Mailman 3 November 2021 - NumPy-Discussion

win32 wheels for Python 3.10
by Aivar Annamaa Nov. 14, 2021

Nov. 14, 2021

Has it been decided to stop publishing win32 wheels for Python 3.10? Numpy 1.21.4 currently misses win32 wheel for Python 3.10 on PyPI. Is this temporary? I'm confused, because https://www.mail-archive.com/numpy-discussion@python.org/msg05512.html says: > We will continue to offer 32 wheels on Windows as it remains popular there.

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Conversion from C-layout to Fortran-layout in Cython
by Ilhan Polat Nov. 12, 2021

Nov. 12, 2021

I've asked this in Cython mailing list but probably I should also get some feedback here too. I have the following function defined in Cython and using flat memory pointers to hold n by n array data. cdef some_C_layout_func(double[:, :, ::1] Am) nogil: # ... cdef double * work1 = <double*>malloc(n*n*sizeof(double)) cdef double *work2 = <double*> malloc(n*n*sizeof(double)) # ... # Lots of C-layout operations here # ... dgetrs(<char*>'T', &n, &n, &work1[0], &n, &ipiv[0], &work2[0], &n, &info ) dcopy(&n2, &work2[0], &int1, &Am[0, 0, 0], &int1) free(...) Here, I have done everything in C layout with work1 and work2 but I have to convert work2 into Fortran layout to be able to solve AX = B. A can be transposed in Lapack internally via the flag 'T' so the only obstacle I have now is to shuffle work2 which holds B transpose in the eyes of Fortran since it is still in C layout. If I go naively and make loops to get one layout to the other that actually spoils all the speed benefits from this Cythonization due to cache misses. In fact 60% of the time is spent in that naive loop across the whole function. Same goes for the copy_fortran() of memoryviews. I have measured the regular NumPy np.asfortranarray() and the performance is quite good enough compared to the actual linear solve. Hence whatever it is doing underneath I would like to reach out and do the same possibly via the C-API. But my C knowledge basically failed me around this line https://github.com/numpy/numpy/blob/8dbd507fb6c854b362c26a0dd056cd04c9c10f2… I have found the SO post from https://stackoverflow.com/questions/45143381/making-a-memoryview-c-contiguo… but I am not sure if that is the canonical way to do it in newer Python versions. Can anyone show me how to go about it without interacting with Python objects? Best, ilhan

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NumPy Community Meeting Wednesday (For those in the US: end of daylight saving means this is one hour earlier)
by Sebastian Berg Nov. 9, 2021

Nov. 9, 2021

Hi all, There will be a NumPy Community meeting Wednesday November 10th at 16:30 UTC. Everyone is invited and encouraged to join in and edit the work-in-progress meeting topics and notes at: https://hackmd.io/76o-IxCjQX2mOXO_wwkcpg?both Best wishes Sebastian

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branching NumPy 1.22.x
by Charles R Harris Nov. 8, 2021

Nov. 8, 2021

Hi All, I am aiming to branch NumPy 1.22.x next weekend. If there are any PRs that you think need to be merged before the branch, please raise the issue. Chuck

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Make the pickle default protocol 4.
by Charles R Harris Nov. 8, 2021

Nov. 8, 2021

Hi All, I'd like to propose making the NumPy default pickle protocol 4, the same as the Python 3.8 default. That would have the advantage of supporting large pickles. The current default protocol is 2, last the default in Python 2.7. Thoughts? Chuck

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Deprecate np.MachAr?
by bas van beek Nov. 8, 2021

Nov. 8, 2021

Hi all, The subject of `MachAr` recently came up in https://github.com/numpy/numpy/pull/20132 and an earlier community meeting, more notably: it’s questionably role as public (and even private?) API. Ever since the introduction of hard-coded `finfo` parameters back in numpy/numpy#8504 there has been progressively less need for computing machine parameters during runtime, to the point where `MachAr` is effectively unused in the numpy codebase itself[1]. From a user-API point of view, the main difference between ` finfo` and `MachAr` these days is that the latter produces the same results roughly 4 orders of magnitude slower than the former… Are there any thoughts about deprecating it? Regards, Bas [1] It’s still used as fallback for `longdouble` types with unknown bytes-representations, rare cases that probably deserve their own pull request.

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Percentile/Quantile "interpolation" refactor
by Sebastian Berg Nov. 8, 2021

Nov. 8, 2021

Hi all, after a long time Abel has helped us and refactored the quantile and percentile functions' `interpolation` keyword. This was long overdue since NumPy implements three (the non-default) interpolation methods that appear to be very much non-standard. On the other hand, NumPy currently has no unbiased methods (i.e. population estimate). There are two main questions right now with respect to the API. First which names to use for the methods and second, how to deal with "outliers". The PR https://github.com/numpy/numpy/pull/19857#issuecomment-939852134 adds the methods and gives them (currently) the following names (sorted by the R methods) – the names will be used as string identifiers: 1. inverted cdf 2. averaged inverted cdf 3. closest observation 4. interpolated inverted cdf 5. hazen (name from wolfram) 6. weibull (name from wolfram) 7. linear (default! Better name deferred) 8. median unbiased 9. normal unbiased And additionally the four ones we currently have: * lower * higher * nearest * midpoint Number 5. and 6. are named "exclusive" and "inclusive" by Python in their `method` keyword argument. While I like the name `method=` and may want to move to it, I am not sure I like "inclusive" and "exclusive". The current plan was to defer the kwarg rename into a followup, although it should be discussed before the next release. The second main question is how to deal with outliers (this does not affect the default method 7, which finds the sample quantiles and not a population estimate). Wikipedia says this: Packages differ in how they estimate quantiles beyond the lowest and highest values in the sample, i.e. p < 1/N and p > (N − 1)/N. Choices include returning an error value, computing linear extrapolation, or assuming a constant value. The current choice is clipping (assuming a constant value), but this could be modified. Any feedback is appreciated! Otherwise, this will probably move forward in the current state for the next release. Cheers, Sebastian

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ENH: add functionality NpyAppendArray to numpy.format
by Michael Siebert Nov. 7, 2021

Nov. 7, 2021

Dear all, I'd like to add the NpyAppendArray functionality, compare https://github.com/xor2k/npy-append-array (15 Stars so far) and https://stackoverflow.com/a/64403144/2755796 (10 Upvotes so far) I have prepared a pull request and want to "test the waters" as suggested by the message I have received when creating the pull request. So what is NpyAppendArray about? I love the .npy file format. It is really great! I cannot appreciate the .npy capabilities mentioned in https://numpy.org/devdocs/reference/generated/numpy.lib.format.html enough, especially its simplicity. No comparison with the struggles we had with HDF5. However, there is one feature Numpy currently does not provide: a simple, efficient, easy-to-use and safe option to append to .npy (here the text I've used in the Github repository above): Appending to an array created by np.save might be possible under certain circumstances, since the .npy total header byte count is required to be evenly divisible by 64. Thus, there might be some spare space to grow the shape entry in the array descriptor. However, this is not guaranteed and might randomly fail. Initialize the array with NpyAppendArray(filename) directly so the header will be created with 64 byte of spare header space for growth. Will this be enough? It allows for up to 10^64 >= 2^212 array entries or data bits. Indeed, this is less than the number of atoms in the universe. However, fully populating such an array, due to limits imposed by quantum mechanics, would require more energy than would be needed to boil the oceans, compare https://hbfs.wordpress.com/2009/02/10/to-boil-the-oceans Therefore, a wide range of use cases should be coverable with this approach. Who could use that? I developed and use NpyAppendArray to efficiently create .npy arrays which are larger than the main memory and can be loaded by memory mapping later, e.g. for Deep Learning workflows. Another use case are binary log files, which could be created on low end embedded devices and later be processed without parsing, optionally again using memory maps. How does the code look like? Here some demo code of how this would look like in practice (taken from the test file): def test_NpyAppendArray(tmpdir): arr1 = np.array([[1,2],[3,4]]) arr2 = np.array([[1,2],[3,4],[5,6]]) fname = os.path.join(tmpdir, 'npaa.npy') with format.NpyAppendArray(fname) as npaa: npaa.append(arr1) npaa.append(arr2) npaa.append(arr2) arr = np.load(fname, mmap_mode="r") arr_ref = np.concatenate([arr1, arr2, arr2]) assert_array_equal(arr, arr_ref) Some more aspects: 1. appending efficiently only works along axis=0 at least for c order (probably different for Fortran order) 2. One could also add the 64 bytes of spare space right on np.save. However, I cannot really judge on how much of an issue that would be to the users of np.save and it is not really necessary since users who want to append to .npy files would create them with NpyAppendArray anyway. 3. Probably I have forgotten something here, some time has passed since the initial Github commit. So what do you think? Yes/No/Maybe? It would be really nice to get some feedback on the mailing list here! Although this might not be perfectly consistent with the protocol, I've created the pull request already, just to force myself to finish this up and I'm prepared to fail if there is no interest to get NpyAppendArray directly into numpy ;) Best from Berlin, Michael

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ANN: SciPy 1.7.2
by Tyler Reddy Nov. 6, 2021

Nov. 6, 2021

Hi all, On behalf of the SciPy development team I'm pleased to announce the release of SciPy 1.7.2, which is a bug fix release that includes wheels for Python 3.10 on many platforms. Many thanks to upstream developers in the ecosystem for their assistance in making this possible. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.7.2 <https://github.com/scipy/scipy/releases/tag/v1.6.3> <https://github.com/scipy/scipy/releases/tag/v1.6.1> One of a few ways to install this release with pip: pip install scipy==1.7.2 ==================== SciPy 1.7.2 Release Notes ==================== SciPy 1.7.2 is a bug-fix release with no new features compared to 1.7.1. Notably, the release includes wheels for Python 3.10, and wheels are now built with a newer version of OpenBLAS, 0.3.17. Python 3.10 wheels are provided for MacOS x86_64 (thin, not universal2 or arm64 at this time), and Windows/Linux 64-bit. Many wheels are now built with newer versions of manylinux, which may require newer versions of pip. Authors ====== * Peter Bell * da-woods + * Isuru Fernando * Ralf Gommers * Matt Haberland * Nicholas McKibben * Ilhan Polat * Judah Rand + * Tyler Reddy * Pamphile Roy * Charles Harris * Matti Picus * Hugo van Kemenade * Jacob Vanderplas A total of 14 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 1.7.2 ------------------------------ * `#6019 <https://github.com/scipy/scipy/issues/6019>`__: minimize_scalar doesn't seem to honor "disp" option * `#14321 <https://github.com/scipy/scipy/issues/14321>`__: BUG: Indexing of CSR matrices with many rows is much slower than... * `#14465 <https://github.com/scipy/scipy/issues/14465>`__: BUG: n-d interpolation parameter provided to geometric_slerp * `#14599 <https://github.com/scipy/scipy/issues/14599>`__: SciPy 1.7 builds as zipped egg, ruining imports * `#14606 <https://github.com/scipy/scipy/issues/14606>`__: BUG: crash / core dump when calling scipy.stats.beta.ppf with... * `#14732 <https://github.com/scipy/scipy/issues/14732>`__: CI, TST: pre-release failures for scipy/interpolate/tests/test_rbfinterp.py * `#14802 <https://github.com/scipy/scipy/issues/14802>`__: CI: Azure Main coverage job failure * `#14829 <https://github.com/scipy/scipy/issues/14829>`__: macOS CI failing with \`ld: library not found for -lSystem\` * `#14887 <https://github.com/scipy/scipy/issues/14887>`__: BUG: scipy.stats.multivariate_normal.logpdf mutates some inputs Pull requests for 1.7.2 ------------------------------ * `#14207 <https://github.com/scipy/scipy/pull/14207>`__: DOC: stats: remove 'Methods' section from \`binomtest\` docstring... * `#14316 <https://github.com/scipy/scipy/pull/14316>`__: MAINT: Update \`openblas_support.py\` to support Apple Silicon * `#14323 <https://github.com/scipy/scipy/pull/14323>`__: BUG: Speed up sparse compressed indexing with very many rows * `#14333 <https://github.com/scipy/scipy/pull/14333>`__: MAINT: Use /usr/bin/linux32 so that sysconfig.get_platform()... * `#14478 <https://github.com/scipy/scipy/pull/14478>`__: BUG: geometric_slerp t ndim guard * `#14605 <https://github.com/scipy/scipy/pull/14605>`__: MAINT: Skip some interpolative decomposition tests * `#14616 <https://github.com/scipy/scipy/pull/14616>`__: REL: update build dependency versions in pyproject.toml for 1.7.2 * `#14618 <https://github.com/scipy/scipy/pull/14618>`__: FIX: raise RuntimeWarning when Boost evaluation_error is encountered * `#14672 <https://github.com/scipy/scipy/pull/14672>`__: BLD: add \`zip_safe=False\` to the \`setup()\` call * `#14791 <https://github.com/scipy/scipy/pull/14791>`__: MAINT: SciPy 1.7.2 prep/backports * `#14803 <https://github.com/scipy/scipy/pull/14803>`__: MAINT: disable include/source coverage warning. * `#14813 <https://github.com/scipy/scipy/pull/14813>`__: Added missing np.import_array() * `#14831 <https://github.com/scipy/scipy/pull/14831>`__: CI: Add stdlib to LD_LIBRARY_PATH * `#14893 <https://github.com/scipy/scipy/pull/14893>`__: BUG: Fix alignment errors due to relaxed stride checking * `#14897 <https://github.com/scipy/scipy/pull/14897>`__: BUG: avoid mutating inputs in multivariate distributions * `#14921 <https://github.com/scipy/scipy/pull/14921>`__: MAINT: "backport" 3.10 support * `#14937 <https://github.com/scipy/scipy/pull/14937>`__: MAINT: 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ndenumerate for masked arrays
by Jouke Witteveen Nov. 5, 2021

Nov. 5, 2021

Hi all, Using `np.ndenumerate` on masked arrays gives unexpected results. For instance, next(np.ndenumerate(np.ma.masked_all(()))) does *not* equal `((), np.ma.masked)`, but instead contains whatever value happens to be in the uninitialized data part of the masked array. Even better than yielding `((), np.ma.masked)` would be for `ndenumerate` to skip masked entries altogether. After all, we are also getting the index of the entries we are iterating over. I went ahead and implemented this specialization of `ndenumerate` for masked arrays: https://github.com/numpy/numpy/pull/20020 If there is anything I can do to advance this pull request, please let me know. Regards, - Jouke

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