Mailman 3 December 2019 - NumPy-Discussion

Invalid value encoutered : how to prevent numpy.where to do this?
by Eric Emsellem 18 Feb '23

18 Feb '23

Dear all, I have a code using lots of "numpy.where" to make some constrained calculations as in: data = arange(10) result = np.where(data == 0, 0., 1./data) # or data1 = arange(10) data2 = arange(10)+1.0 result = np.where(data1 > data2, np.sqrt(data1-data2), np.sqrt(data2-data2)) which then produces warnings like: /usr/bin/ipython:1: RuntimeWarning: invalid value encountered in sqrt or for the first example: /usr/bin/ipython:1: RuntimeWarning: divide by zero encountered in divide How do I avoid these messages to appear? I know that I could in principle use numpy.seterr. However, I do NOT want to remove these warnings for other potential divide/multiply/sqrt etc errors. Only when I am using a "where", to in fact avoid such warnings! Note that the warnings only happen once, but since I am going to release that code, I would like to avoid the user to get such messages which are irrelevant here (because I am testing, with the where, when NOT to divide by zero or take a sqrt of a negative number). thanks! Eric

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Re: [Numpy-discussion] example reading binary Fortran file
by Neil Martinsen-Burrell 22 Jul '21

22 Jul '21

David Froger <david.froger.info <at> gmail.com> writes: > Hy,My question is about reading Fortran binary file (oh no this question > again...) I've posted this before, but I finally got it cleaned up for the Cookbook. For this purpose I use a subclass of file that has methods for reading unformatted Fortran data. See http://www.scipy.org/Cookbook/FortranIO/FortranFile. I'd gladly see this in numpy or scipy somewhere, but I'm not sure where it belongs. > program makeArray > implicit none > integer,parameter:: nx=10,ny=20 > real(4),dimension(nx,ny):: ux,uy,p > integer :: i,j > open(11,file='uxuyp.bin',form='unformatted') > do i = 1,nx > do j = 1,ny > ux(i,j) = real(i*j) > uy(i,j) = real(i)/real(j) > p (i,j) = real(i) + real(j) > enddo > enddo > write(11) ux,uy > write(11) p > close(11) > end program makeArray When I run the above program compiled with gfortran on my Intel Mac, I can read it back with:: >>> import numpy as np >>> from fortranfile import FortranFile >>> f=FortranFile('uxuyp.bin', endian='<') >>> uxuy = f.readReals(prec='f') # 'f' for default reals >>> len(uxuy) 400 >>> ux = np.array(uxuy[:200]).reshape((20,10)).T >>> uy = np.array(uxuy[200:]).reshape((20,10)).T >>> p = f.readReals('f').reshape((20,10)).T >>> ux array([[ 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20.], [ 2., 4., 6., 8., 10., 12., 14., 16., 18., 20., 22., 24., 26., 28., 30., 32., 34., 36., 38., 40.], [ 3., 6., 9., 12., 15., 18., 21., 24., 27., 30., 33., 36., 39., 42., 45., 48., 51., 54., 57., 60.], [ 4., 8., 12., 16., 20., 24., 28., 32., 36., 40., 44., 48., 52., 56., 60., 64., 68., 72., 76., 80.], [ 5., 10., 15., 20., 25., 30., 35., 40., 45., 50., 55., 60., 65., 70., 75., 80., 85., 90., 95., 100.], [ 6., 12., 18., 24., 30., 36., 42., 48., 54., 60., 66., 72., 78., 84., 90., 96., 102., 108., 114., 120.], [ 7.,Proxy-Connection: keep-alive Cache-Control: max-age=0 14., 21., 28., 35., 42., 49., 56., 63., 70., 77., 84., 91., 98., 105., 112., 119., 126., 133., 140.], [ 8., 16., 24., 32., 40., 48., 56., 64., 72., 80., 88., 96., 104., 112., 120., 128., 136., 144., 152., 160.], [ 9., 18., 27., 36., 45., 54., 63., 72., 81., 90., 99., 108., 117., 126., 135., 144., 153., 162., 171., 180.], [ 10., 20., 30., 40., 50., 60., 70., 80., 90., 100., 110., 120., 130., 140., 150., 160., 170., 180., 190., 200.]]) >>> uy array([[ 1. , 0.5 , 0.33333334, 0.25 , 0.2 , 0.16666667, 0.14285715, 0.125 , 0.11111111, 0.1 , 0.09090909, 0.08333334, 0.07692308, 0.07142857, 0.06666667, 0.0625 , 0.05882353, 0.05555556, 0.05263158, 0.05 ], [ 2. , 1. , 0.66666669, 0.5 , 0.40000001, 0.33333334, 0.2857143 , 0.25 , 0.22222222, 0.2 , 0.18181819, 0.16666667, 0.15384616, 0.14285715, 0.13333334, 0.125 , 0.11764706, 0.11111111, 0.10526316, 0.1 ], [ 3. , 1.5 , 1. , 0.75 , 0.60000002, 0.5 , 0.42857143, 0.375 , 0.33333334, 0.30000001, 0.27272728, 0.25 , 0.23076923, 0.21428572, 0.2 , 0.1875 , 0.17647059, 0.16666667, 0.15789473, 0.15000001], [ 4. , 2. , 1.33333337, 1. , 0.80000001, 0.66666669, 0.5714286 , 0.5 , 0.44444445, 0.40000001, 0.36363637, 0.33333334, 0.30769232, 0.2857143 , 0.26666668, 0.25 , 0.23529412, 0.22222222, 0.21052632, 0.2 ], [ 5. , 2.5 , 1.66666663, 1.25 , 1. , 0.83333331, 0.71428573, 0.625 , 0.55555558, 0.5 , 0.45454547, 0.41666666, 0.38461539, 0.35714287, 0.33333334, 0.3125 , 0.29411766, 0.27777779, 0.2631579 , 0.25 ], [ 6. , 3. , 2. , 1.5 , 1.20000005, 1. , 0.85714287, 0.75 , 0.66666669, 0.60000002, 0.54545456, 0.5 , 0.46153846, 0.42857143, 0.40000001, 0.375 , 0.35294119, 0.33333334, 0.31578946, 0.30000001], [ 7. , 3.5 , 2.33333325, 1.75 , 1.39999998, 1.16666663, 1. , 0.875 , 0.77777779, 0.69999999, 0.63636363, 0.58333331, 0.53846157, 0.5 , 0.46666667, 0.4375 , 0.41176471, 0.3888889 , 0.36842105, 0.34999999], [ 8. , 4. , 2.66666675, 2. , 1.60000002, 1.33333337, 1.14285719, 1. , 0.8888889 , 0.80000001, 0.72727275, 0.66666669, 0.61538464, 0.5714286 , 0.53333336, 0.5 , 0.47058824, 0.44444445, 0.42105263, 0.40000001], [ 9. , 4.5 , 3. , 2.25 , 1.79999995, 1.5 , 1.28571427, 1.125 , 1. , 0.89999998, 0.81818181, 0.75 , 0.69230771, 0.64285713, 0.60000002, 0.5625 , 0.52941179, 0.5 , 0.47368422, 0.44999999], [ 10. , 5. , 3.33333325, 2.5 , 2. , 1.66666663, 1.42857146, 1.25 , 1.11111116, 1. , 0.90909094, 0.83333331, 0.76923078, 0.71428573, 0.66666669, 0.625 , 0.58823532, 0.55555558, 0.52631581, 0.5 ]]) >>> p array([[ 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21.], [ 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22.], [ 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23.], [ 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24.], [ 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25.], [ 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26.], [ 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27.], [ 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28.], [ 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28., 29.], [ 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28., 29., 30.]]) Note that you have to provide the shape information for ux and uy because fortran writes them together as a stream of 400 numbers. -Neil

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NumPy 1.16.6 release.
by Charles R Harris 30 Dec '19

30 Dec '19

Hi All, On behalf of the NumPy team I am pleased to announce that NumPy 1.16.6 has been released. This release fixes bugs reported against the 1.16.5 release and backports several enhancements from master that seem appropriate for an LTS series. The supported Python versions are 2.7, 3.5-3.7. This is the last release planned that supports Python 2.7. Wheels for this release can be downloaded from PyPI <https://pypi.org/project/numpy/1.16.6>, source archives and release notes are available from Github <https://github.com/numpy/numpy/releases/tag/v1.16.6>. Downstream developers building this release should use Cython >= 0.29.2 and, if using OpenBLAS, OpenBLAS >= v0.3.7. *Highlights* - The ``np.testing.utils`` functions have been updated from 1.19.0-dev0. This improves the function documentation and error messages as well extending the ``assert_array_compare`` function to additional types. *Contributors* A total of 10 people contributed to this release. - CakeWithSteak - Charles Harris - Chris Burr - Eric Wieser - Fernando Saravia - Lars Grueter - Matti Picus - Maxwell Aladago - Qiming Sun - Warren Weckesser *Pull requests merged* A total of 14 pull requests were merged for this release. - `#14211 <https://github.com/numpy/numpy/pull/14211>`__: BUG: Fix uint-overflow if padding with linear_ramp and negative... - `#14275 <https://github.com/numpy/numpy/pull/14275>`__: BUG: fixing to allow unpickling of PY3 pickles from PY2 - `#14340 <https://github.com/numpy/numpy/pull/14340>`__: BUG: Fix misuse of .names and .fields in various places (backport... - `#14423 <https://github.com/numpy/numpy/pull/14423>`__: BUG: test, fix regression in converting to ctypes. - `#14434 <https://github.com/numpy/numpy/pull/14434>`__: BUG: Fixed maximum relative error reporting in assert_allclose - `#14509 <https://github.com/numpy/numpy/pull/14509>`__: BUG: Fix regression in boolean matmul. - `#14686 <https://github.com/numpy/numpy/pull/14686>`__: BUG: properly define PyArray_DescrCheck - `#14853 <https://github.com/numpy/numpy/pull/14853>`__: BLD: add 'apt update' to shippable - `#14854 <https://github.com/numpy/numpy/pull/14854>`__: BUG: Fix _ctypes class circular reference. (#13808) - `#14856 <https://github.com/numpy/numpy/pull/14856>`__: BUG: Fix `np.einsum` errors on Power9 Linux and z/Linux - `#14863 <https://github.com/numpy/numpy/pull/14863>`__: BLD: Prevent -flto from optimising long double representation... - `#14864 <https://github.com/numpy/numpy/pull/14864>`__: BUG: lib: Fix histogram problem with signed integer arrays. - `#15172 <https://github.com/numpy/numpy/pull/15172>`__: ENH: Backport improvements to testing functions. - `#15191 <https://github.com/numpy/numpy/pull/15191>`__: REL: Prepare for 1.16.6 release. Cheers, Charles Harris

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Upcoming NumPy 1.16.6 release.
by Charles R Harris 27 Dec '19

27 Dec '19

Hi All, The NumPy 1.16.6 release is under preparation. The release notes and changelog may be found at #15191 <https://github.com/numpy/numpy/pull/15191>. Because this is the last planned release that supports Python 2.7 it is important to make sure it has all the relevant fixes, so if this affects you, please review the notes and comment if you think a needed fix has been omitted. Chuck

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Reverse parameter in ordering functions
by mpro 24 Dec '19

24 Dec '19

Hi all, I created pull request #14989, which adds reverse parameter in np.sort function. As suggested in the comments, I want to ask for some feedback on adding parameter 'reverse' . Not only in sort, but in ordering functions in general. Magdalena -- Sent from: http://numpy-discussion.10968.n7.nabble.com/

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ANN: SfePy 2019.4
by Robert Cimrman 23 Dec '19

23 Dec '19

I am pleased to announce release 2019.4 of SfePy. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by the finite element method or by the isogeometric analysis (limited support). It is distributed under the new BSD license. Home page: http://sfepy.org Mailing list: https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/ Git (source) repository, issue tracker: https://github.com/sfepy/sfepy Highlights of this release -------------------------- - support surface terms in 1D problems - improved Gmsh mesh format support (write .msh files) - new updating procedure in nonlinear homogenization - improved/faster log plotter For full release notes see [1]. Cheers, Robert Cimrman [1] http://docs.sfepy.org/doc/release_notes.html#id1 --- Contributors to this release in alphabetical order: Robert Cimrman Vladimir Lukes Matyas Novak Tomáš Zítka

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BIDS-NumPy progress reports, 2018/2019
by Stefan van der Walt 23 Dec '19

23 Dec '19

Dear colleagues, I'd like to thank everyone who contributed to NumPy over the past year. NumPy is a complex undertaking that requires inputs from many spheres to progress. Your contribution, however big or small, is important, and we appreciate you taking the time to make it. As we look back over the past year, I would like to share with you the two grant reports we've written, reporting on our work done with the community: 2018: http://doi.org/10.5281/zenodo.3585761 2019: http://doi.org/10.5281/zenodo.3585767 I fully appreciate that none of this work could have happened in isolation, and that we depend on the community to help set a development agenda, review code, establish regular meetings, do outreach, and much more. Thank you. We look forward to seeing you on 8 January for the next community call. With Ralf's CZI award coming into play, 2020 promises to be an exciting year for NumPy! Happy holidays, Stéfan

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NumPy 1.18.0 release
by Charles R Harris 22 Dec '19

22 Dec '19

Hi All, On behalf of the NumPy team I am pleased to announce that NumPy 1.18.0 has been released. In addition to the usual bug fixes, this NumPy release cleans up and documents the new random C-API, expires a large number of old deprecations, and improves the appearance and organization of the documentation. The Python versions supported are 3.5-3.8. This is the last NumPy release series that will support Python 3.5. The highlights of this release are: - the C-API for ``numpy.random`` has been defined and documented, - basic infrastructure for linking with 64 bit BLAS and LAPACK libraries, - many documentation improvements. Downstream developers should use Cython >= 0.29.14 for Python 3.8 support and OpenBLAS >= 3.7 to avoid wrong results on the Skylake architecture. The NumPy Wheels for this release can be downloaded from PyPI <https://pypi.org/project/numpy/1.18.0/>, source archives and release notes are available from Github <https://github.com/numpy/numpy/releases/tag/v1.18.0>. *Highlights* - The C-API for ``numpy.random`` has been defined and documented. - Basic infrastructure for linking with 64 bit BLAS and LAPACK libraries. - Many documentation improvements. *Contributors* A total of 114 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - Abhinav Sagar - Alex Henrie + - Alexander Jung + - Allan Haldane - Andrea Pattori - Andrew Liu + - Anis Ladram + - Anne Bonner + - Antoine Dechaume + - Aryan Naraghi + - Bastian Eichenberger + - Brian Wignall + - Brigitta Sipocz - CakeWithSteak + - Charles Harris - Chris Barker - Chris Burr + - Chris Markiewicz + - Christoph Gohlke - Christopher Whelan - Colin Snyder - Dan Allan - Daniel Ching - David Stansby + - David Zwicker + - Dieter Werthmüller - Disconnect3d + - Dmytro + - Doug Davis + - Eric Larson - Eric Wieser - Esben Haabendal + - Eugene Prilepin + - Felix Divo + - Gary Gurlaskie - Gina + - Giuseppe Cuccu + - Grzegorz Bokota + - Guanqun Lu + - Guilherme Leobas + - Guillaume Horel - Géraud Le Falher + - Hameer Abbasi - Harmon - Hiroyuki V. Yamazaki - Huang, Guangtai + - Hugo + - Hyeonguk Ryu + - Ilhan Polat + - Isaac Virshup - Jack J. Woehr + - Jack Woehr + - Jackie Leng - Jaime Fernandez - Jeff Hale + - Johann Faouzi + - Jon Dufresne + - Joseph Fox-Rabinovitz - Joseph R. Fox-Rabinovitz + - João Marcos Gris + - Justus Magin + - Jérémie du Boisberranger - Kai Striega - Kevin Sheppard - Kexuan Sun - Kmol Yuan + - Kriti Singh - Larry Bradley + - Lars Grueter - Luis Pedro Coelho - MSeifert04 - Magdalena Proszewska + - Manny + - Mark Harfouche - Martin Reinecke - Martin Thoma - Matt Haberland + - Matt McCormick + - Matthias Bussonnier - Matti Picus - Max Bolingbroke + - Maxwell Aladago + - Michael Hudson-Doyle + - Oleksandr Pavlyk - Omar Merghany + - Pauli Virtanen - Peter Andreas Entschev - Peter Bell - Peter Cock + - Pradeep Reddy Raamana + - Qiming Sun + - Raghuveer Devulapalli - Ralf Gommers - Samesh + - Samesh Lakhotia + - Sebastian Berg - Sergei Lebedev - Seth Troisi + - Siddhesh Poyarekar + - Simon + - Simon Notley + - Stefan van der Walt - Stephan Hoyer - Steve Stagg - Thomas A Caswell - Thomas Kluyver - Tim Hoffmann + - Tirth Patel + - Tyler Reddy - Vladimir Pershin + - Warren Weckesser - Yadong Zhang + - Zieji Pohz + - Zolisa Bleki + Cheers, Charles Harris

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[ANN] pvlib-python v0.7.0: predicting power for solar energy
by Dr. Mark Alexander Mikofski PhD 19 Dec '19

19 Dec '19

pvlib has a new major release, v0.7.0 Release Notes: https://pvlib-python.readthedocs.io/en/v0.7.0/whatsnew.html PyPI: https://pypi.org/project/pvlib/ Read the Docs: https://pvlib-python.readthedocs.io/en/latest/ GitHub: https://github.com/pvlib/pvlib-python Here's a quick summary: - dropped support for Python-2.7 - new `ivtools` module for fitting solar panel parameters - new implementation of the cloud wavelet variability model (WVM) - new functions for temperature and incidence angle modifier (IAM) models - updated solar panel and inverter parameters databases from National Renewable Energy Lab (NREL) Also note this is a major release so there are a few breaking API changes. Users should probably read the release notes and check their code before updating: https://pvlib-python.readthedocs.io/en/v0.7.0/whatsnew.html#api-breaking-ch… -- Mark Mikofski, PhD (2005) *Fiat Lux*

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ANN: SciPy 1.4.1
by Tyler Reddy 19 Dec '19

19 Dec '19

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Hi all, On behalf of the SciPy development team I'm pleased to announce the release of SciPy 1.4.1, 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/v1.4.1 One of a few ways to install this release with pip: pip install scipy==1.4.1 ========================== SciPy 1.4.1 Release Notes ========================== SciPy 1.4.1 is a bug-fix release with no new features compared to 1.4.0. Importantly, it aims to fix a problem where an older version of pybind11 may cause a segmentation fault when imported alongside incompatible libraries. Authors ====== * Ralf Gommers * Tyler Reddy Issues closed for 1.4.1 --------------------------------- * `#11237 <https://github.com/scipy/scipy/issues/11237>`__: Seg fault when importing torch Pull requests for 1.4.1 -------------------------------- * `#11238 <https://github.com/scipy/scipy/pull/11238>`__: BLD: update minimum pybind11 version to 2.4.0. 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NumPy-Discussion December 2019