MAINT: 1.9.1 backports #16901
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MAINT: 1.9.1 backports #16901
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…uild files (scipy#16749) * BLD: remove a warning suppression flag for HiGHS extension This is no longer necessary, the PR linked in the removed comment is included in our `highs` git submodule now. * BLD: remove an outdated FIXME from the scipy/integrate/meson.build This was fixed I believe (there are no skipped or xfailed tests either), and the comment isn't very informative. * BLD: remove another FIXME in `cython_optimize/meson.build`, it's not broken The code can be simplified once the upstream feature is added, but that's not a FIXME. * BLD: remove comments about c++14/c++11 support We can rely on C++14 unconditionally since 2021, see http://scipy.github.io/devdocs/dev/toolchain.html#c-language-standards * BLD: update info on including all license files as separate files * BLD: install missing `scipy/*.pxd` files No tests were failing, so something is fairly badly wrong in the test suite. Also add `optimize.cython_optimize` to the list of submodules that are public API. * BLD: remove FIXME about version string generation This was fixed when adding `--git-dir` to the git invocation, that made the result independent from the current directory when invoking the build. * BLD: remove TODO about `-fallow-argument-mismatch` This flag is added implicitly via 'fortran_std=legacy' in the top-level `meson.build`. Warnings that show up are silenced in multiple modules, so there's no need for a separate TODO here. * BLD: remove TODO for UNU.RAN version string This isn't a very useful today, given that we don't use this version string. The corresponding `setup.py` file also does the same and doesn't have a TODO. * BLD: update FIXME to a TODO in `linalg/meson.build`
This is a fallback detection path, in case pkg-config fails to find `openblas`. CMake uses the camelcase version of the name. If CMake is installed and it finds OpenBLAS, the result looks like: ``` Determining dependency 'OpenBLAS' with pkg-config executable '/home/rgommers/anaconda3/envs/scipy-dev/bin/pkg-config' env[PKG_CONFIG_PATH]: Called `/home/rgommers/anaconda3/envs/scipy-dev/bin/pkg-config --modversion OpenBLAS` -> 1 CMake binary for 1 is cached. Determining dependency 'OpenBLAS' with CMake executable '/home/rgommers/anaconda3/envs/scipy-dev/bin/cmake' Try CMake generator: auto Calling CMake (['/home/rgommers/anaconda3/envs/scipy-dev/bin/cmake']) in /home/rgommers/code/scipy/build/meson-private/cmake_OpenBLAS with: - "-DNAME=OpenBLAS" - "-DARCHS=libpyldb-util.cpython-310-x86-64-linux-gnu.so;libpyldb-util.cpython-310-x86-64-linux-gnu.so.2;libpyldb-util.cpython-310-x86-64-linux-gnu.so.2.5.0;libpytalloc-util.cpython-310-x86-64-linux-gnu.so;libpytalloc-util.cpython-310-x86-64-linux-gnu.so.2;libpytalloc-util.cpython-310-x86-64-linux-gnu.so.2.3.3;libsamba-policy.cpython-310-x86-64-linux-gnu.so;libsamba-policy.cpython-310-x86-64-linux-gnu.so.0;libsamba-policy.cpython-310-x86-64-linux-gnu.so.0.0.1" - "-DVERSION=" - "-DCOMPS=" - "--trace-expand" - "--trace-format=json-v1" - "--no-warn-unused-cli" - "--trace-redirect=cmake_trace.txt" - "-DCMAKE_TOOLCHAIN_FILE=/home/rgommers/code/scipy/build/meson-private/cmake_OpenBLAS/CMakeMesonToolchainFile.cmake" - "." - "-DCMAKE_PREFIX_PATH=/home/rgommers/anaconda3/envs/scipy-dev;/home/rgommers/anaconda3/envs/scipy-dev/x86_64-conda-linux-gnu/sysroot/usr" using old-style CMake variables for dependency OpenBLAS Include Dirs: ['/home/rgommers/anaconda3/envs/scipy-dev/include'] Compiler Definitions: [] Libraries: ['/home/rgommers/anaconda3/envs/scipy-dev/lib/libopenblas.so'] Run-time dependency openblas found: YES 0.3.20 ``` This follows up on comments in scipygh-16308
Instead of string concatenation, use Meson's path operator, which was designed based on the same concept as pathlib.Path and uses the / operator overload (but effectively using .as_posix() for consistency). This guarantees consistent handling, and also avoids e.g. introspection files containing duplicated path separators such as `.../site-packages//scipy/...` This is also required in order for Meson to internally track when an install_dir string comes from py3.get_install_dir() after path-based joining semantics, which is needed for improvements to the mesonpy build backend.
…gainst Closes scipygh-16787 [ci skip]
This mirrors the change in scipy/oldest-supported-numpy#61 NumPy 1.23.3 is the first numpy version with 3.11 wheels on PyPI.
The Schur decomposition is not unique, so testing the result of linalg.schur against hard-coded matrices is not reliable. The updated tests check that the desired properties of the result are satisfied, and that the order of the diagonal elements of the triangular matrix agrees with the given 'sort' parameter. Closes scipygh-14517
tylerjereddy
requested review from
person142,
andyfaff,
ev-br,
larsoner,
ilayn and
rgommers
as code owners
tylerjereddy
commented
Aug 26, 2022
There was a problem hiding this comment.
The other CI failure is:
/opt/hostedtoolcache/Python/3.8.13/x64/lib/python3.8/site-packages/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py:355: in test_tolerance_float32
assert_allclose(eigvals, -np.arange(1, 1 + m), atol=1.5e-5)
E AssertionError:
E Not equal to tolerance rtol=1e-07, atol=1.5e-05
E
E Mismatched elements: 1 / 3 (33.3%)
E Max absolute difference: 1.6450882e-05
E Max relative difference: 5.48362732e-06
E x: array([-1. , -2.000003, -3.000016], dtype=float32)
E y: array([-1, -2, -3])
A = <50x50 sparse matrix of type '<class 'numpy.float32'>'
with 50 stored elements (1 diagonals) in DIAgonal format>
X = array([[ 1.7640524 , 0.4001572 , 0.978738 ],
[ 2.2408931 , 1.867558 , -0.9772779 ],
[ 0.95008844, -...03146],
[ 2.3831449 , 0.94447947, -0.91282225],
[ 1.1170163 , -1.3159074 , -0.4615846 ]], dtype=float32)
_ = array([[ 1.00000000e+00, -4.98104975e-13, -1.17866172e-07],
[-6.63076853e-13, -1.00000000e+00, -2.94708485e-07]...091e-09, 4.23395043e-08, 3.24512008e-08],
[ 1.32321158e-08, -1.75330488e-08, -2.44689122e-08]], dtype=float32)
eigvals = array([-1. , -2.000003 , -3.0000165], dtype=float32)
m = 3
n = 50
rnd = RandomState(MT19937) at 0x7FE549992440
vals = array([ -1, -2, -3, -4, -5, -6, -7, -8, -9, -10, -11, -12, -13,
-14, -15, -16, -17, -18, -19, -20, -21,..., -29, -30, -31, -32, -33, -34, -35, -36, -37, -38, -39,
-40, -41, -42, -43, -44, -45, -46, -47, -48, -49, -50])
mdhaber
reviewed
Aug 26, 2022
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@tylerjereddy @rgommers I think we also need 49cac09 to be cherry picked. |
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For the |
…nce_float32' (scipy#16755) This test has been failing occasionally in CI, with errors slightly greater than the requested tolerances. (cherry picked from commit f71e7fa)
I think this will fix the issue with commit count being zero reported in scipygh-16702. (cherry picked from commit 97ee16d)
rgommers
approved these changes
Aug 26, 2022
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Thanks @tylerjereddy & all. I included all the suggested fixes and added one more backported commit (the version numbering robustness one).
This all LGTM provided it comes back green. I'll open a separate PR for updated dependency ranges.
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CI was green and I've manually cleared out the related backport candidate labels as well. |
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Backports the following PRs, which are all currently-merged PRs with an active backport label, for which there were no merge conflicts observed during cherry-picking. It looks like we'll delay Python
3.11wheels to SciPy1.9.2. In the absence of a compelling reason to delay/issue in the wheels repo (etc.), I think the plan is to try to get a release out this weekend for1.9.1..pxdfiles, and update TODOs/FIXMEs in meson.build files #16749interp1d. #16825odrandczt#16862