internlm/SWE-Fixer-Train-110K huggingface dataset:
Repository: Qiskit/qiskit

Issue:
UnitaryOverlap cannot handle barriers
### Environment

- **Qiskit Terra version**: 0.45.0rc1
- **Python version**: 3.10
- **Operating system**: macOS


### What is happening?

UnitaryOverlap circuit breaks when input circuits contain barriers

### How can we reproduce the issue?

```
from qiskit.circuit import QuantumCircuit
from qiskit.circuit.library import UnitaryOverlap

qc1 = QuantumCircuit(2)
qc1.ry(np.pi/2, qc1.qubits)
qc1.cx(0, 1)
qc1.barrier()
qc1.rz(np.pi/2, qc1.qubits)

# Create the overlap circuit
overlap = UnitaryOverlap(qc1, qc1)
```

results in:
```CircuitError: 'One or more instructions cannot be converted to a gate. "barrier" is not a gate instruction```

### What should happen?

UnitaryOverlap should be able to handle circuits with barriers as if they weren't there.

### Any suggestions?

_No response_


Discussion:
Yeah ok, this one is probably on me for letting it through review: https://github.com/Qiskit/qiskit/pull/10734#pullrequestreview-1687299774.

Resolving patch:
diff --git a/qiskit/circuit/library/overlap.py b/qiskit/circuit/library/overlap.py
--- a/qiskit/circuit/library/overlap.py
+++ b/qiskit/circuit/library/overlap.py
@@ -15,6 +15,7 @@
 from qiskit.circuit import QuantumCircuit, Gate
 from qiskit.circuit.parametervector import ParameterVector
 from qiskit.circuit.exceptions import CircuitError
+from qiskit.circuit import Barrier
 
 
 class UnitaryOverlap(QuantumCircuit):
@@ -101,7 +102,7 @@ def _check_unitary(circuit):
     """Check a circuit is unitary by checking if all operations are of type ``Gate``."""
 
     for instruction in circuit.data:
-        if not isinstance(instruction.operation, Gate):
+        if not isinstance(instruction.operation, (Gate, Barrier)):
             raise CircuitError(
                 (
                     "One or more instructions cannot be converted to"


Test patch:
diff --git a/test/python/circuit/library/test_overlap.py b/test/python/circuit/library/test_overlap.py
--- a/test/python/circuit/library/test_overlap.py
+++ b/test/python/circuit/library/test_overlap.py
@@ -82,6 +82,15 @@ def test_partial_parameterized_inputs2(self):
         overlap = UnitaryOverlap(unitary1, unitary2)
         self.assertEqual(overlap.num_parameters, unitary1.num_parameters)
 
+    def test_barrier(self):
+        """Test that barriers on input circuits are well handled"""
+        unitary1 = EfficientSU2(1, reps=0)
+        unitary1.barrier()
+        unitary2 = EfficientSU2(1, reps=1)
+        unitary2.barrier()
+        overlap = UnitaryOverlap(unitary1, unitary2)
+        self.assertEqual(overlap.num_parameters, unitary1.num_parameters + unitary2.num_parameters)
+
     def test_measurements(self):
         """Test that exception is thrown for measurements"""
         unitary1 = EfficientSU2(2)
Repository: Qiskit/qiskit

Issue:
Incorrect list of parameters in `PauliTwoDesign` documentation
### Environment

- **Qiskit Terra version**: 0.45.1
- **Python version**:  3.10.8
- **Operating system**: openSUSE Tumbleweed  


### What is happening?

The list of parameters in the _Parameter_ section of the [PauliTwoDesign circuit](https://docs.quantum.ibm.com/api/qiskit/qiskit.circuit.library.PauliTwoDesign) documentation page does not correspond with the actual function.
The function only accepts `num_qubits`, `reps`, `seed`, `insert_barriers` and `name`. 
The list of parameters appears to be the one for the [TwoLocal circuit](https://docs.quantum.ibm.com/api/qiskit/qiskit.circuit.library.TwoLocal).

### How can we reproduce the issue?

- Visit the [PauliTwoDesign circuit](https://docs.quantum.ibm.com/api/qiskit/qiskit.circuit.library.PauliTwoDesign) documentation page and scroll down to the _Parameters_ section (below the _References_ section).
- Notice `skip_unentangeld_qubits` is mentioned as a parameter for this circuit
- Try creating a circuit with this parameter.
```
>>> from qiskit.circuit.library import PauliTwoDesign
>>> circuit = PauliTwoDesign(3, reps=1, seed=5, skip_unentangled_qubits=True)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: PauliTwoDesign.__init__() got an unexpected keyword argument 'skip_unentangled_qubits'

```

### What should happen?

The documentation should list the correct parameters for the `PauliTwoDesign` function.

### Any suggestions?

Add a `Args` docstring with the correct parameters to the `init` function of `PauliTwoDesign`.


Discussion:

Resolving patch:
diff --git a/qiskit/circuit/library/n_local/pauli_two_design.py b/qiskit/circuit/library/n_local/pauli_two_design.py
--- a/qiskit/circuit/library/n_local/pauli_two_design.py
+++ b/qiskit/circuit/library/n_local/pauli_two_design.py
@@ -75,6 +75,16 @@ def __init__(
         insert_barriers: bool = False,
         name: str = "PauliTwoDesign",
     ):
+        """
+        Args:
+            num_qubits: The number of qubits of the Pauli Two-Design circuit.
+            reps: Specifies how often a block consisting of a rotation layer and entanglement
+                layer is repeated.
+            seed: The seed for randomly choosing the axes of the Pauli rotations.
+            insert_barriers: If ``True``, barriers are inserted in between each layer. If ``False``,
+                no barriers are inserted. Defaults to ``False``.
+
+        """
         from qiskit.circuit.library import RYGate  # pylint: disable=cyclic-import
 
         # store a random number generator


Test patch:
Repository: Qiskit/qiskit

Issue:
Default values for `approximation_degree` differ in `transpile` and `generate_preset_pass_manager`
### Environment

- **Qiskit version**: 0.45
- **Python version**: 
- **Operating system**: 


### What is happening?

The `transpile` function has a default value of `approximation_degree=1.0` while the `generate_preset_pass_manager` function has `approximation_degree=None`. This can lead to drastically different default behavior when transpiling with these two functions on certain backends which was found by some recent researchers using the pass manager based code.

### How can we reproduce the issue?

To quote the example I was given:
> we had circuits with ~700 gates when  using v1 backends and/or transpile, but this dropped down to ~200 gates when using the preset pm.
on top of this, the approximation is also dependent on the actual 2Q unitary.

### What should happen?

The default values should be consistent between `transpile` and the preset pass manager.

### Any suggestions?

I believe the intended behavior is what is done in `transpile` (no approximation), so the preset pass manager should be updated to have a default kwarg value of `approximation_degree=1.0` to match


Discussion:
Yeah, this sounds very surprising in a very bad way, and we (eventually) did come to the conclusion that `approximation_degree=None` was a bad default.  Flicking quickly through the history, it looks like we changed the `transpile` default in #8595 and missed doing `generate_preset_pass_manager`, which was quite new at the time.

I think we can quickly fold this into 1.0 - I think it's better to squeeze in the "bug fix" API break after the feature-freeze deadline than to navigate a changing default through the 1.0 stability policy.

Resolving patch:
diff --git a/qiskit/transpiler/preset_passmanagers/__init__.py b/qiskit/transpiler/preset_passmanagers/__init__.py
--- a/qiskit/transpiler/preset_passmanagers/__init__.py
+++ b/qiskit/transpiler/preset_passmanagers/__init__.py
@@ -84,7 +84,7 @@ def generate_preset_pass_manager(
     routing_method=None,
     translation_method=None,
     scheduling_method=None,
-    approximation_degree=None,
+    approximation_degree=1.0,
     seed_transpiler=None,
     unitary_synthesis_method="default",
     unitary_synthesis_plugin_config=None,


Test patch:
Repository: Qiskit/qiskit

Issue:
`parallel_map` documents Events that it no longer publishes
https://github.com/Qiskit/qiskit/blob/a73bf7c3be3d6a105b10b4f7c2c7b0d7e62102c4/qiskit/tools/parallel.py#L133-L136

I had been looking to update the parallel_map usage in Nature, given the change in location for 1.0 and noticed it still has these documented (we use TextProgressBar too that will have to go - it was just in logging so no big deal)


Discussion:
Thanks - we can squash a documentation-only change in after 1.0.0rc1.

Resolving patch:
diff --git a/qiskit/utils/parallel.py b/qiskit/utils/parallel.py
--- a/qiskit/utils/parallel.py
+++ b/qiskit/utils/parallel.py
@@ -1,6 +1,6 @@
 # This code is part of Qiskit.
 #
-# (C) Copyright IBM 2017, 2018.
+# (C) Copyright IBM 2017, 2024.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory
@@ -129,11 +129,6 @@ def parallel_map(  # pylint: disable=dangerous-default-value
     Raises:
         QiskitError: If user interrupts via keyboard.
 
-    Events:
-        terra.parallel.start: The collection of parallel tasks are about to start.
-        terra.parallel.update: One of the parallel task has finished.
-        terra.parallel.finish: All the parallel tasks have finished.
-
     Examples:
 
         .. code-block:: python


Test patch:
Repository: Qiskit/qiskit

Issue:
Documentation of RVGate is incorrect
### Environment

N/A

### What is happening?

Received this in an email:
>Hi, I think I found some errors in the Qiskit documentation at
<https://docs.quantum.ibm.com/api/qiskit/qiskit.circuit.library.RVGate>
and I'm contacting you because you look like the two people who most recently edited the source file at
<https://github.com/Qiskit/qiskit/blob/stable/0.46/qiskit/circuit/library/generalized_gates/rv.py>
The matrix representation given in the documentation seems to be wrong.  I compared it to the definition given in
<https://arxiv.org/pdf/2104.14875.pdf>
on page 4, equation 1, we see the definition of the rotation matrix.  It almost matches the definition given in the documentation at
<https://docs.quantum.ibm.com/api/qiskit/qiskit.circuit.library.RVGate>
except for two mistakes: the "sinc" function should be "sin", and the angle should be divided by two.  This can be compared to the source code at
<https://github.com/Qiskit/qiskit/blob/stable/0.46/qiskit/circuit/library/generalized_gates/rv.py>
at lines 86 and 87, where we see the angle divided by two, and we see the use of the sin and cos functions.

### How can we reproduce the issue?

N/A

### What should happen?

N/A

### Any suggestions?

_No response_


Discussion:

Resolving patch:
diff --git a/qiskit/circuit/library/generalized_gates/rv.py b/qiskit/circuit/library/generalized_gates/rv.py
--- a/qiskit/circuit/library/generalized_gates/rv.py
+++ b/qiskit/circuit/library/generalized_gates/rv.py
@@ -18,7 +18,7 @@
 
 
 class RVGate(Gate):
-    r"""Rotation around arbitrary rotation axis :math:`v` where :math:`|v|` is
+    r"""Rotation around arbitrary rotation axis :math:`\vec{v}` where :math:`\|\vec{v}\|_2` is
     angle of rotation in radians.
 
     Can be applied to a :class:`~qiskit.circuit.QuantumCircuit`
@@ -36,14 +36,17 @@ class RVGate(Gate):
 
     .. math::
 
-        \newcommand{\rotationangle}{|\vec{v}|}
-        \newcommand{\sinc}{\text{sinc}}
-            R(\vec{v}) = e^{-i \vec{v}\cdot\vec{\sigma}} =
+        \newcommand{\rotationangle}{\frac{\|\vec{v}\|_2}{2}}
+            R(\vec{v}) = e^{-i \vec{v}\cdot\vec{\sigma} / 2} =
                 \begin{pmatrix}
-                    \cos\left(\rotationangle\right) -i v_z \sinc\left(\rotationangle\right)
-                    & -(i v_x + v_y) \sinc\left(\rotationangle\right) \\
-                    -(i v_x - v_y) \sinc\left(\rotationangle\right)
-                    & \cos\left(\rotationangle\right) + i v_z \sinc\left(\rotationangle\right)
+                    \cos\left(\rotationangle\right)
+                    -i \frac{v_z}{\|\vec{v}\|_2} \sin\left(\rotationangle\right)
+                    & -(i \frac{v_x}{\|\vec{v}\|_2}
+                    + \frac{v_y}{\|\vec{v}\|_2}) \sin\left(\rotationangle\right) \\
+                    -(i \frac{v_x}{\|\vec{v}\|_2}
+                    - \frac{v_y}{\|\vec{v}\|_2}) \sin\left(\rotationangle\right)
+                    & \cos\left(\rotationangle\right)
+                    + i \frac{v_z}{\|\vec{v}\|_2} \sin\left(\rotationangle\right)
                 \end{pmatrix}
     """
 


Test patch:
Repository: Qiskit/qiskit

Issue:
add `graphviz` to the visualization tool dependency
### Environment

- **Qiskit version**: 1.0.0
- **Python version**: 3.11.6
- **Operating system**: macOS


### What is happening?

When calling function `plot_circuit_layout` in the module `qiskit.visualization`, got the following error: 
```
MissingOptionalLibraryError: "The 'graphviz' library is required to use 'plot_coupling_map'. You can install it with ''brew install c' if on Mac, or by downloding it from their website'."
```

### How can we reproduce the issue?

A minimal working example
```
import numpy as np
from qiskit import QuantumCircuit
from qiskit_ibm_runtime.fake_provider import FakeSherbrooke
from qiskit import transpile
from qiskit.visualization import plot_circuit_layout
backend = FakeSherbrooke()
 
qc = QuantumCircuit(2, 1)
 
qc.h(0)
qc.x(1)
qc.cp(np.pi/4, 0, 1)
qc.h(0)
qc.measure([0], [0])
qc.draw(output='mpl')
qct = transpile(qc, backend)
plot_circuit_layout(qct, backend)
```

### What should happen?

Add the `graphviz` package to the `pyproject.toml` file for the `visualization` dependency under the section `[project.optional-dependencies]`.

### Any suggestions?

_No response_


Discussion:
The Python `graphviz` package is not the actual Graphviz executable, which is what's required - the error message should hopefully explain this.
I see. In the case, it is desirable to add the `graphviz` [python wrapper ](https://pypi.org/project/graphviz/) to the `qiskit.visualization` dependency?
Not really, unfortunately - we don't use the Python wrapper from within Qiskit, and installing the wrapper doesn't install Graphviz, so it wouldn't really change the situation.  If you've got more helpful wording for the error that would make it more understandable, we could change that?

Resolving patch:
diff --git a/qiskit/utils/optionals.py b/qiskit/utils/optionals.py
--- a/qiskit/utils/optionals.py
+++ b/qiskit/utils/optionals.py
@@ -307,8 +307,12 @@
 
 HAS_GRAPHVIZ = _LazySubprocessTester(
     ("dot", "-V"),
-    name="graphviz",
-    install="'brew install graphviz' if on Mac, or by downloding it from their website",
+    name="Graphviz",
+    msg=(
+        "To install, follow the instructions at https://graphviz.org/download/."
+        " Qiskit needs the Graphviz binaries, which the 'graphviz' package on pip does not install."
+        " You must install the actual Graphviz software"
+    ),
 )
 HAS_PDFLATEX = _LazySubprocessTester(
     ("pdflatex", "-version"),


Test patch:
Repository: Qiskit/qiskit

Issue:
preset passmanagers should perform gate optimization before routing
### What should we add?

Consider the following circuit:

```python
qc = QuantumCircuit(N)
for kk in range(N - 1):
    qc.cx(kk, N - 1)
qc.x(N - 1)
qc.z(N - 2)
for kk in range(N - 2, -1, -1):
    qc.cx(kk, N - 1)
```

This circuit should collapse down to a pair of X and Z gates via commutation and collapsing pairs of CX gates.  However, the preset passmanagers do not catch this.  Instead, collapsing requires the routing passes to find the correct mapping that allows for later clean up to be successful.  Other SDKs do this, and the performance is markedly better because routing is not required.


Discussion:
This is very easy to do (just add the pass to the `DefaultInitPassManager` as needed) and I agree it makes a ton of sense. I'm thinking we should do this at optimization levels 2 and 3, as that's where we currently do commutative cancellation today. What do you think?
I think that makes sense.  I do agree that this is low-hanging fruit.  I think where it is added depends on what is the proposed "default" preset passmanger.  Namely, other SDKs defaults will do the same, so I my thinking is we should be able to do the same "by default", and let more advance users do custom PMs 

Oh, sorry my comment was more left as a hint for where to put it in the code so it gets pulled in by `transpile` and `generate_preset_pass_manager` for everyone. It's the name of the plugin class we use for the init stage by default: 
https://github.com/Qiskit/qiskit/blob/d47a227d982710e7933d744dfd95f6550ff07ed2/qiskit/transpiler/preset_passmanagers/builtin_plugins.py#L68 we just need to add either `CommutativeCancellation` or `CommutativeInverseCancellation` to the pass manager construction there to do this.

Resolving patch:
diff --git a/qiskit/transpiler/preset_passmanagers/builtin_plugins.py b/qiskit/transpiler/preset_passmanagers/builtin_plugins.py
--- a/qiskit/transpiler/preset_passmanagers/builtin_plugins.py
+++ b/qiskit/transpiler/preset_passmanagers/builtin_plugins.py
@@ -123,6 +123,8 @@ def pass_manager(self, pass_manager_config, optimization_level=None) -> PassMana
                     ]
                 )
             )
+            if optimization_level == 2:
+                init.append(CommutativeCancellation())
 
         elif optimization_level == 3:
             init = common.generate_unroll_3q(
@@ -153,6 +155,7 @@ def pass_manager(self, pass_manager_config, optimization_level=None) -> PassMana
                     ]
                 )
             )
+            init.append(CommutativeCancellation())
 
         else:
             return TranspilerError(f"Invalid optimization level {optimization_level}")


Test patch:
Repository: Qiskit/qiskit

Issue:
`BackendSamplerV2` fails to run with empty classical register
### Environment

- **Qiskit version**: `main`
- **Python version**: 3.11
- **Operating system**: Linux


### What is happening?

The new `BackendSamplerV2` primitive fails to run if provided a circuit where at least one classical register contains zero bits.

### How can we reproduce the issue?

```python
from qiskit.circuit import QuantumCircuit, QuantumRegister, ClassicalRegister
from qiskit.primitives import BackendSamplerV2
from qiskit_aer import AerSimulator

qreg = QuantumRegister(1)
creg0 = ClassicalRegister(0)
creg1 = ClassicalRegister(1)
qc = QuantumCircuit(qreg, creg0, creg1)
qc.h(0)
qc.measure(0, 0)

backend = AerSimulator()
sampler = BackendSamplerV2(backend=backend)
sampler.run([qc], shots=1024).result()
```

### What should happen?

Successful execution

### Any suggestions?

Don't assume it's safe to lookup index 0 of the `creg` at
https://github.com/Qiskit/qiskit/blob/194cc8fb9aedc24a5082eff351fcb7b70da59f17/qiskit/primitives/backend_sampler_v2.py#L189


Discussion:

Resolving patch:
diff --git a/qiskit/primitives/backend_sampler_v2.py b/qiskit/primitives/backend_sampler_v2.py
--- a/qiskit/primitives/backend_sampler_v2.py
+++ b/qiskit/primitives/backend_sampler_v2.py
@@ -186,7 +186,10 @@ def _analyze_circuit(circuit: QuantumCircuit) -> tuple[list[_MeasureInfo], int]:
     for creg in circuit.cregs:
         name = creg.name
         num_bits = creg.size
-        start = circuit.find_bit(creg[0]).index
+        if num_bits != 0:
+            start = circuit.find_bit(creg[0]).index
+        else:
+            start = 0
         meas_info.append(
             _MeasureInfo(
                 creg_name=name,


Test patch:
diff --git a/test/python/primitives/test_backend_sampler_v2.py b/test/python/primitives/test_backend_sampler_v2.py
--- a/test/python/primitives/test_backend_sampler_v2.py
+++ b/test/python/primitives/test_backend_sampler_v2.py
@@ -656,6 +656,21 @@ def test_no_cregs(self, backend):
         self.assertEqual(len(result), 1)
         self.assertEqual(len(result[0].data), 0)
 
+    @combine(backend=BACKENDS)
+    def test_empty_creg(self, backend):
+        """Test that the sampler works if provided a classical register with no bits."""
+        # Test case for issue #12043
+        q = QuantumRegister(1, "q")
+        c1 = ClassicalRegister(0, "c1")
+        c2 = ClassicalRegister(1, "c2")
+        qc = QuantumCircuit(q, c1, c2)
+        qc.h(0)
+        qc.measure(0, 0)
+
+        sampler = BackendSamplerV2(backend=backend, options=self._options)
+        result = sampler.run([qc], shots=self._shots).result()
+        self.assertEqual(result[0].data.c1.array.shape, (self._shots, 0))
+
 
 if __name__ == "__main__":
     unittest.main()
Repository: Qiskit/qiskit

Issue:
Typo: Change Block to Bloc
https://github.com/Qiskit/qiskit/blob/8121aaef61077221d2e612c2c9e54bbfcdb19d07/qiskit/primitives/__init__.py#L113

@kevinsung opened an issue [here](https://github.com/Qiskit/documentation/issues/1066) to change the spelling of Block to Bloc, for consistency.


Discussion:

Resolving patch:
diff --git a/qiskit/primitives/__init__.py b/qiskit/primitives/__init__.py
--- a/qiskit/primitives/__init__.py
+++ b/qiskit/primitives/__init__.py
@@ -110,7 +110,7 @@
 :class:`~BaseSamplerV2` is a primitive that samples outputs of quantum circuits.
 
 Following construction, a sampler is used by calling its :meth:`~.BaseSamplerV2.run` method
-with a list of pubs (Primitive Unified Blocks). Each pub contains values that, together,
+with a list of pubs (Primitive Unified Blocs). Each pub contains values that, together,
 define a computational unit of work for the sampler to complete:
 
 * A single :class:`~qiskit.circuit.QuantumCircuit`, possibly parameterized.


Test patch: