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

Issue:
Add documentation on how to setup the dag drawer for different OSs
_For reference, this was originally posted by @jaygambetta in https://github.com/Qiskit/qiskit-terra/issues/2281#issuecomment-489417445_

> @ajavadia and @mtreinish  it has been lost where to find how to add this dependencies outside pip. It is in the doc for the function https://github.com/Qiskit/qiskit-terra/blob/master/qiskit/visualization/dag_visualization.py but I think we need to make this clearer in the documentation in the Qiskit repo. 
>
> I would split this into two issues -- 
> 1. In terra add better error messaging. If you call drag_drawer and you don't have graphviz give that this dependency needs to be installed on your system. 
> 2. in qiskit add a documentation on how to setup the dag drawer for different operating systems.

This is issue is about the second item. 


Discussion:
I agree this needs to be done but it should  be put in the source code of the dag_drawer.  This is in terra. 
can you add to the source and it should be added here now?

https://qiskit.org/documentation/api/qiskit.visualization.dag_drawer.html#qiskit.visualization.dag_drawer
Let me rephrase to be sure I'm following: you think the `qiskit.visualization.dag_drawer` docstring should include details in how to install Graphviz in different OSs. Is that correct? In that case, should this issue be moved to terra?
yes and yes. 

Resolving patch:
diff --git a/qiskit/visualization/dag_visualization.py b/qiskit/visualization/dag_visualization.py
--- a/qiskit/visualization/dag_visualization.py
+++ b/qiskit/visualization/dag_visualization.py
@@ -32,6 +32,10 @@ def dag_drawer(dag, scale=0.7, filename=None, style='color'):
     means that having `Graphviz <https://www.graphviz.org/>`_ installed on your
     system is required for this to work.
 
+    The current release of Graphviz can be downloaded here: <https://graphviz.gitlab.io/download/>.
+    Download the version of the sotware that matches your environment and follow the instructions to
+    install Graph Visualization Software (Graphviz) on your operating system.
+
     Args:
         dag (DAGCircuit): The dag to draw.
         scale (float): scaling factor


Test patch:
Repository: Qiskit/qiskit

Issue:
Plot_state_city origin axis not centered
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### Information

- **Qiskit Terra version**: 0.9.0
- **Python version**: 3.7.3
- **Operating system**: MacOS

### What is the current behavior?
When creating a real or imaginary plot with both positive and negative values, the origin axis is not centered.

<img width="1405" alt="Screen Shot 2019-09-23 at 9 45 25 AM" src="https://user-images.githubusercontent.com/54714046/65779051-04a51000-e115-11e9-8d79-7edb5d73d717.png">


### Steps to reproduce the problem

Create a plot_state_city plot that has both positive and negative values.

### What is the expected behavior?

On a previous version of plot_state_city (#1540), the origin axis does not appear to have an offset.

<img width="966" alt="50148613-f0c7a600-0286-11e9-9734-baeab0a059bf" src="https://user-images.githubusercontent.com/54714046/65779450-c52af380-e115-11e9-9bfd-cf741e2fd1b5.png">



### Suggested solutions

Currently looking through the older version to try and identify the source of change.



Discussion:

Resolving patch:
diff --git a/qiskit/visualization/state_visualization.py b/qiskit/visualization/state_visualization.py
--- a/qiskit/visualization/state_visualization.py
+++ b/qiskit/visualization/state_visualization.py
@@ -385,10 +385,6 @@ def plot_state_city(rho, title="", figsize=None, color=None,
         ax1 = None
         ax2 = ax_imag
 
-    x = [0, max(xpos)+0.5, max(xpos)+0.5, 0]
-    y = [0, 0, max(ypos)+0.5, max(ypos)+0.5]
-    z = [0, 0, 0, 0]
-    verts = [list(zip(x, y, z))]
     max_dzr = max(dzr)
     min_dzr = min(dzr)
     min_dzi = np.min(dzi)
@@ -406,6 +402,12 @@ def plot_state_city(rho, title="", figsize=None, color=None,
                            alpha=alpha, zorder=zorder)
             b1.set_facecolors(fc1[6*idx:6*idx+6])
 
+        xlim, ylim = ax1.get_xlim(), ax1.get_ylim()
+        x = [xlim[0], xlim[1], xlim[1], xlim[0]]
+        y = [ylim[0], ylim[0], ylim[1], ylim[1]]
+        z = [0, 0, 0, 0]
+        verts = [list(zip(x, y, z))]
+
         pc1 = Poly3DCollection(verts, alpha=0.15, facecolor='k',
                                linewidths=1, zorder=1)
 
@@ -439,6 +441,12 @@ def plot_state_city(rho, title="", figsize=None, color=None,
                            alpha=alpha, zorder=zorder)
             b2.set_facecolors(fc2[6*idx:6*idx+6])
 
+        xlim, ylim = ax2.get_xlim(), ax2.get_ylim()
+        x = [xlim[0], xlim[1], xlim[1], xlim[0]]
+        y = [ylim[0], ylim[0], ylim[1], ylim[1]]
+        z = [0, 0, 0, 0]
+        verts = [list(zip(x, y, z))]
+
         pc2 = Poly3DCollection(verts, alpha=0.2, facecolor='k',
                                linewidths=1, zorder=1)
 


Test patch:
Repository: Qiskit/qiskit

Issue:
Misaligned Tick Labels for state_plot_city
### What is the expected enhancement?
At the moment, when plotting a statevector using state_plot_city, the assigned labels on the bottom axes are misaligned with the corresponding ticks. This is particularly apparent on the y-axis and when using a larger number of qubits (see below). 

### Proposed Workaround
Add horizontal and vertical alignments arguments to the calls of set_ticklabels() in state_plot_city. This aligns the labels on the x- and y-axes. The results are shown in comparison below for 2 and 4 qubits (before: left, after: right).

![2qubit_version](https://user-images.githubusercontent.com/54772951/66530318-8e86ad00-eb07-11e9-97db-ce907f660971.png)

![4qubit_version](https://user-images.githubusercontent.com/54772951/66530332-a0685000-eb07-11e9-80ff-574c07ad8fc4.png)







Discussion:

Resolving patch:
diff --git a/qiskit/visualization/state_visualization.py b/qiskit/visualization/state_visualization.py
--- a/qiskit/visualization/state_visualization.py
+++ b/qiskit/visualization/state_visualization.py
@@ -423,8 +423,10 @@ def plot_state_city(rho, title="", figsize=None, color=None,
             else:
                 ax1.axes.set_zlim3d(auto=True)
         ax1.get_autoscalez_on()
-        ax1.w_xaxis.set_ticklabels(row_names, fontsize=14, rotation=45)
-        ax1.w_yaxis.set_ticklabels(column_names, fontsize=14, rotation=-22.5)
+        ax1.w_xaxis.set_ticklabels(row_names, fontsize=14, rotation=45,
+                                   ha='right', va='top')
+        ax1.w_yaxis.set_ticklabels(column_names, fontsize=14, rotation=-22.5,
+                                   ha='left', va='center')
         ax1.set_zlabel('Re[$\\rho$]', fontsize=14)
         for tick in ax1.zaxis.get_major_ticks():
             tick.label.set_fontsize(14)
@@ -452,7 +454,6 @@ def plot_state_city(rho, title="", figsize=None, color=None,
 
         if min(dzi) < 0 < max(dzi):
             ax2.add_collection3d(pc2)
-
         ax2.set_xticks(np.arange(0.5, lx+0.5, 1))
         ax2.set_yticks(np.arange(0.5, ly+0.5, 1))
         if min_dzi != max_dzi:
@@ -465,8 +466,11 @@ def plot_state_city(rho, title="", figsize=None, color=None,
                 ax2.axes.set_zlim3d(np.min(dzi), max(np.max(dzr)+1e-9, np.max(dzi)+eps))
             else:
                 ax2.axes.set_zlim3d(auto=True)
-        ax2.w_xaxis.set_ticklabels(row_names, fontsize=14, rotation=45)
-        ax2.w_yaxis.set_ticklabels(column_names, fontsize=14, rotation=-22.5)
+
+        ax2.w_xaxis.set_ticklabels(row_names, fontsize=14, rotation=45,
+                                   ha='right', va='top')
+        ax2.w_yaxis.set_ticklabels(column_names, fontsize=14, rotation=-22.5,
+                                   ha='left', va='center')
         ax2.set_zlabel('Im[$\\rho$]', fontsize=14)
         for tick in ax2.zaxis.get_major_ticks():
             tick.label.set_fontsize(14)


Test patch:
Repository: Qiskit/qiskit

Issue:
Latex drawer leaves too much space at end of circuit
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### Information

- **Qiskit Terra version**: 0.9.0
- **Python version**: 3.7.4
- **Operating system**: Windows 10 [18362]

### What is the current behavior?
The latex drawer draws too much "empty circuit" after the last gate.
It's already visible on a small circuit:
![toolong1](https://user-images.githubusercontent.com/29467667/66515901-35575300-eae0-11e9-868e-09571798902c.png)

But the larger the circuit, the more noticeable it gets:
![toolong2](https://user-images.githubusercontent.com/29467667/66515934-46a05f80-eae0-11e9-80df-a0383a5fe560.png)


### Steps to reproduce the problem
Draw any circuit using the latex drawer.


### What is the expected behavior?
Draw the circuit shorter after the last gate.


### Suggested solutions





Discussion:

Resolving patch:
diff --git a/qiskit/visualization/latex.py b/qiskit/visualization/latex.py
--- a/qiskit/visualization/latex.py
+++ b/qiskit/visualization/latex.py
@@ -276,8 +276,14 @@ def _get_image_depth(self):
         # wires in the beginning and end
         columns = 2
 
-        # all gates take up 1 column except from those with labels (cu1) which take 2
-        columns += sum([2 if nd.name == 'cu1' else 1 for layer in self.ops for nd in layer])
+        # all gates take up 1 column except from those with labels (ie cu1)
+        # which take 2 columns
+        for layer in self.ops:
+            column_width = 1
+            for nd in layer:
+                if nd.name in ['cu1', 'rzz']:
+                    column_width = 2
+            columns += column_width
 
         # every 3 characters is roughly one extra 'unit' of width in the cell
         # the gate name is 1 extra 'unit'


Test patch:
Repository: Qiskit/qiskit

Issue:
Latex drawer qubit index subscripts only apply to single character
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### Information

- **Qiskit Terra version**: Master
- **Python version**: Any
- **Operating system**: Any

### What is the current behavior?
When drawing a circuit with >= 10 bits in a register the subscript is only applied to the first character in the index. For example:

![66655756-a72bbb80-ec0a-11e9-89e7-7c88ab141a37](https://user-images.githubusercontent.com/2447371/66656378-dc84d900-ec0b-11e9-99c7-dd1bd62c0387.png)

The entire index should be included in the subscript, for example like:

![latex](https://user-images.githubusercontent.com/2447371/66656399-e7d80480-ec0b-11e9-96b1-281e8e23a111.png)



### Steps to reproduce the problem
Visualize a circuit with >=10 bits in a register using the latex output.


### What is the expected behavior?
The subscript applies to all characters in the index


### Suggested solutions
Fix the bug (it's a one line fix)


Discussion:

Resolving patch:
diff --git a/qiskit/visualization/latex.py b/qiskit/visualization/latex.py
--- a/qiskit/visualization/latex.py
+++ b/qiskit/visualization/latex.py
@@ -221,7 +221,7 @@ def _initialize_latex_array(self, aliases=None):
                                     ": 0}"
             else:
                 if self.layout is None:
-                    self._latex[i][0] = "\\lstick{{ {}_{} : \\ket{{0}} }}".format(
+                    self._latex[i][0] = "\\lstick{{ {}_{{{}}} : \\ket{{0}} }}".format(
                         self.ordered_regs[i].register.name, self.ordered_regs[i].index)
                 else:
                     self._latex[i][0] = "\\lstick{{({}_{{{}}})~q_{{{}}} : \\ket{{0}} }}".format(


Test patch:
Repository: Qiskit/qiskit

Issue:
Assemble docs not formatted correctly 
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### Information

- **Qiskit Terra version**: master
- **Python version**:
- **Operating system**:

### What is the current behavior?
Similar to #3256 

<img width="1081" alt="Screen Shot 2019-10-14 at 5 00 39 AM" src="https://user-images.githubusercontent.com/1249193/66766482-312e8b00-ee7c-11e9-8f03-b5da403be38c.png">



### Steps to reproduce the problem



### What is the expected behavior?



### Suggested solutions





Discussion:

Resolving patch:
diff --git a/qiskit/execute.py b/qiskit/execute.py
--- a/qiskit/execute.py
+++ b/qiskit/execute.py
@@ -146,7 +146,7 @@ def execute(experiments, backend,
         default_meas_los (list):
             List of default meas lo frequencies
 
-        schedule_los (None or list[Union[Dict[PulseChannel, float], LoConfig]] or
+        schedule_los (None or list[Union[Dict[PulseChannel, float], LoConfig]] or \
                       Union[Dict[PulseChannel, float], LoConfig]):
             Experiment LO configurations
 
@@ -169,7 +169,7 @@ def execute(experiments, backend,
             The delay between experiments will be rep_time.
             Must be from the list provided by the device.
 
-        parameter_binds (list[dict{Parameter: Value}]):
+        parameter_binds (list[dict]):
             List of Parameter bindings over which the set of experiments will be
             executed. Each list element (bind) should be of the form
             {Parameter1: value1, Parameter2: value2, ...}. All binds will be


Test patch:
Repository: Qiskit/qiskit

Issue:
plot_circuit_layout output seems to be dependent on the layout order
The function `plot_circuit_layout` (in `qiskit/visualization/gate_map.py`) calls `plot_gate_map` with `qubit_labels`. The `qubit_labels` variable seems to be dependent of the `Layout` "order". In my local machine:
```
Layout({
0: Qubit(QuantumRegister(10, 'qr'), 0),
2: Qubit(QuantumRegister(10, 'qr'), 1),
4: Qubit(QuantumRegister(10, 'qr'), 2),
6: Qubit(QuantumRegister(10, 'qr'), 3),
8: Qubit(QuantumRegister(10, 'qr'), 4),
10: Qubit(QuantumRegister(10, 'qr'), 5),
12: Qubit(QuantumRegister(10, 'qr'), 6),
14: Qubit(QuantumRegister(10, 'qr'), 7),
16: Qubit(QuantumRegister(10, 'qr'), 8),
18: Qubit(QuantumRegister(10, 'qr'), 9)
})
qubit_labels = [0, None, 1, None, 2, None, 3, None, 4, None, 5, None, 6, None, 7, None, 8, None, 9, None]
``` 
![20_plot_circuit_layout](https://user-images.githubusercontent.com/766693/62714483-b0ab6400-b9cc-11e9-9b5c-0372d8797ba4.png)

While in the CI (see [output here](https://dev.azure.com/qiskit-ci/qiskit-terra/_build/results?buildId=1578&view=logs&jobId=8494c7a7-fba7-5345-1d98-c01d59819600&taskId=39a01fa0-e074-53f1-ec0d-d58f2c66d95b&lineStart=13&lineEnd=25&colStart=90&colEnd=91)):
```
Layout({
0: Qubit(QuantumRegister(10, 'qr'), 0),
16: Qubit(QuantumRegister(10, 'qr'), 8),
2: Qubit(QuantumRegister(10, 'qr'), 1),
4: Qubit(QuantumRegister(10, 'qr'), 2),
6: Qubit(QuantumRegister(10, 'qr'), 3),
8: Qubit(QuantumRegister(10, 'qr'), 4),
10: Qubit(QuantumRegister(10, 'qr'), 5),
12: Qubit(QuantumRegister(10, 'qr'), 6),
18: Qubit(QuantumRegister(10, 'qr'), 9),
14: Qubit(QuantumRegister(10, 'qr'), 7)
})
qubit_labels = [4, None, 3, None, 1, None, 8, None, 2, None, 0, None, 7, None, 5, None, 9, None, 6, None]
```
![temp](https://user-images.githubusercontent.com/766693/62714449-9ec9c100-b9cc-11e9-91c8-043cf674e992.png)



Discussion:

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
@@ -313,12 +313,10 @@ def plot_circuit_layout(circuit, backend, view='virtual'):
     qubit_labels = [None] * n_qubits
 
     if view == 'virtual':
-        idx = 0
         for key, val in circuit._layout.get_virtual_bits().items():
             if key.register.name != 'ancilla':
                 qubits.append(val)
-                qubit_labels[val] = idx
-            idx += 1
+                qubit_labels[val] = key.index
 
     elif view == 'physical':
         for key, val in circuit._layout.get_physical_bits().items():


Test patch:
Repository: Qiskit/qiskit

Issue:
Latex drawer leaves too much space at end of circuit
<!-- ⚠️ If you do not respect this template, your issue will be closed -->
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### Information

- **Qiskit Terra version**: 0.9.0
- **Python version**: 3.7.4
- **Operating system**: Windows 10 [18362]

### What is the current behavior?
The latex drawer draws too much "empty circuit" after the last gate.
It's already visible on a small circuit:
![toolong1](https://user-images.githubusercontent.com/29467667/66515901-35575300-eae0-11e9-868e-09571798902c.png)

But the larger the circuit, the more noticeable it gets:
![toolong2](https://user-images.githubusercontent.com/29467667/66515934-46a05f80-eae0-11e9-80df-a0383a5fe560.png)


### Steps to reproduce the problem
Draw any circuit using the latex drawer.


### What is the expected behavior?
Draw the circuit shorter after the last gate.


### Suggested solutions





Discussion:
#3243 should fix this issue. Running the circuit example above with that fix yields:

![latex](https://user-images.githubusercontent.com/2447371/66655756-a72bbb80-ec0a-11e9-89e7-7c88ab141a37.png)

Although I actually see another bug in that image, the subscript is only on the first numeral in the label for register indexes >=10 this causes a rendering problem, I'll open another issue and fix for that shortly.
> 
> 
> #3243 should fix this issue. Running the circuit example above with that fix yields:
> 
> 
Looks great!


Resolving patch:
diff --git a/qiskit/visualization/latex.py b/qiskit/visualization/latex.py
--- a/qiskit/visualization/latex.py
+++ b/qiskit/visualization/latex.py
@@ -276,8 +276,14 @@ def _get_image_depth(self):
         # wires in the beginning and end
         columns = 2
 
-        # all gates take up 1 column except from those with labels (cu1) which take 2
-        columns += sum([2 if nd.name == 'cu1' else 1 for layer in self.ops for nd in layer])
+        # all gates take up 1 column except from those with labels (ie cu1)
+        # which take 2 columns
+        for layer in self.ops:
+            column_width = 1
+            for nd in layer:
+                if nd.name in ['cu1', 'rzz']:
+                    column_width = 2
+            columns += column_width
 
         # every 3 characters is roughly one extra 'unit' of width in the cell
         # the gate name is 1 extra 'unit'


Test patch:
Repository: Qiskit/qiskit

Issue:
Schedule plot has final duration of final schedule duration even if channels are not plotted
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### Information

- **Qiskit Terra version**:
- **Python version**:
- **Operating system**:

### What is the current behavior?
The domain is not adjusted if channel is dropped.

### Steps to reproduce the problem
```python
import qiskit.pulse as pulse
import qiskit.pulse.pulse_lib as pulse_lib
sched = pulse.Schedule()
sched += pulse_lib.square(1000, 1.0)(pulse.DriveChannel(0))
sched += pulse_lib.square(10, 1.0)(pulse.DriveChannel(1))
sched.draw(channels_to_plot=[pulse.DriveChannel(1)])
```
![image](https://user-images.githubusercontent.com/1553846/68097739-ba871b00-fe86-11e9-9ba8-5b96f904d8cf.png)


### What is the expected behavior?
Adjust the domain of plot if the channel is dropped.


### Suggested solutions





Discussion:
I will look into this further. I played around with the pulse visualization files and I think I may know how to fix this.
Awesome, thanks a lot!

Resolving patch:
diff --git a/qiskit/visualization/pulse/matplotlib.py b/qiskit/visualization/pulse/matplotlib.py
--- a/qiskit/visualization/pulse/matplotlib.py
+++ b/qiskit/visualization/pulse/matplotlib.py
@@ -584,7 +584,12 @@ def draw(self, schedule, dt, interp_method, plot_range,
             # when input schedule is empty or comprises only frame changes,
             # we need to overwrite pulse duration by an integer greater than zero,
             # otherwise waveform returns empty array and matplotlib will be crashed.
-            tf = schedule.stop_time or 1
+            if channels_to_plot:
+                tf = schedule.timeslots.ch_duration(*channels_to_plot)
+            else:
+                tf = schedule.stop_time
+            tf = tf or 1
+
         # prepare waveform channels
         (channels, output_channels,
          snapshot_channels) = self._build_channels(schedule, channels_to_plot, t0, tf)


Test patch:
Repository: Qiskit/qiskit

Issue:
Job Monitor fails in possible race condition
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### Information

- **Qiskit Terra version**: 0.11.0.dev0+cf9c3f8
- **Python version**: Python 3.6.8
- **Operating system**: Linux 4.15.0-66-generic #75-Ubuntu SMP Tue Oct 1 05:24:09 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 

### What is the current behavior?
Job monitor fails unrepeatably in a fashion suggesting that if the job has finished right at the instant the job monitor loops it ends up comparing `None` with an `int`.

```
Job Status: job is queuedTraceback (most recent call last):
  File "qyq.py", line 348, in <module>
    job_monitor(job_exp)
  File "/home/jax/work/QISKit/DEV/qiskit-terra/qiskit/tools/monitor/job_monitor.py", line 84, in job_monitor
    quiet=quiet, output=output)
  File "/home/jax/work/QISKit/DEV/qiskit-terra/qiskit/tools/monitor/job_monitor.py", line 49, in _text_checker
    interval = max(job.queue_position(), 2)
TypeError: '>' not supported between instances of 'int' and 'NoneType'
```
### Steps to reproduce the problem
Not reproduceable on-demand.
This occured on `ibmq_london`

### What is the expected behavior?
Job monitor survive any value returned by backend.


### Suggested solutions
None at present.




Discussion:
It looks like `None` is a valid return from `job.queue_position()` ( https://github.com/Qiskit/qiskit-ibmq-provider/blob/2216e758d65e48a8cab49826dd769c14de5619e8/qiskit/providers/ibmq/job/ibmqjob.py#L347 ) so the monitoring tools should handle this case.

Resolving patch:
diff --git a/qiskit/tools/jupyter/jupyter_magics.py b/qiskit/tools/jupyter/jupyter_magics.py
--- a/qiskit/tools/jupyter/jupyter_magics.py
+++ b/qiskit/tools/jupyter/jupyter_magics.py
@@ -57,7 +57,9 @@ def _html_checker(job_var, interval, status, header,
         else:
             if job_status_name == 'QUEUED':
                 job_status_msg += ' (%s)' % job_var.queue_position()
-                if not _interval_set:
+                if job_var.queue_position() is None:
+                    interval = 2
+                elif not _interval_set:
                     interval = max(job_var.queue_position(), 2)
             else:
                 if not _interval_set:
diff --git a/qiskit/tools/monitor/job_monitor.py b/qiskit/tools/monitor/job_monitor.py
--- a/qiskit/tools/monitor/job_monitor.py
+++ b/qiskit/tools/monitor/job_monitor.py
@@ -45,7 +45,9 @@ def _text_checker(job, interval, _interval_set=False, quiet=False, output=sys.st
 
         if status.name == 'QUEUED':
             msg += ' (%s)' % job.queue_position()
-            if not _interval_set:
+            if job.queue_position() is None:
+                interval = 2
+            elif not _interval_set:
                 interval = max(job.queue_position(), 2)
         else:
             if not _interval_set:


Test patch: