Fix CI for mypy and add explicit shape for COO

[woodsp-ibm]

Summary

To fix CI. I tested the changes on a couple of machines 1 with 3.9 the other 3.12 and it seems to pass checks locally.

Fixes #917

Details and comments

1. There was a unit test failure around shape. See Nightly tests failing around sparse COO #917 so I added shape parameter explicitly to COO. This had been noted in a deprecation warning that shape would become required and did so in the lastest sparse which is where things broke. It still works with the earlier sparse versions where its optional.

2. There are several mypy failures as below. These do not show up in 3.9 and my first attempt was to add a type: ignore comment for the incompatible type ones which passed under 3.12 but under 3.9 gave error: Unused "type: ignore" comment [unused-ignore] as it does not fail under the older mypy which is still in use by 3.9. Given the code works, though I guess the newer mypy notes the type differences from what it sees to start with being assigned to what is done to the same variable later I simply added an Any type to the variable which passes mypy now under 3.9 and 3.12 since it allows all (any) types.

For the pegagos_svc failure I cast the return of the algorithm_globals.random.integers call to an int type so as to avoid the later use of it in the get being unable to match appropriately.

qiskit_machine_learning/optimizers/aqgd.py:170: error: Incompatible types in assignment (expression has type "ndarray[tuple[int, ...], dtype[Any]] | ndarray[tuple[int, ...], dtype[float64]]", variable has type "list[ndarray[tuple[int, ...], dtype[Any]] | ndarray[tuple[int, ...], dtype[float64]]]")  [assignment]
qiskit_machine_learning/optimizers/adam_amsgrad.py:187: error: Incompatible types in assignment (expression has type "ndarray[tuple[int, ...], dtype[Any]]", variable has type "ndarray[tuple[int], dtype[float64]]")  [assignment]
qiskit_machine_learning/optimizers/adam_amsgrad.py:189: error: Incompatible types in assignment (expression has type "ndarray[tuple[int, ...], dtype[Any]]", variable has type "ndarray[tuple[int], dtype[float64]]")  [assignment]
qiskit_machine_learning/optimizers/adam_amsgrad.py:190: error: Incompatible types in assignment (expression has type "ndarray[tuple[int, ...], dtype[Any]]", variable has type "ndarray[tuple[int], dtype[float64]]")  [assignment]
qiskit_machine_learning/optimizers/adam_amsgrad.py:216: error: Incompatible types in assignment (expression has type "ndarray[tuple[int, ...], dtype[float64]]", variable has type "ndarray[tuple[int], dtype[float64]]")  [assignment]
qiskit_machine_learning/optimizers/adam_amsgrad.py:217: error: Incompatible types in assignment (expression has type "ndarray[tuple[int, ...], dtype[float64]]", variable has type "ndarray[tuple[int], dtype[float64]]")  [assignment]
qiskit_machine_learning/optimizers/adam_amsgrad.py:219: error: Incompatible types in assignment (expression has type "ndarray[tuple[int, ...], dtype[float64]]", variable has type "ndarray[tuple[int], dtype[float64]]")  [assignment]
qiskit_machine_learning/optimizers/adam_amsgrad.py:234: error: Incompatible types in assignment (expression has type "ndarray[tuple[int, ...], dtype[Any]]", variable has type "ndarray[tuple[int], dtype[float64]]")  [assignment]
qiskit_machine_learning/neural_networks/effective_dimension.py:177: error: Incompatible types in assignment (expression has type "ndarray[tuple[int, ...], dtype[float64]]", variable has type "ndarray[tuple[int, int, int], dtype[float64]]")  [assignment]
qiskit_machine_learning/neural_networks/effective_dimension.py:178: error: Incompatible types in assignment (expression has type "ndarray[tuple[int, ...], dtype[float64]]", variable has type "ndarray[tuple[int, int], dtype[float64]]")  [assignment]
qiskit_machine_learning/algorithms/classifiers/pegasos_qsvc.py:198: error: Argument 1 to "_compute_weighted_kernel_sum" of "PegasosQSVC" has incompatible type "signedinteger[_64Bit]"; expected "int"  [arg-type]
qiskit_machine_learning/algorithms/classifiers/pegasos_qsvc.py:202: error: Invalid index type "signedinteger[_64Bit]" for "dict[int, int]"; expected type "int"  [index]
qiskit_machine_learning/algorithms/classifiers/pegasos_qsvc.py:202: error: No overload variant of "get" of "dict" matches argument types "signedinteger[_64Bit]", "int"  [call-overload]
qiskit_machine_learning/algorithms/classifiers/pegasos_qsvc.py:202: note: Possible overload variants:
qiskit_machine_learning/algorithms/classifiers/pegasos_qsvc.py:202: note:     def get(self, int, /) -> int
qiskit_machine_learning/algorithms/classifiers/pegasos_qsvc.py:202: note:     def get(self, int, int, /) -> int
qiskit_machine_learning/algorithms/classifiers/pegasos_qsvc.py:202: note:     def [_T] get(self, int, _T, /) -> int | _T

[woodsp-ibm]

Seems this just failed per #903 (ie randomly). I'll note it here but its outside of any changes done by this PR. I'll re-run once all tests are done and it should (hopefully) pass ok then.

Update: I re-ran that failed check and the test now passed as expected.

test.gradients.test_estimator_gradient.TestEstimatorGradientV2.test_gradient_parameter_coefficient_2_LinCombEstimatorGradient
-----------------------------------------------------------------------------------------------------------------------------

Captured traceback:
~~~~~~~~~~~~~~~~~~~
    Traceback (most recent call last):

      File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/ddt.py", line 221, in wrapper
    return func(self, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^

      File "/Users/runner/work/qiskit-machine-learning/qiskit-machine-learning/test/gradients/test_estimator_gradient.py", line 614, in test_gradient_parameter_coefficient
    np.testing.assert_allclose(gradients, correct_results[i], atol=1e-1, rtol=1e-1)

      File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/numpy/testing/_private/utils.py", line 1715, in assert_allclose
    assert_array_compare(compare, actual, desired, err_msg=str(err_msg),

      File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/numpy/testing/_private/utils.py", line 921, in assert_array_compare
    raise AssertionError(msg)

    AssertionError: 
Not equal to tolerance rtol=0.1, atol=0.1

Mismatched elements: 1 / 4 (25%)
Max absolute difference among violations: 0.18941639
Max relative difference among violations: 0.26066525
 ACTUAL: array([-0.537249, -0.424078, -0.003906, -0.919434])
 DESIRED: array([-0.726665, -0.490513, -0.006861, -0.922888])

[coveralls]

Pull Request Test Coverage Report for Build 15005482575

Details

• 10 of 10 (100.0%) changed or added relevant lines in 5 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage remained the same at 90.857%

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Totals
Change from base Build 13973547049:	0.0%
Covered Lines:	4482
Relevant Lines:	4933

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💛 - Coveralls