still pursuing this in a separate effort. My opinion is that users will benefit from both efforts: (1) a ufunc newton and (2) a cython newton that takes a cython typed callback function. I understand that some are concerned about the tedium of vectorizing and correctly hanging the halting conditions. However there are only a few changes needed for newton because there is no branching*. Simply wrapping the inputs with no.asarray is enough. For halting conditions we look for the max Newton step to be below the tolerance. For division by zero, we look for any derivative that is zero. IMO the proposed code is cleaner, and as a plus it has less lines. Please consider commenting on the mailing list, on PR 8357, or the related issue 8354 Thanks,Mark MikofskiPrincipal Engineer - Solar ServicesDNV-GL * The original newton uses the parabolic Halley's method which has a branch if the discriminant is negative. Replacing this with the traditional Halley's method removed this condition and possibly resolved issue 5922. On Sat, Feb 3, 2018 at 2:41 PM, Mark Mikofski wrote: I've submitted a pull request to allow arrays to be used in scipy.optimize.newton:BUG: ENH: vectorize scalar zero-search-functions by mikofski ? Pull Request #8357 ? scipy/scipy I would love to hear your comments. Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Wed Feb 7 21:06:19 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Thu, 8 Feb 2018 13:06:19 +1100 Subject: [SciPy-Dev] Proposal - optimize callback given a state keyword Message-ID: Hi all, I propose that the optimize callbacks be asked to accept a new state keyword in the future. The state keyword will be an `OptimizeResult` giving the state of the optimizer at that point. i.e. n_iterations, n_fun, (n_jac?), x, fun, etc. To aid the transition I propose that the user callbacks are wrapped with something along the lines of: class OptimizerCallback(object): def __init__(self, callback): self.callback = callback argspec = _getargspec(callback) self.accepts_state = True if 'state' not in argspec.varkw: warnings.warn(FutureWarning, "In future versions of scipy the" " optimizer callback should accept" "a state kwd") self.accepts_state = False def __call__(self, x, state): if self.accepts_state: self.callback(x, state) else: self.callback(x) and the optimizers be modified appropriately. Thoughts, comments? _____________________________________ Dr. Andrew Nelson _____________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.frio at gmail.com Thu Feb 8 07:37:35 2018 From: jaime.frio at gmail.com (=?UTF-8?Q?Jaime_Fern=C3=A1ndez_del_R=C3=ADo?=) Date: Thu, 08 Feb 2018 12:37:35 +0000 Subject: [SciPy-Dev] Proposal - optimize callback given a state keyword In-Reply-To: References: Message-ID: On Thu, Feb 8, 2018 at 3:06 AM Andrew Nelson wrote: > > Hi all, > I propose that the optimize callbacks be asked to accept a new state keyword in the future. > The state keyword will be an `OptimizeResult` giving the state of the optimizer at that point. > i.e. n_iterations, n_fun, (n_jac?), x, fun, etc. > > To aid the transition I propose that the user callbacks are wrapped with something along the lines of: > > class OptimizerCallback(object): > def __init__(self, callback): > self.callback = callback > argspec = _getargspec(callback) > self.accepts_state = True > if 'state' not in argspec.varkw: > warnings.warn(FutureWarning, "In future versions of scipy the" > " optimizer callback should accept" > "a state kwd") > self.accepts_state = False > > def __call__(self, x, state): > if self.accepts_state: > self.callback(x, state) > else: > self.callback(x) > > and the optimizers be modified appropriately. > > Thoughts, comments? If we do implement callback on steroids, I'd also suggest: - Letting that class wrap a None (which would make calling it a no-op) would allow us to get rid of all those `if callback is not None:` in the optimizer loops. - Another interesting addition for such an OptimizeResult would be to make the typical stopping conditions (gradient norm, relative function change...) available. - This would be especially useful if we allowed the callback to terminate the optimization early, e.g. by returning False instead of None. While I think all of this would be a step in the right direction, I wonder if cramming more functionality into the callback is the way to go. After a few months of using optimize A LOT at work, I am pretty much convinced that the architecture of the library is,, let's call it suboptimal... I haven't fully fleshed it out, but I think it would be much better if, instead of black box functions that run through to convergence, with only the callback function to shed light on what may be going on, we exposed some form of Optimizer object, that would know how to perform a single optimization step. There should still be a form of automatically running these to convergence, but it would allow advanced users to do things that now are impossible, like e.g. running two different algorithms on the same problem with the exact same termination conditions. Jaime -------------- next part -------------- An HTML attachment was scrubbed... URL: From josh.craig.wilson at gmail.com Thu Feb 8 09:12:44 2018 From: josh.craig.wilson at gmail.com (Joshua Wilson) Date: Thu, 8 Feb 2018 08:12:44 -0600 Subject: [SciPy-Dev] Proposal - optimize callback given a state keyword In-Reply-To: References: Message-ID: > we exposed some form of Optimizer object, that would know how to perform a single optimization step I think that's a wonderful idea, and one that has a lot of historical precedent since it's generally how Fortran optimizers worked because there were no function pointers. (Which conveniently means a lot of things in SciPy work that way under-the-hood already.) Just a random comment from the peanut gallery, Josh On Thu, Feb 8, 2018 at 6:37 AM, Jaime Fern?ndez del R?o wrote: > On Thu, Feb 8, 2018 at 3:06 AM Andrew Nelson wrote: >> >> Hi all, >> I propose that the optimize callbacks be asked to accept a new state >> keyword in the future. >> The state keyword will be an `OptimizeResult` giving the state of the >> optimizer at that point. >> i.e. n_iterations, n_fun, (n_jac?), x, fun, etc. >> >> To aid the transition I propose that the user callbacks are wrapped with >> something along the lines of: >> >> class OptimizerCallback(object): >> def __init__(self, callback): >> self.callback = callback >> argspec = _getargspec(callback) >> self.accepts_state = True >> if 'state' not in argspec.varkw: >> warnings.warn(FutureWarning, "In future versions of scipy the" >> " optimizer >> callback should accept" >> "a state >> kwd") >> self.accepts_state = False >> >> def __call__(self, x, state): >> if self.accepts_state: >> self.callback(x, state) >> else: >> self.callback(x) >> >> and the optimizers be modified appropriately. >> >> Thoughts, comments? > > If we do implement callback on steroids, I'd also suggest: > > Letting that class wrap a None (which would make calling it a no-op) would > allow us to get rid of all those `if callback is not None:` in the optimizer > loops. > Another interesting addition for such an OptimizeResult would be to make the > typical stopping conditions (gradient norm, relative function change...) > available. > This would be especially useful if we allowed the callback to terminate the > optimization early, e.g. by returning False instead of None. > > While I think all of this would be a step in the right direction, I wonder > if cramming more functionality into the callback is the way to go. After a > few months of using optimize A LOT at work, I am pretty much convinced that > the architecture of the library is,, let's call it suboptimal... I haven't > fully fleshed it out, but I think it would be much better if, instead of > black box functions that run through to convergence, with only the callback > function to shed light on what may be going on, we exposed some form of > Optimizer object, that would know how to perform a single optimization step. > There should still be a form of automatically running these to convergence, > but it would allow advanced users to do things that now are impossible, like > e.g. running two different algorithms on the same problem with the exact > same termination conditions. > > Jaime > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > From sievert.scott at gmail.com Thu Feb 8 12:19:56 2018 From: sievert.scott at gmail.com (Scott Sievert) Date: Thu, 8 Feb 2018 12:19:56 -0500 Subject: [SciPy-Dev] Proposal - optimize callback given a state keyword In-Reply-To: References: Message-ID: > we exposed some form of Optimizer object, that would know how to perform a single optimization step I think that's a wonderful idea, and one that has a lot of historical precedent Another +1, and I?d be happy to help implement this. More precedent is that popular deep learning libraries implement their optimizers with classes (PyTorch source , Tensorflow source ). >From where I sit this is hugely beneficial because it allows interacting with an optimization as an object. I?m involved in optimization research, and I often want to compute some value after an optimization step or modify the step size at every iteration or something similar. I also desire this in the scipy.optimize interface, and have moved away from scipy.optimize. I started my own implementation then moved to PyTorch. Scott On February 8, 2018 at 8:13:58 AM, Joshua Wilson ( josh.craig.wilson at gmail.com) wrote: > we exposed some form of Optimizer object, that would know how to perform a single optimization step I think that's a wonderful idea, and one that has a lot of historical precedent since it's generally how Fortran optimizers worked because there were no function pointers. (Which conveniently means a lot of things in SciPy work that way under-the-hood already.) Just a random comment from the peanut gallery, Josh On Thu, Feb 8, 2018 at 6:37 AM, Jaime Fern?ndez del R?o wrote: > On Thu, Feb 8, 2018 at 3:06 AM Andrew Nelson wrote: >> >> Hi all, >> I propose that the optimize callbacks be asked to accept a new state >> keyword in the future. >> The state keyword will be an `OptimizeResult` giving the state of the >> optimizer at that point. >> i.e. n_iterations, n_fun, (n_jac?), x, fun, etc. >> >> To aid the transition I propose that the user callbacks are wrapped with >> something along the lines of: >> >> class OptimizerCallback(object): >> def __init__(self, callback): >> self.callback = callback >> argspec = _getargspec(callback) >> self.accepts_state = True >> if 'state' not in argspec.varkw: >> warnings.warn(FutureWarning, "In future versions of scipy the" >> " optimizer >> callback should accept" >> "a state >> kwd") >> self.accepts_state = False >> >> def __call__(self, x, state): >> if self.accepts_state: >> self.callback(x, state) >> else: >> self.callback(x) >> >> and the optimizers be modified appropriately. >> >> Thoughts, comments? > > If we do implement callback on steroids, I'd also suggest: > > Letting that class wrap a None (which would make calling it a no-op) would > allow us to get rid of all those `if callback is not None:` in the optimizer > loops. > Another interesting addition for such an OptimizeResult would be to make the > typical stopping conditions (gradient norm, relative function change...) > available. > This would be especially useful if we allowed the callback to terminate the > optimization early, e.g. by returning False instead of None. > > While I think all of this would be a step in the right direction, I wonder > if cramming more functionality into the callback is the way to go. After a > few months of using optimize A LOT at work, I am pretty much convinced that > the architecture of the library is,, let's call it suboptimal... I haven't > fully fleshed it out, but I think it would be much better if, instead of > black box functions that run through to convergence, with only the callback > function to shed light on what may be going on, we exposed some form of > Optimizer object, that would know how to perform a single optimization step. > There should still be a form of automatically running these to convergence, > but it would allow advanced users to do things that now are impossible, like > e.g. running two different algorithms on the same problem with the exact > same termination conditions. > > Jaime > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From antonior92 at gmail.com Thu Feb 8 12:22:02 2018 From: antonior92 at gmail.com (Antonio Ribeiro) Date: Thu, 8 Feb 2018 15:22:02 -0200 Subject: [SciPy-Dev] Proposal - optimize callback given a state keyword In-Reply-To: References: Message-ID: <226DE38A-B6F7-49BB-8B61-B2A04388DA4D@gmail.com> Hi All, I have a few comments regarding the newcallback: 1. I have started a PR changing this: https://github.com/scipy/scipy/pull/7425 . By what I remember you are helping with it as well Andrew. I never finished because I gave priority to other projects, but I may go back to work on it after finishing PR 8328. 2. By what I remember the methods that could easily benefit from the modification are: Powell, Nelder-Mead, CG, BFGS, Newton-CG, trust-ncg, trust-exact, dogleg. 3. I think we should allow the termination of the optimization solver by returning `True` (or False) in the callback function. 4. For the solver me and Nikolay are working right now (https://github.com/scipy/scipy/pull/8328) this option is already implemented. Please take a look at the new `minimize` documentation after the modifications we have introduced: https://5466-1460385-gh.circle-artifacts.com/0/home/ubuntu/scipy/doc/build/html-scipyorg/generated/scipy.optimize.minimize.html#scipy.optimize.minimize Best, Ant?nio > On Feb 8, 2018, at 15:00, scipy-dev-request at python.org wrote: > > Send SciPy-Dev mailing list submissions to > scipy-dev at python.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.python.org/mailman/listinfo/scipy-dev > or, via email, send a message with subject or body 'help' to > scipy-dev-request at python.org > > You can reach the person managing the list at > scipy-dev-owner at python.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SciPy-Dev digest..." > > > Today's Topics: > > 1. Proposal - optimize callback given a state keyword (Andrew Nelson) > 2. Re: Proposal - optimize callback given a state keyword > (Jaime Fern?ndez del R?o) > 3. Re: Proposal - optimize callback given a state keyword > (Joshua Wilson) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 8 Feb 2018 13:06:19 +1100 > From: Andrew Nelson > To: scipy-dev > Subject: [SciPy-Dev] Proposal - optimize callback given a state > keyword > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi all, > I propose that the optimize callbacks be asked to accept a new state > keyword in the future. > The state keyword will be an `OptimizeResult` giving the state of the > optimizer at that point. > i.e. n_iterations, n_fun, (n_jac?), x, fun, etc. > > To aid the transition I propose that the user callbacks are wrapped with > something along the lines of: > > class OptimizerCallback(object): > def __init__(self, callback): > self.callback = callback > argspec = _getargspec(callback) > self.accepts_state = True > if 'state' not in argspec.varkw: > warnings.warn(FutureWarning, "In future versions of scipy the" > " optimizer > callback should accept" > "a state kwd") > self.accepts_state = False > > def __call__(self, x, state): > if self.accepts_state: > self.callback(x, state) > else: > self.callback(x) > > and the optimizers be modified appropriately. > > Thoughts, comments? > > > > _____________________________________ > Dr. Andrew Nelson > > > _____________________________________ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Thu, 08 Feb 2018 12:37:35 +0000 > From: Jaime Fern?ndez del R?o > To: SciPy Developers List > Subject: Re: [SciPy-Dev] Proposal - optimize callback given a state > keyword > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > On Thu, Feb 8, 2018 at 3:06 AM Andrew Nelson wrote: >> >> Hi all, >> I propose that the optimize callbacks be asked to accept a new state > keyword in the future. >> The state keyword will be an `OptimizeResult` giving the state of the > optimizer at that point. >> i.e. n_iterations, n_fun, (n_jac?), x, fun, etc. >> >> To aid the transition I propose that the user callbacks are wrapped with > something along the lines of: >> >> class OptimizerCallback(object): >> def __init__(self, callback): >> self.callback = callback >> argspec = _getargspec(callback) >> self.accepts_state = True >> if 'state' not in argspec.varkw: >> warnings.warn(FutureWarning, "In future versions of scipy the" >> " optimizer > callback should accept" >> "a state > kwd") >> self.accepts_state = False >> >> def __call__(self, x, state): >> if self.accepts_state: >> self.callback(x, state) >> else: >> self.callback(x) >> >> and the optimizers be modified appropriately. >> >> Thoughts, comments? > > If we do implement callback on steroids, I'd also suggest: > > - Letting that class wrap a None (which would make calling it a no-op) > would allow us to get rid of all those `if callback is not None:` in the > optimizer loops. > - Another interesting addition for such an OptimizeResult would be to > make the typical stopping conditions (gradient norm, relative function > change...) available. > - This would be especially useful if we allowed the callback to > terminate the optimization early, e.g. by returning False instead of None. > > While I think all of this would be a step in the right direction, I wonder > if cramming more functionality into the callback is the way to go. After a > few months of using optimize A LOT at work, I am pretty much convinced that > the architecture of the library is,, let's call it suboptimal... I haven't > fully fleshed it out, but I think it would be much better if, instead of > black box functions that run through to convergence, with only the callback > function to shed light on what may be going on, we exposed some form of > Optimizer object, that would know how to perform a single optimization > step. There should still be a form of automatically running these to > convergence, but it would allow advanced users to do things that now are > impossible, like e.g. running two different algorithms on the same problem > with the exact same termination conditions. > > Jaime > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 3 > Date: Thu, 8 Feb 2018 08:12:44 -0600 > From: Joshua Wilson > To: SciPy Developers List > Subject: Re: [SciPy-Dev] Proposal - optimize callback given a state > keyword > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > >> we exposed some form of Optimizer object, that would know how to perform a single optimization step > > I think that's a wonderful idea, and one that has a lot of historical > precedent since it's generally how Fortran optimizers worked because > there were no function pointers. (Which conveniently means a lot of > things in SciPy work that way under-the-hood already.) > > Just a random comment from the peanut gallery, > Josh > > On Thu, Feb 8, 2018 at 6:37 AM, Jaime Fern?ndez del R?o > wrote: >> On Thu, Feb 8, 2018 at 3:06 AM Andrew Nelson wrote: >>> >>> Hi all, >>> I propose that the optimize callbacks be asked to accept a new state >>> keyword in the future. >>> The state keyword will be an `OptimizeResult` giving the state of the >>> optimizer at that point. >>> i.e. n_iterations, n_fun, (n_jac?), x, fun, etc. >>> >>> To aid the transition I propose that the user callbacks are wrapped with >>> something along the lines of: >>> >>> class OptimizerCallback(object): >>> def __init__(self, callback): >>> self.callback = callback >>> argspec = _getargspec(callback) >>> self.accepts_state = True >>> if 'state' not in argspec.varkw: >>> warnings.warn(FutureWarning, "In future versions of scipy the" >>> " optimizer >>> callback should accept" >>> "a state >>> kwd") >>> self.accepts_state = False >>> >>> def __call__(self, x, state): >>> if self.accepts_state: >>> self.callback(x, state) >>> else: >>> self.callback(x) >>> >>> and the optimizers be modified appropriately. >>> >>> Thoughts, comments? >> >> If we do implement callback on steroids, I'd also suggest: >> >> Letting that class wrap a None (which would make calling it a no-op) would >> allow us to get rid of all those `if callback is not None:` in the optimizer >> loops. >> Another interesting addition for such an OptimizeResult would be to make the >> typical stopping conditions (gradient norm, relative function change...) >> available. >> This would be especially useful if we allowed the callback to terminate the >> optimization early, e.g. by returning False instead of None. >> >> While I think all of this would be a step in the right direction, I wonder >> if cramming more functionality into the callback is the way to go. After a >> few months of using optimize A LOT at work, I am pretty much convinced that >> the architecture of the library is,, let's call it suboptimal... I haven't >> fully fleshed it out, but I think it would be much better if, instead of >> black box functions that run through to convergence, with only the callback >> function to shed light on what may be going on, we exposed some form of >> Optimizer object, that would know how to perform a single optimization step. >> There should still be a form of automatically running these to convergence, >> but it would allow advanced users to do things that now are impossible, like >> e.g. running two different algorithms on the same problem with the exact >> same termination conditions. >> >> Jaime >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > > ------------------------------ > > End of SciPy-Dev Digest, Vol 172, Issue 7 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From newville at cars.uchicago.edu Thu Feb 8 12:41:35 2018 From: newville at cars.uchicago.edu (Matt Newville) Date: Thu, 8 Feb 2018 11:41:35 -0600 Subject: [SciPy-Dev] SciPy-Dev Digest, Vol 172, Issue 7 In-Reply-To: References: Message-ID: Hi Andrew, All, Apologies for replying to the digest.... On Thu, Feb 8, 2018 at 11:00 AM, wrote: > > > Message: 1 > Date: Thu, 8 Feb 2018 13:06:19 +1100 > From: Andrew Nelson > To: scipy-dev > Subject: [SciPy-Dev] Proposal - optimize callback given a state > keyword > Message-ID: > com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > I propose that the optimize callbacks be asked to accept a new state > keyword in the future. > The state keyword will be an `OptimizeResult` giving the state of the > optimizer at that point. > i.e. n_iterations, n_fun, (n_jac?), x, fun, etc. > Are you sure you want an OptimizeResult? Maybe it would be sufficient and clearer to have the callback given "the current iteration number" (a somewhat fuzzy concept, but useful nonetheless) and "the current set of values for the variables", and maybe "the current value of the residual"? Is there more that is actually reliable while the fit is proceeding and that a callback could use? How would you expect a callback function to use the current value of Jacobian, for example? --Matt Newville -------------- next part -------------- An HTML attachment was scrubbed... URL: From xoviat at gmail.com Thu Feb 8 17:45:38 2018 From: xoviat at gmail.com (xoviat) Date: Thu, 8 Feb 2018 16:45:38 -0600 Subject: [SciPy-Dev] CoC incidents Message-ID: <5a7cd312.0aa6ca0a.4f991.2fe4@mx.google.com> The purpose of this email is to give an email address such that I can respond to any Code of Conduct incidents that may arise. I am open to discuss this in public, but will be more than happy to discuss issues in private if asked. -------------- next part -------------- An HTML attachment was scrubbed... URL: From njs at pobox.com Thu Feb 8 18:03:19 2018 From: njs at pobox.com (Nathaniel Smith) Date: Thu, 8 Feb 2018 15:03:19 -0800 Subject: [SciPy-Dev] CoC incidents In-Reply-To: References: <5a7cd312.0aa6ca0a.4f991.2fe4@mx.google.com> Message-ID: Please send messages like this to the CoC committee address at scipy-conduct at googlegroups.com, not scipy-dev. On Feb 8, 2018 14:48, "xoviat" wrote: The purpose of this email is to give an email address such that I can respond to any Code of Conduct incidents that may arise. I am open to discuss this in public, but will be more than happy to discuss issues in private if asked. _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Thu Feb 8 20:35:11 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Fri, 9 Feb 2018 12:35:11 +1100 Subject: [SciPy-Dev] Proposal - optimize callback given a state keyword In-Reply-To: <226DE38A-B6F7-49BB-8B61-B2A04388DA4D@gmail.com> References: <226DE38A-B6F7-49BB-8B61-B2A04388DA4D@gmail.com> Message-ID: The `differential_evolution` function is backed by the (as yet) **non public** DifferentialEvolution solver object. This has different modes of operation (by virtue of implementing __next__ and __iter__): ``` def ackley(x): arg1 = -0.2 * np.sqrt(0.5 * (x[0] ** 2 + x[1] ** 2)) arg2 = 0.5 * (np.cos(2. * np.pi * x[0]) + np.cos(2. * np.pi * x[1])) return -20. * np.exp(arg1) - np.exp(arg2) + 20. + np.e bounds = [(-5, 5), (-5, 5)] solver = DifferentialEvolutionSolver(ackley, bounds) # run's through to completion res = solver.solve() # control how many iterations you want for idx in range(10): x, fun = next(solver) # amend internal state of solver if you know what you're doing # keep on going until you decide to stop for x, fun in solver: print(x, fun) intol = (np.std(solver.population_energies) <= solver.atol + solver.tol * np.abs(np.mean(solver.population_energies))) if intol: break ``` It seems like this could be a useful design pattern going forwards, as I think it meets Jaime's points. However, this is obviously a large package of work. Another possibilitiy is to take the existing code and make them into generators by yielding when the existing callback is used. That way one can step through, but doesn't offer the possibility of modifying internals. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.frio at gmail.com Fri Feb 9 03:48:42 2018 From: jaime.frio at gmail.com (=?UTF-8?Q?Jaime_Fern=C3=A1ndez_del_R=C3=ADo?=) Date: Fri, 09 Feb 2018 08:48:42 +0000 Subject: [SciPy-Dev] Proposal - optimize callback given a state keyword In-Reply-To: References: <226DE38A-B6F7-49BB-8B61-B2A04388DA4D@gmail.com> Message-ID: On Fri, Feb 9, 2018 at 2:35 AM Andrew Nelson wrote: > The `differential_evolution` function is backed by the (as yet) **non > public** DifferentialEvolution solver object. > > This has different modes of operation (by virtue of implementing __next__ > and __iter__): > > ``` > def ackley(x): > arg1 = -0.2 * np.sqrt(0.5 * (x[0] ** 2 + x[1] ** 2)) > arg2 = 0.5 * (np.cos(2. * np.pi * x[0]) + np.cos(2. * np.pi * x[1])) > return -20. * np.exp(arg1) - np.exp(arg2) + 20. + np.e > > bounds = [(-5, 5), (-5, 5)] > > solver = DifferentialEvolutionSolver(ackley, bounds) > > # run's through to completion > res = solver.solve() > > # control how many iterations you want > for idx in range(10): > x, fun = next(solver) > # amend internal state of solver if you know what you're doing > > # keep on going until you decide to stop > for x, fun in solver: > print(x, fun) > intol = (np.std(solver.population_energies) <= > solver.atol + > solver.tol * np.abs(np.mean(solver.population_energies))) > if intol: > break > ``` > > It seems like this could be a useful design pattern going forwards, as I > think it meets Jaime's points. However, this is obviously a large package > of work. > It looks very nice indeed. I will try to find some time to look into the approach in differential evolution and see if I can find inspiration there to turn my thoughts into a more articulate proposal. It certainly looks like it would be a lot of work, but I think there is a chance I could convince my manager to work on some of this on his dime. Jaime -- (\__/) ( O.o) ( > <) Este es Conejo. Copia a Conejo en tu firma y ay?dale en sus planes de dominaci?n mundial. -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Fri Feb 9 03:53:11 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Fri, 9 Feb 2018 19:53:11 +1100 Subject: [SciPy-Dev] Proposal - optimize callback given a state keyword In-Reply-To: References: <226DE38A-B6F7-49BB-8B61-B2A04388DA4D@gmail.com> Message-ID: Jaime, I'm just messing around at the moment, https://github.com/andyfaff/scipy/tree/OPTIMIZE. It won't work, but you'll get another outline idea of what I'm thinking about. On 9 February 2018 at 19:48, Jaime Fern?ndez del R?o wrote: > On Fri, Feb 9, 2018 at 2:35 AM Andrew Nelson wrote: > >> The `differential_evolution` function is backed by the (as yet) **non >> public** DifferentialEvolution solver object. >> >> This has different modes of operation (by virtue of implementing __next__ >> and __iter__): >> >> ``` >> def ackley(x): >> arg1 = -0.2 * np.sqrt(0.5 * (x[0] ** 2 + x[1] ** 2)) >> arg2 = 0.5 * (np.cos(2. * np.pi * x[0]) + np.cos(2. * np.pi * x[1])) >> return -20. * np.exp(arg1) - np.exp(arg2) + 20. + np.e >> >> bounds = [(-5, 5), (-5, 5)] >> >> solver = DifferentialEvolutionSolver(ackley, bounds) >> >> # run's through to completion >> res = solver.solve() >> >> # control how many iterations you want >> for idx in range(10): >> x, fun = next(solver) >> # amend internal state of solver if you know what you're doing >> >> # keep on going until you decide to stop >> for x, fun in solver: >> print(x, fun) >> intol = (np.std(solver.population_energies) <= >> solver.atol + >> solver.tol * np.abs(np.mean(solver.population_energies))) >> if intol: >> break >> ``` >> >> It seems like this could be a useful design pattern going forwards, as I >> think it meets Jaime's points. However, this is obviously a large package >> of work. >> > > It looks very nice indeed. I will try to find some time to look into the > approach in differential evolution and see if I can find inspiration there > to turn my thoughts into a more articulate proposal. It certainly looks > like it would be a lot of work, but I think there is a chance I could > convince my manager to work on some of this on his dime. > > Jaime > > -- > (\__/) > ( O.o) > ( > <) Este es Conejo. Copia a Conejo en tu firma y ay?dale en sus planes > de dominaci?n mundial. > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -- _____________________________________ Dr. Andrew Nelson _____________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.frio at gmail.com Fri Feb 9 03:56:27 2018 From: jaime.frio at gmail.com (=?UTF-8?Q?Jaime_Fern=C3=A1ndez_del_R=C3=ADo?=) Date: Fri, 09 Feb 2018 08:56:27 +0000 Subject: [SciPy-Dev] Proposal - optimize callback given a state keyword In-Reply-To: References: <226DE38A-B6F7-49BB-8B61-B2A04388DA4D@gmail.com> Message-ID: Thanks, will certainly take a look! On Fri, Feb 9, 2018 at 9:53 AM Andrew Nelson wrote: > Jaime, > I'm just messing around at the moment, > https://github.com/andyfaff/scipy/tree/OPTIMIZE. It won't work, but > you'll get another outline idea of what I'm thinking about. > > On 9 February 2018 at 19:48, Jaime Fern?ndez del R?o > wrote: > >> On Fri, Feb 9, 2018 at 2:35 AM Andrew Nelson wrote: >> >>> The `differential_evolution` function is backed by the (as yet) **non >>> public** DifferentialEvolution solver object. >>> >>> This has different modes of operation (by virtue of implementing >>> __next__ and __iter__): >>> >>> ``` >>> def ackley(x): >>> arg1 = -0.2 * np.sqrt(0.5 * (x[0] ** 2 + x[1] ** 2)) >>> arg2 = 0.5 * (np.cos(2. * np.pi * x[0]) + np.cos(2. * np.pi * x[1])) >>> return -20. * np.exp(arg1) - np.exp(arg2) + 20. + np.e >>> >>> bounds = [(-5, 5), (-5, 5)] >>> >>> solver = DifferentialEvolutionSolver(ackley, bounds) >>> >>> # run's through to completion >>> res = solver.solve() >>> >>> # control how many iterations you want >>> for idx in range(10): >>> x, fun = next(solver) >>> # amend internal state of solver if you know what you're doing >>> >>> # keep on going until you decide to stop >>> for x, fun in solver: >>> print(x, fun) >>> intol = (np.std(solver.population_energies) <= >>> solver.atol + >>> solver.tol * np.abs(np.mean(solver.population_energies))) >>> if intol: >>> break >>> ``` >>> >>> It seems like this could be a useful design pattern going forwards, as I >>> think it meets Jaime's points. However, this is obviously a large package >>> of work. >>> >> >> It looks very nice indeed. I will try to find some time to look into the >> approach in differential evolution and see if I can find inspiration there >> to turn my thoughts into a more articulate proposal. It certainly looks >> like it would be a lot of work, but I think there is a chance I could >> convince my manager to work on some of this on his dime. >> >> Jaime >> >> -- >> (\__/) >> ( O.o) >> ( > <) Este es Conejo. Copia a Conejo en tu firma y ay?dale en sus planes >> de dominaci?n mundial. >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> >> > > > -- > _____________________________________ > Dr. Andrew Nelson > > > _____________________________________ > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > -- (\__/) ( O.o) ( > <) Este es Conejo. Copia a Conejo en tu firma y ay?dale en sus planes de dominaci?n mundial. -------------- next part -------------- An HTML attachment was scrubbed... URL: From marc.barbry at mailoo.org Fri Feb 9 04:57:08 2018 From: marc.barbry at mailoo.org (marc) Date: Fri, 9 Feb 2018 10:57:08 +0100 Subject: [SciPy-Dev] lgmres tolerance Message-ID: <9cedbb40-d19d-34b1-7b7d-1d3c6be9e647@mailoo.org> Dear Scipy developers, I have a question regarding the tolerance of the lgmres function. From the documentation, it is written, *tol* : float, optional Tolerance to achieve. The algorithm terminates when either the relative or the absolute residual is below /tol/. For technical issues, I would like the algorithm to ignore the relative residual and to terminates only when the absolute residual is below tol. Do there is a way to do this? Best regards, Marc Barbry -------------- next part -------------- An HTML attachment was scrubbed... URL: From pav at iki.fi Fri Feb 9 08:31:56 2018 From: pav at iki.fi (Pauli Virtanen) Date: Fri, 9 Feb 2018 14:31:56 +0100 Subject: [SciPy-Dev] lgmres tolerance In-Reply-To: <9cedbb40-d19d-34b1-7b7d-1d3c6be9e647@mailoo.org> References: <9cedbb40-d19d-34b1-7b7d-1d3c6be9e647@mailoo.org> Message-ID: <1f94e45b-a2dc-0d8f-407c-18aec2034b3a@iki.fi> marc kirjoitti 09.02.2018 klo 10:57: [clip]> For technical issues, I would like the algorithm to ignore the relative > residual and to terminates only when the absolute residual is below tol. > Do there is a way to do this? Normalizing the right-hand size vector to length 1 should do it: b_scale = np.linalg.norm(b) x = lgmres(A, b/b_scale, ...) x *= b_scale -- Pauli Virtanen From bwana.marko at yahoo.com Sat Feb 10 14:07:38 2018 From: bwana.marko at yahoo.com (Mark Mikofski) Date: Sat, 10 Feb 2018 19:07:38 +0000 (UTC) Subject: [SciPy-Dev] Help for scalar univariate zeros functions References: <412042109.2415645.1518289658984.ref@mail.yahoo.com> Message-ID: <412042109.2415645.1518289658984@mail.yahoo.com> Hi, I model?photovoltaics (PV) for solar?energy rooftop and utility systems, and I also contribute to a Sandia National Labs sponsored, open-source PV modeling Python package called pvlib. I need help with the scalar, univariate zeros functions in scipy.optimize.? 1st a little background: The main governing equation in PV is Shockley's diode equation, which is implicit for either current or voltage. For a one diode model of a solar cell, we can use scipy.special.lambertw, but for a two diode model, we need a scalar, univariate root finding method like scipy.optimize.newton or scipy.optimize.brentq. In fact we can also use these methods for the one diode model in lieu of Lambert-W transform, and it is very fast for a single calculation. However, I often have to calculate thousands if not millions of these solar cell models, and looping over either Newton or brentq is slow. I tried using multi-processing and a multivariate root method like hybrj, hybrd, and Nelder-Mead, but they are just as slow. I've also tried cythonizing the Newton method, and it does run faster. But the LambertW function in scipy.special can take numpy arrays as arguments, and since scipy.optimize.newton is pure Python it is easy to edit it to also take numpy arrays, which runs faster than any other option by 10x. I think this is because doing each operation in the objective function on the entire array optimizes the use of cpu cache and simd registers, maybe? The pvlib maintainers and I agree, we would rather use a scipy method than a custom one so we are hoping that someone will take an interest in PR #8357. I'm also working on a cython optimize branch but I haven't had a chance to submit another PR yet. If you are interested in either of there's branches, I urge you to respond with your comments on the mailing list, on the PR, or issue #8354. Thanks! Best regards, Mark Mikofski, principal Engineer, DNV-GL, solar services -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Tue Feb 13 22:21:00 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Wed, 14 Feb 2018 14:21:00 +1100 Subject: [SciPy-Dev] WIP: Class based Optimizers Message-ID: The #8414 PR on github (https://github.com/scipy/scipy/pull/8414) introduces an `Optimize` class for `scipy.optimize`. The `Optimize` class can be advanced like an iterator, or be advanced to convergence with the `solve` method. The PR is intended to provide a cleaner interface to the minimisation process, with the user being able to interact with the solver during iteration. This allows the variation of solver hyper-parameters, or other user definable interactions. As such `callback`s become redundant, as you can access all the optimizer information required. Other historical parameters may become redundant in these objects, such as `disp`. This is also a chance for a ground-zero approach to how people interact with optimizers. The PR is intended as a Request For Comment to gain feedback on architecture of the solvers. Given that it's a key part of infrastructure this may create a large amount of feedback, if I don't reply to it all bear in mind that I don't have unlimited time resource. In it's current state I've implemented `Optimizer`, `Function`, `LBFGS` and `NelderMead` classes. `LBFGS` and `NelderMead` are being called by the corresponding functions already in existence. The current test suite passes, but no unit tests have been written for the functionality. I'd prefer to add such a specific test suite once the overall architecture is settled. These optimisers were straightforward to translate. However, I don't know how this approach would translate to other minimisers, or things like `least_squares`. If a design could be agreed, then perhaps the best approach would be to tackle the remaining optimizers on a case by case basis once this PR is merged. -------------- next part -------------- An HTML attachment was scrubbed... URL: From xoviat at gmail.com Tue Feb 13 22:52:01 2018 From: xoviat at gmail.com (xoviat) Date: Tue, 13 Feb 2018 21:52:01 -0600 Subject: [SciPy-Dev] WIP: Class based Optimizers In-Reply-To: References: Message-ID: <5a83b261.07e2ca0a.ea29f.922d@mx.google.com> I can use the MATLAB optimizers and solve_ivp as points of reference. When compared to MATLAB, the current interface stacks up pretty well. However, both MATLAB and `scipy.optimize` have a less-than-ideal interface for gathering optimization history. Perhaps it would be more useful to align `scipy.optimize` with `solve_ivp`. In both cases you?re calculating a new point using the history of the previous points (though of course the goal?and the formulas?are different). The difference in user interface means that `scipy.optimize` only returns the last point, whereas `solve_ivp` returns the entire solution history. It?s obvious why: a solution to a set of differential equations mathematically must span the domain of interest whereas an optimization result mathematically only consists of a single point. But there no reason, at least that I can tell, not to return all the points that we tried while running the optimizer. It would at least provide a much simpler way to understand what the optimizer is doing. From: Andrew Nelson Sent: Tuesday, February 13, 2018 9:21 PM To: scipy-dev Subject: [SciPy-Dev] WIP: Class based Optimizers The #8414 PR on github (https://github.com/scipy/scipy/pull/8414) introduces an `Optimize` class for `scipy.optimize`. The `Optimize` class can be advanced like an iterator, or be advanced to convergence with the `solve` method. The PR is intended to provide a cleaner interface to the minimisation process, with the user being able to interact with the solver during iteration. This allows the variation of solver hyper-parameters, or other user definable interactions. As such `callback`s become redundant, as you can access all the optimizer information required.? Other historical parameters may become redundant in these objects, such as `disp`. This is also a chance for a ground-zero approach to how people interact with optimizers. The PR is intended as a Request For Comment to gain feedback on architecture of the solvers. Given that it's a key part of infrastructure this may create a large amount of feedback, if I don't reply to it all bear in mind that I don't have unlimited time resource. In it's current state I've implemented `Optimizer`, `Function`, `LBFGS` and `NelderMead` classes. `LBFGS` and `NelderMead` are being called by the corresponding functions already in existence. The current test suite passes, but no unit tests have been written for the functionality. I'd prefer to add such a specific test suite once the overall architecture is settled. These optimisers were straightforward to translate. However, I don't know how this approach would translate to other minimisers, or things like `least_squares`. If a design could be agreed, then perhaps the best approach would be to tackle the remaining optimizers on a case by case basis once this PR is merged. -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Tue Feb 13 23:25:01 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Wed, 14 Feb 2018 15:25:01 +1100 Subject: [SciPy-Dev] WIP: Class based Optimizers In-Reply-To: <5a83b261.07e2ca0a.ea29f.922d@mx.google.com> References: <5a83b261.07e2ca0a.ea29f.922d@mx.google.com> Message-ID: The iteration based nature will allow the interested user to keep all history. But atm they'll have to do it themselves. One suggestion was to create an optimisation runner to control how the iteration runs through. This is also a golden opportunity to change things on how we specify bounds, etc. On 14 Feb. 2018 15:01, "xoviat" wrote: > I can use the MATLAB optimizers and solve_ivp as points of reference. When > compared to MATLAB, the current interface stacks up pretty well. However, > both MATLAB and `scipy.optimize` have a less-than-ideal interface for > gathering optimization history. > > > > Perhaps it would be more useful to align `scipy.optimize` with > `solve_ivp`. In both cases you?re calculating a new point using the history > of the previous points (though of course the goal?and the formulas?are > different). The difference in user interface means that `scipy.optimize` > only returns the last point, whereas `solve_ivp` returns the entire > solution history. It?s obvious why: a solution to a set of differential > equations mathematically must span the domain of interest whereas an > optimization result mathematically only consists of a single point. But > there no reason, at least that I can tell, not to return all the points > that we tried while running the optimizer. It would at least provide a much > simpler way to understand what the optimizer is doing. > > > > *From: *Andrew Nelson > *Sent: *Tuesday, February 13, 2018 9:21 PM > *To: *scipy-dev > *Subject: *[SciPy-Dev] WIP: Class based Optimizers > > > > The #8414 PR on github (https://github.com/scipy/scipy/pull/8414) > introduces an `Optimize` class for `scipy.optimize`. The `Optimize` class > can be advanced like an iterator, or be advanced to convergence with the > `solve` method. > > The PR is intended to provide a cleaner interface to the minimisation > process, with the user being able to interact with the solver during > iteration. This allows the variation of solver hyper-parameters, or other > user definable interactions. As such `callback`s become redundant, as you > can access all the optimizer information required. > > Other historical parameters may become redundant in these objects, such as > `disp`. This is also a chance for a ground-zero approach to how people > interact with optimizers. > > > > The PR is intended as a Request For Comment to gain feedback on > architecture of the solvers. Given that it's a key part of infrastructure > this may create a large amount of feedback, if I don't reply to it all bear > in mind that I don't have unlimited time resource. > > In it's current state I've implemented `Optimizer`, `Function`, `LBFGS` > and `NelderMead` classes. `LBFGS` and `NelderMead` are being called by the > corresponding functions already in existence. The current test suite > passes, but no unit tests have been written for the functionality. I'd > prefer to add such a specific test suite once the overall architecture is > settled. > > > > These optimisers were straightforward to translate. However, I don't know > how this approach would translate to other minimisers, or things like > `least_squares`. If a design could be agreed, then perhaps the best > approach would be to tackle the remaining optimizers on a case by case > basis once this PR is merged. > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lagru at mailbox.org Wed Feb 14 07:04:04 2018 From: lagru at mailbox.org (Lars G.) Date: Wed, 14 Feb 2018 13:04:04 +0100 Subject: [SciPy-Dev] ENH: Extend peak finding capabilities in scipy.signal (#8264) In-Reply-To: References: Message-ID: On 26.01.2018 20:49, Lars G. wrote: > Dear SciPy devs, > > I'd like to highlight my current pull request which extends SciPy's peak > finding capabilities in the signal module. > https://github.com/scipy/scipy/pull/8264 > I've tried to address all feedback that was given (until now) in said > PR. > [...] I am quite confident with the current state and would encourage a last review. So feel free to chime in if you have some tweaks or refactoring to suggest. The only outstanding question is about the name of `find_peaks`. As the discussion on this hasn't really yielded an agreed upon solution I'm going to leave the name as it is for the time being. Going forward I'd like to build on this with new PRs: - Some parts (especially inside the big loops in `peak_prominences` and `peak_widths`) would profit from one or two private functions written in Cython. I get noticeable speed ups if I just replace a few steps of the algorithms with Cython. `find_peaks` would profit from this as well. I think this is worthwhile because prominence is a very useful parameter and it shouldn't be to much work (unit tests and PYX file already exist). - A tutorial that shows some more complicated use cases for the new functions and peak finding in general. If I feel confident, I may even give some examples and guidelines for `find_peaks_cwt` whose documentation was described as confusing in the past. Best regards, Lars From larson.eric.d at gmail.com Wed Feb 14 07:25:26 2018 From: larson.eric.d at gmail.com (Eric Larson) Date: Wed, 14 Feb 2018 07:25:26 -0500 Subject: [SciPy-Dev] ENH: Extend peak finding capabilities in scipy.signal (#8264) In-Reply-To: References: Message-ID: Thanks for working on this. That sounds like a good plan to me. I should be able to review this week. Eric On Feb 14, 2018 7:11 AM, "Lars G." wrote: > On 26.01.2018 20:49, Lars G. wrote: > > Dear SciPy devs, > > > > I'd like to highlight my current pull request which extends SciPy's peak > > finding capabilities in the signal module. > > https://github.com/scipy/scipy/pull/8264 > > I've tried to address all feedback that was given (until now) in said > > PR. > > [...] > > I am quite confident with the current state and would encourage a last > review. So feel free to chime in if you have some tweaks or refactoring > to suggest. > > The only outstanding question is about the name of `find_peaks`. As the > discussion on this hasn't really yielded an agreed upon solution I'm > going to leave the name as it is for the time being. > > Going forward I'd like to build on this with new PRs: > > - Some parts (especially inside the big loops in `peak_prominences` and > `peak_widths`) would profit from one or two private functions written in > Cython. I get noticeable speed ups if I just replace a few steps of the > algorithms with Cython. `find_peaks` would profit from this as well. I > think this is worthwhile because prominence is a very useful parameter > and it shouldn't be to much work (unit tests and PYX file already exist). > > - A tutorial that shows some more complicated use cases for the new > functions and peak finding in general. If I feel confident, I may even > give some examples and guidelines for `find_peaks_cwt` whose > documentation was described as confusing in the past. > > Best regards, > Lars > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bwana.marko at yahoo.com Wed Feb 14 11:17:06 2018 From: bwana.marko at yahoo.com (Mark Mikofski) Date: Wed, 14 Feb 2018 16:17:06 +0000 (UTC) Subject: [SciPy-Dev] Hello and thank you! References: <1028660122.897944.1518625026063.ref@mail.yahoo.com> Message-ID: <1028660122.897944.1518625026063@mail.yahoo.com> Hi everyone, my name is Mark Mikofski. I am a mechanical engineer, and have been modeling energy transfer for over 15 years. You can learn more about me at https://mikofski.github.io . I wanted to thank you all very much for your contributions to SciPy, and for allowing me to join this mailing list. From reading the posts I can tell this is a vibrant group of creative individuals who share a positive and respectful curiosity for science, math, and numerical computation. I will try to make equally positive and respectful contributions as well. Best regards! Sent from Yahoo Mail on Android -------------- next part -------------- An HTML attachment was scrubbed... URL: From pav at iki.fi Wed Feb 14 16:11:22 2018 From: pav at iki.fi (Pauli Virtanen) Date: Wed, 14 Feb 2018 22:11:22 +0100 Subject: [SciPy-Dev] WIP: Class based Optimizers In-Reply-To: References: Message-ID: <1518642682.8666.18.camel@iki.fi> Hi, ke, 2018-02-14 kello 14:21 +1100, Andrew Nelson kirjoitti: > The #8414 PR on github (https://github.com/scipy/scipy/pull/8414) > introduces an `Optimize` class for `scipy.optimize`. The `Optimize` > class > can be advanced like an iterator, or be advanced to convergence with > the > `solve` method. I think it would be necessary to make clearly a case what is actually gained with such reorganization. This would be the third optimizer API to the same solvers, and at first sight it's not clear to me if there is a strong need for it. One point that one can argue is that solver = ... for foo in solver: some_code is identical with regard to functionality to def callback(.., solver_info): some_code solver(..., callback=callback) with the difference that the latter does not leak unnecessary private implementation details to the user code, requires only small API changes, and won't require extensive code reorganization. The use cases where one needs to continuously monitor convergence in minimization are also somewhat expert-oriented, and for most users I expect such API will not be as useful. (The situation with ODE solvers is I think somewhat different, as with them one e.g. often does not even know the time up to which to integrate a priori.) Writing class-based solvers requires rewriting code in a reverse- communication style, which inverts the structure of control flow. This can result to code that is more complex, and more difficult to maintain. There are some tricks one can do to retain more natural structure such as using generators/coroutines, but these are not always so nice to use in practice in Python in my experience, and also bring more complexity. The existing solvers in Scipy apart from L-BFGS-B are IIRC not written in a reverse-communication style, and converting them would be significant rewrite, particularly so for the solvers written in C/Fortran. The same applies also for tuning solver parameters during the iteration. The solvers AFAIK have not been designed with parameters that can be adjusted during run, and one would probably have to think carefully about each one (instead of e.g. exposing them as class attributes). So, I think there are several questions that one should consider here. Pauli From xoviat at gmail.com Wed Feb 14 16:16:01 2018 From: xoviat at gmail.com (xoviat) Date: Wed, 14 Feb 2018 15:16:01 -0600 Subject: [SciPy-Dev] WIP: Class based Optimizers In-Reply-To: <1518642682.8666.18.camel@iki.fi> References: <1518642682.8666.18.camel@iki.fi> Message-ID: <5a84a711.05cfca0a.4a242.4608@mx.google.com> Pauli, What do you think about returning the entire optimization history, similar to what is done with the ODE solvers, as I suggested? I think it would be necessary to make clearly a case what is actually gained with such reorganization. This would be the third optimizer API to the same solvers, and at first sight it's not clear to me if there is a strong need for it. I agree. The ODE solvers were previously implemented with the iterative method, which was found to be less-than-ideal. From: Pauli Virtanen Sent: Wednesday, February 14, 2018 3:12 PM To: scipy-dev at python.org Subject: Re: [SciPy-Dev] WIP: Class based Optimizers Hi, ke, 2018-02-14 kello 14:21 +1100, Andrew Nelson kirjoitti: > The #8414 PR on github (https://github.com/scipy/scipy/pull/8414) > introduces an `Optimize` class for `scipy.optimize`. The `Optimize` > class > can be advanced like an iterator, or be advanced to convergence with > the > `solve` method. I think it would be necessary to make clearly a case what is actually gained with such reorganization. This would be the third optimizer API to the same solvers, and at first sight it's not clear to me if there is a strong need for it. One point that one can argue is that solver = ... for foo in solver: some_code is identical with regard to functionality to def callback(.., solver_info): some_code solver(..., callback=callback) with the difference that the latter does not leak unnecessary private implementation details to the user code, requires only small API changes, and won't require extensive code reorganization. The use cases where one needs to continuously monitor convergence in minimization are also somewhat expert-oriented, and for most users I expect such API will not be as useful. (The situation with ODE solvers is I think somewhat different, as with them one e.g. often does not even know the time up to which to integrate a priori.) Writing class-based solvers requires rewriting code in a reverse- communication style, which inverts the structure of control flow. This can result to code that is more complex, and more difficult to maintain. There are some tricks one can do to retain more natural structure such as using generators/coroutines, but these are not always so nice to use in practice in Python in my experience, and also bring more complexity. The existing solvers in Scipy apart from L-BFGS-B are IIRC not written in a reverse-communication style, and converting them would be significant rewrite, particularly so for the solvers written in C/Fortran. The same applies also for tuning solver parameters during the iteration. The solvers AFAIK have not been designed with parameters that can be adjusted during run, and one would probably have to think carefully about each one (instead of e.g. exposing them as class attributes). So, I think there are several questions that one should consider here. Pauli _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Wed Feb 14 16:30:22 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Thu, 15 Feb 2018 08:30:22 +1100 Subject: [SciPy-Dev] WIP: Class based Optimizers In-Reply-To: <5a84a711.05cfca0a.4a242.4608@mx.google.com> References: <1518642682.8666.18.camel@iki.fi> <5a84a711.05cfca0a.4a242.4608@mx.google.com> Message-ID: On 15 February 2018 at 08:16, xoviat wrote: > > > I agree. The ODE solvers were previously implemented with the iterative > method, which was found to be less-than-ideal. > What was the experience on that? How were the ODE solvers advanced? -------------- next part -------------- An HTML attachment was scrubbed... URL: From sievert.scott at gmail.com Wed Feb 14 18:00:49 2018 From: sievert.scott at gmail.com (Scott Sievert) Date: Wed, 14 Feb 2018 15:00:49 -0800 Subject: [SciPy-Dev] WIP: Class based Optimizers In-Reply-To: <5a84a711.05cfca0a.4a242.4608@mx.google.com> References: <1518642682.8666.18.camel@iki.fi> <5a84a711.05cfca0a.4a242.4608@mx.google.com> Message-ID: This would be the third optimizer API to the same solvers I agree. The ODE solvers were previously implemented with the iterative method, which was found to be less-than-ideal. What references are there on these? I?ve found [PR #6326] on the ODE solvers. What else is out there? Scott [PR #6326]: https://github.com/scipy/scipy/pull/6326 On February 14, 2018 at 3:16:53 PM, xoviat (xoviat at gmail.com) wrote: Pauli, What do you think about returning the entire optimization history, similar to what is done with the ODE solvers, as I suggested? I think it would be necessary to make clearly a case what is actually gained with such reorganization. This would be the third optimizer API to the same solvers, and at first sight it's not clear to me if there is a strong need for it. I agree. The ODE solvers were previously implemented with the iterative method, which was found to be less-than-ideal. *From: *Pauli Virtanen *Sent: *Wednesday, February 14, 2018 3:12 PM *To: *scipy-dev at python.org *Subject: *Re: [SciPy-Dev] WIP: Class based Optimizers Hi, ke, 2018-02-14 kello 14:21 +1100, Andrew Nelson kirjoitti: > The #8414 PR on github (https://github.com/scipy/scipy/pull/8414) > introduces an `Optimize` class for `scipy.optimize`. The `Optimize` > class > can be advanced like an iterator, or be advanced to convergence with > the > `solve` method. I think it would be necessary to make clearly a case what is actually gained with such reorganization. This would be the third optimizer API to the same solvers, and at first sight it's not clear to me if there is a strong need for it. One point that one can argue is that solver = ... for foo in solver: some_code is identical with regard to functionality to def callback(.., solver_info): some_code solver(..., callback=callback) with the difference that the latter does not leak unnecessary private implementation details to the user code, requires only small API changes, and won't require extensive code reorganization. The use cases where one needs to continuously monitor convergence in minimization are also somewhat expert-oriented, and for most users I expect such API will not be as useful. (The situation with ODE solvers is I think somewhat different, as with them one e.g. often does not even know the time up to which to integrate a priori.) Writing class-based solvers requires rewriting code in a reverse- communication style, which inverts the structure of control flow. This can result to code that is more complex, and more difficult to maintain. There are some tricks one can do to retain more natural structure such as using generators/coroutines, but these are not always so nice to use in practice in Python in my experience, and also bring more complexity. The existing solvers in Scipy apart from L-BFGS-B are IIRC not written in a reverse-communication style, and converting them would be significant rewrite, particularly so for the solvers written in C/Fortran. The same applies also for tuning solver parameters during the iteration. The solvers AFAIK have not been designed with parameters that can be adjusted during run, and one would probably have to think carefully about each one (instead of e.g. exposing them as class attributes). So, I think there are several questions that one should consider here. Pauli _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From bwana.marko at yahoo.com Thu Feb 15 06:39:36 2018 From: bwana.marko at yahoo.com (Mark Mikofski) Date: Thu, 15 Feb 2018 11:39:36 +0000 (UTC) Subject: [SciPy-Dev] cython_optimize.zeros concept References: <1682843065.1464472.1518694776430.ref@mail.yahoo.com> Message-ID: <1682843065.1464472.1518694776430@mail.yahoo.com> Hi, I need to run a loop around the scipy.optimize.zeros functions like brentq and newton. Looping 100k takes a long time, so I started to try to cythonize some of the zeros functions. I've started with newton and bisect. Newton works, but bisect?gives me "Illegal Instruction 4" on my mac running Python 2.7 and Xcode. If anyone has any feedback that would help a lot.?https://github.com/mikofski/scipy/tree/cython_optimize/scipy/optimize/cython_optimize Thanks! ?As I breath in, I calm my body, as I breath out, I smile? - Thich_Nhat_Hanh -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Thu Feb 15 14:26:42 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Fri, 16 Feb 2018 06:26:42 +1100 Subject: [SciPy-Dev] Use of approx_derivative (rel_step) vs approx_fprime (absolute step) in optimize Message-ID: The default for bfgs, lbfgs, and cg scalar function minimizers in optimize is to use the same absolute step size, `sqrt(numpy.finfo(float).eps)` for all values in `x` when estimating the gradient. One can provide an array of step sizes, but I guess that the large majority of people would just use the default. The absolute step value is used by `approx_fprime` to work out the gradient. In contrast `approx_derivative` in optimize/_numdiff.py uses relative steps for all values in `x`. For values in `x` that could encompass values of different magnitudes, including those down to, or below, the default absolute step size, the latter approach of using relative steps seems more robust. Q1 - I'm wondering why the scalar minimizers don't use relative steps in calculating the gradient? Q2 - Might a better default be to use a relative step, reverting to absolute step if requested? This behaviour may not surprise those familiar with these optimizers operate, but I can guarantee that this behaviour will trip up the unwary (i.e. me) just looking to minimize a function, not knowing that the step could be close to a given value in x, and suffer crazy gradients as a result. -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Fri Feb 16 05:18:14 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Fri, 16 Feb 2018 21:18:14 +1100 Subject: [SciPy-Dev] scipep repo Message-ID: Scott Sievert and I are writing an enhancement proposal, think of it as a scipep, to make an Optimizer class. Is it worth keeping such proposals in it's own repo, e.g. scipy/scipep? I'm not sure I can create that myself. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Fri Feb 16 09:59:27 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Fri, 16 Feb 2018 06:59:27 -0800 Subject: [SciPy-Dev] scipep repo In-Reply-To: References: Message-ID: On Fri, Feb 16, 2018 at 2:18 AM, Andrew Nelson wrote: > Scott Sievert and I are writing an enhancement proposal, think of it as a > scipep, to make an Optimizer class. Is it worth keeping such proposals in > it's own repo, e.g. scipy/scipep? > That seems like a good idea. It follows Python, NumPy, etc. - no need to reinvent this wheel. > I'm not sure I can create that myself. > No, only owners can create new repos. What should it be called? "seps" is a bit ambiguous, maybe just go for a long name "scipy-enhancement-proposals"? Ralf > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sievert.scott at gmail.com Fri Feb 16 12:12:22 2018 From: sievert.scott at gmail.com (Scott Sievert) Date: Fri, 16 Feb 2018 12:12:22 -0500 Subject: [SciPy-Dev] scipep repo In-Reply-To: References: Message-ID: What should it be called? "seps" is a bit ambiguous, maybe just go for a long name "scipy-enhancement-proposals"? I?ve been calling it ?scipeps? for ?Scientific Python Enhancement Proposals? because I think it plays well with the acronym ?SciPy?. But the NumPy and Matplotlib have NEPs and MEPs for {NumPy, Matplotlib} Enhancement Proposals respectively. On GitHub, they?re folders (not repos) of names ?neps?[1] and ?MEP?[2]. Scott [1]: https://github.com/numpy/numpy/tree/master/doc/neps [2]: https://github.com/matplotlib/matplotlib/tree/master/doc/devel/MEP On February 16, 2018 at 9:00:22 AM, Ralf Gommers (ralf.gommers at gmail.com) wrote: On Fri, Feb 16, 2018 at 2:18 AM, Andrew Nelson wrote: > Scott Sievert and I are writing an enhancement proposal, think of it as a > scipep, to make an Optimizer class. Is it worth keeping such proposals in > it's own repo, e.g. scipy/scipep? > That seems like a good idea. It follows Python, NumPy, etc. - no need to reinvent this wheel. > I'm not sure I can create that myself. > No, only owners can create new repos. What should it be called? "seps" is a bit ambiguous, maybe just go for a long name "scipy-enhancement-proposals"? Ralf > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Fri Feb 16 14:56:22 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Sat, 17 Feb 2018 06:56:22 +1100 Subject: [SciPy-Dev] scipep repo In-Reply-To: References: Message-ID: All but one of those suggestions (seps) works for me. On 17 February 2018 at 04:12, Scott Sievert wrote: > What should it be called? "seps" is a bit ambiguous, maybe just go for a > long name "scipy-enhancement-proposals"? > > I?ve been calling it ?scipeps? for ?Scientific Python Enhancement > Proposals? because I think it plays well with the acronym ?SciPy?. But the > NumPy and Matplotlib have NEPs and MEPs for {NumPy, Matplotlib} Enhancement > Proposals respectively. On GitHub, they?re folders (not repos) of names > ?neps?[1] and ?MEP?[2]. > Scott > > [1]: https://github.com/numpy/numpy/tree/master/doc/neps > [2]: https://github.com/matplotlib/matplotlib/tree/master/doc/devel/MEP > > On February 16, 2018 at 9:00:22 AM, Ralf Gommers (ralf.gommers at gmail.com) > wrote: > > > > On Fri, Feb 16, 2018 at 2:18 AM, Andrew Nelson wrote: > >> Scott Sievert and I are writing an enhancement proposal, think of it as a >> scipep, to make an Optimizer class. Is it worth keeping such proposals in >> it's own repo, e.g. scipy/scipep? >> > > That seems like a good idea. It follows Python, NumPy, etc. - no need to > reinvent this wheel. > > >> I'm not sure I can create that myself. >> > > No, only owners can create new repos. What should it be called? "seps" is > a bit ambiguous, maybe just go for a long name > "scipy-enhancement-proposals"? > > Ralf > > >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> >> > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -- _____________________________________ Dr. Andrew Nelson _____________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthieu.brucher at gmail.com Sat Feb 17 09:31:20 2018 From: matthieu.brucher at gmail.com (Matthieu Brucher) Date: Sat, 17 Feb 2018 14:31:20 +0000 Subject: [SciPy-Dev] WIP: Class based Optimizers In-Reply-To: References: <1518642682.8666.18.camel@iki.fi> <5a84a711.05cfca0a.4a242.4608@mx.google.com> Message-ID: A long time ago, I wrote a class-based optimization framework. Not sure if people actually care about class-based optimizers. But if you want to create one, I would suggest you take a look at scikits.optimization if classes is what you are looking for here. Cheers, Matthieu 2018-02-14 23:00 GMT+00:00 Scott Sievert : > This would be the third optimizer API to the same solvers > > I agree. The ODE solvers were previously implemented with the iterative > method, which was found to be less-than-ideal. > > What references are there on these? I?ve found [PR #6326] on the ODE > solvers. What else is out there? > Scott > > [PR #6326]: https://github.com/scipy/scipy/pull/6326 > > > On February 14, 2018 at 3:16:53 PM, xoviat (xoviat at gmail.com) wrote: > > Pauli, > > > > What do you think about returning the entire optimization history, similar > to what is done with the ODE solvers, as I suggested? > > > > I think it would be necessary to make clearly a case what is actually > > gained with such reorganization. This would be the third optimizer API > > to the same solvers, and at first sight it's not clear to me if there > > is a strong need for it. > > > > I agree. The ODE solvers were previously implemented with the iterative > method, which was found to be less-than-ideal. > > > > *From: *Pauli Virtanen > *Sent: *Wednesday, February 14, 2018 3:12 PM > *To: *scipy-dev at python.org > *Subject: *Re: [SciPy-Dev] WIP: Class based Optimizers > > > > Hi, > > > > ke, 2018-02-14 kello 14:21 +1100, Andrew Nelson kirjoitti: > > > The #8414 PR on github (https://github.com/scipy/scipy/pull/8414) > > > introduces an `Optimize` class for `scipy.optimize`. The `Optimize` > > > class > > > can be advanced like an iterator, or be advanced to convergence with > > > the > > > `solve` method. > > > > I think it would be necessary to make clearly a case what is actually > > gained with such reorganization. This would be the third optimizer API > > to the same solvers, and at first sight it's not clear to me if there > > is a strong need for it. > > > > One point that one can argue is that > > > > solver = ... > > for foo in solver: > > some_code > > > > is identical with regard to functionality to > > > > def callback(.., solver_info): > > some_code > > solver(..., callback=callback) > > > > with the difference that the latter does not leak unnecessary private > > implementation details to the user code, requires only small API > > changes, and won't require extensive code reorganization. > > > > The use cases where one needs to continuously monitor convergence in > > minimization are also somewhat expert-oriented, and for most users I > > expect such API will not be as useful. (The situation with ODE solvers > > is I think somewhat different, as with them one e.g. often does not > > even know the time up to which to integrate a priori.) > > > > Writing class-based solvers requires rewriting code in a reverse- > > communication style, which inverts the structure of control flow. This > > can result to code that is more complex, and more difficult to > > maintain. There are some tricks one can do to retain more natural > > structure such as using generators/coroutines, but these are not always > > so nice to use in practice in Python in my experience, and also bring > > more complexity. > > > > The existing solvers in Scipy apart from L-BFGS-B are IIRC not written > > in a reverse-communication style, and converting them would be > > significant rewrite, particularly so for the solvers written in > > C/Fortran. > > > > The same applies also for tuning solver parameters during the > > iteration. The solvers AFAIK have not been designed with parameters > > that can be adjusted during run, and one would probably have to think > > carefully about each one (instead of e.g. exposing them as class > > attributes). > > > > So, I think there are several questions that one should consider here. > > > > Pauli > > > > _______________________________________________ > > SciPy-Dev mailing list > > SciPy-Dev at python.org > > https://mail.python.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -- Quantitative analyst, Ph.D. Blog: http://blog.audio-tk.com/ LinkedIn: http://www.linkedin.com/in/matthieubrucher -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Sun Feb 18 06:40:05 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Sun, 18 Feb 2018 22:40:05 +1100 Subject: [SciPy-Dev] Documentation to use LowLevelCallable from cython Message-ID: I was wondering if there was a guide to demonstrate how to use a LowLevelCallable from cython? Is it possible, and does it lead to any speed benefits if all looping is done from cython? -- _____________________________________ Dr. Andrew Nelson _____________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From josh.craig.wilson at gmail.com Sun Feb 18 08:49:37 2018 From: josh.craig.wilson at gmail.com (Joshua Wilson) Date: Sun, 18 Feb 2018 07:49:37 -0600 Subject: [SciPy-Dev] Deprecate hyp2f0, hyp1f2, and hyp3f0 Message-ID: Hello everyone, I would like to draw your attention to https://github.com/scipy/scipy/issues/8443 which proposes deprecating the hypergeometric functions hyp2f0, hyp1f2, and hyp3f0. It appears that they were intended to be internal helper functions for Cephes and got included in the SciPy API by accident (see issue for more details). Note that I am *not* proposing we deprecate the important hypergeometric functions, namely `hyp0f1` (confluent hypergeometric limit function), `hyp1f1`, `hyperu` (confluent hypergeometric functions), and `hyp2f1` (Gaussian hypergeometric function). - Josh From pav at iki.fi Sun Feb 18 09:03:31 2018 From: pav at iki.fi (Pauli Virtanen) Date: Sun, 18 Feb 2018 15:03:31 +0100 Subject: [SciPy-Dev] Documentation to use LowLevelCallable from cython In-Reply-To: References: Message-ID: <1518962611.2541.5.camel@iki.fi> su, 2018-02-18 kello 22:40 +1100, Andrew Nelson kirjoitti: > I was wondering if there was a guide to demonstrate how to use a > LowLevelCallable from cython? Is it possible, and does it lead to any > speed > benefits if all looping is done from cython? There are some examples in the source code: https://github.com/scipy/scipy/blob/master/scipy/_lib/_ccallback_c.pyx# L107 I'm not sure what you precisely mean by "all looping is done from cython", but using direct C calls instead of Python calls will give a speedup. The main point of this all is to allow *users* to pass in C callback routines using whatever FFI they are using, including Cython. Cython itself AFAIK does not have something similar builtin --- you cannot pass in a Cython cdef routine to another Cython routine from Python. Pauli From stefanv at berkeley.edu Sun Feb 18 13:37:45 2018 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Sun, 18 Feb 2018 10:37:45 -0800 Subject: [SciPy-Dev] Documentation to use LowLevelCallable from cython In-Reply-To: References: Message-ID: <20180218183745.gkksn6u3iucbfw6e@fastmail.com> Hi Andrew On Sun, 18 Feb 2018 22:40:05 +1100, Andrew Nelson wrote: > I was wondering if there was a guide to demonstrate how to use a > LowLevelCallable from cython? Is it possible, and does it lead to any speed > benefits if all looping is done from cython? I have an example of how to use LowLevelCallable with Cython (and Numba--courtesy of Juan Nunez-Iglesias) in this notebook: https://github.com/scikit-image/skimage-tutorials/blob/master/lectures/other_libraries.ipynb Best regards St?fan From andyfaff at gmail.com Sun Feb 18 16:08:29 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Mon, 19 Feb 2018 08:08:29 +1100 Subject: [SciPy-Dev] Documentation to use LowLevelCallable from cython In-Reply-To: <20180218183745.gkksn6u3iucbfw6e@fastmail.com> References: <20180218183745.gkksn6u3iucbfw6e@fastmail.com> Message-ID: Sorry if I wasn't clear. I'll look at those two places. What I was hoping to do is have a generic way of calling a LowLevelCallable in cython: cpdef func_caller(LowLevelCallable func, a, b, c, ...): return_value = func(a, b, c) return return_value On 19 February 2018 at 05:37, Stefan van der Walt wrote: > Hi Andrew > > On Sun, 18 Feb 2018 22:40:05 +1100, Andrew Nelson wrote: > > I was wondering if there was a guide to demonstrate how to use a > > LowLevelCallable from cython? Is it possible, and does it lead to any > speed > > benefits if all looping is done from cython? > > I have an example of how to use LowLevelCallable with Cython (and > Numba--courtesy of Juan Nunez-Iglesias) in this notebook: > > https://github.com/scikit-image/skimage-tutorials/blob/ > master/lectures/other_libraries.ipynb > > Best regards > St?fan > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > -- _____________________________________ Dr. Andrew Nelson _____________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From pav at iki.fi Sun Feb 18 18:02:50 2018 From: pav at iki.fi (Pauli Virtanen) Date: Mon, 19 Feb 2018 00:02:50 +0100 Subject: [SciPy-Dev] Documentation to use LowLevelCallable from cython In-Reply-To: References: <20180218183745.gkksn6u3iucbfw6e@fastmail.com> Message-ID: <1518994970.12667.6.camel@iki.fi> ma, 2018-02-19 kello 08:08 +1100, Andrew Nelson kirjoitti: > Sorry if I wasn't clear. I'll look at those two places. What I was > hoping > to do is have a generic way of calling a LowLevelCallable in cython: > > > > cpdef func_caller(LowLevelCallable func, a, b, c, ...): > > return_value = func(a, b, c) > > return return_value That's the `test_thunk_cython` routine in `_ccallback_c.pyx`. See also `test_call_cython` on how to get `ccallback_t` from a user-provided callable (which may be a LowLevelCallable). Of course, when you are not writing callbacks for some 3rd party library, a more sensible signature for the caller routine would be along the lines `test_thunk_cython(ccallback_t *callback, double a)`. Note that you need to write a separate "caller" routine to do the call for each specific type of callback function you have. There's no generic way to do it, as that would require online code generation. Pauli From serge.guelton at telecom-bretagne.eu Mon Feb 19 05:17:57 2018 From: serge.guelton at telecom-bretagne.eu (Serge Guelton) Date: Mon, 19 Feb 2018 11:17:57 +0100 Subject: [SciPy-Dev] Documentation to use LowLevelCallable from cython In-Reply-To: References: Message-ID: <20180219101757.GI12331@lakota> On Sun, Feb 18, 2018 at 10:40:05PM +1100, Andrew Nelson wrote: > I was wondering if there was a guide to demonstrate how to use a > LowLevelCallable from cython? Is it possible, and does it lead to any speed > benefits if all looping is done from cython? Alternatively, here is a documentation on how to use the Pythran compiler to interact with LowLevelCallable: http://serge-sans-paille.github.io/pythran-stories/the-capsule-corporation.html#capsule-and-numpy Best, serge From smkjain8 at gmail.com Mon Feb 19 07:57:06 2018 From: smkjain8 at gmail.com (Samyak Jain) Date: Mon, 19 Feb 2018 18:27:06 +0530 Subject: [SciPy-Dev] Contributing to scipy Message-ID: Hi, I am new to open source and very keen in contributing towards open source. I have started contributing in scipy solving some small DOC issues but I want to solve some major issues too. Can you suggest how do I start with this and also what all I need to know apart from python to start contributing in this org. I am also applying for GSOC'18 by contributing with this org hence I need to know how can I contact the mentors as on the IRC no one is replying. Is there any other way to contact them ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From gdp.1807 at gmail.com Tue Feb 20 04:58:59 2018 From: gdp.1807 at gmail.com (GAGANDEEP SINGH) Date: Tue, 20 Feb 2018 15:28:59 +0530 Subject: [SciPy-Dev] Project Idea for GSoC 2018 In-Reply-To: References: Message-ID: Dear developers, I want to contribute to SciPy via participating in GSoC, 2018. I have gone through the Project Ideas presented on the page, https://github.com/scipy/scipy/wiki/GSoC-2018-project-ideas. As it was written at the end of the same page, I have thought of a new idea and I want to share the same with the GSoC mentors of SciPy for the year 2018. It will be nice of you if you help me in getting touch with them. Waiting for a positive response. With Regards, Gagandeep Singh -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Tue Feb 20 20:21:32 2018 From: charlesr.harris at gmail.com (Charles R Harris) Date: Tue, 20 Feb 2018 18:21:32 -0700 Subject: [SciPy-Dev] NumPy 1.14.1 released Message-ID: Hi All, On behalf of the NumPy team, I am pleased to announce NumPy 1.14.1. This is a bugfix release for some problems reported following the 1.14.0 release. The major problems fixed are the following. - Problems with the new array printing, particularly the printing of complex values, Please report any additional problems that may turn up. - Problems with ``np.einsum`` due to the new ``optimized=True`` default. Some fixes for optimization have been applied and ``optimize=False`` is now the default. - The sort order in ``np.unique`` when ``axis=`` will now always be lexicographic in the subarray elements. In previous NumPy versions there was an optimization that could result in sorting the subarrays as unsigned byte strings. - The change in 1.14.0 that multi-field indexing of structured arrays returns a view instead of a copy has been reverted but remains on track for NumPy 1.15. Affected users should read the 1.14.1 Numpy User Guide section "basics/structured arrays/accessing multiple fields" for advice on how to manage this transition. This release supports Python 2.7 and 3.4 - 3.6. Wheels for the release are available on PyPI. Source tarballs, zipfiles, release notes, and the changelog are available on github . *Contributors* A total of 14 people contributed to this release. People with a "+" by their names contributed a patch for the first time. * Allan Haldane * Charles Harris * Daniel Smith * Dennis Weyland + * Eric Larson * Eric Wieser * Jarrod Millman * Kenichi Maehashi + * Marten van Kerkwijk * Mathieu Lamarre * Sebastian Berg * Simon Conseil * Simon Gibbons * xoviat Cheers, Charles Harris -------------- next part -------------- An HTML attachment was scrubbed... URL: From schakravorty846 at gmail.com Thu Feb 22 01:36:00 2018 From: schakravorty846 at gmail.com (schakravorty846) Date: Thu, 22 Feb 2018 12:06:00 +0530 Subject: [SciPy-Dev] Add MCDA module to SciPy Message-ID: Hello, I am Shivanjan Chakravorty,I am an 8th semester Computer Science Engineering student. I have been using libraries under SciPy for quite a long time now. I wish to contribute to SciPy packages for GSoC by adding all the Multi Criteria Decision Analysis methods listed in MCDA Wikipedia page here . The similar package scikit-criteria exists but it contains only WSM model implementation. I wish to provide all the methods listed in the Wiki Page and make it a core part of SciPy as this has a wide range of application in multiple domains. I am open to suggestions and discussion on this. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.frio at gmail.com Thu Feb 22 15:36:24 2018 From: jaime.frio at gmail.com (=?UTF-8?Q?Jaime_Fern=C3=A1ndez_del_R=C3=ADo?=) Date: Thu, 22 Feb 2018 20:36:24 +0000 Subject: [SciPy-Dev] Change the return of ndimage functions Message-ID: Hi, For some odd reason, several ndimage functions only return the output array if it has been allocated by the function itself, not if you have passed a preallocated array to the function, e.g.: ndimage.correlate1d([1, 2, 3], [1, 1, 1]) # returns [4, 6, 8] out = np.empty(3) ndimage.correlate1d([1, 2, 3], [1, 1, 1], output=out) # returns None (but writes [4, 6, 8] to out) I find this to be an annoying, unintuitive behaviour, that differs from what e.g. numpy ufuncs do, and that often requires special handling, see e.g. the review comments in #8455 . It is furthermore not consistently implemented, as several functions do return the output array always. I have submitted #8461 changing this behaviour so that the output array is always returned, regardless if it was given by the user or allocated by the function. It probably says more about the poor coverage of the tests than anything else, but the change did not make any of the current tests fail. I doubt this change will be problematic to any user, but it is indeed a change to a longstanding, documented behavior, so it probably deserves more discussion than would happen in the PR alone. Any objections anyone? Jaime -- (\__/) ( O.o) ( > <) Este es Conejo. Copia a Conejo en tu firma y ay?dale en sus planes de dominaci?n mundial. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikegraham at gmail.com Thu Feb 22 15:48:55 2018 From: mikegraham at gmail.com (Mike Graham) Date: Thu, 22 Feb 2018 15:48:55 -0500 Subject: [SciPy-Dev] SciPy IRC channel lacks moderation Message-ID: Hi, The SciPy IRC channel on Freenode has been without moderation for a while. On rare occasion, we get trolls in the channel. For example, recently we had a couple instances of a troll posting the n-word in channel and tagging many users (most likely with the intent of sending them notifications). It would also be nice if someone could do things like fix dead links in the channel's topic statement. I would suggest that either the channel be discontinued (and removed from https://www.scipy.org/scipylib/mailing-lists.html ) or that the SciPy organization appoint a "Group Contact" with Freenode to administrate the channel. (Freenode requires the organization a channel is named after to notify them of the desired GC.) Nathan Goldbaum and Nathaniel J. Smith are channel regulars -- if you are looking for someone to appoint as GC, you might try to recruit one of them. Best, Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Thu Feb 22 20:36:15 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Thu, 22 Feb 2018 17:36:15 -0800 Subject: [SciPy-Dev] Change the return of ndimage functions In-Reply-To: References: Message-ID: On Thu, Feb 22, 2018 at 12:36 PM, Jaime Fern?ndez del R?o < jaime.frio at gmail.com> wrote: > Hi, > > For some odd reason, several ndimage functions only return the output > array if it has been allocated by the function itself, not if you have > passed a preallocated array to the function, e.g.: > > ndimage.correlate1d([1, 2, 3], [1, 1, 1]) # returns [4, 6, 8] > > out = np.empty(3) > ndimage.correlate1d([1, 2, 3], [1, 1, 1], output=out) # returns None (but > writes [4, 6, 8] to out) > > > I find this to be an annoying, unintuitive behaviour, that differs from > what e.g. numpy ufuncs do, and that often requires special handling, see > e.g. the review comments in #8455 > . It is furthermore not > consistently implemented, as several functions do return the output array > always. > I have submitted #8461 > changing this behaviour so that the output array is always returned, > regardless if it was given by the user or allocated by the function. It > probably says more about the poor coverage of the tests than anything else, > but the change did not make any of the current tests fail. > > I doubt this change will be problematic to any user, but it is indeed a > change to a longstanding, documented behavior, so it probably deserves more > discussion than would happen in the PR alone. Any objections anyone? > Makes sense to me, no objections. Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Fri Feb 23 01:08:40 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Thu, 22 Feb 2018 22:08:40 -0800 Subject: [SciPy-Dev] Add MCDA module to SciPy In-Reply-To: References: Message-ID: Hi Shivanjan, Thanks for your interest in SciPy and coming up with your own idea. On Wed, Feb 21, 2018 at 10:36 PM, schakravorty846 wrote: > Hello, > > I am Shivanjan Chakravorty,I am an 8th semester Computer Science > Engineering student. I have been using libraries under SciPy for quite a > long time now. I wish to contribute to SciPy packages for GSoC by adding > all the Multi Criteria Decision Analysis methods listed in MCDA Wikipedia > page here > . > The similar package scikit-criteria exists but it contains only WSM model > implementation. I wish to provide all the methods listed in the Wiki Page > and make it a core part of SciPy as this has a wide range of application in > multiple domains. I am open to suggestions and discussion on this. Thank > you. > MCDA methods are out of scope for SciPy I would say. It's very rare for us to add a whole new module, and if we do then it's usually an extension of something already present (e.g. linalg.cython_blas, sparse.csgraph). It would fit better in Pyomo for example. Also, contributing to scikit-criteria would make sense - if there's already a package like that, we don't want to overlap with their scope. Sorry to not be able to give you a positive answer. I'd encourage you to contact one of those projects; they may still be able to sign up under the PSF umbrella and accept you as a student. Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Fri Feb 23 01:13:33 2018 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Thu, 22 Feb 2018 22:13:33 -0800 Subject: [SciPy-Dev] Change the return of ndimage functions In-Reply-To: References: Message-ID: <161c14b9ac8.2815.acf34a9c767d7bb498a799333be0433e@fastmail.com> On 22 February 2018 5:38:24 PM Ralf Gommers wrote: > On Thu, Feb 22, 2018 at 12:36 PM, Jaime Fern?ndez del R?o < > jaime.frio at gmail.com> wrote: > >> Hi, >> >> For some odd reason, several ndimage functions only return the output >> array if it has been allocated by the function itself, not if you have >> passed a preallocated array to the function, e.g.: >> >> ndimage.correlate1d([1, 2, 3], [1, 1, 1]) # returns [4, 6, 8] >> >> out = np.empty(3) >> ndimage.correlate1d([1, 2, 3], [1, 1, 1], output=out) # returns None (but >> writes [4, 6, 8] to out) >> >> >> I find this to be an annoying, unintuitive behaviour, that differs from >> what e.g. numpy ufuncs do, and that often requires special handling, see >> e.g. the review comments in #8455 >> . It is furthermore not >> consistently implemented, as several functions do return the output array >> always. >> I have submitted #8461 >> changing this behaviour so that the output array is always returned, >> regardless if it was given by the user or allocated by the function. It >> probably says more about the poor coverage of the tests than anything else, >> but the change did not make any of the current tests fail. >> >> I doubt this change will be problematic to any user, but it is indeed a >> change to a longstanding, documented behavior, so it probably deserves more >> discussion than would happen in the PR alone. Any objections anyone? >> > > Makes sense to me, no objections. Same here. Best regards St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Fri Feb 23 01:15:46 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Thu, 22 Feb 2018 22:15:46 -0800 Subject: [SciPy-Dev] Contributing to scipy In-Reply-To: References: Message-ID: Hi Samyak, Welcome! On Mon, Feb 19, 2018 at 4:57 AM, Samyak Jain wrote: > Hi, I am new to open source and very keen in contributing towards open > source. I have started contributing in scipy solving some small DOC issues > but I want to solve some major issues too. Can you suggest how do I start > with this > Is there a particular area or submodule of SciPy you are interested in? We have no shortage of issues, but it would probably be best to work on one that's related to your interests or potential gsoc topic. > and also what all I need to know apart from python to start contributing > in this org. > A general skill you need is use of git/Github. Beyond that, it depends on the topic. Some parts of SciPy are pure Python, for others you may need to know Cython, C, C++ or Fortran. I am also applying for GSOC'18 by contributing with this org hence I need > to know how can I contact the mentors as on the IRC no one is replying. Is > there any other way to contact them ? > IRC is a very old channel, not many (none?) of the developers are on it regularly. We didn't list IRC on the ideas page or http://python-gsoc.org as a method to contact the scipy developers. Where did you see a link to it? Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Fri Feb 23 01:18:55 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Thu, 22 Feb 2018 22:18:55 -0800 Subject: [SciPy-Dev] Project Idea for GSoC 2018 In-Reply-To: References: Message-ID: Hi Gagandeep, Welcome! On Tue, Feb 20, 2018 at 1:58 AM, GAGANDEEP SINGH wrote: > Dear developers, > > I want to contribute to SciPy via participating in GSoC, 2018. I have gone > through the Project Ideas presented on the page, https://github.com/ > scipy/scipy/wiki/GSoC-2018-project-ideas. > > As it was written at the end of the same page, I have thought of a new > idea and I want to share the same with the GSoC mentors of SciPy for the > year 2018. It will be nice of you if you help me in getting touch with > them. > You found us:) All SciPy developers read this mailing list, so this is the best place to share your idea. Please let us know what it is, and we'll try to give you feedback quickly. Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Fri Feb 23 01:25:32 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Thu, 22 Feb 2018 22:25:32 -0800 Subject: [SciPy-Dev] SciPy IRC channel lacks moderation In-Reply-To: References: Message-ID: On Thu, Feb 22, 2018 at 12:48 PM, Mike Graham wrote: > Hi, > > The SciPy IRC channel on Freenode has been without moderation for a while. > On rare occasion, we get trolls in the channel. For example, recently we > had a couple instances of a troll posting the n-word in channel and tagging > many users (most likely with the intent of sending them notifications). It > would also be nice if someone could do things like fix dead links in the > channel's topic statement. > Thanks for bringing this up. > > I would suggest that either the channel be discontinued (and removed from > https://www.scipy.org/scipylib/mailing-lists.html ) > yes good idea > or that the SciPy organization appoint a "Group Contact" with Freenode to > administrate the channel. (Freenode requires the organization a channel is > named after to notify them of the desired GC.) > > Nathan Goldbaum and Nathaniel J. Smith are channel regulars -- if you are > looking for someone to appoint as GC, you might try to recruit one of them. > I'm fine with either option, discontinuing or moderation. Either way we should make it clear that scipy devs don't hang out there. Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From njs at pobox.com Fri Feb 23 01:42:38 2018 From: njs at pobox.com (Nathaniel Smith) Date: Thu, 22 Feb 2018 22:42:38 -0800 Subject: [SciPy-Dev] SciPy IRC channel lacks moderation In-Reply-To: References: Message-ID: On Thu, Feb 22, 2018 at 12:48 PM, Mike Graham wrote: > Nathan Goldbaum and Nathaniel J. Smith are channel regulars -- if you are > looking for someone to appoint as GC, you might try to recruit one of them. Thanks for the thought, but I don't have the bandwidth to take this on right now, sorry. -n -- Nathaniel J. Smith -- https://vorpus.org From gdp.1807 at gmail.com Fri Feb 23 11:19:19 2018 From: gdp.1807 at gmail.com (GAGANDEEP SINGH) Date: Fri, 23 Feb 2018 21:49:19 +0530 Subject: [SciPy-Dev] Project Details for GSoC 2018 Message-ID: Dear developers, As suggested by Ralf Gommers, I am presenting my project idea details for GSoC 2018 for contributing to SciPy. I want to add a module to scipy which will allow to perform various computations related to Complex Analysis. You can see more details in the attached file. Waiting for feedbacks from mentors. With Regards, Gagandeep Singh -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Project_Idea.pdf Type: application/pdf Size: 101277 bytes Desc: not available URL: From josh.craig.wilson at gmail.com Fri Feb 23 12:57:33 2018 From: josh.craig.wilson at gmail.com (Joshua Wilson) Date: Fri, 23 Feb 2018 11:57:33 -0600 Subject: [SciPy-Dev] Project Details for GSoC 2018 In-Reply-To: References: Message-ID: A couple of comments: as Ralf mentioned on a recent thread, adding new top-level modules to SciPy is pretty much out of the question, so you probably want to focus on enhancing existing modules. Some of the operations you propose (checking continuity, checking analyticity) are not particularly useful for scientific computing (the nature of floating point means they won't be very reliable); they might be more appropriate for a symbolic library. Now, computing high-order derivatives of analytic functions is an interesting topic because it can be done to high precision using Cauchy's integral formula. Something like this might fit in `scipy.integrate`. The thing I'm not sure of is whether this is enough material for a GSoC; determining this would require looking through the relevant literature. On Fri, Feb 23, 2018 at 10:19 AM, GAGANDEEP SINGH wrote: > Dear developers, > > As suggested by Ralf Gommers, I am presenting my project idea details for > GSoC 2018 for contributing to SciPy. > I want to add a module to scipy which will allow to perform various > computations related to Complex Analysis. > You can see more details in the attached file. > > Waiting for feedbacks from mentors. > > With Regards, > Gagandeep Singh > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > From ralf.gommers at gmail.com Fri Feb 23 14:28:04 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Fri, 23 Feb 2018 11:28:04 -0800 Subject: [SciPy-Dev] Project Details for GSoC 2018 In-Reply-To: References: Message-ID: On Fri, Feb 23, 2018 at 9:57 AM, Joshua Wilson wrote: > A couple of comments: as Ralf mentioned on a recent thread, adding new > top-level modules to SciPy is pretty much out of the question, so you > probably want to focus on enhancing existing modules. Some of the > operations you propose (checking continuity, checking analyticity) are > not particularly useful for scientific computing (the nature of > floating point means they won't be very reliable); they might be more > appropriate for a symbolic library. Indeed. My first thought after reading the proposal was that this could be a good fit with Sympy. Sympy participates in GSoC as well, so you could try with them. Cheers, Ralf > Now, computing high-order > derivatives of analytic functions is an interesting topic because it > can be done to high precision using Cauchy's integral formula. > Something like this might fit in `scipy.integrate`. The thing I'm not > sure of is whether this is enough material for a GSoC; determining > this would require looking through the relevant literature. > > On Fri, Feb 23, 2018 at 10:19 AM, GAGANDEEP SINGH > wrote: > > Dear developers, > > > > As suggested by Ralf Gommers, I am presenting my project idea details for > > GSoC 2018 for contributing to SciPy. > > I want to add a module to scipy which will allow to perform various > > computations related to Complex Analysis. > > You can see more details in the attached file. > > > > Waiting for feedbacks from mentors. > > > > With Regards, > > Gagandeep Singh > > > > _______________________________________________ > > SciPy-Dev mailing list > > SciPy-Dev at python.org > > https://mail.python.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Fri Feb 23 15:32:31 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Sat, 24 Feb 2018 07:32:31 +1100 Subject: [SciPy-Dev] scipep repo In-Reply-To: References: Message-ID: Undergoing the agony of writing one of these scipeps has made me realise its usefulness in examining the merits of proposed large changes to the codebase. I would recommend it for things like GSOC projects (instead of project proposal?), and for other large changes (of the size of #8328). This would help publicise the proposed changes to the wider scipy community. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vishstar88 at gmail.com Fri Feb 23 20:27:14 2018 From: vishstar88 at gmail.com (Vishal Gupta) Date: Sat, 24 Feb 2018 06:57:14 +0530 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism Message-ID: Hey. My name is Vishal Gupta and I'm a 3rd year CSE undergrad. Here's a list of almost everything I've worked on, so far : py-ranoid.github.io/Resume I'd like to contribute to Scipy by working on this project : https://github.com/scipy/scipy/wiki/GSoC-2018-project-ideas#rotation-formalism-in-3-dimensions How can I get in touch with the mentors (Eric Larson and Nikolay Mayorov) ? Thanks Vishal Gupta -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Sat Feb 24 00:40:46 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Fri, 23 Feb 2018 21:40:46 -0800 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: References: Message-ID: On Fri, Feb 23, 2018 at 5:27 PM, Vishal Gupta wrote: > Hey. > My name is Vishal Gupta and I'm a 3rd year CSE undergrad. > Here's a list of almost everything I've worked on, so far : > py-ranoid.github.io/Resume > > I'd like to contribute to Scipy by working on this project : > https://github.com/scipy/scipy/wiki/GSoC-2018-project- > ideas#rotation-formalism-in-3-dimensions > > How can I get in touch with the mentors (Eric Larson and Nikolay Mayorov) > ? > Hi Vishal, this list is the best way to communicate about your questions and ideas. Eric, Nikolay and all the other SciPy developers read this list. Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From gdp.1807 at gmail.com Sat Feb 24 02:59:10 2018 From: gdp.1807 at gmail.com (GAGANDEEP SINGH) Date: Sat, 24 Feb 2018 13:29:10 +0530 Subject: [SciPy-Dev] Changes Incurred in the Project Idea In-Reply-To: References: Message-ID: Dear developers, After working on feedbacks received from the developers I have made changes in my Project Idea for GSoC 2018 for SciPy. This time it is based on extending scipy.integrate. You can see the attachment for details. Waiting for feedbacks. With Regards, Gagandeep Singh -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Project_Idea_1.pdf Type: application/pdf Size: 89678 bytes Desc: not available URL: From nikolay.mayorov at zoho.com Sat Feb 24 04:06:06 2018 From: nikolay.mayorov at zoho.com (Nikolay Mayorov) Date: Sat, 24 Feb 2018 14:06:06 +0500 Subject: [SciPy-Dev] Changes Incurred in the Project Idea In-Reply-To: References: Message-ID: <161c70ff3e5.1108465f535463.495670897355477861@zoho.com> Hi Gagandeep! I read the PDF you attached. I want to point out to you several points: 1) You mentioned serval mathematical constructs: curve, surface, volume. These don't directly translated to Python, you need to define some representation/API for that. And obviously defining any of these is very tricky. If you want to continue to develop this idea you need to provide a detailed information about that: how do you define curve/surface/volume, will it be practical and general enough, will it be convenient for a user. 2) Next, scipy is a numerical library and we are interested for an established and effective numerical methods. Your descriptions doesn't say anything about which numerical methods exist for solving problems you described. Some problems formulated in a mathematical form are just not suitable for numerical methods. 3) This is rather minor, but don't use double underscores for your methods (they indicate special "magic" methods). Please don't consider this as a discouragement. If you are interested in scipy.integrate and numerical integration I'm sure there are enough things you can work on, we can discuss and come up with something. Best, Nikolay ---- On Sat, 24 Feb 2018 12:59:10 +0500 GAGANDEEP SINGH <gdp.1807 at gmail.com> wrote ---- Dear developers, After working on feedbacks received from the developers I have made changes in my Project Idea for GSoC 2018 for SciPy. This time it is based on extending scipy.integrate. You can see the attachment for details. Waiting for feedbacks. With Regards, Gagandeep Singh _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From nikolay.mayorov at zoho.com Sat Feb 24 04:31:55 2018 From: nikolay.mayorov at zoho.com (Nikolay Mayorov) Date: Sat, 24 Feb 2018 14:31:55 +0500 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: References: Message-ID: <161c7279428.c8b3e6f835586.3157607271633216880@zoho.com> Hi, Vishal! I think you are interested to know how to make a good application for GSoC with scipy. I believe there are only two things: 1) Write a good proposal: expand what is already suggested, give your own perspective, provide a detailed and sound time schedule, determine whether it will be enough to work on or you need to add another related topic (like if this is scipy.spatial.transform what else can be generally useful there). I think what I wrote about the class Rotation is all reasonable, but the algorithms parts is more questionable and here where your own perspective is valuable. Also check this http://turnbull.sk.tsukuba.ac.jp/Blog/SPAM.txt#how-to-spam-in-detail Note that you can work on your proposal right in scipy wiki (but probably keep the initial text intact, just create a new page). 2) Become active with scipy development. If you are making good changes in your pull requests, show intelligence and communicate well --- this all is extremely valuable when deciding which proposals to accept. Best, Nikolay ---- On Sat, 24 Feb 2018 10:40:46 +0500 Ralf Gommers <ralf.gommers at gmail.com> wrote ---- On Fri, Feb 23, 2018 at 5:27 PM, Vishal Gupta <vishstar88 at gmail.com> wrote: Hey. My name is Vishal Gupta and I'm a 3rd year CSE undergrad. Here's a list of almost everything I've worked on, so far : py-ranoid.github.io/Resume I'd like to contribute to Scipy by working on this project : https://github.com/scipy/scipy/wiki/GSoC-2018-project-ideas#rotation-formalism-in-3-dimensions How can I get in touch with the mentors (Eric Larson and Nikolay Mayorov) ? Hi Vishal, this list is the best way to communicate about your questions and ideas. Eric, Nikolay and all the other SciPy developers read this list. Cheers, Ralf _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From smkjain8 at gmail.com Sat Feb 24 07:21:56 2018 From: smkjain8 at gmail.com (Samyak Jain) Date: Sat, 24 Feb 2018 17:51:56 +0530 Subject: [SciPy-Dev] Contributing to scipy In-Reply-To: References: Message-ID: There is no particular submodule that I am interested in but I would like to do issues involving some work in python. Can someone suggest which type of issues I should start with? I have started solving some DOC issues but now I want to fix some bugs. Also how can I understand the structure of scipy how other modules are correlated with each other? On Fri, Feb 23, 2018 at 11:45 AM, Ralf Gommers wrote: > Hi Samyak, > > Welcome! > > On Mon, Feb 19, 2018 at 4:57 AM, Samyak Jain wrote: > >> Hi, I am new to open source and very keen in contributing towards open >> source. I have started contributing in scipy solving some small DOC issues >> but I want to solve some major issues too. Can you suggest how do I start >> with this >> > > Is there a particular area or submodule of SciPy you are interested in? We > have no shortage of issues, but it would probably be best to work on one > that's related to your interests or potential gsoc topic. > > >> and also what all I need to know apart from python to start contributing >> in this org. >> > > A general skill you need is use of git/Github. Beyond that, it depends on > the topic. Some parts of SciPy are pure Python, for others you may need to > know Cython, C, C++ or Fortran. > > I am also applying for GSOC'18 by contributing with this org hence I need >> to know how can I contact the mentors as on the IRC no one is replying. Is >> there any other way to contact them ? >> > > IRC is a very old channel, not many (none?) of the developers are on it > regularly. We didn't list IRC on the ideas page or http://python-gsoc.org > as a method to contact the scipy developers. Where did you see a link to it? > > Cheers, > Ralf > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From josh.craig.wilson at gmail.com Sat Feb 24 09:59:40 2018 From: josh.craig.wilson at gmail.com (Joshua Wilson) Date: Sat, 24 Feb 2018 08:59:40 -0600 Subject: [SciPy-Dev] Changes Incurred in the Project Idea In-Reply-To: <161c70ff3e5.1108465f535463.495670897355477861@zoho.com> References: <161c70ff3e5.1108465f535463.495670897355477861@zoho.com> Message-ID: Just to second what Nikolay said, there are are lots of interesting numerical integration things to work on. One thing I've been wanting to see is more PRs along the lines of https://github.com/scipy/scipy/pull/4587 which added support for very high order Gauss-Hermite quadrature. Currently all of the other Gaussian quadrature methods are done by computing the eigenvalues of a tridiagonal matrix, which works fine for low orders but becomes inaccurate/slow for very high orders. There's been recent research on how to improve on that, see for example http://epubs.siam.org/doi/abs/10.1137/120889873?journalCode=sjoce3 I think this could make a very nice summer project. - Josh On Sat, Feb 24, 2018 at 3:06 AM, Nikolay Mayorov wrote: > Hi Gagandeep! > > I read the PDF you attached. I want to point out to you several points: > > 1) You mentioned serval mathematical constructs: curve, surface, volume. > These don't directly translated to Python, you need to define some > representation/API for that. And obviously defining any of these is very > tricky. If you want to continue to develop this idea you need to provide a > detailed information about that: how do you define curve/surface/volume, > will it be practical and general enough, will it be convenient for a user. > > 2) Next, scipy is a numerical library and we are interested for an > established and effective numerical methods. Your descriptions doesn't say > anything about which numerical methods exist for solving problems you > described. Some problems formulated in a mathematical form are just not > suitable for numerical methods. > > 3) This is rather minor, but don't use double underscores for your methods > (they indicate special "magic" methods). > > Please don't consider this as a discouragement. If you are interested in > scipy.integrate and numerical integration I'm sure there are enough things > you can work on, we can discuss and come up with something. > > Best, > Nikolay > > > ---- On Sat, 24 Feb 2018 12:59:10 +0500 GAGANDEEP SINGH > wrote ---- > > Dear developers, > > After working on feedbacks received from the developers I have made changes > in my Project Idea for GSoC 2018 for SciPy. > This time it is based on extending scipy.integrate. You can see the > attachment for details. > > Waiting for feedbacks. > > With Regards, > Gagandeep Singh > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > From ilhanpolat at gmail.com Sat Feb 24 13:01:34 2018 From: ilhanpolat at gmail.com (Ilhan Polat) Date: Sat, 24 Feb 2018 19:01:34 +0100 Subject: [SciPy-Dev] Contributing to scipy In-Reply-To: References: Message-ID: You can start reading about the open issues and try to read the relevant source code. If you think you can handle something then fork and branch scipy locally and check whether you actually handled.the problem (maybe adding extra tests). Modules are except some minor cases mutually exclusive so that won't be a problem. On Feb 24, 2018 13:22, "Samyak Jain" wrote: > There is no particular submodule that I am interested in but I would like > to do issues involving some work in python. Can someone suggest which type > of issues I should start with? I have started solving some DOC issues but > now I want to fix some bugs. Also how can I understand the structure of > scipy how other modules are correlated with each other? > > On Fri, Feb 23, 2018 at 11:45 AM, Ralf Gommers > wrote: > >> Hi Samyak, >> >> Welcome! >> >> On Mon, Feb 19, 2018 at 4:57 AM, Samyak Jain wrote: >> >>> Hi, I am new to open source and very keen in contributing towards open >>> source. I have started contributing in scipy solving some small DOC issues >>> but I want to solve some major issues too. Can you suggest how do I start >>> with this >>> >> >> Is there a particular area or submodule of SciPy you are interested in? >> We have no shortage of issues, but it would probably be best to work on one >> that's related to your interests or potential gsoc topic. >> >> >>> and also what all I need to know apart from python to start contributing >>> in this org. >>> >> >> A general skill you need is use of git/Github. Beyond that, it depends on >> the topic. Some parts of SciPy are pure Python, for others you may need to >> know Cython, C, C++ or Fortran. >> >> I am also applying for GSOC'18 by contributing with this org hence I need >>> to know how can I contact the mentors as on the IRC no one is replying. Is >>> there any other way to contact them ? >>> >> >> IRC is a very old channel, not many (none?) of the developers are on it >> regularly. We didn't list IRC on the ideas page or http://python-gsoc.org >> as a method to contact the scipy developers. Where did you see a link to it? >> >> Cheers, >> Ralf >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> >> > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From phillip.m.feldman at gmail.com Sat Feb 24 13:54:13 2018 From: phillip.m.feldman at gmail.com (Phillip Feldman) Date: Sat, 24 Feb 2018 10:54:13 -0800 Subject: [SciPy-Dev] Contributing to scipy In-Reply-To: References: Message-ID: When you say "correlated", are you referring to dependencies? If you are interested in working on interpolation, I can suggest some things to be done and also contribute some code. Phillip M. Feldman On Sat, Feb 24, 2018 at 4:21 AM, Samyak Jain wrote: > There is no particular submodule that I am interested in but I would like > to do issues involving some work in python. Can someone suggest which type > of issues I should start with? I have started solving some DOC issues but > now I want to fix some bugs. Also how can I understand the structure of > scipy how other modules are correlated with each other? > > On Fri, Feb 23, 2018 at 11:45 AM, Ralf Gommers > wrote: > >> Hi Samyak, >> >> Welcome! >> >> On Mon, Feb 19, 2018 at 4:57 AM, Samyak Jain wrote: >> >>> Hi, I am new to open source and very keen in contributing towards open >>> source. I have started contributing in scipy solving some small DOC issues >>> but I want to solve some major issues too. Can you suggest how do I start >>> with this >>> >> >> Is there a particular area or submodule of SciPy you are interested in? >> We have no shortage of issues, but it would probably be best to work on one >> that's related to your interests or potential gsoc topic. >> >> >>> and also what all I need to know apart from python to start contributing >>> in this org. >>> >> >> A general skill you need is use of git/Github. Beyond that, it depends on >> the topic. Some parts of SciPy are pure Python, for others you may need to >> know Cython, C, C++ or Fortran. >> >> I am also applying for GSOC'18 by contributing with this org hence I need >>> to know how can I contact the mentors as on the IRC no one is replying. Is >>> there any other way to contact them ? >>> >> >> IRC is a very old channel, not many (none?) of the developers are on it >> regularly. We didn't list IRC on the ideas page or http://python-gsoc.org >> as a method to contact the scipy developers. Where did you see a link to it? >> >> Cheers, >> Ralf >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> >> > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From phillip.m.feldman at gmail.com Sat Feb 24 13:57:42 2018 From: phillip.m.feldman at gmail.com (Phillip Feldman) Date: Sat, 24 Feb 2018 10:57:42 -0800 Subject: [SciPy-Dev] Contributing to scipy In-Reply-To: References: Message-ID: Actually, the code that I have is for integration--not interpolation. But, I'd like to see support for interpolating irregularly spaced data in two and higher dimensions. On Sat, Feb 24, 2018 at 10:54 AM, Phillip Feldman < phillip.m.feldman at gmail.com> wrote: > When you say "correlated", are you referring to dependencies? > > If you are interested in working on interpolation, I can suggest some > things to be done and also contribute some code. > > Phillip M. Feldman > > On Sat, Feb 24, 2018 at 4:21 AM, Samyak Jain wrote: > >> There is no particular submodule that I am interested in but I would like >> to do issues involving some work in python. Can someone suggest which type >> of issues I should start with? I have started solving some DOC issues but >> now I want to fix some bugs. Also how can I understand the structure of >> scipy how other modules are correlated with each other? >> >> On Fri, Feb 23, 2018 at 11:45 AM, Ralf Gommers >> wrote: >> >>> Hi Samyak, >>> >>> Welcome! >>> >>> On Mon, Feb 19, 2018 at 4:57 AM, Samyak Jain wrote: >>> >>>> Hi, I am new to open source and very keen in contributing towards open >>>> source. I have started contributing in scipy solving some small DOC issues >>>> but I want to solve some major issues too. Can you suggest how do I start >>>> with this >>>> >>> >>> Is there a particular area or submodule of SciPy you are interested in? >>> We have no shortage of issues, but it would probably be best to work on one >>> that's related to your interests or potential gsoc topic. >>> >>> >>>> and also what all I need to know apart from python to start >>>> contributing in this org. >>>> >>> >>> A general skill you need is use of git/Github. Beyond that, it depends >>> on the topic. Some parts of SciPy are pure Python, for others you may need >>> to know Cython, C, C++ or Fortran. >>> >>> I am also applying for GSOC'18 by contributing with this org hence I >>>> need to know how can I contact the mentors as on the IRC no one is >>>> replying. Is there any other way to contact them ? >>>> >>> >>> IRC is a very old channel, not many (none?) of the developers are on it >>> regularly. We didn't list IRC on the ideas page or >>> http://python-gsoc.org as a method to contact the scipy developers. >>> Where did you see a link to it? >>> >>> Cheers, >>> Ralf >>> >>> >>> _______________________________________________ >>> SciPy-Dev mailing list >>> SciPy-Dev at python.org >>> https://mail.python.org/mailman/listinfo/scipy-dev >>> >>> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nikolay.mayorov at zoho.com Sun Feb 25 05:39:52 2018 From: nikolay.mayorov at zoho.com (Nikolay Mayorov) Date: Sun, 25 Feb 2018 15:39:52 +0500 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: References: Message-ID: <161cc8c27cf.e16b927b42372.6259257951918238853@zoho.com> Hi, Vishal! 1.You should reply to scipy-dev at python.org, check if it works for you. I'm replying to this address now as well. 2. It doesn't seem that many people here use IRC, e-mail for now is totally fine. 3. Fine, looking forward to the updates :) 4. It will be good to see some technical details: like what methods you want to introduce, there general logic and fine points, what difficulties you expect, possible different approaches and their pros and cons. It is valuable if you can think in terms of the actual implementation. Besides that, we are interested in your motivation of working with scipy and this idea in particular. 5. Generally both, there are no hard rules. Perhaps work on your proposal draft first, see if you are in fact interested in working on this idea. Best, Nikolay ---- On Sun, 25 Feb 2018 14:04:56 +0500 Vishal Gupta <vishstar88 at gmail.com> wrote ---- Hey. 1. I'm drafting a new mail, because I've subscribed to scipy-dev digests and I wasn't sure how I could reference or reply to mails in digests. 2. Honestly, I haven't used the IRC a lot, so I hope it's fine to communicate within this mail thread :) 3. I've created a Wiki for the project here : https://github.com/scipy/scipy/wiki/GSoC-Proposal-:-Rotation-Formalism 4. I will expand on the existing idea and give my own perspective over the next 3-4 days. Hopefully, I should have a rough idea of what it might take and also be able to draft a rough time schedule in a week. 5. Since you also mentioned "Become active with scipy development", do I work on the above... or resolving issues and raising PRs ? Thanks Vishal Gupta -------------- next part -------------- An HTML attachment was scrubbed... URL: From vishstar88 at gmail.com Sun Feb 25 06:46:51 2018 From: vishstar88 at gmail.com (Vishal Gupta) Date: Sun, 25 Feb 2018 17:16:51 +0530 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: <161cc8c27cf.e16b927b42372.6259257951918238853@zoho.com> References: <161cc8c27cf.e16b927b42372.6259257951918238853@zoho.com> Message-ID: Hey Here's a bunch of ideas that I have 1. Create a new Vector class primarily for vector algebraic operations (instead of numpy arrays). This could be used any and every vector operation. - Vector Product - Scalar Product - Translation - Rotation - Magnitude - Distance from other Vector objects - Convert to and from numpy array - - asd On Sun, Feb 25, 2018 at 4:09 PM, Nikolay Mayorov wrote: > Hi, Vishal! > > 1.You should reply to scipy-dev at python.org, check if it works for you. > I'm replying to this address now as well. > 2. It doesn't seem that many people here use IRC, e-mail for now is > totally fine. > 3. Fine, looking forward to the updates :) > 4. It will be good to see some technical details: like what methods you > want to introduce, there general logic and fine points, what difficulties > you expect, possible different approaches and their pros and cons. It is > valuable if you can think in terms of the actual implementation. Besides > that, we are interested in your motivation of working with scipy and this > idea in particular. > 5. Generally both, there are no hard rules. Perhaps work on your proposal > draft first, see if you are in fact interested in working on this idea. > > Best, > Nikolay > > ---- On Sun, 25 Feb 2018 14:04:56 +0500 *Vishal Gupta > >* wrote ---- > > Hey. > > 1. I'm drafting a new mail, because I've subscribed to scipy-dev digests > and I wasn't sure how I could reference or reply to mails in digests. > 2. Honestly, I haven't used the IRC a lot, so I hope it's fine to > communicate within this mail thread :) > 3. I've created a Wiki for the project here : https://github.com/scipy/ > scipy/wiki/GSoC-Proposal-:-Rotation-Formalism > 4. I will expand on the existing idea and give my own perspective over the > next 3-4 days. Hopefully, I should have a rough idea of what it might take > and also be able to draft a rough time schedule in a week. > 5. Since you also mentioned "Become active with scipy development", do I > work on the above... or resolving issues and raising PRs ? > Thanks > Vishal Gupta > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vishstar88 at gmail.com Sun Feb 25 06:53:55 2018 From: vishstar88 at gmail.com (Vishal Gupta) Date: Sun, 25 Feb 2018 17:23:55 +0530 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: References: <161cc8c27cf.e16b927b42372.6259257951918238853@zoho.com> Message-ID: Here's a bunch of ideas that I have 1. Create a new Vector class primarily for vector algebraic operations (instead of numpy arrays). This could be used any and every vector operation. - Vector Product - Scalar Product - Translation - Rotation (Different methods for each formalism) - Magnitude - Distance from other Vector objects - Convert to and from numpy array (This could probably be extended to a Plane class for planar operations and transformations) 2. Create a module in scipy.spatial.rotation that has a different method for each formalism and accepts (vector to be rotated as) Vector or numpy.ndarray along with arguments for the rotation as a numpy.ndarray Thanks, Vishal PS. Sorry for 2 mails. Didn't realize Ctrl+Enter sends a mail in Gmail -------------- next part -------------- An HTML attachment was scrubbed... URL: From smkjain8 at gmail.com Sun Feb 25 07:15:50 2018 From: smkjain8 at gmail.com (Samyak Jain) Date: Sun, 25 Feb 2018 17:45:50 +0530 Subject: [SciPy-Dev] Contributing to scipy In-Reply-To: References: Message-ID: Since I am also applying for GSOC'18 for the project "Rotation formalism in 3 dimensions" so if I can get some help in that area too would be helpful. On Sun, Feb 25, 2018 at 5:42 PM, Samyak Jain wrote: > Yes, I am referring to dependencies. Also I can work on interpolation and > integration. I just need some guidelines on what to do and what things I > need to know for contributing in these types of issues. > > Thanks, > Samyak > > On Sun, Feb 25, 2018 at 12:27 AM, Phillip Feldman < > phillip.m.feldman at gmail.com> wrote: > >> Actually, the code that I have is for integration--not interpolation. >> >> But, I'd like to see support for interpolating irregularly spaced data in >> two and higher dimensions. >> >> On Sat, Feb 24, 2018 at 10:54 AM, Phillip Feldman < >> phillip.m.feldman at gmail.com> wrote: >> >>> When you say "correlated", are you referring to dependencies? >>> >>> If you are interested in working on interpolation, I can suggest some >>> things to be done and also contribute some code. >>> >>> Phillip M. Feldman >>> >>> On Sat, Feb 24, 2018 at 4:21 AM, Samyak Jain wrote: >>> >>>> There is no particular submodule that I am interested in but I would >>>> like to do issues involving some work in python. Can someone suggest which >>>> type of issues I should start with? I have started solving some DOC issues >>>> but now I want to fix some bugs. Also how can I understand the structure of >>>> scipy how other modules are correlated with each other? >>>> >>>> On Fri, Feb 23, 2018 at 11:45 AM, Ralf Gommers >>>> wrote: >>>> >>>>> Hi Samyak, >>>>> >>>>> Welcome! >>>>> >>>>> On Mon, Feb 19, 2018 at 4:57 AM, Samyak Jain >>>>> wrote: >>>>> >>>>>> Hi, I am new to open source and very keen in contributing towards >>>>>> open source. I have started contributing in scipy solving some small DOC >>>>>> issues but I want to solve some major issues too. Can you suggest how do I >>>>>> start with this >>>>>> >>>>> >>>>> Is there a particular area or submodule of SciPy you are interested >>>>> in? We have no shortage of issues, but it would probably be best to work on >>>>> one that's related to your interests or potential gsoc topic. >>>>> >>>>> >>>>>> and also what all I need to know apart from python to start >>>>>> contributing in this org. >>>>>> >>>>> >>>>> A general skill you need is use of git/Github. Beyond that, it depends >>>>> on the topic. Some parts of SciPy are pure Python, for others you may need >>>>> to know Cython, C, C++ or Fortran. >>>>> >>>>> I am also applying for GSOC'18 by contributing with this org hence I >>>>>> need to know how can I contact the mentors as on the IRC no one is >>>>>> replying. Is there any other way to contact them ? >>>>>> >>>>> >>>>> IRC is a very old channel, not many (none?) of the developers are on >>>>> it regularly. We didn't list IRC on the ideas page or >>>>> http://python-gsoc.org as a method to contact the scipy developers. >>>>> Where did you see a link to it? >>>>> >>>>> Cheers, >>>>> Ralf >>>>> >>>>> >>>>> _______________________________________________ >>>>> SciPy-Dev mailing list >>>>> SciPy-Dev at python.org >>>>> https://mail.python.org/mailman/listinfo/scipy-dev >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> SciPy-Dev mailing list >>>> SciPy-Dev at python.org >>>> https://mail.python.org/mailman/listinfo/scipy-dev >>>> >>>> >>> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nikolay.mayorov at zoho.com Sun Feb 25 07:25:37 2018 From: nikolay.mayorov at zoho.com (Nikolay Mayorov) Date: Sun, 25 Feb 2018 17:25:37 +0500 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: References: <161cc8c27cf.e16b927b42372.6259257951918238853@zoho.com> Message-ID: <161ccecf8c8.cdd73e9f215404.6065335874476503115@zoho.com> Hi, Vishal!? Sorry, but I don't like this idea about Vector. And I don't think anyone will like it. A vector in 3D is just a numpy array with 3 elements, it has powerful and well designed API and supports all operations you have listed (besides transforms, which should be applied to it in some way). Also I believe we should represent a set of n vectors as (n, 3).? As for your second point, it is not super clear as stated. I don't think you need to make each rotation representation a "first-class citizen". For example, Euler angles are convenient for defining or interpreting a rotation, but to compose or apply rotations you can't use them directly. Please consider carefully the design I proposed and read the two first references to get a better intuition. If you see any flaws in it - we are ready for discussion.? Best,? Nikolay ---- On Sun, 25 Feb 2018 16:53:55 +0500 vishstar88 at gmail.com wrote ---- Here's a bunch of ideas that I have Create a new Vector class primarily for vector algebraic operations (instead of numpy arrays). This could be used any and every vector operation. Vector Product Scalar Product Translation Rotation (Different methods for each formalism) Magnitude Distance from other Vector objects Convert to and from numpy array (This could probably be extended to a Plane class for planar operations and transformations) Create a module in scipy.spatial.rotation that has a different method for each formalism and accepts (vector to be rotated as) Vector or numpy.ndarray along with arguments for the rotation as a numpy.ndarray Thanks, Vishal PS. Sorry for 2 mails. Didn't realize Ctrl+Enter sends a mail in Gmail -------------- next part -------------- An HTML attachment was scrubbed... URL: From smkjain8 at gmail.com Sun Feb 25 07:12:16 2018 From: smkjain8 at gmail.com (Samyak Jain) Date: Sun, 25 Feb 2018 17:42:16 +0530 Subject: [SciPy-Dev] Contributing to scipy In-Reply-To: References: Message-ID: Yes, I am referring to dependencies. Also I can work on interpolation and integration. I just need some guidelines on what to do and what things I need to know for contributing in these types of issues. Thanks, Samyak On Sun, Feb 25, 2018 at 12:27 AM, Phillip Feldman < phillip.m.feldman at gmail.com> wrote: > Actually, the code that I have is for integration--not interpolation. > > But, I'd like to see support for interpolating irregularly spaced data in > two and higher dimensions. > > On Sat, Feb 24, 2018 at 10:54 AM, Phillip Feldman < > phillip.m.feldman at gmail.com> wrote: > >> When you say "correlated", are you referring to dependencies? >> >> If you are interested in working on interpolation, I can suggest some >> things to be done and also contribute some code. >> >> Phillip M. Feldman >> >> On Sat, Feb 24, 2018 at 4:21 AM, Samyak Jain wrote: >> >>> There is no particular submodule that I am interested in but I would >>> like to do issues involving some work in python. Can someone suggest which >>> type of issues I should start with? I have started solving some DOC issues >>> but now I want to fix some bugs. Also how can I understand the structure of >>> scipy how other modules are correlated with each other? >>> >>> On Fri, Feb 23, 2018 at 11:45 AM, Ralf Gommers >>> wrote: >>> >>>> Hi Samyak, >>>> >>>> Welcome! >>>> >>>> On Mon, Feb 19, 2018 at 4:57 AM, Samyak Jain >>>> wrote: >>>> >>>>> Hi, I am new to open source and very keen in contributing towards >>>>> open source. I have started contributing in scipy solving some small DOC >>>>> issues but I want to solve some major issues too. Can you suggest how do I >>>>> start with this >>>>> >>>> >>>> Is there a particular area or submodule of SciPy you are interested in? >>>> We have no shortage of issues, but it would probably be best to work on one >>>> that's related to your interests or potential gsoc topic. >>>> >>>> >>>>> and also what all I need to know apart from python to start >>>>> contributing in this org. >>>>> >>>> >>>> A general skill you need is use of git/Github. Beyond that, it depends >>>> on the topic. Some parts of SciPy are pure Python, for others you may need >>>> to know Cython, C, C++ or Fortran. >>>> >>>> I am also applying for GSOC'18 by contributing with this org hence I >>>>> need to know how can I contact the mentors as on the IRC no one is >>>>> replying. Is there any other way to contact them ? >>>>> >>>> >>>> IRC is a very old channel, not many (none?) of the developers are on it >>>> regularly. We didn't list IRC on the ideas page or >>>> http://python-gsoc.org as a method to contact the scipy developers. >>>> Where did you see a link to it? >>>> >>>> Cheers, >>>> Ralf >>>> >>>> >>>> _______________________________________________ >>>> SciPy-Dev mailing list >>>> SciPy-Dev at python.org >>>> https://mail.python.org/mailman/listinfo/scipy-dev >>>> >>>> >>> >>> _______________________________________________ >>> SciPy-Dev mailing list >>> SciPy-Dev at python.org >>> https://mail.python.org/mailman/listinfo/scipy-dev >>> >>> >> > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From h.klemm at gmx.de Sun Feb 25 09:20:38 2018 From: h.klemm at gmx.de (Hanno Klemm) Date: Sun, 25 Feb 2018 15:20:38 +0100 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: <161ccecf8c8.cdd73e9f215404.6065335874476503115@zoho.com> References: <161cc8c27cf.e16b927b42372.6259257951918238853@zoho.com> <161ccecf8c8.cdd73e9f215404.6065335874476503115@zoho.com> Message-ID: <90842321-0EF5-4040-86D4-80825731FD81@gmx.de> Hi Vishai, from a user?s point of view: Please don?t create a vector class: Just one more casting I have to keep track off. On a different note: Although of course 3D rotations are most common (and many complexities such as Euler angles and so forth are mostly done in 3D only), it might be a good idea to design the underlying framework in such a way that it can be used more generally: A rotation is essentially only an application of a particular representation of a continuous group (potentially plus a discrete transformation such as reflection). If we can think of a well thought out design, it might be easier, to subclass to nD rotations (I need a lot of 2D rotations, for example), and even Lorentz transformations for special relativity. Although the implementations might require tricky special cases, the underlying concepts are quite similar. Just a thought, Hanno > On 25 Feb 2018, at 13.25, Nikolay Mayorov wrote: > > Hi, Vishal! > > Sorry, but I don't like this idea about Vector. And I don't think anyone will like it. A vector in 3D is just a numpy array with 3 elements, it has powerful and well designed API and supports all operations you have listed (besides transforms, which should be applied to it in some way). Also I believe we should represent a set of n vectors as (n, 3). > > As for your second point, it is not super clear as stated. I don't think you need to make each rotation representation a "first-class citizen". For example, Euler angles are convenient for defining or interpreting a rotation, but to compose or apply rotations you can't use them directly. Please consider carefully the design I proposed and read the two first references to get a better intuition. If you see any flaws in it - we are ready for discussion. > > Best, > Nikolay > > > ---- On Sun, 25 Feb 2018 16:53:55 +0500 vishstar88 at gmail.com wrote ---- > > Here's a bunch of ideas that I have > ? Create a new Vector class primarily for vector algebraic operations (instead of numpy arrays). > This could be used any and every vector operation. > ? Vector Product > ? Scalar Product > ? Translation > ? Rotation (Different methods for each formalism) > ? Magnitude > ? Distance from other Vector objects > ? Convert to and from numpy array > (This could probably be extended to a Plane class for planar operations and transformations) > > ? Create a module in scipy.spatial.rotation that has a different method for each formalism and accepts (vector to be rotated as) Vector or numpy.ndarray along with arguments for the rotation as a numpy.ndarray > > > Thanks, > Vishal > > PS. Sorry for 2 mails. Didn't realize Ctrl+Enter sends a mail in Gmail > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev From ilhanpolat at gmail.com Sun Feb 25 11:18:12 2018 From: ilhanpolat at gmail.com (Ilhan Polat) Date: Sun, 25 Feb 2018 17:18:12 +0100 Subject: [SciPy-Dev] Contributing to scipy In-Reply-To: References: Message-ID: Can you elaborate on what kind of help you are looking for? On Sun, Feb 25, 2018 at 1:15 PM, Samyak Jain wrote: > Since I am also applying for GSOC'18 for the project "Rotation formalism > in 3 dimensions" so if I can get some help in that area too would be > helpful. > > On Sun, Feb 25, 2018 at 5:42 PM, Samyak Jain wrote: > >> Yes, I am referring to dependencies. Also I can work on interpolation and >> integration. I just need some guidelines on what to do and what things I >> need to know for contributing in these types of issues. >> >> Thanks, >> Samyak >> >> On Sun, Feb 25, 2018 at 12:27 AM, Phillip Feldman < >> phillip.m.feldman at gmail.com> wrote: >> >>> Actually, the code that I have is for integration--not interpolation. >>> >>> But, I'd like to see support for interpolating irregularly spaced data >>> in two and higher dimensions. >>> >>> On Sat, Feb 24, 2018 at 10:54 AM, Phillip Feldman < >>> phillip.m.feldman at gmail.com> wrote: >>> >>>> When you say "correlated", are you referring to dependencies? >>>> >>>> If you are interested in working on interpolation, I can suggest some >>>> things to be done and also contribute some code. >>>> >>>> Phillip M. Feldman >>>> >>>> On Sat, Feb 24, 2018 at 4:21 AM, Samyak Jain >>>> wrote: >>>> >>>>> There is no particular submodule that I am interested in but I would >>>>> like to do issues involving some work in python. Can someone suggest which >>>>> type of issues I should start with? I have started solving some DOC issues >>>>> but now I want to fix some bugs. Also how can I understand the structure of >>>>> scipy how other modules are correlated with each other? >>>>> >>>>> On Fri, Feb 23, 2018 at 11:45 AM, Ralf Gommers >>>> > wrote: >>>>> >>>>>> Hi Samyak, >>>>>> >>>>>> Welcome! >>>>>> >>>>>> On Mon, Feb 19, 2018 at 4:57 AM, Samyak Jain >>>>>> wrote: >>>>>> >>>>>>> Hi, I am new to open source and very keen in contributing towards >>>>>>> open source. I have started contributing in scipy solving some small DOC >>>>>>> issues but I want to solve some major issues too. Can you suggest how do I >>>>>>> start with this >>>>>>> >>>>>> >>>>>> Is there a particular area or submodule of SciPy you are interested >>>>>> in? We have no shortage of issues, but it would probably be best to work on >>>>>> one that's related to your interests or potential gsoc topic. >>>>>> >>>>>> >>>>>>> and also what all I need to know apart from python to start >>>>>>> contributing in this org. >>>>>>> >>>>>> >>>>>> A general skill you need is use of git/Github. Beyond that, it >>>>>> depends on the topic. Some parts of SciPy are pure Python, for others you >>>>>> may need to know Cython, C, C++ or Fortran. >>>>>> >>>>>> I am also applying for GSOC'18 by contributing with this org hence I >>>>>>> need to know how can I contact the mentors as on the IRC no one is >>>>>>> replying. Is there any other way to contact them ? >>>>>>> >>>>>> >>>>>> IRC is a very old channel, not many (none?) of the developers are on >>>>>> it regularly. We didn't list IRC on the ideas page or >>>>>> http://python-gsoc.org as a method to contact the scipy developers. >>>>>> Where did you see a link to it? >>>>>> >>>>>> Cheers, >>>>>> Ralf >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> SciPy-Dev mailing list >>>>>> SciPy-Dev at python.org >>>>>> https://mail.python.org/mailman/listinfo/scipy-dev >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> SciPy-Dev mailing list >>>>> SciPy-Dev at python.org >>>>> https://mail.python.org/mailman/listinfo/scipy-dev >>>>> >>>>> >>>> >>> >>> _______________________________________________ >>> SciPy-Dev mailing list >>> SciPy-Dev at python.org >>> https://mail.python.org/mailman/listinfo/scipy-dev >>> >>> >> > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pinakinathc at gmail.com Sun Feb 25 13:34:10 2018 From: pinakinathc at gmail.com (Pinaki Nath Chowdhury) Date: Mon, 26 Feb 2018 00:04:10 +0530 Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: no lapack/blas resources found Message-ID: Hi I am trying to build Scipy package in virtualenv and getting the following error message: ``` Traceback (most recent call last): File "setup.py", line 467, in setup_package() File "setup.py", line 463, in setup_package setup(**metadata) File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "setup.py", line 381, in configuration config.add_subpackage('scipy') File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage caller_level = 2) File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage caller_level = caller_level + 1) File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 15, in configuration config.add_subpackage('linalg') File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage caller_level = 2) File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage caller_level = caller_level + 1) File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/linalg/setup.py", line 19, in configuration raise NotFoundError('no lapack/blas resources found') numpy.distutils.system_info.NotFoundError: no lapack/blas resources found ``` The following is details of my system: ``` *python --verison :* Python 2.7.12 *pip freeze :* alabaster==0.7.10 Babel==2.5.3 certifi==2018.1.18 chardet==3.0.4 Cython==0.27.3 docutils==0.14 idna==2.6 imagesize==1.0.0 Jinja2==2.10 MarkupSafe==1.0 numpy==1.14.1 packaging==16.8 Pygments==2.2.0 pyparsing==2.2.0 pytz==2018.3 requests==2.18.4 six==1.11.0 snowballstemmer==1.2.1 Sphinx==1.7.1 sphinxcontrib-websupport==1.0.1 typing==3.6.4 urllib3==1.22 ``` Hope the above information is sufficient. Thanks Pinaki -------------- next part -------------- An HTML attachment was scrubbed... URL: From xoviat at gmail.com Sun Feb 25 13:36:43 2018 From: xoviat at gmail.com (xoviat) Date: Sun, 25 Feb 2018 12:36:43 -0600 Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: no lapack/blas resources found In-Reply-To: References: Message-ID: What is your OS? On Feb 25, 2018 12:34 PM, "Pinaki Nath Chowdhury" wrote: > Hi > I am trying to build Scipy package in virtualenv and getting the following > error message: > > ``` > Traceback (most recent call last): > File "setup.py", line 467, in > setup_package() > File "setup.py", line 463, in setup_package > setup(**metadata) > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/core.py", > line 135, in setup > config = configuration() > File "setup.py", line 381, in configuration > config.add_subpackage('scipy') > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 1024, in add_subpackage > caller_level = 2) > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 993, in get_subpackage > caller_level = caller_level + 1) > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 930, in _get_configuration_from_setup_py > config = setup_module.configuration(*args) > File "scipy/setup.py", line 15, in configuration > config.add_subpackage('linalg') > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 1024, in add_subpackage > caller_level = 2) > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 993, in get_subpackage > caller_level = caller_level + 1) > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 930, in _get_configuration_from_setup_py > config = setup_module.configuration(*args) > File "scipy/linalg/setup.py", line 19, in configuration > raise NotFoundError('no lapack/blas resources found') > numpy.distutils.system_info.NotFoundError: no lapack/blas resources found > ``` > > The following is details of my system: > ``` > *python --verison :* Python 2.7.12 > > *pip freeze :* > > alabaster==0.7.10 > Babel==2.5.3 > certifi==2018.1.18 > chardet==3.0.4 > Cython==0.27.3 > docutils==0.14 > idna==2.6 > imagesize==1.0.0 > Jinja2==2.10 > MarkupSafe==1.0 > numpy==1.14.1 > packaging==16.8 > Pygments==2.2.0 > pyparsing==2.2.0 > pytz==2018.3 > requests==2.18.4 > six==1.11.0 > snowballstemmer==1.2.1 > Sphinx==1.7.1 > sphinxcontrib-websupport==1.0.1 > typing==3.6.4 > urllib3==1.22 > ``` > > Hope the above information is sufficient. > > Thanks > Pinaki > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pinakinathc at gmail.com Sun Feb 25 13:59:36 2018 From: pinakinathc at gmail.com (Pinaki Nath Chowdhury) Date: Mon, 26 Feb 2018 00:29:36 +0530 Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: no lapack/blas resources found In-Reply-To: References: Message-ID: Hi I use Ubuntu 16.04 (64 bit) My OS information: ``` uname -a: Linux Krishna 4.4.0-112-generic #135-Ubuntu SMP Fri Jan 19 11:48:36 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux hardware (if required): (lshw) ``` H/W path Device Class Description ===================================================== system HP Pavilion Notebook (M2W72PA#ACJ) /0 bus 8096 /0/0 memory 128KiB BIOS /0/4 processor Intel(R) Core(TM) i5-5200U CPU @ 2.20GHz /0/4/6 memory 32KiB L1 cache /0/4/7 memory 256KiB L2 cache /0/4/8 memory 3MiB L3 cache /0/5 memory 32KiB L1 cache /0/16 memory 4GiB System Memory /0/16/0 memory 4GiB SODIMM DDR3 Synchronous 1600 MHz (0.6 ns) /0/16/1 memory Synchronous [empty] /0/100 bridge Broadwell-U Host Bridge -OPI /0/100/2 display Broadwell-U Integrated Graphics /0/100/3 multimedia Broadwell-U Audio Controller /0/100/4 generic Broadwell-U Camarillo Device /0/100/14 bus Wildcat Point-LP USB xHCI Controller /0/100/14/0 usb2 bus xHCI Host Controller /0/100/14/1 usb1 bus xHCI Host Controller /0/100/14/1/3 multimedia HP Truevision HD /0/100/14/1/7 communication Bluetooth Radio /0/100/16 communication Wildcat Point-LP MEI Controller #1 /0/100/1b multimedia Wildcat Point-LP High Definition Audio Controller /0/100/1c bridge Wildcat Point-LP PCI Express Root Port #1 /0/100/1c.1 bridge Wildcat Point-LP PCI Express Root Port #2 /0/100/1c.2 bridge Wildcat Point-LP PCI Express Root Port #3 /0/100/1c.2/0 wlo1 network RTL8723BE PCIe Wireless Network Adapter /0/100/1c.3 bridge Wildcat Point-LP PCI Express Root Port #4 /0/100/1c.3/0 eno1 network RTL8101/2/6E PCI Express Fast/Gigabit Ethernet controller /0/100/1c.4 bridge Wildcat Point-LP PCI Express Root Port #5 /0/100/1c.4/0 display GM108M [GeForce 940M] /0/100/1f bridge Wildcat Point-LP LPC Controller /0/100/1f.2 storage Wildcat Point-LP SATA Controller [AHCI Mode] /0/100/1f.3 bus Wildcat Point-LP SMBus Controller /0/1 scsi0 storage /0/1/0.0.0 /dev/sda disk 1TB ST1000LM024 HN-M /0/1/0.0.0/1 /dev/sda1 volume 649MiB Windows NTFS volume /0/1/0.0.0/2 /dev/sda2 volume 259MiB Windows FAT volume /0/1/0.0.0/3 /dev/sda3 volume 127MiB reserved partition /0/1/0.0.0/4 /dev/sda4 volume 183GiB Windows NTFS volume /0/1/0.0.0/5 /dev/sda5 volume 1018MiB Windows NTFS volume /0/1/0.0.0/6 /dev/sda6 volume 239GiB Windows NTFS volume /0/1/0.0.0/7 /dev/sda7 volume 239GiB Windows NTFS volume /0/1/0.0.0/8 /dev/sda8 volume 27GiB Windows NTFS volume /0/1/0.0.0/9 /dev/sda9 volume 235GiB EXT4 volume /0/1/0.0.0/a /dev/sda10 volume 4017MiB Linux swap volume /0/2 scsi1 storage /0/2/0.0.0 /dev/cdrom disk DVDRW DU8A6SH /1 power KI04041 /2 power OEM Define 5 ``` Thanks Pinaki On Mon, Feb 26, 2018 at 12:06 AM, xoviat wrote: > What is your OS? > > On Feb 25, 2018 12:34 PM, "Pinaki Nath Chowdhury" > wrote: > >> Hi >> I am trying to build Scipy package in virtualenv and getting the >> following error message: >> >> ``` >> Traceback (most recent call last): >> File "setup.py", line 467, in >> setup_package() >> File "setup.py", line 463, in setup_package >> setup(**metadata) >> File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/core.py", >> line 135, in setup >> config = configuration() >> File "setup.py", line 381, in configuration >> config.add_subpackage('scipy') >> File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 1024, in add_subpackage >> caller_level = 2) >> File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 993, in get_subpackage >> caller_level = caller_level + 1) >> File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 930, in _get_configuration_from_setup_py >> config = setup_module.configuration(*args) >> File "scipy/setup.py", line 15, in configuration >> config.add_subpackage('linalg') >> File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 1024, in add_subpackage >> caller_level = 2) >> File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 993, in get_subpackage >> caller_level = caller_level + 1) >> File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 930, in _get_configuration_from_setup_py >> config = setup_module.configuration(*args) >> File "scipy/linalg/setup.py", line 19, in configuration >> raise NotFoundError('no lapack/blas resources found') >> numpy.distutils.system_info.NotFoundError: no lapack/blas resources found >> ``` >> >> The following is details of my system: >> ``` >> *python --verison :* Python 2.7.12 >> >> *pip freeze :* >> >> alabaster==0.7.10 >> Babel==2.5.3 >> certifi==2018.1.18 >> chardet==3.0.4 >> Cython==0.27.3 >> docutils==0.14 >> idna==2.6 >> imagesize==1.0.0 >> Jinja2==2.10 >> MarkupSafe==1.0 >> numpy==1.14.1 >> packaging==16.8 >> Pygments==2.2.0 >> pyparsing==2.2.0 >> pytz==2018.3 >> requests==2.18.4 >> six==1.11.0 >> snowballstemmer==1.2.1 >> Sphinx==1.7.1 >> sphinxcontrib-websupport==1.0.1 >> typing==3.6.4 >> urllib3==1.22 >> ``` >> >> Hope the above information is sufficient. >> >> Thanks >> Pinaki >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> >> > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From xoviat at gmail.com Sun Feb 25 14:02:17 2018 From: xoviat at gmail.com (xoviat) Date: Sun, 25 Feb 2018 13:02:17 -0600 Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: nolapack/blas resources found In-Reply-To: References: Message-ID: <5a930838.332b9d0a.6403c.86bd@mx.google.com> Run: sudo apt-get install libblas-dev liblapack-dev gfortran From: Pinaki Nath Chowdhury Sent: Sunday, February 25, 2018 1:00 PM To: SciPy Developers List Subject: Re: [SciPy-Dev] Error while trying to build scipy: NotFoundError: nolapack/blas resources found Hi I use Ubuntu 16.04 (64 bit) My OS information: ``` uname -a:?Linux Krishna 4.4.0-112-generic #135-Ubuntu SMP Fri Jan 19 11:48:36 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux hardware (if required): (lshw) ``` H/W path? ? ? ?Device? ? ? Class? ? ? ? ? Description ===================================================== ? ? ? ? ? ? ? ? ? ? ? ? ? ?system? ? ? ? ?HP Pavilion Notebook (M2W72PA#ACJ) /0? ? ? ? ? ? ? ? ? ? ? ? ?bus? ? ? ? ? ? 8096 /0/0? ? ? ? ? ? ? ? ? ? ? ?memory? ? ? ? ?128KiB BIOS /0/4? ? ? ? ? ? ? ? ? ? ? ?processor? ? ? Intel(R) Core(TM) i5-5200U CPU @ 2.20GHz /0/4/6? ? ? ? ? ? ? ? ? ? ?memory? ? ? ? ?32KiB L1 cache /0/4/7? ? ? ? ? ? ? ? ? ? ?memory? ? ? ? ?256KiB L2 cache /0/4/8? ? ? ? ? ? ? ? ? ? ?memory? ? ? ? ?3MiB L3 cache /0/5? ? ? ? ? ? ? ? ? ? ? ?memory? ? ? ? ?32KiB L1 cache /0/16? ? ? ? ? ? ? ? ? ? ? memory? ? ? ? ?4GiB System Memory /0/16/0? ? ? ? ? ? ? ? ? ? memory? ? ? ? ?4GiB SODIMM DDR3 Synchronous 1600 MHz (0.6 ns) /0/16/1? ? ? ? ? ? ? ? ? ? memory? ? ? ? ?Synchronous [empty] /0/100? ? ? ? ? ? ? ? ? ? ?bridge? ? ? ? ?Broadwell-U Host Bridge -OPI /0/100/2? ? ? ? ? ? ? ? ? ?display? ? ? ? Broadwell-U Integrated Graphics /0/100/3? ? ? ? ? ? ? ? ? ?multimedia? ? ?Broadwell-U Audio Controller /0/100/4? ? ? ? ? ? ? ? ? ?generic? ? ? ? Broadwell-U Camarillo Device /0/100/14? ? ? ? ? ? ? ? ? bus? ? ? ? ? ? Wildcat Point-LP USB xHCI Controller /0/100/14/0? ? usb2? ? ? ? bus? ? ? ? ? ? xHCI Host Controller /0/100/14/1? ? usb1? ? ? ? bus? ? ? ? ? ? xHCI Host Controller /0/100/14/1/3? ? ? ? ? ? ? multimedia? ? ?HP Truevision HD /0/100/14/1/7? ? ? ? ? ? ? communication? Bluetooth Radio /0/100/16? ? ? ? ? ? ? ? ? communication? Wildcat Point-LP MEI Controller #1 /0/100/1b? ? ? ? ? ? ? ? ? multimedia? ? ?Wildcat Point-LP High Definition Audio Controller /0/100/1c? ? ? ? ? ? ? ? ? bridge? ? ? ? ?Wildcat Point-LP PCI Express Root Port #1 /0/100/1c.1? ? ? ? ? ? ? ? bridge? ? ? ? ?Wildcat Point-LP PCI Express Root Port #2 /0/100/1c.2? ? ? ? ? ? ? ? bridge? ? ? ? ?Wildcat Point-LP PCI Express Root Port #3 /0/100/1c.2/0? wlo1? ? ? ? network? ? ? ? RTL8723BE PCIe Wireless Network Adapter /0/100/1c.3? ? ? ? ? ? ? ? bridge? ? ? ? ?Wildcat Point-LP PCI Express Root Port #4 /0/100/1c.3/0? eno1? ? ? ? network? ? ? ? RTL8101/2/6E PCI Express Fast/Gigabit Ethernet controller /0/100/1c.4? ? ? ? ? ? ? ? bridge? ? ? ? ?Wildcat Point-LP PCI Express Root Port #5 /0/100/1c.4/0? ? ? ? ? ? ? display? ? ? ? GM108M [GeForce 940M] /0/100/1f? ? ? ? ? ? ? ? ? bridge? ? ? ? ?Wildcat Point-LP LPC Controller /0/100/1f.2? ? ? ? ? ? ? ? storage? ? ? ? Wildcat Point-LP SATA Controller [AHCI Mode] /0/100/1f.3? ? ? ? ? ? ? ? bus? ? ? ? ? ? Wildcat Point-LP SMBus Controller /0/1? ? ? ? ? ?scsi0? ? ? ?storage? ? ? ?? /0/1/0.0.0? ? ?/dev/sda? ? disk? ? ? ? ? ?1TB ST1000LM024 HN-M /0/1/0.0.0/1? ?/dev/sda1? ?volume? ? ? ? ?649MiB Windows NTFS volume /0/1/0.0.0/2? ?/dev/sda2? ?volume? ? ? ? ?259MiB Windows FAT volume /0/1/0.0.0/3? ?/dev/sda3? ?volume? ? ? ? ?127MiB reserved partition /0/1/0.0.0/4? ?/dev/sda4? ?volume? ? ? ? ?183GiB Windows NTFS volume /0/1/0.0.0/5? ?/dev/sda5? ?volume? ? ? ? ?1018MiB Windows NTFS volume /0/1/0.0.0/6? ?/dev/sda6? ?volume? ? ? ? ?239GiB Windows NTFS volume /0/1/0.0.0/7? ?/dev/sda7? ?volume? ? ? ? ?239GiB Windows NTFS volume /0/1/0.0.0/8? ?/dev/sda8? ?volume? ? ? ? ?27GiB Windows NTFS volume /0/1/0.0.0/9? ?/dev/sda9? ?volume? ? ? ? ?235GiB EXT4 volume /0/1/0.0.0/a? ?/dev/sda10? volume? ? ? ? ?4017MiB Linux swap volume /0/2? ? ? ? ? ?scsi1? ? ? ?storage? ? ? ?? /0/2/0.0.0? ? ?/dev/cdrom? disk? ? ? ? ? ?DVDRW? DU8A6SH /1? ? ? ? ? ? ? ? ? ? ? ? ?power? ? ? ? ? KI04041 /2? ? ? ? ? ? ? ? ? ? ? ? ?power? ? ? ? ? OEM Define 5 ``` Thanks Pinaki On Mon, Feb 26, 2018 at 12:06 AM, xoviat wrote: What is your OS? On Feb 25, 2018 12:34 PM, "Pinaki Nath Chowdhury" wrote: Hi I am trying to build Scipy package in virtualenv and getting the following error message: ``` Traceback (most recent call last): ? File "setup.py", line 467, in ? ? setup_package() ? File "setup.py", line 463, in setup_package ? ? setup(**metadata) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup ? ? config = configuration() ? File "setup.py", line 381, in configuration ? ? config.add_subpackage('scipy') ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage ? ? caller_level = 2) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage ? ? caller_level = caller_level + 1) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py ? ? config = setup_module.configuration(*args) ? File "scipy/setup.py", line 15, in configuration ? ? config.add_subpackage('linalg') ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage ? ? caller_level = 2) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage ? ? caller_level = caller_level + 1) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py ? ? config = setup_module.configuration(*args) ? File "scipy/linalg/setup.py", line 19, in configuration ? ? raise NotFoundError('no lapack/blas resources found') numpy.distutils.system_info.NotFoundError: no lapack/blas resources found ``` The following is details of my system: ``` python --verison : Python 2.7.12 pip freeze : alabaster==0.7.10 Babel==2.5.3 certifi==2018.1.18 chardet==3.0.4 Cython==0.27.3 docutils==0.14 idna==2.6 imagesize==1.0.0 Jinja2==2.10 MarkupSafe==1.0 numpy==1.14.1 packaging==16.8 Pygments==2.2.0 pyparsing==2.2.0 pytz==2018.3 requests==2.18.4 six==1.11.0 snowballstemmer==1.2.1 Sphinx==1.7.1 sphinxcontrib-websupport==1.0.1 typing==3.6.4 urllib3==1.22 ``` Hope the above information is sufficient. Thanks Pinaki _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From bwana.marko at yahoo.com Sun Feb 25 14:02:50 2018 From: bwana.marko at yahoo.com (Mark Mikofski) Date: Sun, 25 Feb 2018 19:02:50 +0000 (UTC) Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: no lapack/blas resources found In-Reply-To: References: Message-ID: <1344227097.5689800.1519585370493@mail.yahoo.com> Hi Pinaki, Building SciPy from source requires BLAS and LAPACK development libraries, and aFORTRAN compiler. That seems to me to be what your traceback is complaint about. Can you use a wheel instead? There are wheels for every platform at pypi:?https://pypi.python.org/pypi/scipy? Can you tell us what platform you are using? If it is Ubuntu Linux try libblas-dev, liblapack-dev, libopenblas-dev, and gfortran by using `sudo apt install `. In rhel/fedora the names are slightly different. If you're in Mac osx, building from source then you probably will need homebrew to install the dev libraries and gcc (which different from clang that shops with xcode) Try reading the dev docs on building SciPy from source here:?https://scipy.github.io/devdocs/building/index.html Another thought is if you are missing conda and pip, it's possible you have different sources of BLAS and LAPACK. Start your Python interpreter, import numpy and execute `numpy.show_config()` to see what numpy was built with. You will have to match the configuration for scipy. Hope this helps? Sent from Yahoo Mail on Android On Sun, Feb 25, 2018 at 10:34 AM, Pinaki Nath Chowdhury wrote: HiI am trying to build Scipy package in virtualenv and getting the following error message: ```Traceback (most recent call last):? File "setup.py", line 467, in ? ? setup_package()? File "setup.py", line 463, in setup_package? ? setup(**metadata)? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup? ? config = configuration()? File "setup.py", line 381, in configuration? ? config.add_subpackage('scipy')? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage? ? caller_level = 2)? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage? ? caller_level = caller_level + 1)? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py? ? config = setup_module.configuration(*args)? File "scipy/setup.py", line 15, in configuration? ? config.add_subpackage('linalg')? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage? ? caller_level = 2)? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage? ? caller_level = caller_level + 1)? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py? ? config = setup_module.configuration(*args)? File "scipy/linalg/setup.py", line 19, in configuration? ? raise NotFoundError('no lapack/blas resources found')numpy.distutils.system_info.NotFoundError: no lapack/blas resources found``` The following is details of my system:```python --verison : Python 2.7.12 pip freeze : alabaster==0.7.10Babel==2.5.3certifi==2018.1.18chardet==3.0.4Cython==0.27.3docutils==0.14idna==2.6imagesize==1.0.0Jinja2==2.10MarkupSafe==1.0numpy==1.14.1packaging==16.8Pygments==2.2.0pyparsing==2.2.0pytz==2018.3requests==2.18.4six==1.11.0snowballstemmer==1.2.1Sphinx==1.7.1sphinxcontrib-websupport==1.0.1typing==3.6.4urllib3==1.22``` Hope the above information is sufficient. ThanksPinaki_______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Untitled URL: From pinakinathc at gmail.com Sun Feb 25 15:15:30 2018 From: pinakinathc at gmail.com (Pinaki Nath Chowdhury) Date: Mon, 26 Feb 2018 01:45:30 +0530 Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: no lapack/blas resources found In-Reply-To: <1344227097.5689800.1519585370493@mail.yahoo.com> References: <1344227097.5689800.1519585370493@mail.yahoo.com> Message-ID: Thank you very much. As you all pointed out, I needed to get BLAS and LAPACK development libraries and fortan compiler. hence the issue was resolved by simply using: `sudo apt-get install libblas-dev liblapack-dev gfortran` But I am a bit worried that this command installed those development libraries in my main system and not in the virtualenv. So just out of curiosity I wanted to ask, if there is some way in which we can completely install all packages in a virtualenv and then start coding? When I no more feel like working, I can simple delete the virtualenv. Thanks Pinaki On Mon, Feb 26, 2018 at 12:32 AM, Mark Mikofski wrote: > Hi Pinaki, > > Building SciPy from source requires BLAS and LAPACK development libraries, > and aFORTRAN compiler. That seems to me to be what your traceback is > complaint about. > > Can you use a wheel instead? There are wheels for every platform at pypi: > https://pypi.python.org/pypi/scipy > > Can you tell us what platform you are using? If it is Ubuntu Linux try > libblas-dev, liblapack-dev, libopenblas-dev, and gfortran by using `sudo > apt install `. In rhel/fedora the names are slightly different. > > If you're in Mac osx, building from source then you probably will need > homebrew to install the dev libraries and gcc (which different from clang > that shops with xcode) > > Try reading the dev docs on building SciPy from source here: > https://scipy.github.io/devdocs/building/index.html > > Another thought is if you are missing conda and pip, it's possible you > have different sources of BLAS and LAPACK. Start your Python interpreter, > import numpy and execute `numpy.show_config()` to see what numpy was built > with. You will have to match the configuration for scipy. > > Hope this helps? > > > Sent from Yahoo Mail on Android > > On Sun, Feb 25, 2018 at 10:34 AM, Pinaki Nath Chowdhury > wrote: > Hi > I am trying to build Scipy package in virtualenv and getting the following > error message: > > ``` > Traceback (most recent call last): > File "setup.py", line 467, in > setup_package() > File "setup.py", line 463, in setup_package > setup(**metadata) > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/core.py", > line 135, in setup > config = configuration() > File "setup.py", line 381, in configuration > config.add_subpackage('scipy') > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 1024, in add_subpackage > caller_level = 2) > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 993, in get_subpackage > caller_level = caller_level + 1) > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 930, in _get_configuration_from_setup_py > config = setup_module.configuration(*args) > File "scipy/setup.py", line 15, in configuration > config.add_subpackage('linalg') > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 1024, in add_subpackage > caller_level = 2) > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 993, in get_subpackage > caller_level = caller_level + 1) > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 930, in _get_configuration_from_setup_py > config = setup_module.configuration(*args) > File "scipy/linalg/setup.py", line 19, in configuration > raise NotFoundError('no lapack/blas resources found') > numpy.distutils.system_info.NotFoundError: no lapack/blas resources found > ``` > > The following is details of my system: > ``` > *python --verison :* Python 2.7.12 > > *pip freeze :* > > alabaster==0.7.10 > Babel==2.5.3 > certifi==2018.1.18 > chardet==3.0.4 > Cython==0.27.3 > docutils==0.14 > idna==2.6 > imagesize==1.0.0 > Jinja2==2.10 > MarkupSafe==1.0 > numpy==1.14.1 > packaging==16.8 > Pygments==2.2.0 > pyparsing==2.2.0 > pytz==2018.3 > requests==2.18.4 > six==1.11.0 > snowballstemmer==1.2.1 > Sphinx==1.7.1 > sphinxcontrib-websupport==1.0.1 > typing==3.6.4 > urllib3==1.22 > ``` > > Hope the above information is sufficient. > > Thanks > Pinaki > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From xoviat at gmail.com Sun Feb 25 15:25:35 2018 From: xoviat at gmail.com (xoviat) Date: Sun, 25 Feb 2018 14:25:35 -0600 Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: nolapack/blas resources found In-Reply-To: References: <1344227097.5689800.1519585370493@mail.yahoo.com> Message-ID: <5a931bbf.230c9d0a.ba835.463c@mx.google.com> You?ve discovered that Python packages can depend on native system libraries, and that sharing libraries globally could be a problem. Of course, as with anything in computer science, you aren?t the first person to discover this problem. If you?re looking for a package manager that can manage system libraries and Python packages, conda is your solution. However, you should consider the cost/benefit of learning conda vs. just keeping your head down and working on whatever issue you would like to work on. Also note that those BLAS and LAPACK packages are for development only and should not be used in production. Distributors will use a more performant BLAS and LAPACK package that?s written in Assembly. Again, it?s a question of whether it?s worth your time to build a performant BLAS and LAPACK library vs. just using one that?s ?good enough? to get you through development. From: Pinaki Nath Chowdhury Sent: Sunday, February 25, 2018 2:15 PM To: bwana.marko at yahoo.com; SciPy Developers List; xoviat at gmail.com Subject: Re: [SciPy-Dev] Error while trying to build scipy: NotFoundError: nolapack/blas resources found Thank you very much. As you all pointed out, I needed to get BLAS and LAPACK development libraries and fortan compiler. hence the issue was resolved by simply using: `sudo apt-get install libblas-dev liblapack-dev gfortran` But I am a bit worried that this command installed those development libraries in my main system and not in the virtualenv. So just out of curiosity I wanted to ask, if there is some way in which we can completely install all packages in a virtualenv and then start coding? When I no more feel like working, I can simple delete the virtualenv. Thanks Pinaki On Mon, Feb 26, 2018 at 12:32 AM, Mark Mikofski wrote: Hi Pinaki, Building SciPy from source requires BLAS and LAPACK development libraries, and aFORTRAN compiler. That seems to me to be what your traceback is complaint about. Can you use a wheel instead? There are wheels for every platform at pypi:?https://pypi.python.org/pypi/scipy? Can you tell us what platform you are using? If it is Ubuntu Linux try libblas-dev, liblapack-dev, libopenblas-dev, and gfortran by using `sudo apt install `. In rhel/fedora the names are slightly different. If you're in Mac osx, building from source then you probably will need homebrew to install the dev libraries and gcc (which different from clang that shops with xcode) Try reading the dev docs on building SciPy from source here:?https://scipy.github.io/devdocs/building/index.html Another thought is if you are missing conda and pip, it's possible you have different sources of BLAS and LAPACK. Start your Python interpreter, import numpy and execute `numpy.show_config()` to see what numpy was built with. You will have to match the configuration for scipy. Hope this helps? Sent from Yahoo Mail on Android On Sun, Feb 25, 2018 at 10:34 AM, Pinaki Nath Chowdhury wrote: Hi I am trying to build Scipy package in virtualenv and getting the following error message: ``` Traceback (most recent call last): ? File "setup.py", line 467, in ? ? setup_package() ? File "setup.py", line 463, in setup_package ? ? setup(**metadata) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup ? ? config = configuration() ? File "setup.py", line 381, in configuration ? ? config.add_subpackage('scipy') ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage ? ? caller_level = 2) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage ? ? caller_level = caller_level + 1) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py ? ? config = setup_module.configuration(*args) ? File "scipy/setup.py", line 15, in configuration ? ? config.add_subpackage('linalg') ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage ? ? caller_level = 2) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage ? ? caller_level = caller_level + 1) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py ? ? config = setup_module.configuration(*args) ? File "scipy/linalg/setup.py", line 19, in configuration ? ? raise NotFoundError('no lapack/blas resources found') numpy.distutils.system_info.NotFoundError: no lapack/blas resources found ``` The following is details of my system: ``` python --verison : Python 2.7.12 pip freeze : alabaster==0.7.10 Babel==2.5.3 certifi==2018.1.18 chardet==3.0.4 Cython==0.27.3 docutils==0.14 idna==2.6 imagesize==1.0.0 Jinja2==2.10 MarkupSafe==1.0 numpy==1.14.1 packaging==16.8 Pygments==2.2.0 pyparsing==2.2.0 pytz==2018.3 requests==2.18.4 six==1.11.0 snowballstemmer==1.2.1 Sphinx==1.7.1 sphinxcontrib-websupport==1.0.1 typing==3.6.4 urllib3==1.22 ``` Hope the above information is sufficient. Thanks Pinaki _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From bennet at umich.edu Sun Feb 25 15:33:03 2018 From: bennet at umich.edu (Bennet Fauber) Date: Sun, 25 Feb 2018 15:33:03 -0500 Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: no lapack/blas resources found In-Reply-To: References: <1344227097.5689800.1519585370493@mail.yahoo.com> Message-ID: Pinaki, I believe that's what virtual machines and containers are best at: providing a fully self-contained environment. Either would replace the virtualenv. Both Docker and Singularity are popular container environments. If you use something like miniconda/anaconda, those will come with their own set of libraries for at least some things, and that might provide the kind of separation from the system that you are looking for. I believe that the Python virtual environments will encapsulate the Python environment only, but that all the system libraries are still system libraries. Only libraries compiled as part of the Python packages would be in the virtual environment. On Sun, Feb 25, 2018 at 3:15 PM, Pinaki Nath Chowdhury wrote: > Thank you very much. > As you all pointed out, I needed to get BLAS and LAPACK development > libraries and fortan compiler. > hence the issue was resolved by simply using: > `sudo apt-get install libblas-dev liblapack-dev gfortran` > > But I am a bit worried that this command installed those development > libraries in my main system and not in the virtualenv. > So just out of curiosity I wanted to ask, if there is some way in which we > can completely install all packages in a virtualenv and then start coding? > When I no more feel like working, I can simple delete the virtualenv. > > Thanks > Pinaki > > On Mon, Feb 26, 2018 at 12:32 AM, Mark Mikofski > wrote: >> >> Hi Pinaki, >> >> Building SciPy from source requires BLAS and LAPACK development libraries, >> and aFORTRAN compiler. That seems to me to be what your traceback is >> complaint about. >> >> Can you use a wheel instead? There are wheels for every platform at pypi: >> https://pypi.python.org/pypi/scipy >> >> Can you tell us what platform you are using? If it is Ubuntu Linux try >> libblas-dev, liblapack-dev, libopenblas-dev, and gfortran by using `sudo apt >> install `. In rhel/fedora the names are slightly different. >> >> If you're in Mac osx, building from source then you probably will need >> homebrew to install the dev libraries and gcc (which different from clang >> that shops with xcode) >> >> Try reading the dev docs on building SciPy from source here: >> https://scipy.github.io/devdocs/building/index.html >> >> Another thought is if you are missing conda and pip, it's possible you >> have different sources of BLAS and LAPACK. Start your Python interpreter, >> import numpy and execute `numpy.show_config()` to see what numpy was built >> with. You will have to match the configuration for scipy. >> >> Hope this helps? >> >> >> Sent from Yahoo Mail on Android >> >> On Sun, Feb 25, 2018 at 10:34 AM, Pinaki Nath Chowdhury >> wrote: >> Hi >> I am trying to build Scipy package in virtualenv and getting the following >> error message: >> >> ``` >> Traceback (most recent call last): >> File "setup.py", line 467, in >> setup_package() >> File "setup.py", line 463, in setup_package >> setup(**metadata) >> File >> "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/core.py", >> line 135, in setup >> config = configuration() >> File "setup.py", line 381, in configuration >> config.add_subpackage('scipy') >> File >> "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 1024, in add_subpackage >> caller_level = 2) >> File >> "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 993, in get_subpackage >> caller_level = caller_level + 1) >> File >> "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 930, in _get_configuration_from_setup_py >> config = setup_module.configuration(*args) >> File "scipy/setup.py", line 15, in configuration >> config.add_subpackage('linalg') >> File >> "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 1024, in add_subpackage >> caller_level = 2) >> File >> "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 993, in get_subpackage >> caller_level = caller_level + 1) >> File >> "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", >> line 930, in _get_configuration_from_setup_py >> config = setup_module.configuration(*args) >> File "scipy/linalg/setup.py", line 19, in configuration >> raise NotFoundError('no lapack/blas resources found') >> numpy.distutils.system_info.NotFoundError: no lapack/blas resources found >> ``` >> >> The following is details of my system: >> ``` >> python --verison : Python 2.7.12 >> >> pip freeze : >> >> alabaster==0.7.10 >> Babel==2.5.3 >> certifi==2018.1.18 >> chardet==3.0.4 >> Cython==0.27.3 >> docutils==0.14 >> idna==2.6 >> imagesize==1.0.0 >> Jinja2==2.10 >> MarkupSafe==1.0 >> numpy==1.14.1 >> packaging==16.8 >> Pygments==2.2.0 >> pyparsing==2.2.0 >> pytz==2018.3 >> requests==2.18.4 >> six==1.11.0 >> snowballstemmer==1.2.1 >> Sphinx==1.7.1 >> sphinxcontrib-websupport==1.0.1 >> typing==3.6.4 >> urllib3==1.22 >> ``` >> >> Hope the above information is sufficient. >> >> Thanks >> Pinaki >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > From bwana.marko at yahoo.com Sun Feb 25 15:34:13 2018 From: bwana.marko at yahoo.com (Mark Mikofski) Date: Sun, 25 Feb 2018 20:34:13 +0000 (UTC) Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: nolapack/blas resources found In-Reply-To: <5a931bbf.230c9d0a.ba835.463c@mx.google.com> References: <1344227097.5689800.1519585370493@mail.yahoo.com> <5a931bbf.230c9d0a.ba835.463c@mx.google.com> Message-ID: <374795626.5736970.1519590853255@mail.yahoo.com> As xoviat says, if you want all libs in your sandboxed environment then either use (1) conda, (2) a docker image, or (3) autotools with `PREFIX=`, from easiest to hardest Sent from Yahoo Mail on Android On Sun, Feb 25, 2018 at 12:25 PM, xoviat wrote: #yiv0637741737 #yiv0637741737 -- _filtered #yiv0637741737 {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv0637741737 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}#yiv0637741737 #yiv0637741737 p.yiv0637741737MsoNormal, #yiv0637741737 li.yiv0637741737MsoNormal, #yiv0637741737 div.yiv0637741737MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;}#yiv0637741737 a:link, #yiv0637741737 span.yiv0637741737MsoHyperlink {color:blue;text-decoration:underline;}#yiv0637741737 a:visited, #yiv0637741737 span.yiv0637741737MsoHyperlinkFollowed {color:#954F72;text-decoration:underline;}#yiv0637741737 .yiv0637741737MsoChpDefault {} _filtered #yiv0637741737 {margin:1.0in 1.0in 1.0in 1.0in;}#yiv0637741737 div.yiv0637741737WordSection1 {}#yiv0637741737 You?ve discovered that Python packages can depend on native system libraries, and that sharing libraries globally could be a problem. Of course, as with anything in computer science, you aren?t the first person to discover this problem. ? If you?re looking for a package manager that can manage system libraries and Python packages, conda is your solution. However, you should consider the cost/benefit of learning conda vs. just keeping your head down and working on whatever issue you would like to work on. ? Also note that those BLAS and LAPACK packages are for development only and should not be used in production. Distributors will use a more performant BLAS and LAPACK package that?s written in Assembly. Again, it?s a question of whether it?s worth your time to build a performant BLAS and LAPACK library vs. just using one that?s ?good enough?? to get you through development. ? From: Pinaki Nath Chowdhury Sent: Sunday, February 25, 2018 2:15 PM To: bwana.marko at yahoo.com; SciPy Developers List; xoviat at gmail.com Subject: Re: [SciPy-Dev] Error while trying to build scipy: NotFoundError: nolapack/blas resources found ? Thank you very much. As you all pointed out, I needed to get BLAS and LAPACK development libraries and fortan compiler. hence the issue was resolved by simply using: `sudo apt-get install libblas-dev liblapack-dev gfortran` ? But I am a bit worried that this command installed those development libraries in my main system and not in the virtualenv. So just out of curiosity I wanted to ask, if there is some way in which we can completely install all packages in a virtualenv and then start coding? When I no more feel like working, I can simple delete the virtualenv. ? Thanks Pinaki ? On Mon, Feb 26, 2018 at 12:32 AM, Mark Mikofski wrote: Hi Pinaki, ? Building SciPy from source requires BLAS and LAPACK development libraries, and aFORTRAN compiler. That seems to me to be what your traceback is complaint about. ? Can you use a wheel instead? There are wheels for every platform at pypi:?https://pypi.python.org/pypi/scipy? ? Can you tell us what platform you are using? If it is Ubuntu Linux try libblas-dev, liblapack-dev, libopenblas-dev, and gfortran by using `sudo apt install `. In rhel/fedora the names are slightly different. ? If you're in Mac osx, building from source then you probably will need homebrew to install the dev libraries and gcc (which different from clang that shops with xcode) ? Try reading the dev docs on building SciPy from source here:?https://scipy.github.io/devdocs/building/index.html ? Another thought is if you are missing conda and pip, it's possible you have different sources of BLAS and LAPACK. Start your Python interpreter, import numpy and execute `numpy.show_config()` to see what numpy was built with. You will have to match the configuration for scipy. ? Hope this helps? ? ? Sent from Yahoo Mail on Android ? On Sun, Feb 25, 2018 at 10:34 AM, Pinaki Nath Chowdhury wrote: Hi I am trying to build Scipy package in virtualenv and getting the following error message: ? ``` Traceback (most recent call last): ? File "setup.py", line 467, in ? ? setup_package() ? File "setup.py", line 463, in setup_package ? ? setup(**metadata) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup ? ? config = configuration() ? File "setup.py", line 381, in configuration ? ? config.add_subpackage('scipy') ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage ? ? caller_level = 2) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage ? ? caller_level = caller_level + 1) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py ? ? config = setup_module.configuration(*args) ? File "scipy/setup.py", line 15, in configuration ? ? config.add_subpackage('linalg') ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage ? ? caller_level = 2) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage ? ? caller_level = caller_level + 1) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py ? ? config = setup_module.configuration(*args) ? File "scipy/linalg/setup.py", line 19, in configuration ? ? raise NotFoundError('no lapack/blas resources found') numpy.distutils.system_info.NotFoundError: no lapack/blas resources found ``` ? The following is details of my system: ``` python --verison : Python 2.7.12 ? pip freeze : ? alabaster==0.7.10 Babel==2.5.3 certifi==2018.1.18 chardet==3.0.4 Cython==0.27.3 docutils==0.14 idna==2.6 imagesize==1.0.0 Jinja2==2.10 MarkupSafe==1.0 numpy==1.14.1 packaging==16.8 Pygments==2.2.0 pyparsing==2.2.0 pytz==2018.3 requests==2.18.4 six==1.11.0 snowballstemmer==1.2.1 Sphinx==1.7.1 sphinxcontrib-websupport==1.0.1 typing==3.6.4 urllib3==1.22 ``` ? Hope the above information is sufficient. ? Thanks Pinaki _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev ? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From bwana.marko at yahoo.com Sun Feb 25 16:21:24 2018 From: bwana.marko at yahoo.com (Mark Mikofski) Date: Sun, 25 Feb 2018 21:21:24 +0000 (UTC) Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: nolapack/blas resources found In-Reply-To: <374795626.5736970.1519590853255@mail.yahoo.com> References: <1344227097.5689800.1519585370493@mail.yahoo.com> <5a931bbf.230c9d0a.ba835.463c@mx.google.com> <374795626.5736970.1519590853255@mail.yahoo.com> Message-ID: <250575993.5761256.1519593684579@mail.yahoo.com> I will also add that it's very important to read the docs that I linked to previously??https://scipy.github.io/devdocs/building/index.html??A lot of information is there that you won't get ad hoc on a mailing list Sent from Yahoo Mail on Android On Sun, Feb 25, 2018 at 12:34 PM, Mark Mikofski wrote: As xoviat says, if you want all libs in your sandboxed environment then either use (1) conda, (2) a docker image, or (3) autotools with `PREFIX=`, from easiest to hardest Sent from Yahoo Mail on Android On Sun, Feb 25, 2018 at 12:25 PM, xoviat wrote: #yiv0637741737 #yiv0637741737 -- _filtered #yiv0637741737 {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv0637741737 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}#yiv0637741737 #yiv0637741737 p.yiv0637741737MsoNormal, #yiv0637741737 li.yiv0637741737MsoNormal, #yiv0637741737 div.yiv0637741737MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;}#yiv0637741737 a:link, #yiv0637741737 span.yiv0637741737MsoHyperlink {color:blue;text-decoration:underline;}#yiv0637741737 a:visited, #yiv0637741737 span.yiv0637741737MsoHyperlinkFollowed {color:#954F72;text-decoration:underline;}#yiv0637741737 .yiv0637741737MsoChpDefault {} _filtered #yiv0637741737 {margin:1.0in 1.0in 1.0in 1.0in;}#yiv0637741737 div.yiv0637741737WordSection1 {}#yiv0637741737 You?ve discovered that Python packages can depend on native system libraries, and that sharing libraries globally could be a problem. Of course, as with anything in computer science, you aren?t the first person to discover this problem. ? If you?re looking for a package manager that can manage system libraries and Python packages, conda is your solution. However, you should consider the cost/benefit of learning conda vs. just keeping your head down and working on whatever issue you would like to work on. ? Also note that those BLAS and LAPACK packages are for development only and should not be used in production. Distributors will use a more performant BLAS and LAPACK package that?s written in Assembly. Again, it?s a question of whether it?s worth your time to build a performant BLAS and LAPACK library vs. just using one that?s ?good enough?? to get you through development. ? From: Pinaki Nath Chowdhury Sent: Sunday, February 25, 2018 2:15 PM To: bwana.marko at yahoo.com; SciPy Developers List; xoviat at gmail.com Subject: Re: [SciPy-Dev] Error while trying to build scipy: NotFoundError: nolapack/blas resources found ? Thank you very much. As you all pointed out, I needed to get BLAS and LAPACK development libraries and fortan compiler. hence the issue was resolved by simply using: `sudo apt-get install libblas-dev liblapack-dev gfortran` ? But I am a bit worried that this command installed those development libraries in my main system and not in the virtualenv. So just out of curiosity I wanted to ask, if there is some way in which we can completely install all packages in a virtualenv and then start coding? When I no more feel like working, I can simple delete the virtualenv. ? Thanks Pinaki ? On Mon, Feb 26, 2018 at 12:32 AM, Mark Mikofski wrote: Hi Pinaki, ? Building SciPy from source requires BLAS and LAPACK development libraries, and aFORTRAN compiler. That seems to me to be what your traceback is complaint about. ? Can you use a wheel instead? There are wheels for every platform at pypi:?https://pypi.python.org/pypi/scipy? ? Can you tell us what platform you are using? If it is Ubuntu Linux try libblas-dev, liblapack-dev, libopenblas-dev, and gfortran by using `sudo apt install `. In rhel/fedora the names are slightly different. ? If you're in Mac osx, building from source then you probably will need homebrew to install the dev libraries and gcc (which different from clang that shops with xcode) ? Try reading the dev docs on building SciPy from source here:?https://scipy.github.io/devdocs/building/index.html ? Another thought is if you are missing conda and pip, it's possible you have different sources of BLAS and LAPACK. Start your Python interpreter, import numpy and execute `numpy.show_config()` to see what numpy was built with. You will have to match the configuration for scipy. ? Hope this helps? ? ? Sent from Yahoo Mail on Android ? On Sun, Feb 25, 2018 at 10:34 AM, Pinaki Nath Chowdhury wrote: Hi I am trying to build Scipy package in virtualenv and getting the following error message: ? ``` Traceback (most recent call last): ? File "setup.py", line 467, in ? ? setup_package() ? File "setup.py", line 463, in setup_package ? ? setup(**metadata) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup ? ? config = configuration() ? File "setup.py", line 381, in configuration ? ? config.add_subpackage('scipy') ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage ? ? caller_level = 2) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage ? ? caller_level = caller_level + 1) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py ? ? config = setup_module.configuration(*args) ? File "scipy/setup.py", line 15, in configuration ? ? config.add_subpackage('linalg') ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1024, in add_subpackage ? ? caller_level = 2) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 993, in get_subpackage ? ? caller_level = caller_level + 1) ? File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 930, in _get_configuration_from_setup_py ? ? config = setup_module.configuration(*args) ? File "scipy/linalg/setup.py", line 19, in configuration ? ? raise NotFoundError('no lapack/blas resources found') numpy.distutils.system_info.NotFoundError: no lapack/blas resources found ``` ? The following is details of my system: ``` python --verison : Python 2.7.12 ? pip freeze : ? alabaster==0.7.10 Babel==2.5.3 certifi==2018.1.18 chardet==3.0.4 Cython==0.27.3 docutils==0.14 idna==2.6 imagesize==1.0.0 Jinja2==2.10 MarkupSafe==1.0 numpy==1.14.1 packaging==16.8 Pygments==2.2.0 pyparsing==2.2.0 pytz==2018.3 requests==2.18.4 six==1.11.0 snowballstemmer==1.2.1 Sphinx==1.7.1 sphinxcontrib-websupport==1.0.1 typing==3.6.4 urllib3==1.22 ``` ? Hope the above information is sufficient. ? Thanks Pinaki _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev ? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From pinakinathc at gmail.com Sun Feb 25 21:14:31 2018 From: pinakinathc at gmail.com (Pinaki Nath Chowdhury) Date: Mon, 26 Feb 2018 07:44:31 +0530 Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: nolapack/blas resources found In-Reply-To: <374795626.5736970.1519590853255@mail.yahoo.com> References: <1344227097.5689800.1519585370493@mail.yahoo.com> <5a931bbf.230c9d0a.ba835.463c@mx.google.com> <374795626.5736970.1519590853255@mail.yahoo.com> Message-ID: Thank you all. I have started with conda by installing Miniconda and it works great!! Pinaki On Mon, Feb 26, 2018 at 2:04 AM, Mark Mikofski wrote: > As xoviat says, if you want all libs in your sandboxed environment then > either use (1) conda, (2) a docker image, or (3) autotools with > `PREFIX=`, from easiest to hardest > > Sent from Yahoo Mail on Android > > > On Sun, Feb 25, 2018 at 12:25 PM, xoviat > wrote: > > You?ve discovered that Python packages can depend on native system > libraries, and that sharing libraries globally could be a problem. Of > course, as with anything in computer science, you aren?t the first person > to discover this problem. > > > > If you?re looking for a package manager that can manage system libraries > and Python packages, conda is your solution. However, you should consider > the cost/benefit of learning conda vs. just keeping your head down and > working on whatever issue you would like to work on. > > > > Also note that those BLAS and LAPACK packages are for development only and > should not be used in production. Distributors will use a more performant > BLAS and LAPACK package that?s written in Assembly. Again, it?s a question > of whether it?s worth your time to build a performant BLAS and LAPACK > library vs. just using one that?s ?good enough? to get you through > development. > > > > *From: *Pinaki Nath Chowdhury > *Sent: *Sunday, February 25, 2018 2:15 PM > *To: *bwana.marko at yahoo.com; SciPy Developers List ; > xoviat at gmail.com > *Subject: *Re: [SciPy-Dev] Error while trying to build scipy: > NotFoundError: nolapack/blas resources found > > > > Thank you very much. > > As you all pointed out, I needed to get BLAS and LAPACK development > libraries and fortan compiler. > > hence the issue was resolved by simply using: > `sudo apt-get install libblas-dev liblapack-dev gfortran` > > > > But I am a bit worried that this command installed those development > libraries in my main system and not in the virtualenv. > > So just out of curiosity I wanted to ask, if there is some way in which we > can completely install all packages in a virtualenv and then start coding? > When I no more feel like working, I can simple delete the virtualenv. > > > > Thanks > > Pinaki > > > > On Mon, Feb 26, 2018 at 12:32 AM, Mark Mikofski > wrote: > > Hi Pinaki, > > > > Building SciPy from source requires BLAS and LAPACK development libraries, > and aFORTRAN compiler. That seems to me to be what your traceback is > complaint about. > > > > Can you use a wheel instead? There are wheels for every platform at pypi: > https://pypi.python.org/pypi/scipy > > > > Can you tell us what platform you are using? If it is Ubuntu Linux try > libblas-dev, liblapack-dev, libopenblas-dev, and gfortran by using `sudo > apt install `. In rhel/fedora the names are slightly different. > > > > If you're in Mac osx, building from source then you probably will need > homebrew to install the dev libraries and gcc (which different from clang > that shops with xcode) > > > > Try reading the dev docs on building SciPy from source here: > https://scipy.github.io/devdocs/building/index.html > > > > Another thought is if you are missing conda and pip, it's possible you > have different sources of BLAS and LAPACK. Start your Python interpreter, > import numpy and execute `numpy.show_config()` to see what numpy was built > with. You will have to match the configuration for scipy. > > > > Hope this helps? > > > > > > Sent from Yahoo Mail on Android > > > > On Sun, Feb 25, 2018 at 10:34 AM, Pinaki Nath Chowdhury > > wrote: > > Hi > > I am trying to build Scipy package in virtualenv and getting the following > error message: > > > > ``` > > Traceback (most recent call last): > > File "setup.py", line 467, in > > setup_package() > > File "setup.py", line 463, in setup_package > > setup(**metadata) > > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/core.py", > line 135, in setup > > config = configuration() > > File "setup.py", line 381, in configuration > > config.add_subpackage('scipy') > > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 1024, in add_subpackage > > caller_level = 2) > > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 993, in get_subpackage > > caller_level = caller_level + 1) > > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 930, in _get_configuration_from_setup_py > > config = setup_module.configuration(*args) > > File "scipy/setup.py", line 15, in configuration > > config.add_subpackage('linalg') > > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 1024, in add_subpackage > > caller_level = 2) > > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 993, in get_subpackage > > caller_level = caller_level + 1) > > File "/home/pinaki/gsoc/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > line 930, in _get_configuration_from_setup_py > > config = setup_module.configuration(*args) > > File "scipy/linalg/setup.py", line 19, in configuration > > raise NotFoundError('no lapack/blas resources found') > > numpy.distutils.system_info.NotFoundError: no lapack/blas resources found > > ``` > > > > The following is details of my system: > > ``` > > *python --verison :* Python 2.7.12 > > > > *pip freeze :* > > > > alabaster==0.7.10 > > Babel==2.5.3 > > certifi==2018.1.18 > > chardet==3.0.4 > > Cython==0.27.3 > > docutils==0.14 > > idna==2.6 > > imagesize==1.0.0 > > Jinja2==2.10 > > MarkupSafe==1.0 > > numpy==1.14.1 > > packaging==16.8 > > Pygments==2.2.0 > > pyparsing==2.2.0 > > pytz==2018.3 > > requests==2.18.4 > > six==1.11.0 > > snowballstemmer==1.2.1 > > Sphinx==1.7.1 > > sphinxcontrib-websupport==1.0.1 > > typing==3.6.4 > > urllib3==1.22 > > ``` > > > > Hope the above information is sufficient. > > > > Thanks > > Pinaki > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From anubhavp28 at gmail.com Mon Feb 26 05:12:35 2018 From: anubhavp28 at gmail.com (Anubhav Patel) Date: Mon, 26 Feb 2018 15:42:35 +0530 Subject: [SciPy-Dev] Contributing to SciPy through GSoC Message-ID: Hi everyone, I want to work on SciPy as part of GSoC and I have few queries. 1. On the Ideas Page, there was a mention of scipy.spatial.transform module. I want to know what will be the exact purpose of this module? 2. Whether the idea for a module for numerical differentiation was dropped completely? 3. Apart from those ideas listed on ideas page, are there any other area where you guys would like to see contribution on? -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Mon Feb 26 05:29:41 2018 From: matthew.brett at gmail.com (Matthew Brett) Date: Mon, 26 Feb 2018 10:29:41 +0000 Subject: [SciPy-Dev] Error while trying to build scipy: NotFoundError: nolapack/blas resources found In-Reply-To: References: <1344227097.5689800.1519585370493@mail.yahoo.com> <5a931bbf.230c9d0a.ba835.463c@mx.google.com> <374795626.5736970.1519590853255@mail.yahoo.com> Message-ID: Hi, On Mon, Feb 26, 2018 at 2:14 AM, Pinaki Nath Chowdhury wrote: > Thank you all. I have started with conda by installing Miniconda and it > works great!! I should point out that, pip wheels do ship with their library dependencies, so if you are not building from source, you get much the same isolation from the two systems. For example, if you do: virtualenv my_venv . ./my_venv/bin/activate pip install numpy you'll get a numpy with its BLAS / LAPACK libraries embedded in the numpy install. Cheers, Matthew From ilhanpolat at gmail.com Mon Feb 26 06:36:52 2018 From: ilhanpolat at gmail.com (Ilhan Polat) Date: Mon, 26 Feb 2018 12:36:52 +0100 Subject: [SciPy-Dev] Contributing to SciPy through GSoC In-Reply-To: References: Message-ID: without being completely wrong, you can safely assume that there is a strong opinion to have no new modules in SciPy but make the existing modules production ready in the short term. That means long waiting issues and missing functionalities. On Mon, Feb 26, 2018 at 11:12 AM, Anubhav Patel wrote: > Hi everyone, > I want to work on SciPy as part of GSoC and I have few queries. > > 1. On the Ideas Page, there was a mention of scipy.spatial.transform > module. I want to know what will be the exact purpose of this module? > > 2. Whether the idea for a module for numerical differentiation was dropped > completely? > > 3. Apart from those ideas listed on ideas page, are there any other area > where you guys would like to see contribution on? > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Mon Feb 26 11:00:16 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Mon, 26 Feb 2018 08:00:16 -0800 Subject: [SciPy-Dev] Contributing to SciPy through GSoC In-Reply-To: References: Message-ID: Hi Anubhev, On Mon, Feb 26, 2018 at 2:12 AM, Anubhav Patel wrote: > Hi everyone, > I want to work on SciPy as part of GSoC and I have few queries. > > 1. On the Ideas Page, there was a mention of scipy.spatial.transform > module. I want to know what will be the exact purpose of this module? > Did you read the whole idea? There's a lot of detail. It says for example "The aim of this project is to create a module which will allow to conveniently describe, apply and compose rotations. ". That answer your question I think. > > 2. Whether the idea for a module for numerical differentiation was dropped > completely? > Yes, for now that's off the table - at least not feasible for a GSoC we've concluded after several attempts. > > 3. Apart from those ideas listed on ideas page, are there any other area > where you guys would like to see contribution on? > Ideas for new features on http://scipy.github.io/devdocs/roadmap.html are of interest, or ones you may have yourself. But given that they're not on the ideas page, it's not guaranteed we can find mentors for those. Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikegraham at gmail.com Mon Feb 26 12:53:35 2018 From: mikegraham at gmail.com (Mike Graham) Date: Mon, 26 Feb 2018 12:53:35 -0500 Subject: [SciPy-Dev] SciPy IRC channel lacks moderation In-Reply-To: References: Message-ID: On Fri, Feb 23, 2018 at 1:25 AM, Ralf Gommers wrote: > > I'm fine with either option, discontinuing or moderation. Either way we > should make it clear that scipy devs don't hang out there. > For what it's worth, people still get help with numpy, scipy, and other scientific programming issues in the channel every day. Nathan remarked that closing the channel was "a really dumb idea". ;) If you want to appoint Nathan (ngoldbaum on Freenode) and/or me (papna on freenode) as group contact to have moderator tools, the freenode people will probably do that if we can point them to this mailing list thread. They will just want to see that it is what the project wants. Thanks, Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From ilhanpolat at gmail.com Mon Feb 26 13:00:52 2018 From: ilhanpolat at gmail.com (Ilhan Polat) Date: Mon, 26 Feb 2018 19:00:52 +0100 Subject: [SciPy-Dev] SciPy IRC channel lacks moderation In-Reply-To: References: Message-ID: Or we can just remove the "official" tone from the channel description, if there is any, and people can still continue getting information without the maintenance or moderation burden on the SciPy team. I don't even know how to get to any IRC channel and I doubt any younger generation does too (just asked 10-15 data scientists aged 25+ish during lunch time, so admittedly not really a comprehensive survey) On Mon, Feb 26, 2018 at 6:53 PM, Mike Graham wrote: > On Fri, Feb 23, 2018 at 1:25 AM, Ralf Gommers > wrote: > >> >> I'm fine with either option, discontinuing or moderation. Either way we >> should make it clear that scipy devs don't hang out there. >> > > For what it's worth, people still get help with numpy, scipy, and other > scientific programming issues in the channel every day. Nathan remarked > that closing the channel was "a really dumb idea". ;) > > If you want to appoint Nathan (ngoldbaum on Freenode) and/or me (papna on > freenode) as group contact to have moderator tools, the freenode people > will probably do that if we can point them to this mailing list thread. > They will just want to see that it is what the project wants. > > Thanks, > Mike > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nikolay.mayorov at zoho.com Mon Feb 26 13:15:15 2018 From: nikolay.mayorov at zoho.com (Nikolay Mayorov) Date: Mon, 26 Feb 2018 23:15:15 +0500 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: <90842321-0EF5-4040-86D4-80825731FD81@gmx.de> References: <161cc8c27cf.e16b927b42372.6259257951918238853@zoho.com> <161ccecf8c8.cdd73e9f215404.6065335874476503115@zoho.com> <90842321-0EF5-4040-86D4-80825731FD81@gmx.de> Message-ID: <161d3536c72.bd3930bb278733.4122577303708210357@zoho.com> Hi, Hanno! I personally don't feel comfortable at all doing anything with rotations in higher than 3 dimensions. Intuitively seems too abstract for a numerical methods library. You mentioned Lorentz transformation, I recall it might be considered as a rotation, but not even in Euclidean space. I think it's too tricky to go to higher dimensions, but perhaps some student can pick it up. But Rotation2D might be a useful little addition, although I'm not sure if it is truly necessary, as it is so simple. Thanks for your input, Nikolay ---- On Sun, 25 Feb 2018 19:20:38 +0500 h.klemm at gmx.de wrote ---- Hi Vishai, from a user?s point of view: Please don?t create a vector class: Just one more casting I have to keep track off. On a different note: Although of course 3D rotations are most common (and many complexities such as Euler angles and so forth are mostly done in 3D only), it might be a good idea to design the underlying framework in such a way that it can be used more generally: A rotation is essentially only an application of a particular representation of a continuous group (potentially plus a discrete transformation such as reflection). If we can think of a well thought out design, it might be easier, to subclass to nD rotations (I need a lot of 2D rotations, for example), and even Lorentz transformations for special relativity. Although the implementations might require tricky special cases, the underlying concepts are quite similar. Just a thought, Hanno > On 25 Feb 2018, at 13.25, Nikolay Mayorov wrote: > > Hi, Vishal! > > Sorry, but I don't like this idea about Vector. And I don't think anyone will like it. A vector in 3D is just a numpy array with 3 elements, it has powerful and well designed API and supports all operations you have listed (besides transforms, which should be applied to it in some way). Also I believe we should represent a set of n vectors as (n, 3). > > As for your second point, it is not super clear as stated. I don't think you need to make each rotation representation a "first-class citizen". For example, Euler angles are convenient for defining or interpreting a rotation, but to compose or apply rotations you can't use them directly. Please consider carefully the design I proposed and read the two first references to get a better intuition. If you see any flaws in it - we are ready for discussion. > > Best, > Nikolay > > > ---- On Sun, 25 Feb 2018 16:53:55 +0500 vishstar88 at gmail.com wrote ---- > > Here's a bunch of ideas that I have > ????? Create a new Vector class primarily for vector algebraic operations (instead of numpy arrays). > This could be used any and every vector operation. > ????????? Vector Product > ????????? Scalar Product > ????????? Translation > ????????? Rotation (Different methods for each formalism) > ????????? Magnitude > ????????? Distance from other Vector objects > ????????? Convert to and from numpy array > (This could probably be extended to a Plane class for planar operations and transformations) > > ????? Create a module in scipy.spatial.rotation that has a different method for each formalism and accepts (vector to be rotated as) Vector or numpy.ndarray along with arguments for the rotation as a numpy.ndarray > > > Thanks, > Vishal > > PS. Sorry for 2 mails. Didn't realize Ctrl+Enter sends a mail in Gmail > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev _______________________________________________ SciPy-Dev mailing list SciPy-Dev at python.org https://mail.python.org/mailman/listinfo/scipy-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From gdp.1807 at gmail.com Mon Feb 26 13:30:05 2018 From: gdp.1807 at gmail.com (GAGANDEEP SINGH) Date: Tue, 27 Feb 2018 00:00:05 +0530 Subject: [SciPy-Dev] GSoC 2018 In-Reply-To: References: Message-ID: Dear developers, As it was said that the surface/volume integrals for arbitrary surfaces/volumes cannot be calculated easily in python. But I am able to do so by applying Simpson rule for Double Integrals and achieved the theoretical answer. If any mentor wants to reconsider my idea on extending scipy.integrate for GSoC 2018, then please discuss with me. Waiting for a positive response. With Regards, Gagandeep Singh -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikegraham at gmail.com Mon Feb 26 13:47:53 2018 From: mikegraham at gmail.com (Mike Graham) Date: Mon, 26 Feb 2018 13:47:53 -0500 Subject: [SciPy-Dev] SciPy IRC channel lacks moderation In-Reply-To: References: Message-ID: On Mon, Feb 26, 2018 at 1:00 PM, Ilhan Polat wrote: > Or we can just remove the "official" tone from the channel description, if > there is any, and people can still continue getting information without the > maintenance or moderation burden on the SciPy team. > It's certainly the team's call whether the channel can continue, but it really seems like relatively little effort not to end it. Freenode will not allow access to moderator tools for a channel called "#scipy" without the project weighing in. I don't even know how to get to any IRC channel and I doubt any younger > generation does too (just asked 10-15 data scientists aged 25+ish during > lunch time, so admittedly not really a comprehensive survey) I do not know what generations most channel participants are, but -- for what it's worth -- many of them are students. Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From pav at iki.fi Mon Feb 26 15:04:18 2018 From: pav at iki.fi (Pauli Virtanen) Date: Mon, 26 Feb 2018 21:04:18 +0100 Subject: [SciPy-Dev] SciPy IRC channel lacks moderation In-Reply-To: References: Message-ID: <1519675458.2780.7.camel@iki.fi> to, 2018-02-22 kello 22:25 -0800, Ralf Gommers kirjoitti: > I'm fine with either option, discontinuing or moderation. Either way > we > should make it clear that scipy devs don't hang out there. I'm still logged on the channel, although I'm not following the discussion actively. I can in principle GC it with freenode, in case we want to continue it, but I'm going to have to leave moderation mostly to volunteers. Pauli From h.klemm at gmx.de Mon Feb 26 15:52:57 2018 From: h.klemm at gmx.de (Hanno Klemm) Date: Mon, 26 Feb 2018 21:52:57 +0100 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: <161d3536c72.bd3930bb278733.4122577303708210357@zoho.com> References: <161cc8c27cf.e16b927b42372.6259257951918238853@zoho.com> <161ccecf8c8.cdd73e9f215404.6065335874476503115@zoho.com> <90842321-0EF5-4040-86D4-80825731FD81@gmx.de> <161d3536c72.bd3930bb278733.4122577303708210357@zoho.com> Message-ID: <3343368F-8FB2-4262-929C-A178BFB6329D@gmx.de> Hi Nikolay, probably, I didn?t make myself clear enough. I don?t want to advocate that we try to implement any non-3D rotations in this GSOC. All I wanted to do, is to mention that it might be useful, if we think about the possibility of other rotations, when we design the underlying classes. Something along the line of class Rotation() #general thing class Rotation3D(Rotation) class Rotation2D(Rotation) I am not completely sure, if this really does make sense, but I think having the fact that 3D rotations are an (important) special case of a more general concept in the back of our minds might help to make good design choices. As I said, just a thought, Best, Hanno > On 26 Feb 2018, at 19.15, Nikolay Mayorov wrote: > > Hi, Hanno! > > I personally don't feel comfortable at all doing anything with rotations in higher than 3 dimensions. Intuitively seems too abstract for a numerical methods library. You mentioned Lorentz transformation, I recall it might be considered as a rotation, but not even in Euclidean space. I think it's too tricky to go to higher dimensions, but perhaps some student can pick it up. > > But Rotation2D might be a useful little addition, although I'm not sure if it is truly necessary, as it is so simple. > > Thanks for your input, > Nikolay > > > ---- On Sun, 25 Feb 2018 19:20:38 +0500 h.klemm at gmx.de wrote ---- > > Hi Vishai, > > from a user?s point of view: Please don?t create a vector class: Just one more casting I have to keep track off. > > On a different note: Although of course 3D rotations are most common (and many complexities such as Euler angles and so forth are mostly done in 3D only), it might be a good idea to design the underlying framework in such a way that it can be used more generally: A rotation is essentially only an application of a particular representation of a continuous group (potentially plus a discrete transformation such as reflection). If we can think of a well thought out design, it might be easier, to subclass to nD rotations (I need a lot of 2D rotations, for example), and even Lorentz transformations for special relativity. Although the implementations might require tricky special cases, the underlying concepts are quite similar. > > Just a thought, > Hanno > > > On 25 Feb 2018, at 13.25, Nikolay Mayorov wrote: > > > > Hi, Vishal! > > > > Sorry, but I don't like this idea about Vector. And I don't think anyone will like it. A vector in 3D is just a numpy array with 3 elements, it has powerful and well designed API and supports all operations you have listed (besides transforms, which should be applied to it in some way). Also I believe we should represent a set of n vectors as (n, 3). > > > > As for your second point, it is not super clear as stated. I don't think you need to make each rotation representation a "first-class citizen". For example, Euler angles are convenient for defining or interpreting a rotation, but to compose or apply rotations you can't use them directly. Please consider carefully the design I proposed and read the two first references to get a better intuition. If you see any flaws in it - we are ready for discussion. > > > > Best, > > Nikolay > > > > > > ---- On Sun, 25 Feb 2018 16:53:55 +0500 vishstar88 at gmail.com wrote ---- > > > > Here's a bunch of ideas that I have > > ? Create a new Vector class primarily for vector algebraic operations (instead of numpy arrays). > > This could be used any and every vector operation. > > ? Vector Product > > ? Scalar Product > > ? Translation > > ? Rotation (Different methods for each formalism) > > ? Magnitude > > ? Distance from other Vector objects > > ? Convert to and from numpy array > > (This could probably be extended to a Plane class for planar operations and transformations) > > > > ? Create a module in scipy.spatial.rotation that has a different method for each formalism and accepts (vector to be rotated as) Vector or numpy.ndarray along with arguments for the rotation as a numpy.ndarray > > > > > > Thanks, > > Vishal > > > > PS. Sorry for 2 mails. Didn't realize Ctrl+Enter sends a mail in Gmail > > > > > > _______________________________________________ > > SciPy-Dev mailing list > > SciPy-Dev at python.org > > https://mail.python.org/mailman/listinfo/scipy-dev > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev From bwana.marko at yahoo.com Mon Feb 26 20:43:46 2018 From: bwana.marko at yahoo.com (Mark Mikofski) Date: Tue, 27 Feb 2018 01:43:46 +0000 (UTC) Subject: [SciPy-Dev] Use more common Halley's method instead of parabolic variant References: <1416540474.6606511.1519695826515.ref@mail.yahoo.com> Message-ID: <1416540474.6606511.1519695826515@mail.yahoo.com> Hi All, I would like to propose that we change the form of the Halley's method in scipy.optimize.zeros from the "parabolic" variant currently in use (see?https://de.wikipedia.org/wiki/Halley-Verfahren?from issue #5922?https://github.com/scipy/scipy/issues/5922?) with the more common form found in several other popular libraries and references (see list at end of email). I think that there are at least four advantages to using the more common form: (1) the parabolic variant has an unnecessary branching condition, which makes the file easier to read, understand and maintain, (2) the proposed changes actually make the `zeros.py` file smaller by removing about 5 lines, (3) the common form seems to have more documentation and widespread usage, so it is easier to find, and should increase confidence in it's usage, and (4) without branching conditions, it is easier to vectorize these methods, so that they can process numerous scalar, univariate cases simulataneously using numpy arrays or in a tight cythonized loop, with exit conditions that are similar to the multivariate case: (a) if derivatives are badly conditioned, then exit or (b) if absoluate max of all of the Newton steps is less than a given tolerance.?? I have made my proposed changes in PR #8489?https://github.com/scipy/scipy/pull/8489 List of libraries and references using the more common form of Halley's method: (1) Boost (http://www.boost.org/doc/libs/1_62_0/libs/math/doc/html/math_toolkit/roots/roots_deriv.html#math_toolkit.roots.roots_deriv.halley), (2) the English language Wikipedia (https://en.wikipedia.org/wiki/Halley%27s_method), (3) Wolfram's (http://mathworld.wolfram.com/HalleysMethod.html), (4) JuliaLang? Roots.jl (https://github.com/JuliaMath/Roots.jl/blob/master/src/newton.jl#L111), and (5) the R pracma package in newton.R (https://cran.r-project.org/web/packages/pracma/index.html) Thank you very much for your consideration! Sincerely,Mark Mikofski ?As I breath in, I calm my body, as I breath out, I smile? - Thich_Nhat_Hanh -------------- next part -------------- An HTML attachment was scrubbed... URL: From gdp.1807 at gmail.com Tue Feb 27 00:53:42 2018 From: gdp.1807 at gmail.com (GAGANDEEP SINGH) Date: Tue, 27 Feb 2018 11:23:42 +0530 Subject: [SciPy-Dev] Code for Surface Integral Message-ID: Dear developers, I have prepared the following code for calculating the surface integral over arbitrary surfaces. In the "Main Code" , just for example, surface integral of a function, G(u,v)=1 is calculated over the surface of Taurus of inner radius 1 unit and outer radius 2 units. Please give your feed backs so that I can improve the code further. Link to the code: https://github.com/czgdp1807/gsoc2108/blob/master/surfintegrate.py Note: I have worked only over the surface integrals. Please don't consider this as my only idea. I will discuss in detail with interested mentors. I feel that SciPy should have these features since it is necessary for various fields in Science and Technology. Waiting for feed backs. With Regards, Gagandeep Singh -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Tue Feb 27 03:39:53 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Tue, 27 Feb 2018 00:39:53 -0800 Subject: [SciPy-Dev] Code for Surface Integral In-Reply-To: References: Message-ID: Hi Gagandeep, I have two requests for making this conversation more productive. First, please don't start new threads with each of your email, but instead reply to previous emails. Second, both Nokolay and Josh have given you concrete feedback and ideas (here: https://mail.python.org/pipermail/scipy-dev/2018-February/022490.html). Please reply to those. Your reply below doesn't show you have taken their feedback into account. Cheers, Ralf On Mon, Feb 26, 2018 at 9:53 PM, GAGANDEEP SINGH wrote: > Dear developers, > > I have prepared the following code for calculating the surface integral > over arbitrary surfaces. In the "Main Code" , just for example, > surface integral of a function, G(u,v)=1 is calculated over the surface of > Taurus of inner radius 1 unit and outer radius 2 units. > Please give your feed backs so that I can improve the code further. > > Link to the code: > https://github.com/czgdp1807/gsoc2108/blob/master/surfintegrate.py > > Note: I have worked only over the surface integrals. Please don't consider > this as my only idea. I will discuss in detail with interested mentors. I > feel that SciPy should have these features since it is necessary for > various fields in Science and Technology. > > Waiting for feed backs. > > With Regards, > Gagandeep Singh > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Tue Feb 27 03:40:48 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Tue, 27 Feb 2018 00:40:48 -0800 Subject: [SciPy-Dev] GSoC 2018 In-Reply-To: References: Message-ID: On Mon, Feb 26, 2018 at 10:30 AM, GAGANDEEP SINGH wrote: > Dear developers, > > As it was said that the surface/volume integrals for arbitrary > surfaces/volumes cannot be calculated easily in python. But I am able to do > so by applying Simpson rule for Double Integrals and achieved the > theoretical answer. > If any mentor wants to reconsider my idea on extending scipy.integrate for > GSoC 2018, then please discuss with me. > > > Waiting for a positive response. > please see my other email on this topic Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From gdp.1807 at gmail.com Tue Feb 27 05:54:32 2018 From: gdp.1807 at gmail.com (GAGANDEEP SINGH) Date: Tue, 27 Feb 2018 16:24:32 +0530 Subject: [SciPy-Dev] Bug Tracker In-Reply-To: References: Message-ID: Dear developers, I came to know about something called Bug Trackers from my seniors. How do I find them on Github? Please someone provide the link or the steps to follow to find the bugs. I am particularly interested in scipy.integrate. Please let me know how to reach out the bugs in that. Waiting for a reply. With Regards, Gagandeep Singh -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.frio at gmail.com Tue Feb 27 06:59:11 2018 From: jaime.frio at gmail.com (=?UTF-8?Q?Jaime_Fern=C3=A1ndez_del_R=C3=ADo?=) Date: Tue, 27 Feb 2018 11:59:11 +0000 Subject: [SciPy-Dev] Spline interpolation in ndimage Message-ID: Hi all, We have been discussing in issue #8465 about the extension modes for the interpolation module of ndimage. As some other issues linked in that one show, this is an old problem, that has been recurringly discussed, and there mostly is agreement on what the correct behavior should be. But as all things ndimage, implementing any change is hard, in this case not only because the code is complicated, but also because of the mathematical subtleties of the interpolation method used. In trying to come up with a way forward for this I think I can handle the code complexity, but am having trouble being sure that I come up with a sound math approach. I think I have more or less figured it out, but I don't have a good academic background on signal processing, so was hoping that someone who does (I'm thinking of you, Chuck!) can read my longish description of things below and validate or correct it. My main source of knowledge has been: M. Unser, "Splines: a perfect fit for signal and image processing," in IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, Nov 1999. Recommendations for bigger, better readings on the subject are also welcome! ----- In what follows I'll assume the input image is 2-D and NxN for simplicity, but I think everything generalizes easily If I'm understanding it right, all of our interpolation functions use B-splines for interpolation. So instead of having NxN discrete values on a grid, we have NxN B-splines centered at the grid points, and we keep the NxN coefficients multiplying each spline to reproduce the original image at the grid points exactly. If the spline order is < 2, the spline coefficients are the same as the image values. But if order >= 2 (and we use 3 by default), these have to be calculated in a non-trivial fashion. This can be done efficiently by applying a separable filter, which is implemented in ndimage.spline_filter. Because B-splines have compact support, when using splines of order n we only need to consider the B-splines on an (n + 1)x(n + 1) grid neighborhood of the point being interpolated. This is more or less straightforward, until you move close to the edges and all of a sudden some of the points in your grid neighborhood fall outside the original image grid. We have our extend mode, which controls how this points outside should be mapped to points inside. But here is where things start getting tricky... When the spline coefficients are computed (i.e. when ndimage.spline_filter is called), assumptions have to be made about boundary conditions. But ndimage.spline_filter does not take a mode parameter to control this! So what I think ndimage does is compute the spline coefficients assuming "mirror symmetric" boundary conditions, i.e.: a b c d c b | a b c d | c b a b c d So if our interpolated point is within the image boundaries, but some of the grid points in its (n + 1)x(n + 1) neighborhood fall outside the boundary, the code uses a mirror symmetric extension mode to fill in those values. This approach has a funny smell to it, but even if it's formally incorrect I think it would only be marginally so, as the values are probably going to be very close to the correct ones. The problem comes when the point being interpolated is outside the boundaries of the image. We cannot use mirror-symmetric spline coefficients to extend if e.g. we have been asked to extend using wrap mode. So what ndimage does is first map the value outside the boundaries to a value within the boundaries, using the given extension mode, then interpolate it as before, using mirror-symmetric coefficients if needed because its (n + 1)x(n + 1) neighborhood extends outside. Again, this smells funny, but it is either correct or very close to correct. This is mostly all good and well, except for the "wrap" and "reflect" extension modes: in these cases the area within one pixel of the image boundaries is different from anything inside the image, so we cannot use that approach. So what ndimage does is basically make shit up and use something similar, but not quite right. "reflect" is mostly correct, except for within that pixel of the boundary, but "wrap" is a surprising and confusing mess. So how do we fix this? I see two ways forward: 1. What seems the more correct approach would be to compute the spline coefficients taking into account the extension mode to be used, then use the same extension mode to fill in the neighborhood values when interpolating for a point outside the boundaries. 1. First question is whether this is doable? I need to work out the math, but for "wrap" it looks like it should be, not 100% sure if also is for "reflect". 2. Assuming it is it has the main advantage of doing things in a more general and understandable way once you have enough background knowledge. 3. It does go a little bit against our API design: you can control whether the input is spline-filtered automatically with a parameter, the idea being that you may want to do the filtering yourself if you are going to apply several different transformations to the same image. If the mode of the filtering has to be synced with the mode of the transformation, letting the user do it themselves is a recipe for disaster, because it's going to lead to very hard to track bugs. 4. As elsewhere in ndimage, the current implementation does a lot of caching, which works because it always interpolates for a point within the image boundaries. If we started interpolating for points outside the boundaries without first mapping to within there may be a performance hit which has to be evaluated. 2. The other approach is, for "wrap" and "reflect" modes, pad the input image with an extra pixel in each direction, then compute our current "mirror symmetric" spline coefficients, and leave things as they are right now, aside from some changes to the mapping of values to take the extra pixels into account. 1. This looks like a nightmare of special cases everywhere and potential off-by-one errors while putting it together, but it would just go along with the ugliness of the existing code. 2. It's unclear what we would do if we are given an input with prefilter=False, so this also breaks the current API, probably even more so. Any thoughts or recommendations are very welcome! Jaime -- (\__/) ( O.o) ( > <) Este es Conejo. Copia a Conejo en tu firma y ay?dale en sus planes de dominaci?n mundial. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rlucente at pipeline.com Tue Feb 27 09:32:17 2018 From: rlucente at pipeline.com (Robert Lucente) Date: Tue, 27 Feb 2018 09:32:17 -0500 (GMT-05:00) Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism Message-ID: <372936706.2127.1519741937865@wamui-jasmine.atl.sa.earthlink.net> You guys are probably aware of the stuff below but just in case. Quaternions and spatial rotation https://en.wikipedia.org/wiki/Quaternions_and_spatial_rotation From divyank.agarwal1993 at gmail.com Tue Feb 27 10:57:41 2018 From: divyank.agarwal1993 at gmail.com (Divyank Agarwal) Date: Tue, 27 Feb 2018 21:27:41 +0530 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: <372936706.2127.1519741937865@wamui-jasmine.atl.sa.earthlink.net> References: <372936706.2127.1519741937865@wamui-jasmine.atl.sa.earthlink.net> Message-ID: Quaternions as a number system is good idea for 3d rotation. It takes away Edge cases issues with Euler angles, like gimbal lock. Quaternions are 4D counterpart of complex numbers. However their non commutativity makes them a challenge to understand and visualize, making mathematics bit complicated. A specific quaternion library already exist on github. https://github.com/moble/quaternion "This Python module adds a quaternion dtype to NumPy." Advanced functionalities could be added above the library. Their are good use cases of Quaternions. If your smartPhone has orientation sensors, It probably uses Quaternions. For advanced users: http://nautil.us/issue/49/the-absurd/chaos-makes-the-multiverse-unnecessary On Tue, Feb 27, 2018 at 8:02 PM, Robert Lucente wrote: > You guys are probably aware of the stuff below but just in case. > > Quaternions and spatial rotation > > https://en.wikipedia.org/wiki/Quaternions_and_spatial_rotation > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Tue Feb 27 11:12:43 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Tue, 27 Feb 2018 08:12:43 -0800 Subject: [SciPy-Dev] Bug Tracker In-Reply-To: References: Message-ID: On Tue, Feb 27, 2018 at 2:54 AM, GAGANDEEP SINGH wrote: > Dear developers, > > I came to know about something called Bug Trackers from my seniors. How do > I find them on Github? > https://github.com/scipy/scipy/issues > Please someone provide the link or the steps to follow to find the bugs. I > am particularly interested in scipy.integrate. Please let me know how to > reach out the bugs in that. > Use the dropdown "Labels" on the page linked above. You'll see https://github.com/scipy/scipy/issues?q=is%3Aopen+is%3Aissue+label%3Ascipy.integrate Ralf > Waiting for a reply. > > With Regards, > Gagandeep Singh > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Nicolas.Rougier at inria.fr Tue Feb 27 12:39:04 2018 From: Nicolas.Rougier at inria.fr (Nicolas Rougier) Date: Tue, 27 Feb 2018 18:39:04 +0100 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: References: <372936706.2127.1519741937865@wamui-jasmine.atl.sa.earthlink.net> Message-ID: <56F42377-BF68-4F8D-AAB0-7603C72A1D37@inria.fr> Just for the record, there?s also the Pyrr library: https://github.com/adamlwgriffiths/Pyrr Nicolas > On 27 Feb 2018, at 16:57, Divyank Agarwal wrote: > > > Quaternions as a number system is good idea for 3d rotation. > It takes away Edge cases issues with Euler angles, like gimbal lock. > > Quaternions are 4D counterpart of complex numbers. > However their non commutativity makes them a challenge to understand and visualize, > making mathematics bit complicated. > > > > A specific quaternion library already exist on github. > https://github.com/moble/quaternion > "This Python module adds a quaternion dtype to NumPy." > > Advanced functionalities could be added above the library. > > > > Their are good use cases of Quaternions. > If your smartPhone has orientation sensors, It probably uses Quaternions. > > For advanced users: > http://nautil.us/issue/49/the-absurd/chaos-makes-the-multiverse-unnecessary > > On Tue, Feb 27, 2018 at 8:02 PM, Robert Lucente wrote: > You guys are probably aware of the stuff below but just in case. > > Quaternions and spatial rotation > > https://en.wikipedia.org/wiki/Quaternions_and_spatial_rotation > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev From matthew.brett at gmail.com Tue Feb 27 17:06:56 2018 From: matthew.brett at gmail.com (Matthew Brett) Date: Tue, 27 Feb 2018 22:06:56 +0000 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: <56F42377-BF68-4F8D-AAB0-7603C72A1D37@inria.fr> References: <372936706.2127.1519741937865@wamui-jasmine.atl.sa.earthlink.net> <56F42377-BF68-4F8D-AAB0-7603C72A1D37@inria.fr> Message-ID: Hi, Also : http://matthew-brett.github.io/transforms3d/ This is mostly Christoph Gohlke's code, but I've been the maintainer for a while: * rotation matrices * quaternions * axis - angle * Euler anges * reflections, shears etc. * decomposing affine matrices into component transformations. Cheers, Matthew On Tue, Feb 27, 2018 at 5:39 PM, Nicolas Rougier wrote: > Just for the record, there?s also the Pyrr library: > https://github.com/adamlwgriffiths/Pyrr > > Nicolas > >> On 27 Feb 2018, at 16:57, Divyank Agarwal wrote: >> >> >> Quaternions as a number system is good idea for 3d rotation. >> It takes away Edge cases issues with Euler angles, like gimbal lock. >> >> Quaternions are 4D counterpart of complex numbers. >> However their non commutativity makes them a challenge to understand and visualize, >> making mathematics bit complicated. >> >> >> >> A specific quaternion library already exist on github. >> https://github.com/moble/quaternion >> "This Python module adds a quaternion dtype to NumPy." >> >> Advanced functionalities could be added above the library. >> >> >> >> Their are good use cases of Quaternions. >> If your smartPhone has orientation sensors, It probably uses Quaternions. >> >> For advanced users: >> http://nautil.us/issue/49/the-absurd/chaos-makes-the-multiverse-unnecessary >> >> On Tue, Feb 27, 2018 at 8:02 PM, Robert Lucente wrote: >> You guys are probably aware of the stuff below but just in case. >> >> Quaternions and spatial rotation >> >> https://en.wikipedia.org/wiki/Quaternions_and_spatial_rotation >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev From pmhobson at gmail.com Tue Feb 27 18:03:03 2018 From: pmhobson at gmail.com (Paul Hobson) Date: Tue, 27 Feb 2018 15:03:03 -0800 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: References: <372936706.2127.1519741937865@wamui-jasmine.atl.sa.earthlink.net> <56F42377-BF68-4F8D-AAB0-7603C72A1D37@inria.fr> Message-ID: Add to the list the affine package from Sean Gilles, geared towards raster GIS datasets: https://pypi.python.org/pypi/affine/2.1.0 On Tue, Feb 27, 2018 at 2:06 PM, Matthew Brett wrote: > Hi, > > Also : http://matthew-brett.github.io/transforms3d/ > > This is mostly Christoph Gohlke's code, but I've been the maintainer > for a while: > > * rotation matrices > * quaternions > * axis - angle > * Euler anges > * reflections, shears etc. > * decomposing affine matrices into component transformations. > > Cheers, > > Matthew > > On Tue, Feb 27, 2018 at 5:39 PM, Nicolas Rougier > wrote: > > Just for the record, there?s also the Pyrr library: > > https://github.com/adamlwgriffiths/Pyrr > > > > Nicolas > > > >> On 27 Feb 2018, at 16:57, Divyank Agarwal < > divyank.agarwal1993 at gmail.com> wrote: > >> > >> > >> Quaternions as a number system is good idea for 3d rotation. > >> It takes away Edge cases issues with Euler angles, like gimbal lock. > >> > >> Quaternions are 4D counterpart of complex numbers. > >> However their non commutativity makes them a challenge to understand > and visualize, > >> making mathematics bit complicated. > >> > >> > >> > >> A specific quaternion library already exist on github. > >> https://github.com/moble/quaternion > >> "This Python module adds a quaternion dtype to NumPy." > >> > >> Advanced functionalities could be added above the library. > >> > >> > >> > >> Their are good use cases of Quaternions. > >> If your smartPhone has orientation sensors, It probably uses > Quaternions. > >> > >> For advanced users: > >> http://nautil.us/issue/49/the-absurd/chaos-makes-the- > multiverse-unnecessary > >> > >> On Tue, Feb 27, 2018 at 8:02 PM, Robert Lucente > wrote: > >> You guys are probably aware of the stuff below but just in case. > >> > >> Quaternions and spatial rotation > >> > >> https://en.wikipedia.org/wiki/Quaternions_and_spatial_rotation > >> _______________________________________________ > >> SciPy-Dev mailing list > >> SciPy-Dev at python.org > >> https://mail.python.org/mailman/listinfo/scipy-dev > >> > >> _______________________________________________ > >> SciPy-Dev mailing list > >> SciPy-Dev at python.org > >> https://mail.python.org/mailman/listinfo/scipy-dev > > > > _______________________________________________ > > SciPy-Dev mailing list > > SciPy-Dev at python.org > > https://mail.python.org/mailman/listinfo/scipy-dev > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vishstar88 at gmail.com Wed Feb 28 00:54:26 2018 From: vishstar88 at gmail.com (Vishal Gupta) Date: Wed, 28 Feb 2018 05:54:26 +0000 Subject: [SciPy-Dev] GSoC 2018 : Rotation formalism In-Reply-To: References: <161cc8c27cf.e16b927b42372.6259257951918238853@zoho.com> Message-ID: Hey. Here's the basis for my proposal 1. Class Rotation will represent any rotation vector 2. Initialsed as Rotation (vector, type, dim) Vector : Rotational Vector (Values corresponding to mentioned formalism) Type : Formalism Name Dim : Dimension Alternatively, have a bunch of Rotation.fromXYZ(**kwargs) function to initialise from different formalisms 3. Similary have Rotation.toXYZ(**kwargs) function to convert internal representation to different formalisms 4. Internally , the entered vector will be converted to Quaternion (or DCM) 5. A Rotation.apply method to rotate or project a vector or a set of vectors (apply Quaternion rotation on vectors) 6. A Rotation.__mul__(rot) method to apply consecutive rotations where rot is another Rotation object Will adding more methods for other algorithms. Thanks, Vishal On Sun, Feb 25, 2018, 5:23 PM Vishal Gupta wrote: > Here's a bunch of ideas that I have > > 1. Create a new Vector class primarily for vector algebraic operations > (instead of numpy arrays). > This could be used any and every vector operation. > > > 1. > - Vector Product > - Scalar Product > - Translation > > > 1. > - Rotation (Different methods for each formalism) > > > 1. > - Magnitude > - Distance from other Vector objects > - Convert to and from numpy array > > > 1. > > (This could probably be extended to a Plane class for planar > operations and transformations) > 2. Create a module in scipy.spatial.rotation that has a different > method for each formalism and accepts (vector to be rotated as) Vector or > numpy.ndarray along with arguments for the rotation as a numpy.ndarray > > > Thanks, > Vishal > > PS. Sorry for 2 mails. Didn't realize Ctrl+Enter sends a mail in Gmail > -------------- next part -------------- An HTML attachment was scrubbed... URL: From smkjain8 at gmail.com Wed Feb 28 01:37:24 2018 From: smkjain8 at gmail.com (Samyak Jain) Date: Wed, 28 Feb 2018 12:07:24 +0530 Subject: [SciPy-Dev] Contributing to scipy In-Reply-To: References: Message-ID: What all I need to study for implementing this module and basic guidelines you follow while building a new module. Also can you suggest some issues I could start solving to understand more about Scipy. On Sun, Feb 25, 2018 at 9:48 PM, Ilhan Polat wrote: > Can you elaborate on what kind of help you are looking for? > > On Sun, Feb 25, 2018 at 1:15 PM, Samyak Jain wrote: > >> Since I am also applying for GSOC'18 for the project "Rotation formalism >> in 3 dimensions" so if I can get some help in that area too would be >> helpful. >> >> On Sun, Feb 25, 2018 at 5:42 PM, Samyak Jain wrote: >> >>> Yes, I am referring to dependencies. Also I can work on interpolation >>> and integration. I just need some guidelines on what to do and what things >>> I need to know for contributing in these types of issues. >>> >>> Thanks, >>> Samyak >>> >>> On Sun, Feb 25, 2018 at 12:27 AM, Phillip Feldman < >>> phillip.m.feldman at gmail.com> wrote: >>> >>>> Actually, the code that I have is for integration--not interpolation. >>>> >>>> But, I'd like to see support for interpolating irregularly spaced data >>>> in two and higher dimensions. >>>> >>>> On Sat, Feb 24, 2018 at 10:54 AM, Phillip Feldman < >>>> phillip.m.feldman at gmail.com> wrote: >>>> >>>>> When you say "correlated", are you referring to dependencies? >>>>> >>>>> If you are interested in working on interpolation, I can suggest some >>>>> things to be done and also contribute some code. >>>>> >>>>> Phillip M. Feldman >>>>> >>>>> On Sat, Feb 24, 2018 at 4:21 AM, Samyak Jain >>>>> wrote: >>>>> >>>>>> There is no particular submodule that I am interested in but I would >>>>>> like to do issues involving some work in python. Can someone suggest which >>>>>> type of issues I should start with? I have started solving some DOC issues >>>>>> but now I want to fix some bugs. Also how can I understand the structure of >>>>>> scipy how other modules are correlated with each other? >>>>>> >>>>>> On Fri, Feb 23, 2018 at 11:45 AM, Ralf Gommers < >>>>>> ralf.gommers at gmail.com> wrote: >>>>>> >>>>>>> Hi Samyak, >>>>>>> >>>>>>> Welcome! >>>>>>> >>>>>>> On Mon, Feb 19, 2018 at 4:57 AM, Samyak Jain >>>>>>> wrote: >>>>>>> >>>>>>>> Hi, I am new to open source and very keen in contributing towards >>>>>>>> open source. I have started contributing in scipy solving some small DOC >>>>>>>> issues but I want to solve some major issues too. Can you suggest how do I >>>>>>>> start with this >>>>>>>> >>>>>>> >>>>>>> Is there a particular area or submodule of SciPy you are interested >>>>>>> in? We have no shortage of issues, but it would probably be best to work on >>>>>>> one that's related to your interests or potential gsoc topic. >>>>>>> >>>>>>> >>>>>>>> and also what all I need to know apart from python to start >>>>>>>> contributing in this org. >>>>>>>> >>>>>>> >>>>>>> A general skill you need is use of git/Github. Beyond that, it >>>>>>> depends on the topic. Some parts of SciPy are pure Python, for others you >>>>>>> may need to know Cython, C, C++ or Fortran. >>>>>>> >>>>>>> I am also applying for GSOC'18 by contributing with this org hence I >>>>>>>> need to know how can I contact the mentors as on the IRC no one is >>>>>>>> replying. Is there any other way to contact them ? >>>>>>>> >>>>>>> >>>>>>> IRC is a very old channel, not many (none?) of the developers are on >>>>>>> it regularly. We didn't list IRC on the ideas page or >>>>>>> http://python-gsoc.org as a method to contact the scipy developers. >>>>>>> Where did you see a link to it? >>>>>>> >>>>>>> Cheers, >>>>>>> Ralf >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> SciPy-Dev mailing list >>>>>>> SciPy-Dev at python.org >>>>>>> https://mail.python.org/mailman/listinfo/scipy-dev >>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> SciPy-Dev mailing list >>>>>> SciPy-Dev at python.org >>>>>> https://mail.python.org/mailman/listinfo/scipy-dev >>>>>> >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> SciPy-Dev mailing list >>>> SciPy-Dev at python.org >>>> https://mail.python.org/mailman/listinfo/scipy-dev >>>> >>>> >>> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> >> > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Wed Feb 28 02:02:37 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Tue, 27 Feb 2018 23:02:37 -0800 Subject: [SciPy-Dev] Contributing to scipy In-Reply-To: References: Message-ID: On Tue, Feb 27, 2018 at 10:37 PM, Samyak Jain wrote: > What all I need to study for implementing this module and basic guidelines > you follow while building a new module. Also can you suggest some issues I > could start solving to understand more about Scipy. > Hi Samyak, there are a number of other threads on that Rotation Formalism project on the mailing list in the last week, and the project idea itself has a lot of details and links. So asking a one line question "can I get some help" doesn't show that you've tried to understand the information already given. Please look into what is already there; if something is not clear or you have questions/ideas, then ask concrete questions. You will need to do a bit of homework here first. Cheers, Ralf > On Sun, Feb 25, 2018 at 9:48 PM, Ilhan Polat wrote: > >> Can you elaborate on what kind of help you are looking for? >> >> On Sun, Feb 25, 2018 at 1:15 PM, Samyak Jain wrote: >> >>> Since I am also applying for GSOC'18 for the project "Rotation formalism >>> in 3 dimensions" so if I can get some help in that area too would be >>> helpful. >>> >>> On Sun, Feb 25, 2018 at 5:42 PM, Samyak Jain wrote: >>> >>>> Yes, I am referring to dependencies. Also I can work on interpolation >>>> and integration. I just need some guidelines on what to do and what things >>>> I need to know for contributing in these types of issues. >>>> >>>> Thanks, >>>> Samyak >>>> >>>> On Sun, Feb 25, 2018 at 12:27 AM, Phillip Feldman < >>>> phillip.m.feldman at gmail.com> wrote: >>>> >>>>> Actually, the code that I have is for integration--not interpolation. >>>>> >>>>> But, I'd like to see support for interpolating irregularly spaced data >>>>> in two and higher dimensions. >>>>> >>>>> On Sat, Feb 24, 2018 at 10:54 AM, Phillip Feldman < >>>>> phillip.m.feldman at gmail.com> wrote: >>>>> >>>>>> When you say "correlated", are you referring to dependencies? >>>>>> >>>>>> If you are interested in working on interpolation, I can suggest some >>>>>> things to be done and also contribute some code. >>>>>> >>>>>> Phillip M. Feldman >>>>>> >>>>>> On Sat, Feb 24, 2018 at 4:21 AM, Samyak Jain >>>>>> wrote: >>>>>> >>>>>>> There is no particular submodule that I am interested in but I would >>>>>>> like to do issues involving some work in python. Can someone suggest which >>>>>>> type of issues I should start with? I have started solving some DOC issues >>>>>>> but now I want to fix some bugs. Also how can I understand the structure of >>>>>>> scipy how other modules are correlated with each other? >>>>>>> >>>>>>> On Fri, Feb 23, 2018 at 11:45 AM, Ralf Gommers < >>>>>>> ralf.gommers at gmail.com> wrote: >>>>>>> >>>>>>>> Hi Samyak, >>>>>>>> >>>>>>>> Welcome! >>>>>>>> >>>>>>>> On Mon, Feb 19, 2018 at 4:57 AM, Samyak Jain >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi, I am new to open source and very keen in contributing towards >>>>>>>>> open source. I have started contributing in scipy solving some small DOC >>>>>>>>> issues but I want to solve some major issues too. Can you suggest how do I >>>>>>>>> start with this >>>>>>>>> >>>>>>>> >>>>>>>> Is there a particular area or submodule of SciPy you are interested >>>>>>>> in? We have no shortage of issues, but it would probably be best to work on >>>>>>>> one that's related to your interests or potential gsoc topic. >>>>>>>> >>>>>>>> >>>>>>>>> and also what all I need to know apart from python to start >>>>>>>>> contributing in this org. >>>>>>>>> >>>>>>>> >>>>>>>> A general skill you need is use of git/Github. Beyond that, it >>>>>>>> depends on the topic. Some parts of SciPy are pure Python, for others you >>>>>>>> may need to know Cython, C, C++ or Fortran. >>>>>>>> >>>>>>>> I am also applying for GSOC'18 by contributing with this org hence >>>>>>>>> I need to know how can I contact the mentors as on the IRC no one is >>>>>>>>> replying. Is there any other way to contact them ? >>>>>>>>> >>>>>>>> >>>>>>>> IRC is a very old channel, not many (none?) of the developers are >>>>>>>> on it regularly. We didn't list IRC on the ideas page or >>>>>>>> http://python-gsoc.org as a method to contact the scipy >>>>>>>> developers. Where did you see a link to it? >>>>>>>> >>>>>>>> Cheers, >>>>>>>> Ralf >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> SciPy-Dev mailing list >>>>>>>> SciPy-Dev at python.org >>>>>>>> https://mail.python.org/mailman/listinfo/scipy-dev >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> SciPy-Dev mailing list >>>>>>> SciPy-Dev at python.org >>>>>>> https://mail.python.org/mailman/listinfo/scipy-dev >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> SciPy-Dev mailing list >>>>> SciPy-Dev at python.org >>>>> https://mail.python.org/mailman/listinfo/scipy-dev >>>>> >>>>> >>>> >>> >>> _______________________________________________ >>> SciPy-Dev mailing list >>> SciPy-Dev at python.org >>> https://mail.python.org/mailman/listinfo/scipy-dev >>> >>> >> >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev at python.org >> https://mail.python.org/mailman/listinfo/scipy-dev >> >> > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lagru at mailbox.org Wed Feb 28 09:32:42 2018 From: lagru at mailbox.org (Lars G.) Date: Wed, 28 Feb 2018 15:32:42 +0100 Subject: [SciPy-Dev] GSoC 2018: Cythonizing Message-ID: <3648ed21-1b43-975c-4ca0-05926d683736@mailbox.org> Dear SciPy devs, I'm currently thinking about an application for this year's GSoC as well. As there already seems to be a large interest in the rotation formalism I'm trying to find another area that matches my interest and skill. I've dug up this proposal in scikit-image from GSoC 2015 https://github.com/scikit-image/scikit-image/wiki/GSoC-2015#rewriting-scipyndimage-in-cython and judging by the state of scipy/ndimage/src/ nobody has worked on this proposal yet (feel free to correct me). Alternatively I could imagine something similar for other sub-packages, e.g. scipy/signal which features many source files in C as well. So basically if there is an interest I could try to port C / Python code to Cython. What I would like to know: - Is there an interest? ;) - Is the original proposal in scikit-image still unfinished and are the potential mentors still interested in mentoring? - If there is a general interest to cythonize C or Python code during a GSoC project, which parts / sub-packages of SciPy would you priorize? As for my current involvement with SciPy: - I've already added a small function written in Cython https://github.com/scipy/scipy/pull/8350 - as part of a larger PR extending the signal module https://github.com/scipy/scipy/pull/8264 which will possibly merged this week. - I already cythonized slow parts of the above PR and plan to add these with new PRs after #8264 is merged. If this receives positive feedback I'd be happy to draft a more complete proposal / application based on the discussion around this. Best regards, Lars From larson.eric.d at gmail.com Wed Feb 28 10:04:23 2018 From: larson.eric.d at gmail.com (Eric Larson) Date: Wed, 28 Feb 2018 10:04:23 -0500 Subject: [SciPy-Dev] GSoC 2018: Cythonizing In-Reply-To: <3648ed21-1b43-975c-4ca0-05926d683736@mailbox.org> References: <3648ed21-1b43-975c-4ca0-05926d683736@mailbox.org> Message-ID: > > - Is there an interest? ;) > I'd be happy to co-mentor on any relevant `scipy.signal` bits at least, as I've done some Cython work there. - Is the original proposal in scikit-image still unfinished and are the > potential mentors still interested in mentoring? > - If there is a general interest to cythonize C or Python code during a > GSoC project, which parts / sub-packages of SciPy would you priorize? > I don't know the answer to either of these questions -- I'll let others respond. If this receives positive feedback I'd be happy to draft a more complete > proposal / application based on the discussion around this. > For GSoC we need to ensure (at least) that the project fits 1) the needs of SciPy, 2) the GSoC program scope / timeline, 3) possible mentors, and 4) your goals. My sense is that a proposal based on code Cythonizing (with proper benchmark testing and regression protection) would be good for SciPy maintainability and could be crafted to have a reasonable scope. In terms of mentors, I feel comfortable mentoring changes to the `signal` module but not `ndimage`, so we'd need to find a qualified primary volunteer mentor if that ends up being the primary proposal direction. Another thing to keep in mind is that the list of GSoC ideas is not meant to be exhaustive. So if you have some other ideas for SciPy functionality, feel free to throw those out for discussion as well. In my experience, genuine intrinsic enthusiasm for a project -- finding something you'd enjoy working on in your free time even if you weren't getting paid to do so -- can help make for successful GSoC applications and experiences. Cheers, Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: From jomsdev at gmail.com Wed Feb 28 10:51:08 2018 From: jomsdev at gmail.com (Jordi Montes) Date: Wed, 28 Feb 2018 16:51:08 +0100 Subject: [SciPy-Dev] GSoC 2018: Blendenpik (A least-square solver) Message-ID: Hello, I am Jordi Montes, an enthusiastic student of discrete mathematics wanting to participate in this GSoC. My idea is to take advantage of the current method for dimensinality reduction of scipy (clarkson_woodruff_transformation) and build a least-square solver on top of it. The principal motivation is that it outperforms the other solvers in many real world applications, even those in LAPACK. I already discussed this in the mailing list before the GSoC admission term started, but I have also written a formal proposal (which is attached in this email). As always, feel free to ask about any doubt that comes to your mind or point to any improvement that you think I could make. Thanks, Jordi. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: GSoC 2018.pdf Type: application/pdf Size: 74490 bytes Desc: not available URL: From jaime.frio at gmail.com Wed Feb 28 11:11:36 2018 From: jaime.frio at gmail.com (=?UTF-8?Q?Jaime_Fern=C3=A1ndez_del_R=C3=ADo?=) Date: Wed, 28 Feb 2018 16:11:36 +0000 Subject: [SciPy-Dev] GSoC 2018: Cythonizing In-Reply-To: <3648ed21-1b43-975c-4ca0-05926d683736@mailbox.org> References: <3648ed21-1b43-975c-4ca0-05926d683736@mailbox.org> Message-ID: On Wed, Feb 28, 2018 at 3:40 PM Lars G. wrote: > Dear SciPy devs, > > I'm currently thinking about an application for this year's GSoC as > well. As there already seems to be a large interest in the rotation > formalism I'm trying to find another area that matches my interest and > skill. > > I've dug up this proposal in scikit-image from GSoC 2015 > > https://github.com/scikit-image/scikit-image/wiki/GSoC-2015#rewriting-scipyndimage-in-cython > and judging by the state of scipy/ndimage/src/ nobody has worked on this > proposal yet (feel free to correct me). > I mentored the not very successful, to put it mildly, GSoC 2015 project about cythonizing ndimage. From that experience, and further work afterwards, I no longer think Cython is the answer to ndimage's problems. The underlying C has a lot of very complicated code making lots of clever (often too clever for everyone's good) uses of pointer magic, that I honestly think are better kept in C. Or would at least need someone with a very deep understanding of both C and Cython, would much exceed the scope of a GSoC project, and I don't think I can commit to properly mentor such a project this summer. What would be nice is to replace the current nd_image.c file that implements the Python interface to the underlying C by a Cython implementation. That is not enough for a GSoC project, and it's not the most exciting thing to work on either. But if you want to put a full project together out of smaller, Cython related, subprojects, this could certainly be a part of it, and I wouldn't mind mentoring that subproject. Jaime > Alternatively I could imagine something similar for other sub-packages, > e.g. scipy/signal which features many source files in C as well. > > So basically if there is an interest I could try to port C / Python code > to Cython. What I would like to know: > > - Is there an interest? ;) > - Is the original proposal in scikit-image still unfinished and are the > potential mentors still interested in mentoring? > - If there is a general interest to cythonize C or Python code during a > GSoC project, which parts / sub-packages of SciPy would you priorize? > > As for my current involvement with SciPy: > > - I've already added a small function written in Cython > https://github.com/scipy/scipy/pull/8350 P.S. Have submitted a small enhancement to your code, could you take a look? https://github.com/scipy/scipy/pull/8499 > - as part of a larger PR extending the signal module > https://github.com/scipy/scipy/pull/8264 > which will possibly merged this week. > - I already cythonized slow parts of the above PR and plan > to add these with new PRs after #8264 is merged. > > If this receives positive feedback I'd be happy to draft a more complete > proposal / application based on the discussion around this. > > Best regards, > Lars > > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at python.org > https://mail.python.org/mailman/listinfo/scipy-dev > -- (\__/) ( O.o) ( > <) Este es Conejo. Copia a Conejo en tu firma y ay?dale en sus planes de dominaci?n mundial. -------------- next part -------------- An HTML attachment was scrubbed... URL: From andyfaff at gmail.com Wed Feb 28 15:56:10 2018 From: andyfaff at gmail.com (Andrew Nelson) Date: Thu, 1 Mar 2018 07:56:10 +1100 Subject: [SciPy-Dev] circleCI 2 Message-ID: Apparently circleCI is sunsetting version 1 and moving to version 2 ( https://circleci.com/sunset1-0/). This will require a migration ( https://circleci.com/docs/2.0/migrating-from-1-2/#validate-yaml) This may require some work for the circle config we use to build documents. -- _____________________________________ Dr. Andrew Nelson _____________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Wed Feb 28 23:49:46 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Wed, 28 Feb 2018 20:49:46 -0800 Subject: [SciPy-Dev] SciPy IRC channel lacks moderation In-Reply-To: References: Message-ID: On Mon, Feb 26, 2018 at 9:53 AM, Mike Graham wrote: > On Fri, Feb 23, 2018 at 1:25 AM, Ralf Gommers > wrote: > >> >> I'm fine with either option, discontinuing or moderation. Either way we >> should make it clear that scipy devs don't hang out there. >> > > For what it's worth, people still get help with numpy, scipy, and other > scientific programming issues in the channel every day. Nathan remarked > that closing the channel was "a really dumb idea". ;) > > If you want to appoint Nathan (ngoldbaum on Freenode) and/or me (papna on > freenode) as group contact to have moderator tools, the freenode people > will probably do that if we can point them to this mailing list thread. > They will just want to see that it is what the project wants. > Okay, that seems fine - if Nathan and you want to do that, and it's helpful for a part of the community, then that seems like a good idea. Thanks for stepping up. Could you please request access to those moderator tools for Nathan and yourself, and point them to this thread? I'll still expand the description of the IRC channel on https://scipy.org/scipylib/mailing-lists.html a bit to make clearer what it's for (getting help, not for SciPy development discussions). Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Wed Feb 28 23:57:29 2018 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Wed, 28 Feb 2018 20:57:29 -0800 Subject: [SciPy-Dev] SciPy IRC channel lacks moderation In-Reply-To: References: Message-ID: On Wed, Feb 28, 2018 at 8:49 PM, Ralf Gommers wrote: > > > On Mon, Feb 26, 2018 at 9:53 AM, Mike Graham wrote: > >> On Fri, Feb 23, 2018 at 1:25 AM, Ralf Gommers >> wrote: >> >>> >>> I'm fine with either option, discontinuing or moderation. Either way we >>> should make it clear that scipy devs don't hang out there. >>> >> >> For what it's worth, people still get help with numpy, scipy, and other >> scientific programming issues in the channel every day. Nathan remarked >> that closing the channel was "a really dumb idea". ;) >> >> If you want to appoint Nathan (ngoldbaum on Freenode) and/or me (papna on >> freenode) as group contact to have moderator tools, the freenode people >> will probably do that if we can point them to this mailing list thread. >> They will just want to see that it is what the project wants. >> > > Okay, that seems fine - if Nathan and you want to do that, and it's > helpful for a part of the community, then that seems like a good idea. > Thanks for stepping up. Could you please request access to those moderator > tools for Nathan and yourself, and point them to this thread? > > I'll still expand the description of the IRC channel on > https://scipy.org/scipylib/mailing-lists.html a bit to make clearer what > it's for (getting help, not for SciPy development discussions). > Description: https://github.com/scipy/scipy.org/pull/246 Ralf -------------- next part -------------- An HTML attachment was scrubbed... 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