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MAINT: SciPy 1.11.3 backports/prep #19279
MAINT: SciPy 1.11.3 backports/prep #19279
Commits on Sep 21, 2023
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BUG: add infeasibility checks to min_weight_full_bipartite_matching
The algorithm is already equipped with a handful of checks for problem infeasibility, but the tests added here show two different examples that were not caught by any of those checks. It is likely possible to dive in and determine infeasibility in `_lapjvsp` itself, as in both examples, the symptom is the algorithm hitting an infinite loop (but a different infinite loop for each case), but here we simply add the catch-all fix of checking that the problem is feasible before even trying to solve it. This does come with a performance hit, but at least the implementation of Hopcroft--Karp that we're using is fast.
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MAINT: specify expected error message in test
Co-authored-by: Jake Bowhay <60778417+j-bowhay@users.noreply.github.com>
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BUG: sparse.csgraph: Support int64 indices in traversal.pyx (scipy#18913
) Closes scipygh-18716 Co-authored-by: Julien Jerphanion <git@jjerphan.xyz>
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BUG: trust-constr Bounds exclusive
Closes scipy#15093 The scipy docs define Bounds as inclusive but trust-constr treats bounds as exclusive. According to Nocedal, Jorge, and Stephen J. Wright. "Numerical optimization" Second Edition (2006), p. 393, interior point methods necessarily treat bounds as exclusive. To work around this limitation of interior point methods and create consistent behavior for Bounds, this PR modifies trust-constr so that Bounds passed to trust-constr are expanded by epsilon.
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Switched from using assert_ to using assert.
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BUG: Fixes scipy#19103 by adding back make_strictly_feasible to lsq trf.
PR scipy#18896 removed make_strictly_feasible because it makes solutions worse if they are close to the boundary. However, the downstream algorithm that eventually solves the optimization problem has some trouble with starting points that are on the boundaries of a bounded optimization problem. This either results in division by zero warnings, see scipy#19102, or in failure of finding the correct solution at all, which is added as a regression test in this commit. This PR brings back make_strictly_feasible but with the smallest possible step from the boundary a floating point allows by setting rstep=0 on the function make_strictly_feasible, which uses np.nextafter to find such a point, hereby respecting the strictly feasible point condition and minimizing boundary effects. See strictly feasible points in interior-point methods for more context https://nmayorov.wordpress.com/2015/06/19/trust-region-reflective-algorithm/
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BLD: Avoid absolute pathnames in .pyx files
to allow for reproducible builds even when (unneeded) .pyx files are installed and shipped in OS packages Fixes: scipy#19101 This patch was done while working on reproducible builds for openSUSE.
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MAINT: signal: Remove the cval parameter from the private function _p…
…ad_test. The parameter `cval` in the private helper function `_pad_test` is not used, so remove it. This change is inspired by a bug in Cython 3.0.1 (see SciPy issue scipygh-19132), and this change is a work-around for that bug, but since the parameter is unused and in a private function, there is no need to revert this change.
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BLD: revert to using published wheels [wheel build] (scipy#19139)
* BLD: revert to using published wheels [wheel build]
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BUG: Support sparse arrays in scipy.sparse.csgraph.laplacian (scipy#1…
…9156) * BUG: Support sparse arrays in scipy.sparse.csgraph.laplacian * TST: Added unit test for laplacian
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BUG: signal: freqz rfft grid fix (scipy#19208)
* TST: for issues scipy#17289 scipy#15273 * BUG/ENH: fix scipy#17289 scipy#15273 * TST: use correct assert * BENCH: Added a benchmark for signal.freqz * TST/BENCH: improved coverage scipy#17289 scipy#15273 * BENCH: removed vectorized input scipy#17289 scipy#15273 * STY: add missing whitespace [skip ci] --------- Co-authored-by: Jake Bowhay <60778417+j-bowhay@users.noreply.github.com>
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DOC, MAINT: update relnotes and build
* update the SciPy 1.11.3 release notes * update our wheel build config per feedback in scipygh-19274 [skip cirrus]
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* fix a doc build failure related to `numpy.ma.row_stack`; should use `vstack` now re: NumPy namespace changes that are happening
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Allow johnsonsu parameters to be floats
Fixes scipy#18782 18782
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MAINT, CI: fix linting + CI issue
* `node_list` was already made private on `main` in `_traversal.pyx`, so just apply that fix here as well, to fix the linter error * pin `pythran` in gcc-8 GHA job, was causing problem in build with isolation disabled because `0.14.0` is now available
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TST: fix
TestODR.test_implicit
test failure with tolerance bump (sc……ipy#19200) This was failing on macOS x86-64 in CI with: ``` E Arrays are not almost equal to 6 decimals E E Mismatched elements: 1 / 25 (4%) E Max absolute difference: 1.52291797e-06 E Max relative difference: 8.81522156e-07 E x: array([[ 2.108927e+00, -1.943767e+00, 7.026353e-02, -4.717525e-02, E 5.251554e-02], E [-1.943767e+00, 2.048149e+00, -6.160049e-02, 4.626880e-02,... E y: array([[ 2.108927e+00, -1.943769e+00, 7.026355e-02, -4.717527e-02, E 5.251558e-02], E [-1.943769e+00, 2.048151e+00, -6.160052e-02, 4.626883e-02,... ``` So it's a very small atol violation (1.52e-6, where decimal=6 implies 1.5e-6). Rather than bump to `decimal=5`, I decided to change the test to `assert_allclose` so the bump could be smaller. [skip ci]
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* update SciPy `1.11.3` release notes after more changes/backports [skip cirrus]
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* pin `meson-python` version in gcc-8 GHA job, because it has build isolation disabled [skip cirrus]
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Commits on Sep 22, 2023
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DOC, TST: update 1.11.3 relnotes, test
* update SciPy `1.11.3` release notes following more backports * `test_int_x0_gh19280()` required a small shim to deal with module import differences vs. `main` [skip cirrus]
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Commits on Sep 26, 2023
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MAINT: fix libquadmath licence (scipy#19299)
* MAINT: linux amendments * MAINT: osx amendments * MAINT: win licence amendments * MAINT: licence typo
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BUG: stats: remove use of
BOOST_MATH_DECLARE_SPECIAL_FUNCTIONS
This macro must not be used in the global scope, but rather in a separate namespace (see, e.g., `boost_math/example/policy_eg_9.cpp`). It caused compilation errors with Clang on Windows in PR 246 on the conda-forge scipy feedback. This bit of code also did not seem necessary, given that these compile flags in `stats/_boost/meson.build` should already achieve the same effect: ``` '-DBOOST_MATH_EVALUATION_ERROR_POLICY=user_error', '-DBOOST_MATH_OVERFLOW_ERROR_POLICY=user_error', ``` That the custom error handling in `func_defs.hpp` is still used can be verified by running for example after modifying the `user_evaluation_error` handler: ``` python dev.py test -t scipy.stats.tests.test_distributions -- -k test_boost_eval_issue_14606 ```
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BLD: add float.h include to
_fpumode.c
, fixes Clang on Windows issueFollow-up to scipygh-8918; the linked CPython code in the discussion on the issue that that PR closes has the same `<float.h>` include. This upstreams a patch from PR 246 to https://github.com/conda-forge/scipy-feedstock Co-authored-by: Uwe L. Korn <uwe.korn@quantco.com>
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BUG: Fix python3.12 distutils dev.py build
Fix scipygh-18689 scipygh-18922 python3.12 removes distutils and scipy dev.py uses distutils for the meson based build in debian python. With python3.12 debian has patched sysconfig and no longer requires dependence on distutils.
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* update the SciPy 1.11.3 release notes following another series of backports [skip cirrus]
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Commits on Sep 27, 2023
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* empty commit to test wheel builds for the SciPy `1.11.3` release process before the backport PR is merged [wheel build]
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