1878 pyquil v5 deprecations

[erichulburd]

Description

pyQuil v5 deprecation warnings as described in #1878

Checklist

• The PR targets the master branch
• The above description motivates these changes.
• The change is atomic and can be described by a single commit (your PR will be squashed on merge).
• All changes to code are covered via unit tests.
• Parameters and return values have type hints with PEP 484 syntax.
• Functions and classes have useful Sphinx-style docstrings.
• Live QPU tests have run via pytest test --live-qpu-access by myself or a reviewer.
• (New Feature) The docs have been updated accordingly.
• (User-visible change) A bullet has been added under "Unreleased" in the changelog.
• (Bugfix) The associated issue is referenced above using auto-close keywords.
• (Release) Version bump and changelog update according to CONTRIBUTING.md.

[github-actions]

☂️ Python Coverage

current status: ❌

Overall Coverage

Lines	Covered	Coverage	Threshold	Status
10396	9342	90%	87%	🟢

New Files

File	Coverage	Status
pyquil/_deprecation.py	100%	🟢
pyquil/_pyqvm.py	74%	🔴
pyquil/_wavefunction.py	80%	🔴
TOTAL	85%	🔴

Modified Files

File	Coverage	Status
pyquil/api/init.py	100%	🟢
pyquil/api/_compiler.py	62%	🟢
pyquil/api/_quantum_computer.py	86%	🟢
pyquil/api/_qvm.py	87%	🟢
pyquil/api/_wavefunction_simulator.py	81%	🟢
pyquil/experiment/init.py	100%	🟢
pyquil/experiment/_group.py	93%	🟢
pyquil/experiment/_main.py	81%	🟢
pyquil/experiment/_memory.py	92%	🟢
pyquil/experiment/_program.py	100%	🟢
pyquil/experiment/_result.py	88%	🟢
pyquil/experiment/_setting.py	95%	🟢
pyquil/latex/init.py	100%	🟢
pyquil/latex/_diagram.py	92%	🟢
pyquil/latex/_ipython.py	35%	🟢
pyquil/latex/_main.py	100%	🟢
pyquil/latex/latex_generation.py	0%	🟢
pyquil/noise/init.py	100%	🟢
pyquil/noise/_legacy_noise.py	95%	🟢
pyquil/noise_gates.py	87%	🟢
pyquil/operator_estimation.py	90%	🟢
pyquil/pyqvm.py	100%	🟢
pyquil/quil.py	85%	🟢
pyquil/simulation/init.py	100%	🟢
pyquil/simulation/_numpy.py	94%	🟢
pyquil/simulation/_reference.py	77%	🟢
pyquil/simulation/tools.py	93%	🟢
pyquil/wavefunction.py	100%	🟢
TOTAL	86%	🟢

updated for commit: ffadd40 by action🐍

[github-actions]

Bencher Report

Project	pyquil
Branch	1878-pyquil_v5_deprecations
Testbed	ci-runner-linux

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Benchmark	Latency	milliseconds (ms)
test/benchmarks/test_program.py::test_copy_everything_except_instructions	📈 view plot ⚠️ NO THRESHOLD	9,730.98 ms
test/benchmarks/test_program.py::test_instructions	📈 view plot ⚠️ NO THRESHOLD	3,186.23 ms
test/benchmarks/test_program.py::test_iteration	📈 view plot ⚠️ NO THRESHOLD	3,241.57 ms
test/benchmarks/test_simulators.py::TestJitCompileTime::test_density_matrix_compile_depth[20L]	📈 view plot ⚠️ NO THRESHOLD	236.98 ms
test/benchmarks/test_simulators.py::TestJitCompileTime::test_density_matrix_compile_depth[40L]	📈 view plot ⚠️ NO THRESHOLD	272.50 ms
test/benchmarks/test_simulators.py::TestJitCompileTime::test_density_matrix_compile_depth[5L]	📈 view plot ⚠️ NO THRESHOLD	225.46 ms
test/benchmarks/test_simulators.py::TestJitCompileTime::test_state_vector_compile_depth[10L]	📈 view plot ⚠️ NO THRESHOLD	212.68 ms
test/benchmarks/test_simulators.py::TestJitCompileTime::test_state_vector_compile_depth[40L]	📈 view plot ⚠️ NO THRESHOLD	200.77 ms
test/benchmarks/test_simulators.py::TestJitCompileTime::test_state_vector_compile_depth[80L]	📈 view plot ⚠️ NO THRESHOLD	217.66 ms
test/benchmarks/test_simulators.py::TestPerformance::test_17q_batch_size[b16]	📈 view plot ⚠️ NO THRESHOLD	136,404.00 ms
test/benchmarks/test_simulators.py::TestPerformance::test_17q_batch_size[b64]	📈 view plot ⚠️ NO THRESHOLD	121,986.08 ms
test/benchmarks/test_simulators.py::TestPerformance::test_17q_batch_size[b8]	📈 view plot ⚠️ NO THRESHOLD	158,369.55 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_batch_size[b16]	📈 view plot ⚠️ NO THRESHOLD	43,649.09 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_batch_size[b64]	📈 view plot ⚠️ NO THRESHOLD	29,006.03 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_batch_size[b8]	📈 view plot ⚠️ NO THRESHOLD	66,021.24 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_depth[10L]	📈 view plot ⚠️ NO THRESHOLD	34,047.79 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_depth[1L]	📈 view plot ⚠️ NO THRESHOLD	14,361.88 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_depth[20L]	📈 view plot ⚠️ NO THRESHOLD	57,055.70 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_depth[3L]	📈 view plot ⚠️ NO THRESHOLD	18,912.89 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_qubits[12q]	📈 view plot ⚠️ NO THRESHOLD	11,570.15 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_qubits[15q]	📈 view plot ⚠️ NO THRESHOLD	35,471.47 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_qubits[3q]	📈 view plot ⚠️ NO THRESHOLD	3,420.66 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_qubits[6q]	📈 view plot ⚠️ NO THRESHOLD	4,978.73 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_qubits[9q]	📈 view plot ⚠️ NO THRESHOLD	6,776.82 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_subsystem_size[s0]	📈 view plot ⚠️ NO THRESHOLD	94,027.28 ms
test/benchmarks/test_simulators.py::TestPerformance::test_scaling_subsystem_size[s1]	📈 view plot ⚠️ NO THRESHOLD	33,232.11 ms
test/benchmarks/test_simulators.py::TestPerformance::test_surface17_depth5_cycle_noise	📈 view plot ⚠️ NO THRESHOLD	80,522.64 ms
test/benchmarks/test_simulators.py::TestPerformance::test_surface17_depth5_cycle_noise_low_trajectory	📈 view plot ⚠️ NO THRESHOLD	5,130.28 ms
test/benchmarks/test_simulators.py::TestPerformance::test_surface17_depth5_cycle_noise_measurements_only_micro	📈 view plot ⚠️ NO THRESHOLD	2,354.60 ms
test/benchmarks/test_simulators.py::TestPerformance::test_surface17_depth5_cycle_noise_micro	📈 view plot ⚠️ NO THRESHOLD	4,372.60 ms
test/benchmarks/test_simulators.py::TestPerformance::test_surface17_depth5_cycle_noise_micro_jit	📈 view plot ⚠️ NO THRESHOLD	61.66 ms
test/benchmarks/test_simulators.py::TestPerformance::test_surface17_depth5_cycle_noise_no_measurements_micro	📈 view plot ⚠️ NO THRESHOLD	2,802.16 ms

🐰 View full continuous benchmarking report in Bencher

[bramathon]

I think quiltwaveforms should be deprecated as there is a quil based implementation coming? @asaites will know

[bramathon]

I believe noise_gates.py should be deprecated