Mailman 3 August 2019 - NumPy-Discussion

NumPy 1.17.1
by Charles R Harris Aug. 19, 2019

Aug. 19, 2019

Hi All, I'm planning on releasing NumPy 1.17.1 this weekend. If there are fixes that you think need to be included that are not currently marked for backport, please let me know. Chuck

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NumPy Community Meeting Wednesday, Aug. 21
by Sebastian Berg Aug. 19, 2019

Aug. 19, 2019

Hi all, There will be a NumPy Community meeting Wednesday August 21 at 11 am Pacific Time. Everyone is invited to join in and edit the work-in- progress meeting topics and notes: https://hackmd.io/76o-IxCjQX2mOXO_wwkcpg?both Best wishes Sebastian

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Season of Docs - welcome Anne, Maja, Brandon
by Ralf Gommers Aug. 19, 2019

Aug. 19, 2019

Hi all, Google has announced the Season of Docs participants for this year [1]. We had a lot of excellent candidates and had to make some hard choices. We applied for extra slots, but unfortunately didn't win the lottery for those; we got one slot for NumPy and one for SciPy. We chose the projects of Anne for NumPy and Maja for SciPy: Anne Bonner, "Making "The Basics" a Little More Basic: Improving the Introductory NumPy Sections" [2] Maja Gwozdz, "User-oriented documentation and thorough restructuring" [3] That's not all though. There was some space left in the budget of the NumPy BIDS grant, and Stéfan has reserved that so we can accept more writers and provide them the same mentoring and funding as they would have gotten through GSoD. We could only start the conversations about that once Google made its decisions, so a further announcement will follow. However, we already have one extra project confirmed, from Brandon: Brandon David, "Improve the documentation of scipy.stats" (project details to be published). I will send out a poll to find a good time for everyone for a kickoff call. Our intent is to build a documentation team with multiple writers and mentors interacting and able to help each other out. And all of this will also interact with the numpy.org website redesign and the people putting energy into that:) I'm very happy to welcome Anne, Maja and Brandon! Cheers, Ralf [1] https://developers.google.com/season-of-docs/docs/participants/ [2] https://developers.google.com/season-of-docs/docs/participants/project-numpy [3] https://developers.google.com/season-of-docs/docs/participants/project-scipy

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Numpy twitter handle?
by Abdur-Rahmaan Janhangeer Aug. 18, 2019

Aug. 18, 2019

Greetings, what is the numpy twitter handle? Thanks! Abdur-Rahmaan Janhangeer Mauritius

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ANN: NumExpr 2.7.0 Release
by Robert McLeod Aug. 14, 2019

Aug. 14, 2019

========================= Announcing Numexpr 2.7.0 ========================= Hi everyone, This is a minor version bump for NumExpr. We would like to highlight the changes made in 2.6.9 (which in retrospect should have been a minor version bump), where the maximum number of threads spawned can be limited by setting the environment variable "NUMEXPR_MAX_THREADS". If this variable is not set, in 2.7.0 the historical limit of 8 threads will be used. The lack of a check caused some problems on very large hosts in cluster environments in 2.6.9. In addition, we are officially dropping Python 2.6 support in this release as we cannot perform continuous integration for it. Project documentation is available at: http://numexpr.readthedocs.io/ Changes from 2.6.9 to 2.7.0 ---------------------------- - The default number of 'safe' threads has been restored to the historical limit of 8, if the environment variable "NUMEXPR_MAX_THREADS" has not been set. - Thanks to @eltoder who fixed a small memory leak. - Support for Python 2.6 has been dropped, as it is no longer available via TravisCI. - A typo in the test suite that had a less than rather than greater than symbol in the NumPy version check has been corrected thanks to dhomeier. - The file `site.cfg` was being accidentally included in the sdists on PyPi. It has now been excluded. What's Numexpr? --------------- Numexpr is a fast numerical expression evaluator for NumPy. With it, expressions that operate on arrays (like "3*a+4*b") are accelerated and use less memory than doing the same calculation in Python. It has multi-threaded capabilities, as well as support for Intel's MKL (Math Kernel Library), which allows an extremely fast evaluation of transcendental functions (sin, cos, tan, exp, log...) while squeezing the last drop of performance out of your multi-core processors. Look here for a some benchmarks of numexpr using MKL: https://github.com/pydata/numexpr/wiki/NumexprMKL Its only dependency is NumPy (MKL is optional), so it works well as an easy-to-deploy, easy-to-use, computational engine for projects that don't want to adopt other solutions requiring more heavy dependencies. Where I can find Numexpr? ------------------------- The project is hosted at GitHub in: https://github.com/pydata/numexpr You can get the packages from PyPI as well (but not for RC releases): http://pypi.python.org/pypi/numexpr Documentation is hosted at: http://numexpr.readthedocs.io/en/latest/ Share your experience --------------------- Let us know of any bugs, suggestions, gripes, kudos, etc. you may have. Enjoy data! -- Robert McLeod robbmcleod(a)gmail.com robert.mcleod(a)hitachi-hhtc.ca

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NumPy Community Meeting Wednesday, August 14
by Sebastian Berg Aug. 14, 2019

Aug. 14, 2019

Hi all, There will be a NumPy Community meeting Wednesday August 14 at 11 am Pacific Time. Everyone is invited to join in and edit the work-in- progress meeting topics and notes: https://hackmd.io/76o-IxCjQX2mOXO_wwkcpg Best wishes Sebastian

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merging empty bins used by histogram(bins='auto') to avoid MemoryErrors
by Alexander Reeves Aug. 9, 2019

Aug. 9, 2019

Hi all, This thread is to do with the github issues raised in #11879, #10297, #8203 of and possibly others that didn't appear in my search. The main issue is that histogram(bins='auto') will sometimes raise a memory error if the number of automatically-generated bin edges is too large. In all documented cases, the conditions producing outsized bin numbers are when the auto-binning defaults to the 'fd' method. I have taken a crack at minimizing the number of bins used by setting bins to 'auto' in numpy's histogram method. Based on suggestions from eric-weiser, the approach merges empty bins. The method works for the sample datasets in all the issues related to the FD estimator (#11879, #10297, #8203). Note that this method produces unequal bin widths. You can see some code I've already written in a comment on issue #11879 in the link below. https://github.com/numpy/numpy/issues/11879#issuecomment-516686087 Thanks for reading this far. Would be happy to turn this into a PR if there is interest. -areeves87

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ANN: SciPy 1.3.1
by Tyler Reddy Aug. 9, 2019

Aug. 9, 2019

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Hi all, On behalf of the SciPy development team I'm pleased to announce the release of SciPy 1.3.1, which is a bug fix release. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.3.1 One of a few ways to install this release with pip: pip install scipy==1.3.1 ========================== SciPy 1.3.1 Release Notes ========================== SciPy 1.3.1 is a bug-fix release with no new features compared to 1.3.0. Authors ======= * Matt Haberland * Geordie McBain * Yu Feng * Evgeni Burovski * Sturla Molden * Tapasweni Pathak * Eric Larson * Peter Bell * Carlos Ramos Carreño + * Ralf Gommers * David Hagen * Antony Lee * Ayappan P * Tyler Reddy * Pauli Virtanen A total of 15 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete. Issues closed for 1.3.1 ------------------------------- * `#5040 <https://github.com/scipy/scipy/issues/5040>`__: BUG: Empty data handling of (c)KDTrees * `#9901 <https://github.com/scipy/scipy/issues/9901>`__: lsoda fails to detect stiff problem when called from solve_ivp * `#10206 <https://github.com/scipy/scipy/issues/10206>`__: sparse matrices indexing with scipy 1.3 * `#10232 <https://github.com/scipy/scipy/issues/10232>`__: Exception in loadarff with quoted nominal attributes in scipy... * `#10292 <https://github.com/scipy/scipy/issues/10292>`__: DOC/REL: Some sections of the release notes are not nested correctly. * `#10303 <https://github.com/scipy/scipy/issues/10303>`__: BUG: optimize: `linprog` failing TestLinprogSimplexBland::test_unbounded_below_no_presolve_corrected * `#10376 <https://github.com/scipy/scipy/issues/10376>`__: TST: Travis CI fails (with pytest 5.0 ?) * `#10384 <https://github.com/scipy/scipy/issues/10384>`__: CircleCI doc build failing on new warnings * `#10398 <https://github.com/scipy/scipy/issues/10398>`__: Scipy 1.3.0 build broken in AIX * `#10501 <https://github.com/scipy/scipy/issues/10501>`__: BUG: scipy.spatial.HalfspaceIntersection works incorrectly * `#10514 <https://github.com/scipy/scipy/issues/10514>`__: BUG: cKDTree GIL handling is incorrect * `#10535 <https://github.com/scipy/scipy/issues/10535>`__: TST: master branch CI failures * `#10572 <https://github.com/scipy/scipy/issues/10572>`__: BUG: ckdtree query_ball_point errors on discontiguous input * `#10597 <https://github.com/scipy/scipy/issues/10597>`__: BUG: No warning on PchipInterpolator changing from bernstein base to local power base Pull requests for 1.3.1 ------------------------------ * `#10071 <https://github.com/scipy/scipy/pull/10071>`__: DOC: reconstruct SuperLU permutation matrices avoiding SparseEfficiencyWarning * `#10196 <https://github.com/scipy/scipy/pull/10196>`__: Fewer checks on xdata for curve_fit. * `#10207 <https://github.com/scipy/scipy/pull/10207>`__: BUG: Compressed matrix indexing should return a scalar * `#10233 <https://github.com/scipy/scipy/pull/10233>`__: Fix for ARFF reader regression (#10232) * `#10306 <https://github.com/scipy/scipy/pull/10306>`__: BUG: optimize: Fix for 10303 * `#10309 <https://github.com/scipy/scipy/pull/10309>`__: BUG: Pass jac=None directly to lsoda * `#10377 <https://github.com/scipy/scipy/pull/10377>`__: TST, MAINT: adjustments for pytest 5.0 * `#10379 <https://github.com/scipy/scipy/pull/10379>`__: BUG: sparse: set writeability to be forward-compatible with numpy>=1.17 * `#10426 <https://github.com/scipy/scipy/pull/10426>`__: MAINT: Fix doc build bugs * `#10431 <https://github.com/scipy/scipy/pull/10431>`__: Update numpy version for AIX * `#10457 <https://github.com/scipy/scipy/pull/10457>`__: BUG: Allow ckdtree to accept empty data input * `#10503 <https://github.com/scipy/scipy/pull/10503>`__: BUG: spatial/qhull: get HalfspaceIntersection.dual_points from the correct array * `#10516 <https://github.com/scipy/scipy/pull/10516>`__: BUG: Use nogil contexts in cKDTree * `#10520 <https://github.com/scipy/scipy/pull/10520>`__: DOC: Proper .rst formatting for deprecated features and Backwards incompatible changes * `#10540 <https://github.com/scipy/scipy/pull/10540>`__: MAINT: Fix Travis and Circle * `#10573 <https://github.com/scipy/scipy/pull/10573>`__: BUG: Fix query_ball_point with discontiguous input * `#10600 <https://github.com/scipy/scipy/pull/10600>`__: BUG: interpolate: fix broken conversions between PPoly/BPoly objects Checksums ========= MD5 ~~~ 818dc6325a4511d656582ff2946eed80 scipy-1.3.1-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 83a11b3127b19e71353ee2a04c4be20c scipy-1.3.1-cp35-cp35m-manylinux1_i686.whl 49c52e00706b47b7311171fe37b9efac scipy-1.3.1-cp35-cp35m-manylinux1_x86_64.whl 015b3d443e2a9e4e664a50af64a7f5b6 scipy-1.3.1-cp35-cp35m-win32.whl 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Reformat the wall-of-text release notes
by Matti Picus Aug. 9, 2019

Aug. 9, 2019

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Re: [Numpy-discussion] [SciPy-Dev] Season of Docs - welcome Anne, Maja, Brandon
by Bennet Fauber Aug. 8, 2019

Aug. 8, 2019

I can offer some time for alpha or beta reading and proofreading. I have experience as a proofreader, copy editor (American Statistical Association), and mathematical typesetter (Wiley, Academic Press, Addison-Wesley, et al.). I've taught statistical software workshops, (very) introductory python, have a Software Carpentry instructor certificate, and work daily with people who are finding themselves needing technical and scientific computing but who don't have strong backgrounds. Hopefully that would be good context for early review of a couple of the projects. I will add my name to the poll, if that's OK? -- bennet On Wed, Aug 7, 2019 at 9:03 PM Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > > > > On Tue, Aug 6, 2019 at 4:46 PM Ralf Gommers <ralf.gommers(a)gmail.com> wrote: >> >> Hi all, >> >> Google has announced the Season of Docs participants for this year [1]. We had a lot of excellent candidates and had to make some hard choices. We applied for extra slots, but unfortunately didn't win the lottery for those; we got one slot for NumPy and one for SciPy. We chose the projects of Anne for NumPy and Maja for SciPy: >> >> Anne Bonner, "Making "The Basics" a Little More Basic: Improving the Introductory NumPy Sections" [2] >> >> Maja Gwozdz, "User-oriented documentation and thorough restructuring" [3] >> >> That's not all though. There was some space left in the budget of the NumPy BIDS grant, and Stéfan has reserved that so we can accept more writers and provide them the same mentoring and funding as they would have gotten through GSoD. We could only start the conversations about that once Google made its decisions, so a further announcement will follow. However, we already have one extra project confirmed, from Brandon: >> >> Brandon David, "Improve the documentation of scipy.stats" (project details to be published). > > > Happy to announce that we have a fourth participant: > > Shekhar Rajak, "numpy.org redesign and high level documentation restructuring for end user focus" > > Welcome Shekhar! > >> I will send out a poll to find a good time for everyone for a kickoff call. Our intent is to build a documentation team with multiple writers and mentors interacting and able to help each other out. And all of this will also interact with the numpy.org website redesign and the people putting energy into that:) > > > Here is the poll link: https://doodle.com/poll/skgbk74gsg8zpziu. I hope we can find a time that works for everyone - we're split over all US timezones, Europe and India. So it's going to be early morning or late evening somewhere. > > Sending this out in public, so anyone who wants to participate is welcome to join. I've Bcc'd all participants and mentors, to make sure they see this. > > Cheers, > Ralf > > >> >> >> I'm very happy to welcome Anne, Maja and Brandon! >> >> Cheers, >> Ralf >> >> >> [1] https://developers.google.com/season-of-docs/docs/participants/ >> [2] https://developers.google.com/season-of-docs/docs/participants/project-numpy >> [3] https://developers.google.com/season-of-docs/docs/participants/project-scipy > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev(a)python.org > https://mail.python.org/mailman/listinfo/scipy-dev

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