Fix ABI3 issues identified during 1.3.0b1 release attempt (#13136)

We recently tried to publish the 1.3.0b1 release unsucessfully. During
the wheel build jobs abi3audit was failing because it correctly
identified a couple of abi violations in the builds. The first was we
were tagging the package incorrectly as being with a minimum level of
Python 3.8 instead of the correct minimum of 3.9. This commit updates
the setup.py tag to match the package metadata with the binary.

The second issue is we were creating `PyInit_*` symbols for submodules
which goes against the abi3 naming recomendations and abi3 audit flags
it as a violation. We had this issue previously in 1.2.0 but was fixed
for that release. However since 1.2.0 and now several stray usages of
`#[pymodule]` on submodules slipped in during development. This commit
fixes those so the bad symbol names won't be created anymore.

Once this commit merges we should tag the new commit as 1.3.0b1.

Co-authored-by: Raynel Sanchez <87539502+raynelfss@users.noreply.github.com>

crates/accelerate/src/circuit_library/mod.rs

@@ -14,7 +14,6 @@ use pyo3::prelude::*;
 
 mod entanglement;
 
-#[pymodule]
 pub fn circuit_library(m: &Bound<PyModule>) -> PyResult<()> {
     m.add_wrapped(wrap_pyfunction!(entanglement::get_entangler_map))?;
     Ok(())

crates/accelerate/src/commutation_analysis.rs

@@ -12,7 +12,7 @@
 
 use pyo3::exceptions::PyValueError;
 use pyo3::prelude::PyModule;
-use pyo3::{pyfunction, pymodule, wrap_pyfunction, Bound, PyResult, Python};
+use pyo3::{pyfunction, wrap_pyfunction, Bound, PyResult, Python};
 use qiskit_circuit::Qubit;
 
 use crate::commutation_checker::CommutationChecker;
@@ -185,7 +185,6 @@ pub(crate) fn analyze_commutations(
     Ok(out_dict.unbind())
 }
 
-#[pymodule]
 pub fn commutation_analysis(m: &Bound<PyModule>) -> PyResult<()> {
     m.add_wrapped(wrap_pyfunction!(analyze_commutations))?;
     Ok(())

crates/accelerate/src/commutation_cancellation.rs

@@ -15,7 +15,7 @@ use std::f64::consts::PI;
 use hashbrown::{HashMap, HashSet};
 use pyo3::exceptions::PyRuntimeError;
 use pyo3::prelude::*;
-use pyo3::{pyfunction, pymodule, wrap_pyfunction, Bound, PyResult, Python};
+use pyo3::{pyfunction, wrap_pyfunction, Bound, PyResult, Python};
 use rustworkx_core::petgraph::stable_graph::NodeIndex;
 use smallvec::{smallvec, SmallVec};
 
@@ -273,7 +273,6 @@ pub(crate) fn cancel_commutations(
     Ok(())
 }
 
-#[pymodule]
 pub fn commutation_cancellation(m: &Bound<PyModule>) -> PyResult<()> {
     m.add_wrapped(wrap_pyfunction!(cancel_commutations))?;
     Ok(())

crates/accelerate/src/commutation_checker.rs

@@ -767,7 +767,6 @@ fn hashable_params(params: &[Param]) -> PyResult<SmallVec<[ParameterKey; 3]>> {
         .collect()
 }
 
-#[pymodule]
 pub fn commutation_checker(m: &Bound<PyModule>) -> PyResult<()> {
     m.add_class::<CommutationLibrary>()?;
     m.add_class::<CommutationChecker>()?;

crates/accelerate/src/gate_direction.rs

@@ -142,7 +142,6 @@ where
     Ok(true)
 }
 
-#[pymodule]
 pub fn gate_direction(m: &Bound<PyModule>) -> PyResult<()> {
     m.add_wrapped(wrap_pyfunction!(py_check_with_coupling_map))?;
     m.add_wrapped(wrap_pyfunction!(py_check_with_target))?;

crates/accelerate/src/remove_diagonal_gates_before_measure.rs

@@ -102,7 +102,6 @@ fn run_remove_diagonal_before_measure(dag: &mut DAGCircuit) -> PyResult<()> {
     Ok(())
 }
 
-#[pymodule]
 pub fn remove_diagonal_gates_before_measure(m: &Bound<PyModule>) -> PyResult<()> {
     m.add_wrapped(wrap_pyfunction!(run_remove_diagonal_before_measure))?;
     Ok(())

setup.py

@@ -51,5 +51,5 @@ setup(
             features=features,
         )
     ],
-    options={"bdist_wheel": {"py_limited_api": "cp38"}},
+    options={"bdist_wheel": {"py_limited_api": "cp39"}},
 )