Mailman 3 October 2019 - SciPy-Dev

Proposed SciPy 1.4.0 Release Schedule
by Tyler Reddy Dec. 7, 2019

Dec. 7, 2019

Hi, SciPy 1.3.0 was released May 17 (5 months ago), and I think we'd like to keep a roughly biannual release cadence. I'd like to propose the following schedule for 1.4.0: - November 14: branch 1.4.x - November 17: rc1 - December 1: rc2 (if needed) - December 10: final release The arrival of Python 3.8 and simultaneous responsibility to get at least one more 1.2.x LTS Python 2.7 release out the door means things will probably be busy on the release front until 2020. As always, it is a good idea to start tagging things that should be in 1.4.0 & please do help with reviewing PRs/issues that are tagged--current counts are: - PRs: 40 open with 1.4.0 milestone - issues: 17 open with 1.4.0 milestone While helping with that, also great if the release notes wiki is updated for appropriate changes: https://github.com/scipy/scipy/wiki/Release-note-entries-for-SciPy-1.4.0 Curating those final notes can be painful if the wiki isn't updated. Thoughts/objections for the schedule? Best wishes, Tyler

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Pythran 0.9.4 - Hollsent
by Serge Guelton Nov. 6, 2019

Nov. 6, 2019

Hi folks, It's always a pleasure to announce a Pythran release, and here we go for a version bump! Short reminder: Pythran is an ahead-of-time compiler for scientific Python, with a focus on high-level numerical kernels, parallelism and vectorisation. Here is a simple kernel example, with a pythran annotation. Note that this kernel is still Python-compatible (from https://stackoverflow.com/questions/50658884): #pythran export euclidean_distance_square(float64[1,:], float64[:,:]) import numpy as np def euclidean_distance_square(x1, x2): return -2*np.dot(x1, x2.T) + np.sum(np.square(x1), axis=1)[:, np.newaxis] + np.sum(np.square(x2), axis=1) The Pythran package is available on PyPI, Github and Conda https://pypi.org/project/pythran/ https://anaconda.org/conda-forge/pythran https://github.com/serge-sans-paille/pythran Packages exist for archlinux and Fedora, they'll probably be updated soon :-) The interested reader can have a look to the changelog for details https://pythran.readthedocs.io/en/latest/Changelog.html Most notably, this release provides support for Python 3.7 and Python 3.8, as well as the ability to use clang-cl as a (better) backend compiler for Windows. Huge thanks to all contributors: paugier Anubhab Haldar Jean Laroche polo and bug reporters: paugier nbecker gdementen mgirardis MordicusEtCubitus Dapid piotrbartman m-romanov slayoo martibosch jeanlaroche

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Documentation: user survey
by Maja Gwozdz Oct. 31, 2019

Oct. 31, 2019

Hi everyone, I'm currently working on improving the SciPy documentation during the Google Season of Docs. One of my projects is about a user survey. The basic idea is to get (documentation) feedback from SciPy users and try to improve our docs accordingly. It'd be great if you could take a look at the survey form and say if you have any comments that could help me. You can access it here: https://docs.google.com/forms/d/e/1FAIpQLSeBAO0UFKDZyKpg2XzRslsLJVHU61ugjc1… Also, I'm compiling a list of websites where I could deploy the survey to get a fair amount of responses. If you know any such websites, please let me know. Your help is much appreciated! All the best, Maja Gwozdz

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Re: [SciPy-Dev] Fishers exact confidence interval
by Jay Moore Oct. 27, 2019

Oct. 27, 2019

Hi Ralf, I have a proposed implementation. Should I collect unit tests and documentation and make a pull request? Best, Jay On Sun, Oct 27, 2019 at 09:00 <scipy-dev-request(a)python.org> wrote: > Send SciPy-Dev mailing list submissions to > scipy-dev(a)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(a)python.org > > You can reach the person managing the list at > scipy-dev-owner(a)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. New to list (Jay Moore) > 2. Re: New to list (Ralf Gommers) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 26 Oct 2019 23:09:38 -0400 > From: Jay Moore <j.alex.moore(a)gmail.com> > To: scipy-dev(a)python.org > Subject: [SciPy-Dev] New to list > Message-ID: > < > CAOz3X_5TnZOOCOsVxGqb4V+zGO+ndfL55crJf0er_pK6OsFD_Q(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I am new to this mailing list and I would like to discuss a new feature I > would like to add to scipy stats. I have never contributed code to open > source projects before so any guidance would be greatly appreciated. > > I would like to add confidence intervals for fisher's exact testing. I've > been working with the code for a couple of months now and would like to > make this available to everyone using this package. > > Best, > Jay Moore >

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New to list
by Jay Moore Oct. 27, 2019

Oct. 27, 2019

Hi all, I am new to this mailing list and I would like to discuss a new feature I would like to add to scipy stats. I have never contributed code to open source projects before so any guidance would be greatly appreciated. I would like to add confidence intervals for fisher's exact testing. I've been working with the code for a couple of months now and would like to make this available to everyone using this package. Best, Jay Moore

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not running CI on merge commits
by Ralf Gommers Oct. 21, 2019

Oct. 21, 2019

Hi all, I propose that we stop running CI on merges. There's a number of reasons for this, the current behavior: - significantly increases our CI resource usage, for little gain - delays CI runs on PRs regularly (many of us tend to do PR review and updates in batches) - causes Azure to send out spammy emails each time I merge a PR, I really don't need to know that a merge commit passed In the very rare case that CI on a PR is green and then fails after merge with a valid failure rather than a flake, we will find out soon enough anyway. So I really can't think of a good reason to keep triggering all CI on merging with master. Thoughts? Cheers, Ralf

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ANN: PyWavelets 1.1.0
by Gregory Lee Oct. 21, 2019

Oct. 21, 2019

Hello all, We are very pleased to announce the release of PyWavelets 1.1. PyWavelets is Python package for wavelet analysis. This release includes enhanced functionality for both the stationary wavelet transforms (``swt``, ``swt2``, ``swtn``) as well as the continuous wavelet transform (``cwt``). In addition, there are a handful of bug fixes. This release has dropped Python 2.7 support and now requires Python >= 3.5. Wheels for Python 3.5-3.8 are currently being uploaded to PyPI. In addition to these changes to the software itself, a paper describing PyWavelets was recently published in The Journal of Open Source Software: https://joss.theoj.org/papers/10.21105/joss.01237 For full details see the release notes at: https://pywavelets.readthedocs.io/en/latest/release.1.1.0.html Cheers, Greg

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Re: [SciPy-Dev] Contribution: Estimating the overlap of a ray with volume-cells (voxels) for e.g. tomography
by Sebastian A. Mueller Oct. 21, 2019

Oct. 21, 2019

On 2019-10-18 15:19, Ralf Gommers wrote: > Thanks for the explanation, makes sense now. Okay, let's forget about > my suggestion then. > > So we're back to: shall we include this in scipy.spatial more or less > in its current form? There does seem to be interest and it does fit. > Would be nice though if we can get someone else to step up to review. Review is good. I would be happy to receive comments. > Matteo had a good question that's still to be answered. Matteo's question is valid. I opened a [feature-request](https://github.com/cherenkov-plenoscope/ray_voxel_overlap/…. Currently the rays have no limits. Adding control over start- and end-points sounds reasonable to address more applications. The effort to implement this feature might be worth the gain in possible users. > Perhaps if he > could review it to make sure it looks good and would be useful for his > use case, that would get it much closer to ready for inclusion? Sure. A review by a potential user is good. > > Cheers, > > Ralf Cheers, Sebastian

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[ANN] SciPy India 2019
by Prabhu Ramachandran Oct. 20, 2019

Oct. 20, 2019

Hello, [Apologies for the cross-posting!] We are pleased to announce the SciPy India conference 2019. SciPy India is an annual conference on using Python for research and education. The conference is currently in its eleventh year and will be held at IIT Bombay on 29 & 30 November, 2019. The registration and call for papers are open. Please visit http://scipy.in to register and submit your proposals. Please spread the word! Call for Papers ============= We look forward to your submissions on the use of Python for scientific computing and education. This includes development of tools for pedagogy, exploration, modeling, and analysis. We welcome contributions from academia as well as industry. For details on the paper submission please see here: http://scipy.in/ Important Dates ================ - Call for proposals end: 25th October 2019 - List of accepted proposals will be announced: 3rd November. We look forward to seeing you at SciPy India. Regards, Prabhu Ramachandran (For the SciPy organizing team)

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NumPy 1.17 3 released
by Charles R Harris Oct. 17, 2019

Oct. 17, 2019

Hi All, On behalf of the NumPy team I am pleased to announce that NumPy 1.17.3 has been released. This is a bugfix release. The Python versions supported in this release are 3.5-3.8. Downstream developers should use Cython >= 0.29.13 for Python 3.8 support and OpenBLAS >= 3.7 to avoid wrong results on the Skylake architecture. The NumP Wheels for this release can be downloaded from PyPI <https://pypi.org/project/numpy/1.17.3/>, source archives and release notes are available from Github <https://github.com/numpy/numpy/releases/tag/v1.17.3>. *Highlights* - Wheels for Python 3.8 - Boolean matmul fixed to use booleans instead of integers. *Compatibility notes* - The seldom used PyArray_DescrCheck macro has been changed/fixed. *Contributors* A total of 7 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - Allan Haldane - Charles Harris - Kevin Sheppard - Matti Picus - Ralf Gommers - Sebastian Berg - Warren Weckesser *Pull requests merged* A total of 12 pull requests were merged for this release. - gh-14456: MAINT: clean up pocketfft modules inside numpy.fft namespace. - gh-14463: BUG: random.hypergeometic assumes npy_long is npy_int64, hung... - gh-14502: BUG: random: Revert gh-14458 and refix gh-14557. - gh-14504: BUG: add a specialized loop for boolean matmul. - gh-14506: MAINT: Update pytest version for Python 3.8 - gh-14512: DOC: random: fix doc linking, was referencing private submodules. - gh-14513: BUG,MAINT: Some fixes and minor cleanup based on clang analysis - gh-14515: BUG: Fix randint when range is 2**32 - gh-14519: MAINT: remove the entropy c-extension module - gh-14563: DOC: remove note about Pocketfft license file (non-existing here). - gh-14578: BUG: random: Create a legacy implementation of random.binomial. - gh-14687: BUG: properly define PyArray_DescrCheck Cheers, Charles Harris

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