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MAINT: backports/prep for 1.13.1 #20632

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Commits on May 2, 2024

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  2. BUG: sync pocketfft again

    * Fixes scipygh-20300 by syncing `pocketfft` again, this time
    to completely disable `aligned_alloc`; see scipy/pocketfft#3
    for details, but in short our more conservative shim
    was not sufficient for `conda-forge`, so let's just do the same
    thing NumPy did...
    
    [skip cirrus] [skip circle]
    tylerjereddy committed May 2, 2024
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  4. DOC: add missing deprecations from 1.13.0 release notes

    [doc only]
    j-bowhay authored and tylerjereddy committed May 2, 2024
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  6. DOC: remove spurious backtic from release notes

    [doc only]
    j-bowhay authored and tylerjereddy committed May 2, 2024
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  7. BUG: linalg: fix ordering of complex conj gen eigenvalues

    This was reported to cause test failures under windows + MKL in conda-forge
    cf scipy#20471
    ev-br authored and tylerjereddy committed May 2, 2024
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  8. TST: interpolate: bump test tolerance in TestRGI::test_derivatives

    A slight tolerance violation was reported on conda-forge in
    scipy#20472
    ev-br authored and tylerjereddy committed May 2, 2024
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  9. TST: interpolate: bump test tolerance in TestInterpN

    A small tolerance violation reported on conda-forge
    in scipy#20472
    ev-br authored and tylerjereddy committed May 2, 2024
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  10. TST: interpolate: bump test tolerance in test_rbfinterp::test_pickleable

    An exact equality was reported as flaky on conda-forge in
    scipy#20472
    
    The tolerance violations are of the order of fp noise (< 2e-16), and I don't
    think that pickling/unpickling guarantees bit-to-bit compatibility.
    In principle, this may invoke recalculations and those may be subject
    to fp noise. So I think it's OK to only require allclose(atol=eps)
    instead of exact equality.
    ev-br authored and tylerjereddy committed May 2, 2024
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  11. TST: sparse/linalg: bump tolerance for an svds test

    tol violation observed on conda-forge on win+blis; suggested in
    scipy#20474 (comment)
    ev-br authored and tylerjereddy committed May 2, 2024
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  13. BUG: linalg: fix eigh(1x1 array, driver='evd') f2py check (scipy#20516)

    f2py check was just too strict;
    LAPACK docs indicate that for N=1, lwork>=1 is acceptable:
    
    *  LWORK   (input) INTEGER
    *          The dimension of the array WORK.
    *          If N <= 1,               LWORK must be at least 1.
    *          If JOBZ = 'N' and N > 1, LWORK must be at least 2*N+1.
    *          If JOBZ = 'V' and N > 1, LWORK must be at least
    *                                                1 + 6*N + 2*N**2.
    
    https://www.netlib.org/lapack/explore-3.1.1-html/ssyevd.f.html
    
    closes scipygh-20512
    ev-br authored and tylerjereddy committed May 2, 2024
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  15. BLD: Fix error message for f2py generation fail (scipy#20530)

    Co-authored-by: Ralf Gommers <ralf.gommers@gmail.com>
    2 people authored and tylerjereddy committed May 2, 2024
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  16. update openblas to 0.3.27

    mattip authored and tylerjereddy committed May 2, 2024
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  17. BUG: Fix error with 180 degree rotation in Rotation.align_vectors() w…

    …ith an infinite weight (scipy#20573)
    
    * Fix exact rotations at 180 deg, improve near 180 deg
    
    Comments
    
    * Tests for exact near 180 deg rotations
    
    * Fix tests
    
    * Code review updates
    
    ---------
    
    Co-authored-by: Scott Shambaugh <scottshambaugh@users.noreply.github.com>
    2 people authored and tylerjereddy committed May 2, 2024
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  19. BUG: spherical_in old patch

    * Apply "old version" of the patch provided
    at scipygh-20527
    tylerjereddy committed May 2, 2024
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  20. DOC: update 1.13.1 relnotes

    * Update the SciPy `1.13.1` release notes following
    a series of backports.
    
    [skip cirrus]
    tylerjereddy committed May 2, 2024
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Commits on May 5, 2024

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  2. BUG: fix Vor/Delaunay segfaults

    * Deals with the `spatial` part of scipygh-20623 (`Voronoi`
    was also affected beyond the originally-reported `Delaunay`
    segfault).
    
    * Both classes are documented to accept arrays with two dimensions
    only, so raise a `ValueError` in cases with other dimensions to
    avoid the segfault.
    
    * Other potential points of confusion here are the differences
    between arrays with two dimensions and two dimensional arrays
    that represent generators with more than two dimensions via
    the number of columns, but this is just how things are for
    most array programming languages of course. Also, the docs
    don't explicitly say array-like for the generators I don't think, but this patch
    only worked if I placed it after the coercion to array type.
    
    [skip circle] [skip ci] [ci skip]
    tylerjereddy committed May 5, 2024
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Commits on May 15, 2024

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  2. MAINT: stats.yulesimon: fix kurtosis

    mdhaber authored and tylerjereddy committed May 15, 2024
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  3. MAINT: stats: update boost to improve skewnorm.ppf (scipy#20643)

    * MAINT: stats: update boost to fix improve `skewnorm.ppf`
    dschmitz89 authored and tylerjereddy committed May 15, 2024
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  4. BUG: sparse: Clean up 1D input handling to sparse array/matrix and ad…

    …d tests (scipy#20444)
    
    * test 1d input to sparse. Add FutureWarnings and ValueErrors
    
    * remove matrix changes. Let them create 2D
    
    * correct imports
    
    * rebase on main and update to support 1D CSR input
    dschult authored and tylerjereddy committed May 15, 2024
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  5. BUG: sparse: Fix summing duplicates for CSR/CSC creation from (data,c…

    …oords) (scipy#20687)
    
    * test and then fix duplicates for CSR/CSC creation from (data,coords)
    
    * remove has_canonical_format check when summing duplicates.
    dschult authored and tylerjereddy committed May 15, 2024
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  6. MAINT: added doc/source/.jupyterlite.doit.db to .gitignore See scipy#…

    Sijo Valayakkad Manikandan authored and tylerjereddy committed May 15, 2024
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  7. MAINT: lint: temporarily disable UP031

    [lint only]
    lucascolley authored and tylerjereddy committed May 15, 2024
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  8. DEV: lint: disable UP031

    Showed up as a linting error in an unrelated PR for me:
    ```
    scipy/interpolate/_interpolate.py:918:30: UP032 [*] Use f-string instead of `format` call
    scipy/interpolate/_interpolate.py:1972:30: UP032 [*] Use f-string instead of `format` call
    ```
    This should not happen; the old code is fine, so this check needs to be
    silenced or fixed separately. Similar to scipygh-20601.
    
    [skip ci]
    rgommers authored and tylerjereddy committed May 15, 2024
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  9. BUG: value_indices unfixed types

    * Fixes scipygh-19423
    
    * Add a few more `case` statements to account for
    the (i.e., Windows) data types that don't have a fixed
    width, and add a regression test.
    
    [skip circle] [skip cirrus]
    tylerjereddy committed May 15, 2024
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  10. MAINT: release branch failures

    * attempt to deal with scipygh-20576
    tylerjereddy committed May 15, 2024
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  11. MAINT: import fixes

    * some minor import fixes following a large
    series of backports
    tylerjereddy committed May 15, 2024
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  13. MAINT: import fixes

    * more import cleanups after backport activity
    to make the linter happy
    tylerjereddy committed May 15, 2024
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Commits on May 16, 2024

  1. TST: Adapt to __array__(copy=True)

    [skip circle]
    thalassemia authored and tylerjereddy committed May 16, 2024
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Commits on May 17, 2024

  1. CI, MAINT: pin Python for MacOS conda

    * We're seeing CI failures related to an undesirable
    bump to Python `3.12` in this job, when the intention
    was clearly to respect the Python version specific
    in the GHA matrix. I didn't check too closely why
    exactly it suddenly started happening, but some
    packages weren't ready for `3.12` yet on this
    job (`scikit-umfpack` in particular) and I don't
    see too much harm in adding an extra pin to
    respect the intention for the Python version.
    tylerjereddy committed May 17, 2024
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Commits on May 18, 2024

  1. CI: MR 20632 revisions

    * attempt to fix `M1 test - openblas` MacOS ARM CI job
    based on some `gfortran` shims applied to a similar
    job on `main`
    tylerjereddy committed May 18, 2024
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Commits on May 19, 2024

  1. CI: PR 20632 revisions [wheel build]

    * This is an empty commit to test the wheel
    building in the above PR.
    
    [wheel build]
    tylerjereddy committed May 19, 2024
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Commits on May 21, 2024

  1. MAINT: PR 20632 revisions [wheel build]

    * Changes needed to get MacOS ARM wheels building
    again, based on debug work on my fork.
    
    [wheel build]
    tylerjereddy committed May 21, 2024
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  2. MAINT: PR 20632 revisions [wheel build]

    * Need to pin `pythran` version in a CI job
    because of a recent new release.
    
    [wheel build]
    tylerjereddy committed May 21, 2024
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Commits on May 22, 2024

  1. CI, MAINT: PR 20632 revisions

    * Increase the Cirrus CI Linux aarch64
    job timeout to 72 minutes; it timed
    out twice in a row via manual restarts.
    tylerjereddy committed May 22, 2024
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  3. BUG: stats: Fix zipf.pmf and zipfian.pmf for int32 k (scipy#20702

    …) [wheel build]
    
    * BUG: fix zipf.pmf for integer k
    
    * ENH: increase range for zipfian.pmf for integer k
    
    ---------
    
    Co-authored-by: Tyler Reddy <tyler.je.reddy@gmail.com>
    
    [wheel build]
    dschmitz89 authored and tylerjereddy committed May 22, 2024
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  4. DOC: PR 20632 updates

    * Update the SciPy `1.13.1` release notes following substantial
    backport activity.
    
    [skip cirrus]
    tylerjereddy committed May 22, 2024
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