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

Issue:
`jupyter-execute` displayed in docs
The `.. jupyter-execute` command is erroneously displayed in the [docs](https://qiskit.org/documentation/stubs/qiskit.circuit.QuantumCircuit.initialize.html?highlight=initialize#qiskit.circuit.QuantumCircuit.initialize).

![image](https://user-images.githubusercontent.com/42675093/176892071-283ba9cd-5aee-47f9-b800-76afdb0067ef.png)

**Source Code**

https://github.com/Qiskit/qiskit-terra/blob/fe8ab43f1218d6997458fb3bf4011045f40932b0/qiskit/extensions/quantum_initializer/initializer.py#L163


Discussion:
Thanks!  This just needs an extra blank line putting in above the `.. jupyter-execute::` line to get it rendered correctly.

Resolving patch:
diff --git a/qiskit/extensions/quantum_initializer/initializer.py b/qiskit/extensions/quantum_initializer/initializer.py
--- a/qiskit/extensions/quantum_initializer/initializer.py
+++ b/qiskit/extensions/quantum_initializer/initializer.py
@@ -159,7 +159,8 @@ class to prepare the qubits in a specified state.
             q_1: ┤1                 ├
                  └──────────────────┘
 
-        Initialize two qubits from an array of complex amplitudes
+        Initialize two qubits from an array of complex amplitudes.
+
         .. jupyter-execute::
 
             import numpy as np


Test patch:
Repository: Qiskit/qiskit

Issue:
Specifying gates to decompose fails
### Environment

- **Qiskit Terra version**: e4e4646f18d6e7d5dae0bc5308bcb5f5c9aa206d
- **Python version**: 3.9.7
- **Operating system**: RHEL 8.6


### What is happening?

See title.

### How can we reproduce the issue?

```python
from qiskit import QuantumCircuit
from qiskit.circuit.library import XGate, XXPlusYYGate

circuit = QuantumCircuit(2)
circuit.append(XGate(), [0])
circuit.append(XXPlusYYGate(0.1), [0, 1])

decomposed = circuit.decompose(gates_to_decompose=XXPlusYYGate)
decomposed.draw()
```
Output:
```
     ┌───┐┌─────────────────┐
q_0: ┤ X ├┤0                ├
     └───┘│  {XX+YY}(0.1,0) │
q_1: ─────┤1                ├
          └─────────────────┘
```

### What should happen?

The specified gates should be decomposed.

### Any suggestions?

_No response_


Discussion:

Resolving patch:
diff --git a/qiskit/transpiler/passes/basis/decompose.py b/qiskit/transpiler/passes/basis/decompose.py
--- a/qiskit/transpiler/passes/basis/decompose.py
+++ b/qiskit/transpiler/passes/basis/decompose.py
@@ -128,9 +128,7 @@ def _should_decompose(self, node) -> bool:
             node.name in gates or any(fnmatch(node.name, p) for p in strings_list)
         ):
             return True
-        elif not has_label and (  # check if Gate type given
-            any(isinstance(node.op, op) for op in gate_type_list)
-        ):
+        elif any(isinstance(node.op, op) for op in gate_type_list):  # check if Gate type given
             return True
         else:
             return False


Test patch:
diff --git a/test/python/circuit/test_circuit_operations.py b/test/python/circuit/test_circuit_operations.py
--- a/test/python/circuit/test_circuit_operations.py
+++ b/test/python/circuit/test_circuit_operations.py
@@ -1265,3 +1265,10 @@ def test_pop_previous_instruction_removes_parameters(self):
         instruction = test._pop_previous_instruction_in_scope()
         self.assertEqual(list(last_instructions), [instruction])
         self.assertEqual({y}, set(test.parameters))
+
+    def test_decompose_gate_type(self):
+        """Test decompose specifying gate type."""
+        circuit = QuantumCircuit(1)
+        circuit.append(SGate(label="s_gate"), [0])
+        decomposed = circuit.decompose(gates_to_decompose=SGate)
+        self.assertNotIn("s", decomposed.count_ops())
Repository: Qiskit/qiskit

Issue:
plot_coupling_map appears to incorrectly plot in docs example
### Environment

the qiskit.org website

### What is happening?

The map does not look like what is expected based on the input:
![image](https://user-images.githubusercontent.com/60495383/188241999-0a2b4b69-d7c0-457b-8b0d-d360943263d4.png)


### How can we reproduce the issue?

view the doc page here: https://qiskit.org/documentation/stubs/qiskit.visualization.plot_coupling_map.html

### What should happen?

In the example, the displayed image and the input should agree. In the image only the first two edges are displayed, but it looks like there are 8 edges in the `coupling_map` list. Possibly the `qubit_coordinates` are being processed incorrectly as well, not sure.

### Any suggestions?

_No response_


Discussion:
Hi there. It seems like the "qubit_coordinates" and "coupling_map" inputs were simply inverted.

Here you go:

<img width="568" alt="image" src="https://user-images.githubusercontent.com/77298980/188272505-38cbf764-8b7b-4a2a-92af-9b2e146c8782.png">


Thanks @dalin27! Would you be interested making a PR to fix the documentation? The lines that need changing are here: https://github.com/Qiskit/qiskit-terra/blob/aca01eb9867ccc08a49efc5a27fd60c2e28b5db3/qiskit/visualization/gate_map.py#L592-L600

Resolving patch:
diff --git a/qiskit/visualization/gate_map.py b/qiskit/visualization/gate_map.py
--- a/qiskit/visualization/gate_map.py
+++ b/qiskit/visualization/gate_map.py
@@ -595,9 +595,9 @@ def plot_coupling_map(
             %matplotlib inline
 
             num_qubits = 8
-            coupling_map = [[0, 1], [1, 2], [2, 3], [3, 5], [4, 5], [5, 6], [2, 4], [6, 7]]
             qubit_coordinates = [[0, 1], [1, 1], [1, 0], [1, 2], [2, 0], [2, 2], [2, 1], [3, 1]]
-            plot_coupling_map(num_qubits, coupling_map, qubit_coordinates)
+            coupling_map = [[0, 1], [1, 2], [2, 3], [3, 5], [4, 5], [5, 6], [2, 4], [6, 7]]
+            plot_coupling_map(num_qubits, qubit_coordinates, coupling_map)
     """
     import matplotlib.pyplot as plt
     import matplotlib.patches as mpatches


Test patch:
Repository: Qiskit/qiskit

Issue:
Document naming of CircuitInstruction and related classes
### What should we add?

I asked @jakelishman why CircuitInstruction is named that way when it is not an Instruction, and why it has an attribute named `operation` which is actually an Instruction. He replied:
>it’s because what’s currently called Instruction shouldn’t really be called that, but we can’t change it without breaking everything.  So instead, the new interface definition for “something that can be added to QuantumCircuit is called Operation, and the container is CircuitInstruction to avoid the naming clash

This should be publicly documented somewhere to mitigate user confusion.


Discussion:

Resolving patch:
diff --git a/qiskit/circuit/quantumcircuitdata.py b/qiskit/circuit/quantumcircuitdata.py
--- a/qiskit/circuit/quantumcircuitdata.py
+++ b/qiskit/circuit/quantumcircuitdata.py
@@ -26,6 +26,28 @@ class CircuitInstruction:
     """A single instruction in a :class:`.QuantumCircuit`, comprised of the :attr:`operation` and
     various operands.
 
+    .. note::
+
+        There is some possible confusion in the names of this class, :class:`~.circuit.Instruction`,
+        and :class:`~.circuit.Operation`, and this class's attribute :attr:`operation`.  Our
+        preferred terminology is by analogy to assembly languages, where an "instruction" is made up
+        of an "operation" and its "operands".
+
+        Historically, :class:`~.circuit.Instruction` came first, and originally contained the qubits
+        it operated on and any parameters, so it was a true "instruction".  Over time,
+        :class:`.QuantumCircuit` became responsible for tracking qubits and clbits, and the class
+        became better described as an "operation".  Changing the name of such a core object would be
+        a very unpleasant API break for users, and so we have stuck with it.
+
+        This class was created to provide a formal "instruction" context object in
+        :class:`.QuantumCircuit.data`, which had long been made of ad-hoc tuples.  With this, and
+        the advent of the :class:`~.circuit.Operation` interface for adding more complex objects to
+        circuits, we took the opportunity to correct the historical naming.  For the time being,
+        this leads to an awkward case where :attr:`.CircuitInstruction.operation` is often an
+        :class:`~.circuit.Instruction` instance (:class:`~.circuit.Instruction` implements the
+        :class:`.Operation` interface), but as the :class:`.Operation` interface gains more use,
+        this confusion will hopefully abate.
+
     .. warning::
 
         This is a lightweight internal class and there is minimal error checking; you must respect


Test patch:
Repository: Qiskit/qiskit

Issue:
Documentation build drops a file in the working directory
### Environment

- **Qiskit Terra version**: main @ 686ba34
- **Python version**: any
- **Operating system**: any


### What is happening?

Running the documentation build (such as by `tox -e docs`) causes a file `new_hist.png` to be dropped in the working directory.  This came from #8569, which added a `jupyter-execute` block to the `qiskit.visualization` documentation that leads a `savefig` command.

### How can we reproduce the issue?

Run the documentation build.

### What should happen?

No files outside the documentation build directory should be created.

### Any suggestions?

The offending `.. jupter-execute` block can just be replaced by a `.. code-block` one, since it doesn't actually output anything visually, or execute code in the IPython kernel that needs persisting to later cells.


Discussion:

Resolving patch:
diff --git a/qiskit/visualization/__init__.py b/qiskit/visualization/__init__.py
--- a/qiskit/visualization/__init__.py
+++ b/qiskit/visualization/__init__.py
@@ -70,7 +70,7 @@
 `matplotlib.figure.Figure.savefig
 <https://matplotlib.org/stable/api/figure_api.html#matplotlib.figure.Figure.savefig>`_ method.
 
-.. jupyter-execute::
+.. code-block:: python
 
    plot_histogram(data, filename='new_hist.png')
 


Test patch:
Repository: Qiskit/qiskit

Issue:
Drawing a circuit with idle_wires=False causes the circuit to break in future draw/qpy events
### Environment

- **Qiskit Terra version**: main
- **Python version**: 3.9.1
- **Operating system**: OSX


### What is happening?

When drawing a circuit with `circuit.draw(idle_wires=False)` the circuit is somehow mutated to fail on future drawing or qpy serialization events.



### How can we reproduce the issue?

Using the circuit below. Message for QPY file.

```python
from qiskit import qpy

with open('test.qpy', 'wb') as fd:
    qpy.dump(transpiled_bit_code_circuit, fd)

with open('test.qpy', 'rb') as fd:
    new_qc = qpy.load(fd)[0]
    
new_qc.draw(idle_wires=False)
new_qc.draw(idle_wires=False)
```



### What should happen?

Circuit should draw twice.

### Any suggestions?

_No response_


Discussion:
The immediate cause of this is the circuit drawer doing `qubits = circuit.qubits` and then mutating its `qubits` list when deciding what to display.  The _root_ cause is that `QuantumCircuit` exposes its _private, mutable_ data store (`_qubits: List[Qubit]`) directly via the `qubits` property, which is what allows this kind of error to occur.

As a simpler example that's effectively the same behaviour:
```python
import qiskit
qc = qiskit.QuantumCircuit(2)
print(qc.num_qubits)  # 2
qc.draw(idle_wires=False)
print(qc.num_qubits)  # 0
```

I can squash this symptom, but fixing the `QuantumCircuit` interface without performance degradations or backwards-compatibility breaks is rather harder and may not be practically possible right now.

Resolving patch:
diff --git a/qiskit/visualization/circuit/_utils.py b/qiskit/visualization/circuit/_utils.py
--- a/qiskit/visualization/circuit/_utils.py
+++ b/qiskit/visualization/circuit/_utils.py
@@ -399,8 +399,8 @@ def _get_layered_instructions(
     # default to left
     justify = justify if justify in ("right", "none") else "left"
 
-    qubits = circuit.qubits
-    clbits = circuit.clbits
+    qubits = circuit.qubits.copy()
+    clbits = circuit.clbits.copy()
     nodes = []
 
     # Create a mapping of each register to the max layer number for all measure ops


Test patch:
diff --git a/test/python/visualization/test_circuit_text_drawer.py b/test/python/visualization/test_circuit_text_drawer.py
--- a/test/python/visualization/test_circuit_text_drawer.py
+++ b/test/python/visualization/test_circuit_text_drawer.py
@@ -3447,6 +3447,13 @@ def test_text_barrier_delay(self):
         circuit.delay(100, qr[2])
         self.assertEqual(str(_text_circuit_drawer(circuit, idle_wires=False)), expected)
 
+    def test_does_not_mutate_circuit(self):
+        """Using 'idle_wires=False' should not mutate the circuit.  Regression test of gh-8739."""
+        circuit = QuantumCircuit(1)
+        before_qubits = circuit.num_qubits
+        circuit.draw(idle_wires=False)
+        self.assertEqual(circuit.num_qubits, before_qubits)
+
 
 class TestTextNonRational(QiskitTestCase):
     """non-rational numbers are correctly represented"""
Repository: Qiskit/qiskit

Issue:
Barrier API documentation is not informative
### What should we add?

A Google search for "[qiskit barrier](https://google.com/search?q=qiskit+barrier)" leads one to [its entry in the API reference](https://qiskit.org/documentation/stubs/qiskit.circuit.library.Barrier.html) as the first hit.  Unfortunately, this page contains only a circular definition, and does not even explain what a barrier does:

> Barrier instruction.
>
> Create new barrier instruction.

There is a much more useful description by @chriseclectic on StackExchange, with tens of upvotes.  I believe a similar explanation should be incorporated into the `Barrier` docstring(s).


Discussion:
For reference, [this is Chris's answer on stackexchange](https://quantumcomputing.stackexchange.com/a/8371/18472).  The relevant docstrings that need updating are the `QuantumCircuit.barrier` method and the `Barrier` class.
How is it going with this issue? I am interested to learn more and contributing.
@faraimazh Do you want to work on this issue? I can assign you.
Hi @HuangJunye , if it's okay, may I work on this? 
I'd like to work on this

Resolving patch:
diff --git a/qiskit/circuit/barrier.py b/qiskit/circuit/barrier.py
--- a/qiskit/circuit/barrier.py
+++ b/qiskit/circuit/barrier.py
@@ -21,7 +21,12 @@
 
 
 class Barrier(Instruction):
-    """Barrier instruction."""
+    """Barrier instruction.
+
+    A barrier is a visual indicator of the grouping of a circuit section.
+    It also acts as a directive for circuit compilation to separate pieces
+    of a circuit so that any optimizations or re-writes are constrained
+    to only act between barriers."""
 
     _directive = True
 


Test patch:
Repository: Qiskit/qiskit

Issue:
Should be able to create CouplingMap from CouplingMap
### Environment

- **Qiskit Terra version**: 0.22rc1
- **Python version**: 3.10.6
- **Operating system**: OSX


### What is happening?

```python
from qiskit.transpiler import CouplingMap
from qiskit.providers.fake_provider import FakeAuckland
backend = FakeAuckland()

CouplingMap(backend.coupling_map)
```

```
TypeError: 'CouplingMap' object is not iterable
```

### How can we reproduce the issue?

run above

### What should happen?

I should be able to create a `CouplingMap` from a `CouplingMap`

### Any suggestions?

It is caused by #8863


Discussion:

Resolving patch:
diff --git a/qiskit/transpiler/coupling.py b/qiskit/transpiler/coupling.py
--- a/qiskit/transpiler/coupling.py
+++ b/qiskit/transpiler/coupling.py
@@ -79,6 +79,9 @@ def get_edges(self):
         """
         return self.graph.edge_list()
 
+    def __iter__(self):
+        return iter(self.graph.edge_list())
+
     def add_physical_qubit(self, physical_qubit):
         """Add a physical qubit to the coupling graph as a node.
 


Test patch:
diff --git a/test/python/transpiler/test_coupling.py b/test/python/transpiler/test_coupling.py
--- a/test/python/transpiler/test_coupling.py
+++ b/test/python/transpiler/test_coupling.py
@@ -442,6 +442,12 @@ def test_subgraph(self):
         expected = [(0, 1), (1, 2), (2, 3)]
         self.assertEqual(expected, edge_list, f"{edge_list} does not match {expected}")
 
+    def test_implements_iter(self):
+        """Test that the object is implicitly iterable."""
+        coupling = CouplingMap.from_line(3)
+        expected = [(0, 1), (1, 0), (1, 2), (2, 1)]
+        self.assertEqual(sorted(coupling), expected)
+
 
 class CouplingVisualizationTest(QiskitVisualizationTestCase):
     @unittest.skipUnless(optionals.HAS_GRAPHVIZ, "Graphviz not installed")
Repository: Qiskit/qiskit

Issue:
QuasiDistribution returned by BackendSampler has incorrect shots
### Environment

- **Qiskit Terra version**: 07e0a2fc79bada7c1fbf0594f4ad33934f70b7e
- **Python version**: 3.10.8
- **Operating system**: Arch Linux


### What is happening?

See title.

### How can we reproduce the issue?

```python
from qiskit.circuit import QuantumCircuit
from qiskit.primitives import BackendSampler
from qiskit.providers.fake_provider import FakeLagos

circuit = QuantumCircuit(2)
circuit.measure_all()

backend = FakeLagos()
sampler = BackendSampler(backend)
result = sampler.run(circuit, shots=100).result()
quasis = result.quasi_dists[0]
print(quasis.shots)
```
```
None
```

### What should happen?

It should print "100", not "None".

### Any suggestions?

_No response_


Discussion:

Resolving patch:
diff --git a/qiskit/primitives/backend_sampler.py b/qiskit/primitives/backend_sampler.py
--- a/qiskit/primitives/backend_sampler.py
+++ b/qiskit/primitives/backend_sampler.py
@@ -14,6 +14,7 @@
 
 from __future__ import annotations
 
+import math
 from collections.abc import Sequence
 from typing import Any, cast
 
@@ -162,14 +163,16 @@ def _postprocessing(self, result: Result, circuits: list[QuantumCircuit]) -> Sam
         counts = _prepare_counts(result)
         shots = sum(counts[0].values())
 
-        probabilies = []
+        probabilities = []
         metadata: list[dict[str, Any]] = [{}] * len(circuits)
         for count in counts:
             prob_dist = {k: v / shots for k, v in count.int_outcomes().items()}
-            probabilies.append(QuasiDistribution(prob_dist))
+            probabilities.append(
+                QuasiDistribution(prob_dist, shots=shots, stddev_upper_bound=math.sqrt(1 / shots))
+            )
             for metadatum in metadata:
                 metadatum["shots"] = shots
-        return SamplerResult(probabilies, metadata)
+        return SamplerResult(probabilities, metadata)
 
     def _transpile(self):
         from qiskit.compiler import transpile


Test patch:
diff --git a/test/python/primitives/test_backend_sampler.py b/test/python/primitives/test_backend_sampler.py
--- a/test/python/primitives/test_backend_sampler.py
+++ b/test/python/primitives/test_backend_sampler.py
@@ -12,6 +12,7 @@
 
 """Tests for BackendSampler."""
 
+import math
 import unittest
 from test import combine
 
@@ -96,11 +97,12 @@ def test_sampler_run(self, backend):
         """Test Sampler.run()."""
         bell = self._circuit[1]
         sampler = BackendSampler(backend=backend)
-        job = sampler.run(circuits=[bell])
+        job = sampler.run(circuits=[bell], shots=1000)
         self.assertIsInstance(job, JobV1)
         result = job.result()
         self.assertIsInstance(result, SamplerResult)
-        # print([q.binary_probabilities() for q in result.quasi_dists])
+        self.assertEqual(result.quasi_dists[0].shots, 1000)
+        self.assertEqual(result.quasi_dists[0].stddev_upper_bound, math.sqrt(1 / 1000))
         self._compare_probs(result.quasi_dists, self._target[1])
 
     @combine(backend=BACKENDS)
Repository: Qiskit/qiskit

Issue:
ClassicalFunction compiler (qiskit.circuit.classicalfunction) Overview Sentence trails off without completion
### Where is the problem?
https://qiskit.org/documentation/apidoc/classicalfunction.html
### What is the problem?
Sentence in Overview trails off without completion:
> Following Qiskit’s little-endian bit ordering convention, the left-most bit (a) is the most significant bit and the right-most bit (d) is the least significant bit. The resulting

... and that's it.
### What would you expect?
Finish the thought!


Discussion:
Any update on the content needed to finish the sentence?
This issue should be posted on the [qiskit-terra repo](https://github.com/Qiskit/qiskit-terra) because they maintain that part of the documentation. @1ucian0 , could you transfer this issue to the terra repo? I don't have permissions to do it. Thank you!

Resolving patch:
diff --git a/qiskit/circuit/classicalfunction/__init__.py b/qiskit/circuit/classicalfunction/__init__.py
--- a/qiskit/circuit/classicalfunction/__init__.py
+++ b/qiskit/circuit/classicalfunction/__init__.py
@@ -21,7 +21,7 @@
 ========
 
 The classical function compiler provides the necessary tools to map a classical
-irreversible functions into quantum circuits.  Below is a simple example of
+potentially irreversible functions into quantum circuits.  Below is a simple example of
 how to synthesize a simple boolean function defined using Python into a
 QuantumCircuit:
 
@@ -34,10 +34,22 @@
       def grover_oracle(a: Int1, b: Int1, c: Int1, d: Int1) -> Int1:
           return (not a and b and not c and d)
 
-      quantum_circuit = grover_oracle.synth()
-
-Following Qiskit's little-endian bit ordering convention, the left-most bit (`a`) is the most
-significant bit and the right-most bit (`d`) is the least significant bit. The resulting
+      quantum_circuit = grover_oracle.synth(registerless=False)
+      quantum_circuit.draw('text')
+
+           a: ──o──
+                │
+           b: ──■──
+                │
+           c: ──o──
+                │
+           d: ──■──
+              ┌─┴─┐
+      return: ┤ X ├
+              └───┘
+
+Following Qiskit's little-endian bit ordering convention, the left-most bit (``a``) is the most
+significant bit and the right-most bit (``d``) is the least significant bit.
 
 Supplementary Information
 =========================


Test patch: