Deprecate loose custom basis gates in preset pm pipieline

[ElePT]

Summary

This PR is a spinoff of #12850 that introduces the deprecation warning for loose custom basis gates as an input to transpile/generate_preset_pm. This is a pre-requisite for eventually merging #12850. Moving forward, users can still provide custom basis gates but they need to be included as part of a Target instance.

Details and comments

The PR also modifies a few oversights found in generate_preset_pass_manager that didn't have user impact but should be corrected to set the stage for a target-only pipeline:

• we were "over-skipping" the target by having a condition with an or instead of an and (fixed in L453/466)
• control flow ops were not included by default in the custom name mapping (this would raise a warning if control flow ops were provided as loose basis gates). This didn't cause issues because the target was often skipped with the previous oversight.

[qiskit-bot]

One or more of the following people are relevant to this code:

• @Qiskit/terra-core

[coveralls]

Pull Request Test Coverage Report for Build 11702502035

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

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• For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

• 42 of 42 (100.0%) changed or added relevant lines in 5 files are covered.
• 147 unchanged lines in 15 files lost coverage.
• Overall coverage increased (+0.06%) to 88.829%

---

Files with Coverage Reduction	New Missed Lines	%
crates/accelerate/src/unitary_synthesis.rs	1	92.2%
crates/qasm2/src/expr.rs	1	94.02%
qiskit/circuit/library/generalized_gates/gms.py	2	94.44%
qiskit/circuit/library/generalized_gates/rv.py	2	84.62%
qiskit/transpiler/preset_passmanagers/builtin_plugins.py	2	95.74%
qiskit/primitives/backend_sampler_v2.py	2	98.53%
qiskit/circuit/library/generalized_gates/diagonal.py	3	95.16%
qiskit/circuit/library/generalized_gates/permutation.py	3	92.73%
crates/qasm2/src/lex.rs	8	91.73%
qiskit/circuit/library/grover_operator.py	9	92.86%

Totals
Change from base Build 11669445061:	0.06%
Covered Lines:	77100
Relevant Lines:	86796

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💛 - Coveralls

[eliarbel]

Overall LGTM, thanks and good catch with the target-skipping condition! I have couple small comments, one is important.

[eliarbel]

Dead code now

[ElePT]

Thanks for the review! Really good catch with transpile. This actually made me notice that it was used internally in the Quantum Shannon Decomposer, so I had to do a small refactoring there. The code should look good now!

[eliarbel]

Overall looks good, thanks for all the changes and for handling the newly exposed deprecation warnings. I've left one question for you to confirm in qsd.py; assuming you will, I think this PR is good to go hence already approving.

[eliarbel]

Previously transpile built a flow containing UnitarySynthesis, HighLevelSynthesis and BasisTranslator. Looking at qs_decomposition seems that this change is safe in the sense that HighLevelSynthesis should be sufficient. Can you just confirm?

[ElePT]

Yes, I believe it is, I also briefly confirmed it with @Cryoris.