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Update to 0.58.1 #128

Merged
merged 10 commits into from
Nov 8, 2023
Merged

Update to 0.58.1 #128

merged 10 commits into from
Nov 8, 2023

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metab0t
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@metab0t metab0t commented Oct 20, 2023

Checklist

  • Used a personal fork of the feedstock to propose changes
  • Bumped the build number (if the version is unchanged)
  • Reset the build number to 0 (if the version changed)
  • Re-rendered with the latest conda-smithy (Use the phrase @conda-forge-admin, please rerender in a comment in this PR for automated rerendering)
  • Ensured the license file is being packaged.

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Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

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Thanks Yue! 🙏

Requesting one change above

Co-authored-by: jakirkham <jakirkham@gmail.com>
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metab0t commented Oct 21, 2023

The failed tests on Linux are caused by +0.0 != -0.0.
It seems to be a numerical issue and too strict equality criteria.
@esc How can we disable some tests in run_tests.sh (python -m numba.tests.test_runtests) ?

@jdblischak jdblischak mentioned this pull request Oct 23, 2023
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@jakirkham jakirkham mentioned this pull request Oct 23, 2023
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We are seeing the following test failures. AFAICT there are small things like -0 that throw the comparison

@stuartarchibald how should we proceed here?

======================================================================
FAIL: test_arcsinh_D_D (numba.tests.test_ufuncs.TestLoopTypesComplex.test_arcsinh_D_D)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1522, in test_template
    self._check_loop(fn, ufunc, loop)
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1468, in _check_loop
    self._check_ufunc_with_dtypes(fn, ufunc, letter_types)
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1507, in _check_ufunc_with_dtypes
    self.assertPreciseEqual(py_arg, c_arg, prec=prec, msg=msg,
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/support.py", line 434, in assertPreciseEqual
    self.fail("when comparing %s and %s: %s" % (first, second, failure_msg))
AssertionError: when comparing [0.        -1.57079633j        nan       +nanj 0.        -1.57079633j
 0.        +0.j         1.44973435+0.73040122j        nan       +nanj
 1.44973435+0.73040122j 0.        +0.j        ] and [-0.        -1.57079633j         nan       +nanj -0.        -1.57079633j
  0.        +0.j          1.44973435+0.73040122j         nan       +nanj
  1.44973435+0.73040122j  0.        +0.j        ]: 0.0 != -0.0 : ufunc 'arcsinh' arrays differ ([array([-0. -1.j ,  nan+nanj, -0. -1.j ,  0. +0.j ,  1.5+1.5j,  nan+nanj,
        1.5+1.5j,  0. +0.j ]), array([-0.        -1.57079633j,         nan       +nanj,
       -0.        -1.57079633j,  0.        +0.j        ,
        1.44973435+0.73040122j,         nan       +nanj,
        1.44973435+0.73040122j,  0.        +0.j        ])]):
args: double
expected [0.        -1.57079633j        nan       +nanj 0.        -1.57079633j
 0.        +0.j         1.44973435+0.73040122j        nan       +nanj
 1.44973435+0.73040122j 0.        +0.j        ]
got [-0.        -1.57079633j         nan       +nanj -0.        -1.57079633j
  0.        +0.j          1.44973435+0.73040122j         nan       +nanj
  1.44973435+0.73040122j  0.        +0.j        ]

======================================================================
FAIL: test_arcsinh_F_F (numba.tests.test_ufuncs.TestLoopTypesComplex.test_arcsinh_F_F)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1522, in test_template
    self._check_loop(fn, ufunc, loop)
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1468, in _check_loop
    self._check_ufunc_with_dtypes(fn, ufunc, letter_types)
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1507, in _check_ufunc_with_dtypes
    self.assertPreciseEqual(py_arg, c_arg, prec=prec, msg=msg,
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/support.py", line 434, in assertPreciseEqual
    self.fail("when comparing %s and %s: %s" % (first, second, failure_msg))
AssertionError: when comparing [0.       -1.5707964j       nan      +nanj 0.       -1.5707964j
 0.       +0.j        1.4497344+0.7304012j       nan      +nanj
 1.4497344+0.7304012j 0.       +0.j       ] and [-0.       -1.5707964j        nan      +nanj -0.       -1.5707964j
  0.       +0.j         1.4497343+0.7304012j        nan      +nanj
  1.4497343+0.7304012j  0.       +0.j       ]: 0.0 != -0.0 : ufunc 'arcsinh' arrays differ ([array([-0. -1.j ,  nan+nanj, -0. -1.j ,  0. +0.j ,  1.5+1.5j,  nan+nanj,
        1.5+1.5j,  0. +0.j ], dtype=complex64), array([-0.       -1.5707964j,        nan      +nanj,
       -0.       -1.5707964j,  0.       +0.j       ,
        1.4497343+0.7304012j,        nan      +nanj,
        1.4497343+0.7304012j,  0.       +0.j       ], dtype=complex64)]):
args: single
expected [0.       -1.5707964j       nan      +nanj 0.       -1.5707964j
 0.       +0.j        1.4497344+0.7304012j       nan      +nanj
 1.4497344+0.7304012j 0.       +0.j       ]
got [-0.       -1.5707964j        nan      +nanj -0.       -1.5707964j
  0.       +0.j         1.4497343+0.7304012j        nan      +nanj
  1.4497343+0.7304012j  0.       +0.j       ]

======================================================================
FAIL: test_arctanh_D_D (numba.tests.test_ufuncs.TestLoopTypesComplex.test_arctanh_D_D)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1522, in test_template
    self._check_loop(fn, ufunc, loop)
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1468, in _check_loop
    self._check_ufunc_with_dtypes(fn, ufunc, letter_types)
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1507, in _check_ufunc_with_dtypes
    self.assertPreciseEqual(py_arg, c_arg, prec=prec, msg=msg,
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/support.py", line 434, in assertPreciseEqual
    self.fail("when comparing %s and %s: %s" % (first, second, failure_msg))
AssertionError: when comparing [0.        -0.78539816j        nan       +nanj 0.        -0.78539816j
 0.        +0.j         0.30594386+1.21648319j        nan       +nanj
 0.30594386+1.21648319j 0.        +0.j        ] and [-0.        -0.78539816j         nan       +nanj -0.        -0.78539816j
  0.        +0.j          0.30594386+1.21648319j         nan       +nanj
  0.30594386+1.21648319j  0.        +0.j        ]: 0.0 != -0.0 : ufunc 'arctanh' arrays differ ([array([-0. -1.j ,  nan+nanj, -0. -1.j ,  0. +0.j ,  1.5+1.5j,  nan+nanj,
        1.5+1.5j,  0. +0.j ]), array([-0.        -0.78539816j,         nan       +nanj,
       -0.        -0.78539816j,  0.        +0.j        ,
        0.30594386+1.21648319j,         nan       +nanj,
        0.30594386+1.21648319j,  0.        +0.j        ])]):
args: double
expected [0.        -0.78539816j        nan       +nanj 0.        -0.78539816j
 0.        +0.j         0.30594386+1.21648319j        nan       +nanj
 0.30594386+1.21648319j 0.        +0.j        ]
got [-0.        -0.78539816j         nan       +nanj -0.        -0.78539816j
  0.        +0.j          0.30594386+1.21648319j         nan       +nanj
  0.30594386+1.21648319j  0.        +0.j        ]

======================================================================
FAIL: test_arctanh_F_F (numba.tests.test_ufuncs.TestLoopTypesComplex.test_arctanh_F_F)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1522, in test_template
    self._check_loop(fn, ufunc, loop)
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1468, in _check_loop
    self._check_ufunc_with_dtypes(fn, ufunc, letter_types)
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/test_ufuncs.py", line 1507, in _check_ufunc_with_dtypes
    self.assertPreciseEqual(py_arg, c_arg, prec=prec, msg=msg,
  File "/home/conda/feedstock_root/build_artifacts/numba_1697850551590/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.11/site-packages/numba/tests/support.py", line 434, in assertPreciseEqual
    self.fail("when comparing %s and %s: %s" % (first, second, failure_msg))
AssertionError: when comparing [0.        -0.7853982j        nan      +nanj 0.        -0.7853982j
 0.        +0.j        0.30594385+1.2164832j        nan      +nanj
 0.30594385+1.2164832j 0.        +0.j       ] and [-0.        -0.7853982j         nan      +nanj -0.        -0.7853982j
  0.        +0.j         0.30594385+1.2164832j         nan      +nanj
  0.30594385+1.2164832j  0.        +0.j       ]: 0.0 != -0.0 : ufunc 'arctanh' arrays differ ([array([-0. -1.j ,  nan+nanj, -0. -1.j ,  0. +0.j ,  1.5+1.5j,  nan+nanj,
        1.5+1.5j,  0. +0.j ], dtype=complex64), array([-0.        -0.7853982j,         nan      +nanj,
       -0.        -0.7853982j,  0.        +0.j       ,
        0.30594385+1.2164832j,         nan      +nanj,
        0.30594385+1.2164832j,  0.        +0.j       ], dtype=complex64)]):
args: single
expected [0.        -0.7853982j        nan      +nanj 0.        -0.7853982j
 0.        +0.j        0.30594385+1.2164832j        nan      +nanj
 0.30594385+1.2164832j 0.        +0.j       ]
got [-0.        -0.7853982j         nan      +nanj -0.        -0.7853982j
  0.        +0.j         0.30594385+1.2164832j         nan      +nanj
  0.30594385+1.2164832j  0.        +0.j       ]

----------------------------------------------------------------------

@PrimozGodec
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If it is just a small numeric error, can tests be disabled for this version (it seems the package builds fine and tests again almost all tests except those small numeric values)? They can be reenabled for the next version when it is fixed in Numba.

@jakirkham
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It's my understanding the Numba team is currently investigating this. So let's give them a little time to follow up

@PrimozGodec
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Is there any new on this one?

@stuartarchibald
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@jakirkham apologies for the delay on this. I've debugged it and think that the issue is actually rooted in a problem in the CF docker container glibc/libm. This program demonstrates:

#include <stdio.h>
#include <complex.h>

int main(void) {
    double complex x = -0.0 - 1.0 * I;
    double complex result;
    printf("Input : (%18.16f, %18.16f)\n", creal(x), cimag(x));
    result = casinh(x);
    printf("Result: (%18.16f, %18.16f)\n", creal(result), cimag(result));
    return 0;
}

which, in the container used for the build, produces:

$ $CC issue128.c -o issue128 -lm
$ ./issue128
Input : (-0.0000000000000000, -1.0000000000000000)
Result: (0.0000000000000000, -1.5707963267948966)

Note that the real part of the result does not copy the sign of the zero from the input. Further, running the failing test in the same container under gdb with a breakpoint set on casinh confirms it's being hit by NumPy and is likely the cause of the mismatch (Numba's implementation is largely internal and IIRC doesn't rely on the casinh symbol, so should just behave consistently invariant of libm's complex function implementations).

This issue was discussed at the Numba maintainer's triage meeting on 2023-10-31 and the conclusion was that if the issue is indeed in libm, then, given the way in which this part of the test suite is written, it would be easiest for Conda-Forge to carry a "skip these tests" style patch.

As an aside, as part of the above discussion, it wasn't clear why the containers are using glibc of version 2.10 and 2.12? I did try and see if there was a ticket tracking the potential libm issue but couldn't find an issue tracker or source that would go back that far (seems to be from around 2015?).

Hope this helps?

@metab0t
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metab0t commented Nov 3, 2023

@jakirkham OK to merge?

@henryiii
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henryiii commented Nov 3, 2023

Can we just skip the broken tests? Skipping all tests on Linux sounds like it could hide future problems.

@metab0t
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metab0t commented Nov 3, 2023

The test system of numba is based on unittests.
It is easy to select a fraction of tests but I don't know how to filter specific tests like pytest.

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esc commented Nov 6, 2023

The test system of numba is based on unittests. It is easy to select a fraction of tests but I don't know how to filter specific tests like pytest.

Numba has a number of convenience functions for skipping specific tests, like this one:

https://github.com/numba/numba/blob/main/numba/tests/support.py#L92

Here is the documentation about how to skip things using unittest:

https://docs.python.org/3/library/unittest.html#skipping-tests-and-expected-failures

So, probably a decorator like:

@unittest.skipIf(sys.platform.startswith('linux'), "Skipping on linux for conda-forge, see issue #128")

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metab0t commented Nov 6, 2023

I don't have the expertise or bandwidth to dig into which parts of tests should be precisely skipped.
Now I use llvmlite from conda-forge channel and numba from numba channel as a temporary solution.

This reverts commit e7d0718.
Signed-off-by: Marcel Bargull <marcel.bargull@udo.edu>
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mbargull commented Nov 6, 2023

@conda-forge-admin, please rerender

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mbargull commented Nov 6, 2023

As an aside, as part of the above discussion, it wasn't clear why the containers are using glibc of version 2.10 and 2.12? I did try and see if there was a ticket tracking the potential libm issue but couldn't find an issue tracker or source that would go back that far (seems to be from around 2015?).

While Anaconda stopped building for CentOS 6 (glibc 2.12) in 2021 after its regular maintenance EOL, conda-forge continues to build for CentOS 6 by default until June next year (RHEL 6 extended support EOL).
We do, however started to only test by default against CentOS 7 (glibc 2.17) about 2 years ago.
For a timeline see:

Due to slight misunderstanding this feedstock continued to be tested against CentOS 6 (we hadn't yet merged a commit to rectify that).


That being said, apparently we have slight regression in NumPy 1.26 regarding arctanh on glibc<=2.17:

python -c 'import numpy as np; print("pass" if np.signbit(np.arctanh(-1j).real) else "fail", np.__version__)'

On CentOS 7:

/usr/lib64/libc.so.6 --version | head -n1
GNU C Library (GNU libc) stable release version 2.17, by Roland McGrath et al.
pass 1.25.2
fail 1.26.0

On Ubuntu 14.04:

/lib/x86_64-linux-gnu/libc-2.19.so --version | head -n1
GNU C Library (Ubuntu EGLIBC 2.19-0ubuntu6.15) stable release version 2.19, by Roland McGrath et al.
pass 1.25.2
pass 1.26.0

Small reproducer showing different behavior in glibc versions like the one given by @stuartarchibald in #128 (comment) :

{ cat << 'EOF' 
#include <stdio.h>
#include <complex.h>
#include <math.h>

void main(void) {
    double complex x = -I;
    if (signbit(creal(catanh(x))))
        printf("pass\n");
    else
        printf("fail\n");
}
EOF
} | $CC -x c - -o issue128 -lm

CentOS 7:

# ./issue128 
fail

Ubuntu 14.04:

# ./issue128 
pass

^-- If anyone wants to report that upstream to NumPy, feel free to do so.

- llvm-openmp is added as a hard dependency via run_exports anyway.
- libgomp is linked to by numba.np.ufunc.omppool.
- tbb cannot be input to pin_compatible since it is not in host reqs.

Signed-off-by: Marcel Bargull <marcel.bargull@udo.edu>
Signed-off-by: Marcel Bargull <marcel.bargull@udo.edu>
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mbargull commented Nov 7, 2023

^-- If anyone wants to report that upstream to NumPy, feel free to do so.

I haven't yet opened an upstream issue but put out conda-forge/numpy-feedstock#304 for further inspection/reference in future upstream issue.


@conda-forge/numba : Anyone opposed to merging?
I added the very specific numpy !=1.26.0 # [linux and x86_64] to the test requirements so that this will be able to test for numpy>1.26.0 builds in the future.

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mbargull commented Nov 7, 2023

I haven't yet opened an upstream issue but put out conda-forge/numpy-feedstock#304 for further inspection/reference in future upstream issue.

Upstream issue: numpy/numpy#25087

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mbargull commented Nov 7, 2023

I've also opened an issue for Numba to test against glibc=2.17 upstream so that we could react to upstream NumPy changes earlier in the future.

xref:
- numba/numba#9270

@jakirkham
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Thanks Stuart for digging into the test issue and following up! 🙏 Agree that we can just ignore those tests

Thanks everyone (especially Marcel) on bringing this up-to-date! 🙏

@beckermr , could you please read over the discussion and changes here? Would appreciate hearing your thoughts (as I think you discovered the GLIBC symbol leak issue previously)

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mbargull commented Nov 7, 2023

(as I think you discovered the GLIBC symbol leak issue previously)

That was a false positive coming from defaults, see #89 (comment) .

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beckermr commented Nov 7, 2023

This feedstock is build with cos6 because when it was built against cos7, it started to carry cos7 symbols and not just the cos6 ones.

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beckermr commented Nov 7, 2023

Ahhh thanks @mbargull! We all missed that apparently. LGTM!

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Thanks all! 🙏

Generally this looks good. Thanks for all the hard work here 👏

Had a couple questions below

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Comment on lines 82 to 84
# Need these for AOT. Do not init msvc as it may not be present
- {{ compiler('c') }} # [not win]
- {{ compiler('cxx') }} # [not win]
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Somewhat unrelated, but do we need to limit this on Windows? We should always have MSVC on CI. Or do we want to keep this around for offline building/testing?

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I guess we could remove it.
It comes from the upstream recipe.
IDK in which way it changes the tests, TBH.

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No strong feelings. Agree dropping altogether seems reasonable. We can always change later if needed

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Ah, I actually meant to drop the selector only but deleted the lines 🤦.

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Oh ok. Thought it was dropped since the current AOT implementation is deprecated

Though ok with continuing to test AOT until it is removed

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Thanks Marcel! 🙏

@jakirkham jakirkham added the automerge Merge the PR when CI passes label Nov 8, 2023
Signed-off-by: Marcel Bargull <marcel.bargull@udo.edu>
@github-actions github-actions bot removed the automerge Merge the PR when CI passes label Nov 8, 2023
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github-actions bot commented Nov 8, 2023

Hi! This is the friendly conda-forge automerge bot!

Commits were made to this PR after the automerge label was added. For security reasons, I have disabled automerge by removing the automerge label. Please add the automerge label again (or ask a maintainer to do so) if you'd like to enable automerge again!

@mbargull mbargull added the automerge Merge the PR when CI passes label Nov 8, 2023
@mbargull mbargull merged commit 172c489 into conda-forge:main Nov 8, 2023
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mbargull commented Nov 8, 2023

I haven't yet opened an upstream issue but put out conda-forge/numpy-feedstock#304 for further inspection/reference in future upstream issue.

Upstream issue: numpy/numpy#25087

Upstream PR to fix it: numpy/numpy#25093

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Thanks for all your efforts @mbargull @jakirkham, great to see this shipped!

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8 participants