Remove reimplementation of np.testing.assert_allclose

[jaharvey8]

Description

I think I got all the unittest_tools.assert_allclose instances

The following files no longer used functions from unittest_tools so I removed the import
tests/link/test_vm.py
tests/tensor/test_variable.py
tests/scalar/test_basic.py
tests/sparse/test_rewriting.py
tests/link/c/test_params_type.py
tests/tensor/rewriting/test_elemwise.py

There was a mention of utt.assert_all close in the creating_an_op document file so I changed that as well.

Related Issue

• Closes Remove reimplementation of np.testing.assert_allclose #551

Checklist

• Checked that the pre-commit linting/style checks pass
• Included tests that prove the fix is effective or that the new feature works
• Added necessary documentation (docstrings and/or example notebooks)
• If you are a pro: each commit corresponds to a [relevant logical changes

Type of change

• New feature / enhancement
• Bug fix
• Documentation
• Maintenance
• Other (please specify):

[ricardoV94]

Seems like the rtol/atol values may need to be tweaked slightly, as some tests are now failing

[jaharvey8]

Seems like the rtol/atol values may need to be tweaked slightly, as some tests are now failing

Potentially dumb question, is that something I need to do?

[ricardoV94]

Yes, we can only merge the changes if all tests pass. You can see which tests failed here on GitHub

[jaharvey8]

Oh ok yeah I just wasn't sure what the atol and rtol values were and if that was something I was supposed to modify. But I'll look and see which tests failed and why. Thanks!

[jaharvey8]

Ok I fixed up some remaining calls to the old unittest_tools assert_allclose function and fixed some typos I had introduced.

On the rtol and atol issues, in the current unittest_tools assert_allclose function, the default values for those are set to 'None'. That is

def assert_allclose(expected, value, rtol=None, atol=None):
    if not _allclose(expected, value, rtol, atol):
        raise WrongValue(expected, value, rtol, atol)

Should I also pass 'None' to the np.testing.assert_allclose function calls (assuming that's allowed)?

[ricardoV94]

Instead of none, we should not specify them at all (unless the test fails, then we need to tweak them)

[ricardoV94]

If things get out of hand, the default atol and rtol were being defined here:

pytensor/pytensor/tensor/math.py

Line 102 in 0ebc83b

def _get_atol_rtol(a, b):

And used here:

pytensor/pytensor/tensor/math.py

Line 117 in 0ebc83b

def _allclose(a, b, rtol=None, atol=None):

[Dhruvanshu-Joshi]

Hi @jaharvey8 Are you still working on this PR? I'd like to take it up if you are not.