Mailman 3 October 2020 - 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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Documentation Team meeting - Monday June 8th
by Melissa Mendonça 03 Dec '22

03 Dec '22

Hi all! A reminder that on Monday, June 8, we have another documentation team meeting at 3PM UTC**. If you wish to join on Zoom, you need to use this link https://zoom.us/j/420005230 Here's the permanent hackmd document with the meeting notes: https://hackmd.io/oB_boakvRqKR-_2jRV-Qjg <https://www.google.com/url?q=https%3A%2F%2Fhackmd.io%2FoB_boakvRqKR-_2jRV-Q…> Hope to see you around (especially if you want to introduce yourself or discuss ideas for Google Season of Docs). ** You can click this link to get the correct time at your timezone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=NumPy+Documentati… - Melissa

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[Feature Request] Add alias of np.concatenate as np.concat
by Iordanis Fostiropoulos 10 May '22

10 May '22

In regard to Feature Request: https://github.com/numpy/numpy/issues/16469 It was suggested to sent to the mailing list. I think I can make a strong point as to why the support for this naming convention would make sense. Such as it would follow other frameworks that often work alongside numpy such as tensorflow. For backward compatibility, it can simply be an alias to np.concatenate I often convert portions of code from tf to np, it is as simple as changing the base module from tf to np. e.g. np.expand_dims -> tf.expand_dims. This is done either in debugging (e.g. converting tf to np without eager execution to debug portion of the code), or during prototyping, e.g. develop in numpy and convert in tf. I find myself more than at one occasion to getting syntax errors because of this particular function np.concatenate. It is unnecessarily long. I imagine there are more people that also run into the same problems. Pandas uses concat (torch on the other extreme uses simply cat, which I don't think is as descriptive).

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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 1.20.x branch in two weeks
by Charles R Harris 01 Dec '20

01 Dec '20

Hi All, Time to start planning for the 1.20.x branch. These are my thoughts at the moment: - Keep support for Python 3.6. Python 3.7 came out in June 2018, which seems too recent to be our oldest supported version. - Drop Python 3.6 for 1.21.x, that will make the oldest supported version about three years old. - Drop manylinux1 for 1.21.x. It would be nice to drop earlier, but manylinux2010 is pretty recent. There were 33 wheels in the 1.19.3 release, I think we can live with that for 1.20.x. I'm more worried about our tools aging out. After Python has settled into its yearly release cycle, I think we will end up supporting the latest 4 versions. Thoughts? Chuck

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Add sliding_window_view method to numpy
by Zimmermann Klaus 27 Nov '20

27 Nov '20

Hello, I would like to draw the attention of this list to PR #17394 [1] that adds the implementation of a sliding window view to numpy. Having a sliding window view in numpy is a longstanding open issue (cf #7753 [2] from 2016). A brief summary of the discussions surrounding it can be found in the description of the PR. This PR implements a sliding window view based on stride tricks. Following the discussion in issue #7753, a first implementation was provided by Fanjin Zeng in PR #10771. After some discussion, that PR stalled and I picked up the issue in the present PR #17394. It is based on the first implementation, but follows the changed API as suggested by Eric Wieser. Code reviews have been provided by Bas van Beek, Stephen Hoyer, and Eric Wieser. Sebastian Berg added the "62 - Python API" label. Do you think this is suitable for inclusion in numpy? Do you consider the PR ready? Do you have suggestions or requests? Thanks for your time and consideration! Klaus [1] https://github.com/numpy/numpy/pull/17394 [2] https://github.com/numpy/numpy/issues/7753

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start of an array (tensor) and dataframe API standardization initiative
by Ralf Gommers 13 Nov '20

13 Nov '20

Hi all, I'd like to share this announcement blog post about the creation of a consortium for array and dataframe API standardization here: https://data-apis.org/blog/announcing_the_consortium/. It's still in the beginning stages, but starting to take shape. We have participation from one or more maintainers of most array and tensor libraries - NumPy, TensorFlow, PyTorch, MXNet, Dask, JAX, Xarray. Stephan Hoyer, Travis Oliphant and myself have been providing input from a NumPy perspective. The effort is very much related to some of the interoperability work we've been doing in NumPy (e.g. it could provide an answer to what's described in https://numpy.org/neps/nep-0037-array-module.html#requesting-restricted-sub… ). At this point we're looking for feedback from maintainers at a high level (see the blog post for details). Also important: the python-record-api tooling and data in its repo has very granular API usage data, of the kind we could really use when making decisions that impact backwards compatibility. Cheers, Ralf

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Ndarray static typing: Order of generic types
by bas van beek 01 Nov '20

01 Nov '20

Hey all, With the recent merging of numpy/numpy#16759<https://github.com/numpy/numpy/pull/16759> we're at the point where `ndarray` can be made generic w.r.t. its dtype and shape. An open question which yet remains is to order in which these two parameters should appear (numpy/numpy#16547<https://github.com/numpy/numpy/issues/16547>): * `ndarray[Dtype, Shape]` * `ndarray[Shape, Dtype]` There has been a some discussion about this question in issue 16547, but a consensus has not yet to be reached. Most people seem to slightly preferring one option over the other. Are there any further thoughts on this subject? Regards, Bas van Beek

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Allow __getitem__ to support custom objects
by Aaron Meurer 30 Oct '20

30 Oct '20

For ndindex (https://quansight.github.io/ndindex/), the biggest issue with the API is that to use an ndindex object to actually index an array, you have to use a[idx.raw] instead of a[idx]. This is because for NumPy arrays, you cannot allow custom objects to be indices. The exception is objects that define __index__, but this only works for integer indices. If __index__ returns anything other than an integer, you get an IndexError. This is annoying because it's easy to forget to do this when working with the ndindex API, and the error message from NumPy isn't informative about what went wrong unless you know to expect it. I'd like to propose an API that would allow custom objects to define how they should be converted to a standard NumPy index, similar to __index__ but that supports all index types. I think there are two options here: - Allow __index__ to return any index type, not just integers. This is the simplest because it reuses an existing API, and __index__ is the best possible name for this API. However, I'm not sure, but this may actually conflict with the text of PEP 357 (https://www.python.org/dev/peps/pep-0357/). Also, some other APIs use __index__ to check if something is an indexable integer, which wouldn't accept generic index. For example, elements of a slice can be any object that defines __index__. - Add a new __numpy_index__ API that works like def __numpy_index__(self): return <tuple, integer, slice, newaxis, ellipsis, or integer or boolean array> In NumPy, __getitem__ and __setitem__ on ndarray would first check if the input index type is one of the known types as it currently does, then it would try __index__, and if neither of those fails, it would call __numpy_index__(index) and use that. Note: there is a more general way that NumPy arrays could allow __getitem__ to be defined on custom objects, which I am NOT proposing. Instead of an API that returns one of the current predefined index types (tuple, integer, slice, newaxis, ellipsis, or integer or boolean array), there could instead be an API that takes the array as input and returns another array (or view) as an output. This would allow an object to define itself as an index in arbitrary ways, even if such an index would not actually be possible via traditional indexing. There are definitely some interesting ideas that could be done with this, but this idea would be much more complicated, and isn't something that I need. Unless the community feels that a more general API like this would be preferred, I would suggest deferring something like it to a later discussion. What would be the best way to go about getting something like this implemented? Is it simple enough that we can just work out the details here and on a pull request, or should I write a NEP? Aaron Meurer

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Multinomial random sampling
by Currurant 29 Oct '20

29 Oct '20

I wonder if there is an efficient way to draw multinomial random samples. For univariate sampling, we can do that for different parameters and desired shape, but neither of rng nor multinomial function in numpy.random is able to achieve that. To be specific, can we draw multinomial samples for different probabilities and different n? I asked the question on Stackoverflow here: https://stackoverflow.com/questions/64529620/is-there-an-efficient-way-to-g…. Seems like there isn't a function to do that. Thank you and appreciate numpy, Daniel -- Sent from: http://numpy-discussion.10968.n7.nabble.com/

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NumPy-Discussion October 2020