Mailman 3 February 2022 - NumPy-Discussion

mixed mode arithmetic
by Neal Becker 11 Jul '23

11 Jul '23

I've been browsing the numpy source. I'm wondering about mixed-mode arithmetic on arrays. I believe the way numpy handles this is that it never does mixed arithmetic, but instead converts arrays to a common type. Arguably, that might be efficient for a mix of say, double and float. Maybe not. But for a mix of complex and a scalar type (say, CDouble * Double), it's clearly suboptimal in efficiency. So, do I understand this correctly? If so, is that something we should improve?

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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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An extension of the .npy file format
by Michael Siebert 25 Aug '22

25 Aug '22

Dear all, originally, I have planned to make an extension of the .npy file format a dedicated follow-up pull request, but I have upgraded my current request instead, since it was not as difficult to implement as I initially thought and probably a more straight-forward solution: https://github.com/numpy/numpy/pull/20321/ What is this pull request about? It is about appending to Numpy .npy files. Why? I see two main use cases: 1. creating .npy files larger than the main memory. They can, once finished, be loaded as memory maps 2. creating binary log files, which can be processed very efficiently without parsing Are there not other good file formats to do this? Theoretically yes, but practically they can be pretty complex and with very little tweaking .npy could do efficient appending too. Use case 1 is already covered by the Pip/Conda package npy-append-array I have created and getting the functionality directly into Numpy was the original goal of the pull request. This would have been possible without introducing a new file format version, just by adding some spare space in the header. During the pull request discussion it turned out that rewriting the header after each append would be desirable in case the writing program crashes to minimize data loss. Use case 2 however would highly profit from a new file format version as it would make rewriting the header unnecessary: since efficient appending can only take place along one axis, setting shape[-1] = -1 in case of Fortran order or shape[0] = -1 otherwise (default) in the .npy header on file creation could indicate that the array size is determined by the file size: when np.load (typically with memory mapping on) gets called, it constructs the ndarray with the actual shape by replacing the -1 in the constructor call. Otherwise, the header is not modified anymore, neither on append nor on file write finish. Concurrent appends to a single file would not be advisable and should be channeled through a single AppendArray instance. Concurrent reads while writes take place however should work relatively smooth: every time an np.load (ideally with mmap) is called, the ndarray would provide access to all data written until that time. Currently, my pull request provides: 1. A definition of .npy version 4.0 that supports -1 in the shape 2. implementations for fortran order and non-fortran order (default) including test cases 3. Updated np.load 4. The AppendArray class that does the actual appending Although there is a certain hassle with introducing a new .npy version, the changes themselves are very small. I could also implement a fallback mode for older Numpy installations, if someone is interested. What do you think about such a feature, would it make sense? Anyone available for some more code review? Best from Berlin, Michael PS thank you so far, I could improve my npy-append-array module as well and from what I have seen so far the Numpy code readability exceeded my already high expectations.

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copy="never" discussion and no deprecation cycle?
by Sebastian Berg 21 Jul '22

21 Jul '22

Hi all, (sorry for the length, details/discussion below) On the triage call, there seemed a preference to just try to skip the deprecation and introduce `copy="never"`, `copy="if_needed"`, and `copy="always"` (i.e. string options for the `copy` keyword argument). Strictly speaking, this is against the typical policy (one year of warning/errors). But nobody could think of a reasonable chance that anyone actually uses it. (For me just "policy" will be enough of an argument to just take it slow.) BUT: If nobody has *any* concerns at all, I think we may just end up introducing the change right away. The PR is: https://github.com/numpy/numpy/pull/19173 ## The Feature There is the idea to add `copy=never` (or similar). This would modify the existing `copy` argument to make it a 3-way decision: * `copy=always` or `copy=True` to force a copy * `copy=if_needed` or `copy=False` to prefer no-copy behavior * `copy=never` to error when no-copy behavior is not possible (this ensures that a view is returned) this would affect the functions: * np.array(object, copy=...) * arr.astype(new_dtype, copy=...) * np.reshape(arr, new_shape, copy=...), and the method arr.reshape() * np.meshgrid and possibly Where `reshape` currently does not have the option and would benefit by allowing for `arr.reshape(-1, copy=never)`, which would guarantee a view. ## The Options We have three options that are currently being discussed: 1. We introduce a new `np.CopyMode` or `np.<something>.Copy` Enum with values `np.CopyMode.NEVER`, `np.CopyMode.IF_NEEDED`, and `np.CopyMode.ALWAYS` * Plus: No compatibility concerns * Downside(?): This would be a first in NumPy, and is untypical API due to that. 2. We introduce `copy="never"`, `copy="if_needed"` and `copy="always"` as strings (all other strings will be a `TypeError`): * Problem: `copy="never"` currently means `copy=True` (the opposite) Which means new code has to take care when it may run on older NumPy versions. And in theory could make old code return the wrong thing. * Plus: Strings are the typical for options in NumPy currently. 3. Same as 2. But we take it very slow: Make strings an error right now and only introduce the new options after two releases as per typical deprecation policy. ## Discussion We discussed it briefly today in the triage call and we were leaning towards strings. I was honestly expecting to converge to option 3 to avoid compatibility issues (mainly surprises with `copy="never"` on older versions). But considering how weird it is to currently pass `copy="never"`, the question was whether we should not change it with a release note. The probability of someone currently passing exactly one of those three (and no other) strings seems exceedingly small. Personally, I don't have a much of an opinion. But if *nobody* voices any concern about just changing the meaning of the string inputs, I think the current default may be to just do it. Cheers, Sebastian

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Changes to `np.loadtxt`
by Sebastian Berg 29 Jun '22

29 Jun '22

Hi all, just a brief heads up that: https://github.com/numpy/numpy/pull/20580 is now merged. This moves `np.loadtxt` to C. Mainly making it much faster. There are also some other improvements and changes though: * It now supports `quotechar='"'` to support Excel dialect CSV. * Parsing some numbers is stricter (e.g. removed support for `_` or hex float parsing by default). * `max_rows` now actually counts rows and not lines. A warning is given if this makes a difference (blank lines). * Some exception will change, parsing failures now (almost) always give an informative `ValueError`. * `converters=callable` is now valid to provide a single converter for all columns. Please test, and let us know if there is any issue or followup you would like to see. We do have possible followups planned * Consider deprecating the `encoding="bytes"` default which exists for Python 2 compatibility. * Consider renaming `skip_rows` to the more precise `skip_lines`. Moving to C unlocks possible further improvement, such as full `csv.Dialect` support. We do not have this on the roadmap, but such contributions are possible now. Similarly, it should be possible to rewrite `genfromtxt` based on this work. Cheers, Sebastian

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Numpy binary wheels and CI for win/arm64 platform
by Niyas Sait 22 Jun '22

22 Jun '22

Hello, Numpy v1.21.2 <https://github.com/numpy/numpy/releases/tag/v1.21.2> added support for windows/arm64 platforms but we still don't have any systems in place to produce binary wheels or test win/arm64 packages. I think it will be good to start looking into this. CPython has an official buildbot worker running for win/arm64 and official python support for the platform will be available from the 3.11 release. It is not yet clear to me how the build and CI system for numpy is deployed and how to enable support for a new platform like win/arm64. One of the main issues in supporting win/arm64 build would be due to the lack of win/arm64 VMs available on the cloud. But I see we have been producing binary wheels for Apple M1 platforms on pypi and conda repository for some time which also lacks the cloud VM support. I think we could take some learnings from Apple M1 support and look at how a similar strategy can be used for win/arm64. I would like to hear if anyone has any thoughts on this topic. Also, any pointers to understand numpy wheel generation and CI flow for similar platforms would be helpful as well. Thanks, Niyas

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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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request to remove the numpy-aarch64 package from PyPI
by Ralf Gommers 14 Mar '22

14 Mar '22

Hi all, FYI, I noticed this package that claimed to be maintained by us: https://pypi.org/project/numpy-aarch64/. That's not ours, so I tried to contact the author (no email provided, but guessed the same username on GitHub) and asked to remove it: https://github.com/tomasriv/DNA_Sequence/issues/1. There are a very large number of packages with "numpy" in the name on PyPI, and there's no way we can audit/police that effectively, but if it's a rebuild that pretends like it's official then I think it's worth doing something about. It could contain malicious code for all we know. Cheers, Ralf

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NumPy community meeting – Wednesday, March 2nd, 2022 at 18:00 (6 pm) UTC
by Inessa Pawson 28 Feb '22

28 Feb '22

Our next NumPy Community meeting is scheduled for Wednesday, March 2nd at 18:00 (6 pm) UTC. Join us via Zoom: https://berkeley.zoom.us/j/762261535 As always, everyone is welcome and encouraged to attend. To add to the meeting agenda the topics you’d like to discuss, follow the link: https://hackmd.io/76o-IxCjQX2mOXO_wwkcpg?both Cheers, Inessa Inessa Pawson Contributor Experience Lead | NumPy

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