internlm/SWE-Fixer-Train-110K huggingface dataset:
Repository: microsoft/Qcodes

Issue:
Get_idn fails for AMI430 3D instrument
the Instrument class implements get_idn by calling ask but that will in general not work on virtual instruments such as the AMI4303D but raise an exception that is handled and logged. 

Virtual instruments should either override get_idn to not fail and respond with something useful or we should rework this so get_idn is not implemented like this for the generic class 


Discussion:

Resolving patch:
diff --git a/qcodes/instrument_drivers/american_magnetics/AMI430.py b/qcodes/instrument_drivers/american_magnetics/AMI430.py
--- a/qcodes/instrument_drivers/american_magnetics/AMI430.py
+++ b/qcodes/instrument_drivers/american_magnetics/AMI430.py
@@ -9,6 +9,7 @@
 from typing import (
     Any,
     Callable,
+    Dict,
     Iterable,
     List,
     Optional,
@@ -758,6 +759,10 @@ def find_ami430_with_name(ami430_name: str) -> AMI430:
 
         self._exit_stack = ExitStack()
 
+    def get_idn(self) -> Dict[str, Optional[str]]:
+        idparts = ["American Magnetics", self.name, None, None]
+        return dict(zip(("vendor", "model", "serial", "firmware"), idparts))
+
     def _set_vector_ramp_rate_units(self, val: float) -> float:
         _, common_ramp_rate_units = self._raise_if_not_same_field_and_ramp_rate_units()
         self.vector_ramp_rate.unit = common_ramp_rate_units
diff --git a/qcodes/instrument_drivers/american_magnetics/AMI430_visa.py b/qcodes/instrument_drivers/american_magnetics/AMI430_visa.py
--- a/qcodes/instrument_drivers/american_magnetics/AMI430_visa.py
+++ b/qcodes/instrument_drivers/american_magnetics/AMI430_visa.py
@@ -809,6 +809,10 @@ def find_ami430_with_name(ami430_name: str) -> AMIModel430:
 
         self._exit_stack = ExitStack()
 
+    def get_idn(self) -> dict[str, str | None]:
+        idparts = ["American Magnetics", self.name, None, None]
+        return dict(zip(("vendor", "model", "serial", "firmware"), idparts))
+
     def _set_vector_ramp_rate_units(self, val: float) -> float:
         _, common_ramp_rate_units = self._raise_if_not_same_field_and_ramp_rate_units()
         self.vector_ramp_rate.unit = common_ramp_rate_units


Test patch:
Repository: microsoft/Qcodes

Issue:
Update Sphinx favicon config
Thanks for using [Sphinx Favicon](https://github.com/tcmetzger/sphinx-favicon) in your project! I just released version 1.0 of the extension, which brings one breaking change: to better conform with Python standards, we changed the module name to `sphinx_favicon` (instead of `sphinx-favicon`). This means you'll have to update the name in the `extensions` list of your conf.py file (https://github.com/QCoDeS/Qcodes/blob/master/docs/conf.py#L81) to use version 1.0. Otherwise, your existing configuration should continue to work!


Discussion:

Resolving patch:
diff --git a/docs/conf.py b/docs/conf.py
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -78,7 +78,7 @@
     "sphinxcontrib.towncrier",
     "autodocsumm",
     "sphinx_issues",
-    "sphinx-favicon",
+    "sphinx_favicon",
 ]
 
 # include special __xxx__ that DO have a docstring


Test patch:
Repository: microsoft/Qcodes

Issue:
Disabling auto_sweep in Keysight N52xx driver broken
The `auto_sweep` function in the Keysight N52xx driver is broken. This feature allows data to be taken directly off screen without running a scan when disabled, which is necessary when measuring multiple parameters at once.

It looks like the check for auto_sweep was accidentally disabled in commit 78a989f

## Expected Behaviour
When running the below snippet the PNA should only take a single measurement
```python3
pna.auto_sweep(False)
qc.dataset.do0d(pna.magnitude, pna.phase)
```

## Actual
The pna will run the trace twice, once for magnitude and once for phase.

@jenshnielsen 


Discussion:

Resolving patch:
diff --git a/qcodes/instrument_drivers/Keysight/N52xx.py b/qcodes/instrument_drivers/Keysight/N52xx.py
--- a/qcodes/instrument_drivers/Keysight/N52xx.py
+++ b/qcodes/instrument_drivers/Keysight/N52xx.py
@@ -112,7 +112,9 @@ def get_raw(self) -> np.ndarray:
         # Check if we should run a new sweep
         auto_sweep = root_instr.auto_sweep()
 
-        prev_mode = self.instrument.run_sweep()
+        prev_mode = ""
+        if auto_sweep:
+            prev_mode = self.instrument.run_sweep()
         # Ask for data, setting the format to the requested form
         self.instrument.format(self.sweep_format)
         data = root_instr.visa_handle.query_binary_values('CALC:DATA? FDATA',
@@ -266,20 +268,20 @@ def __init__(
             "polar",
             sweep_format="POLAR",
             label="Polar",
-            unit="V",
+            unit="ratio",
             parameter_class=FormattedSweep,
             get_parser=self._parse_polar_data,
             vals=Arrays(shape=(self.parent.points,), valid_types=(complex,)),
         )
 
     @staticmethod
-    def _parse_polar_data(data: Sequence[float]) -> np.ndarray:
+    def _parse_polar_data(data: np.ndarray) -> np.ndarray:
         """
         Parse the 2*n-length flat array coming from the instrument
         and convert to n-length array of complex numbers
         """
-        pairs = np.array([data[::2], data[1::2]]).T
-        return np.array([complex(*pair) for pair in pairs])
+        data_shape = data.size
+        return data.reshape((data_shape // 2, 2)).view(dtype=np.complex128).flatten()
 
     def run_sweep(self) -> str:
         """


Test patch:
Repository: microsoft/Qcodes

Issue:
Loading a parameter called "current_time" produces an array that just contains the completed timestamp
We have a custom parameter class whose value is always the current time, basically it just returns `time.time()` (similar to `ElapsedTimeParameter`). When trying to use this parameter in `dond`, we noticed the following strange behavior: if the parameter is called `"current_time"`, the result of `get_parameter_data` will be just strings, which appears to be the completed timestamp of the measurement.

### Steps to reproduce
Run the following code:

```python
import qcodes as qc 
from qcodes import ManualParameter
from qcodes.dataset import dond, ArraySweep

qc.config.core.db_location = "./test.db"

ds, _, _ = dond(
    ArraySweep(qc.ManualParameter("setpoint"), [1, 2, 3]),

    # if this is called something else, it works as expected
    qc.ManualParameter("current_time", initial_value=123),
)

print(ds.get_parameter_data())
```

### Expected behaviour
The loaded data should be whatever the `get()` method of the parameter returned. In the above dummy example, it should print

```
{'current_time': {'current_time': array([123., 123., 123.]), 'setpoint': array([1., 2., 3.])}}
```

### Actual behaviour
The code prints
```
{'current_time': {'current_time': array(['12:07:54', '12:07:54', '12:07:54'], dtype=object), 'setpoint': array([1., 2., 3.])}}
```
The values of the array are strings.

### Additional information

I have no idea where this is coming from. I tried to grep "current_time" in the qcodes codebase but couldn't find anything. The timestamp is always constant, if I add `delay=2` to the ArrayParameter, the value is still the same for all three points, and it's the same as `ds.completed_timestamp()`. The data in the SQLite database is  actually correct, so this is maybe some `getattr` issue when loading the data?

### System

**operating system**: Happens both on Windows and Ubuntu
**qcodes commit**: e66f00173e (current master). Also happens at least with qcodes 0.35.


Discussion:
Aha, it's probably coming from SQLite, from what I can tell (see e.g. [here](https://stackoverflow.com/questions/15473325/inserting-current-date-and-time-in-sqlite-database)), `SELECT current_time FROM ...` will return the current wall clock time as a string, instead of a column named `current_time`.

The [SQLite documentation](https://www.sqlite.org/lang_keywords.html) mentions that `current_time` is a keyword and needs to be quoted.

Resolving patch:
diff --git a/qcodes/dataset/sqlite/queries.py b/qcodes/dataset/sqlite/queries.py
--- a/qcodes/dataset/sqlite/queries.py
+++ b/qcodes/dataset/sqlite/queries.py
@@ -588,7 +588,7 @@ def get_parameter_tree_values(
     # Create the base sql query
     columns = [toplevel_param_name] + list(other_param_names)
     sql = f"""
-           SELECT {','.join(columns)} FROM "{result_table_name}"
+           SELECT "{'","'.join(columns)}" FROM "{result_table_name}"
            WHERE {toplevel_param_name} IS NOT NULL
            LIMIT ? OFFSET ?
            """


Test patch:
Repository: microsoft/Qcodes

Issue:
Cannot exit ipython with running qcodes.Monitor()
### Steps to reproduce
iPython version 8.10, qcodes version 0.42, Windows 10 Pro 22H2

1. open ipython
2. from qcodes import Monitor
monitor = Monitor()
3. exit ipython

It hangs instead of closing iPython. The terminal must be terminated.



Discussion:
I can reproduce this. Not sure what is going on but perhaps related to https://github.com/QCoDeS/Qcodes/issues/3814 

It would be nice to investigate if changing the monitor thread to be a deamon thread would also resolve this issue 
Note that until this is resolved it can be mitigated by explicitly calling join on the monitor thread

```
❯ ipython
Python 3.11.5 | packaged by Anaconda, Inc. | (main, Sep 11 2023, 13:26:23) [MSC v.1916 64 bit (AMD64)]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.18.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from qcodes import Monitor
In [2]: m = Monitor()
In [3]: m.join()
In [4]: exit

~ took 29s
❯
```
I've tested turning the monitor thread into a daemon thread as you suggested, by passing the keyword argument `daemon=True` into the `Monitor` initialization. It appears to resolve this issue. I've also checked that the behaviour of the monitor remains unchanged by add QDAC2 voltage channels to the monitor, and it seems fine.

I don't know if there's any more testing required, but happy to raise a PR for this if you like.
@michaelc12qe In the long term I would like to come up with something slightly cleaner than deamon mode but I agree that in the short term using deamon is the best solution. So please go ahead

Resolving patch:
diff --git a/src/qcodes/monitor/monitor.py b/src/qcodes/monitor/monitor.py
--- a/src/qcodes/monitor/monitor.py
+++ b/src/qcodes/monitor/monitor.py
@@ -147,7 +147,7 @@ def __init__(
             use_root_instrument: Defines if parameters are grouped according to
                                 parameter.root_instrument or parameter.instrument
         """
-        super().__init__()
+        super().__init__(daemon=True)
 
         # Check that all values are valid parameters
         for parameter in parameters:


Test patch:
Repository: microsoft/Qcodes

Issue:
print_readable_snapshot() of instrument modules without parameters broken.
### `print_readable_snapshot()` of instrument modules without parameters fails.

### Steps to reproduce
```python
from qcodes import instrument
bar = instrument.Instrument('bar')
foo = instrument.InstrumentModule(bar, 'foo')
bar.add_submodule('foo', foo)
```
Calling `print_readable_snapshot()` on either the submodule or the parent instrument fails:
```python
>>> bar.print_readable_snapshot()
  File ~\Documents\Qcodes\src\qcodes\instrument\instrument_base.py:406 in print_readable_snapshot
    par_field_len = min(max(par_lengths) + 1, 50)

ValueError: max() arg is an empty sequence
```
This should be resolved by catching the empty sequence here:
https://github.com/QCoDeS/Qcodes/blob/7f114bfc2c8cbb759d0a7266da26945fd66dac43/src/qcodes/instrument/instrument_base.py#L398-L402

Branch: main @ https://github.com/QCoDeS/Qcodes/commit/42c74833d227a85ee45d7812e1ac0f66b8d948b0


Discussion:

Resolving patch:
diff --git a/src/qcodes/instrument/instrument_base.py b/src/qcodes/instrument/instrument_base.py
--- a/src/qcodes/instrument/instrument_base.py
+++ b/src/qcodes/instrument/instrument_base.py
@@ -396,6 +396,8 @@ def print_readable_snapshot(
         snapshot = self.snapshot(update=update)
 
         par_lengths = [len(p) for p in snapshot["parameters"]]
+        # handle the case of no parameters
+        par_lengths = par_lengths or [0]
 
         # Min of 50 is to prevent a super long parameter name to break this
         # function


Test patch:
diff --git a/tests/test_instrument.py b/tests/test_instrument.py
--- a/tests/test_instrument.py
+++ b/tests/test_instrument.py
@@ -14,7 +14,12 @@
 import pytest
 from pytest import FixtureRequest
 
-from qcodes.instrument import Instrument, InstrumentBase, find_or_create_instrument
+from qcodes.instrument import (
+    Instrument,
+    InstrumentBase,
+    InstrumentModule,
+    find_or_create_instrument,
+)
 from qcodes.instrument_drivers.mock_instruments import (
     DummyChannelInstrument,
     DummyFailingInstrument,
@@ -53,6 +58,16 @@ def _dummy_parabola() -> Iterator[MockParabola]:
         instrument.close()
 
 
+@pytest.fixture(name="empty_instrument_with_empty_submodule", scope="function")
+def _empty_instrument_with_empty_submodule() -> Iterator[Instrument]:
+    instrument = Instrument("EmptyInstrument")
+    instrument.add_submodule("A", InstrumentModule(instrument, "B"))
+    try:
+        yield instrument
+    finally:
+        instrument.close()
+
+
 @pytest.fixture(name='close_before_and_after', scope='function')
 def _close_before_and_after():
     Instrument.close_all()
@@ -320,6 +335,10 @@ def test_meta_instrument(parabola) -> None:
     assert re.search(r"gain[ \t]+:[ \t]+2", readable_snap) is not None
 
 
+def test_empty_instrument(empty_instrument_with_empty_submodule: Instrument) -> None:
+    empty_instrument_with_empty_submodule.print_readable_snapshot()
+
+
 def test_find(testdummy) -> None:
     """Test finding an existing instrument"""
Repository: microsoft/Qcodes

Issue:
Ignored exception on ci in windows related to monitor and socket. 
This may be related to the intermitted failures of monitor tests on windows

Observing the following traceback
```
Exception ignored in: <socket.socket fd=1116, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=0, laddr=('127.0.0.1', 55090), raddr=('127.0.0.1', 55091)>
Traceback (most recent call last):
  File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 917, in run
    self._target(*self._args, **self._kwargs)
ResourceWarning: unclosed <socket.socket fd=1116, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=0, laddr=('127.0.0.1', 55090), raddr=('127.0.0.1', 55091)>
```


Discussion:

Resolving patch:
diff --git a/src/qcodes/monitor/monitor.py b/src/qcodes/monitor/monitor.py
--- a/src/qcodes/monitor/monitor.py
+++ b/src/qcodes/monitor/monitor.py
@@ -193,10 +193,8 @@ async def run_loop() -> None:
                 self.handler, "127.0.0.1", WEBSOCKET_PORT, close_timeout=1
             ):
                 self.server_is_started.set()
-                try:
-                    await self._stop_loop_future
-                except asyncio.CancelledError:
-                    log.debug("Websocket server thread shutting down")
+                await self._stop_loop_future
+                log.debug("Websocket server thread shutting down")
 
         try:
             asyncio.run(run_loop())
@@ -234,7 +232,7 @@ def join(self, timeout: float | None = None) -> None:
         try:
             if self.loop is not None and self._stop_loop_future is not None:
                 log.debug("Instructing server to stop event loop.")
-                self.loop.call_soon_threadsafe(self._stop_loop_future.cancel)
+                self.loop.call_soon_threadsafe(self._stop_loop_future.set_result, True)
             else:
                 log.debug("No event loop found. Cannot stop event loop.")
         except RuntimeError:


Test patch:
Repository: RedHatInsights/insights-core

Issue:
Run Flake8 lint on RHEL6
Currently, flake8 is run only on RHEL7 and 8 and not on RHEL6. According to [the documentation](http://flake8.pycqa.org/en/latest/#installation) it is necessary to run flake8 with the exact Python version that is used. Thus to be sure that the syntax is ok even for the older Python version, we have to run in to RHEL6 too.

Tackled in #1251.


Discussion:
Close as complete.
Are you sure? Jenkinsfile on current _master_ doesn’t run `flake8` for the RHEL6 stage. https://github.com/RedHatInsights/insights-core/blob/561841414573e9cfce9b3632fb0c1528630c5f14/Jenkinsfile#L12
@Glutexo My bad. Should I do a PR?
Not necessary, it’ll be just a one-liner, so I’ll do it right away. But thanks!

Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -64,7 +64,7 @@ def maybe_require(pkg):
 ])
 
 linting = set([
-    'flake8==3.3.0',
+    'flake8==2.6.2',
 ])
 
 optional = set([


Test patch:
Repository: RedHatInsights/insights-core

Issue:
Mistake to recognize collected files as missing requirements
When I tried to reformat the output of missing requirements from "-m" option in insights-run, I found that insights-run would recognize collected soft link files from sosreport as missing. For example, when I executed insights-run with a sosreport collected from my local server, the command reported following item in the missing_requirements section:

~~~
<class 'insights.parsers.lsmod.LsMod'>:[[insights.specs.Specs.lsmod],[]]
~~~

That means insights-run thought there was no lsmod file in the sosreport. However, I am pretty sure that the lsmod file exists in the directory. 

~~~
# ls
boot           dmidecode      installed-rpms lib            mount          root           sos_reports    usr
chkconfig      etc            ip_addr        lsmod          netstat        route          sys            var
date           free           java           lsof           proc           sos_commands   uname          version.txt
df             hostname       last           lspci          ps             sos_logs       uptime         vgdisplay
~~~

The item of lsmod in sos_archive.py is "lsmod = simple_file("lsmod")", after changing the item as "lsmod = simple_file("sos_commands/kernel/lsmod")" and execute insights-run again, lsmod missing disappears in the missing_requirements section. So I think there may be issue in handling soft link files in sosreport. 




Discussion:
Hey @wushiqinlou, thanks for bringing this up! It should happen only when analyzing a sos report that's already been extracted to a directory. It's caused by [code that checks to ensure symlinks don't point outside the archive](https://github.com/RedHatInsights/insights-core/blob/master/insights/core/spec_factory.py#L144).

I'll push a fix shortly, but until then, analyzing the archive without extracting it should work as expected.

Resolving patch:
diff --git a/insights/core/spec_factory.py b/insights/core/spec_factory.py
--- a/insights/core/spec_factory.py
+++ b/insights/core/spec_factory.py
@@ -141,7 +141,7 @@ def validate(self):
 
         if os.path.islink(self.path):
             resolved = os.path.realpath(self.path)
-            if not resolved.startswith(self.root):
+            if not resolved.startswith(os.path.realpath(self.root)):
                 msg = "Symbolic link points outside archive: %s -> %s."
                 raise Exception(msg % (self.path, resolved))
 


Test patch:
Repository: RedHatInsights/insights-core

Issue:
Ensure current working directory is on the python path with insights-run
`insights-run` can't invoke arbitrary scripts because it doesn't include the current working directory in the python path like `python -m insights` does.


Discussion:

Resolving patch:
diff --git a/insights/__init__.py b/insights/__init__.py
--- a/insights/__init__.py
+++ b/insights/__init__.py
@@ -2,6 +2,7 @@
 import logging
 import pkgutil
 import os
+import sys
 import yaml
 from .core import Scannable, LogFileOutput, Parser, IniConfigFile  # noqa: F401
 from .core import FileListing, LegacyItemAccess, SysconfigOptions  # noqa: F401
@@ -250,6 +251,8 @@ class Args(object):
 
 
 def main():
+    if "" not in sys.path:
+        sys.path.insert(0, "")
     run(print_summary=True)
 
 


Test patch:
Repository: RedHatInsights/insights-core

Issue:
InstalledRpm.from_package doesn't support 'epoch' correctly
The current `InstalledRpm.from_package` doesn's support generating an Rpm object contains `epoch`

e.g.

```python
In [1]: from insights.parsers.installed_rpms import InstalledRpm

In [2]: bash_rpm = InstalledRpm.from_package('bash-1:4.1.2-12.el7.x86_64')

In [3]: bash_rpm.epoch
Out[3]: '0'

```

The `.epoch` always returns `'0'` even it's specified as `'1'`.



Discussion:

Resolving patch:
diff --git a/insights/parsers/installed_rpms.py b/insights/parsers/installed_rpms.py
--- a/insights/parsers/installed_rpms.py
+++ b/insights/parsers/installed_rpms.py
@@ -339,8 +339,7 @@ def __init__(self, data):
 
         for k, v in data.items():
             setattr(self, k, v)
-        if 'epoch' not in data or data['epoch'] == '(none)':
-            self.epoch = '0'
+        self.epoch = data['epoch'] if 'epoch' in data and data['epoch'] != '(none)' else '0'
 
         """Below is only for version comparison"""
         def _start_of_distribution(rest_split):
@@ -444,6 +443,7 @@ def _parse_package(cls, package_string):
             pkg, arch = (package_string, None)
         pkg, release = rsplit(pkg, '-')
         name, version = rsplit(pkg, '-')
+        epoch, version = version.split(':', 1) if ":" in version else ['0', version]
         # oracleasm packages have a dash in their version string, fix that
         if name.startswith('oracleasm') and name.endswith('.el5'):
             name, version2 = name.split('-', 1)
@@ -452,7 +452,8 @@ def _parse_package(cls, package_string):
             'name': name,
             'version': version,
             'release': release,
-            'arch': arch
+            'arch': arch,
+            'epoch': epoch
         }
 
     @classmethod


Test patch:
diff --git a/insights/parsers/tests/test_installed_rpms.py b/insights/parsers/tests/test_installed_rpms.py
--- a/insights/parsers/tests/test_installed_rpms.py
+++ b/insights/parsers/tests/test_installed_rpms.py
@@ -112,9 +112,18 @@
 
 def test_from_package():
     rpms = InstalledRpms(context_wrap(RPMS_PACKAGE))
-    assert rpms.packages['openssh-server'][0].package == 'openssh-server-5.3p1-104.el6'
     assert not rpms.is_hypervisor
 
+    pkg_rpm = rpms.packages['openssh-server'][0]
+    rpm = InstalledRpm.from_package(pkg_rpm.package)
+    assert rpm.package == 'openssh-server-5.3p1-104.el6'
+    assert pkg_rpm.package == 'openssh-server-5.3p1-104.el6'
+    assert rpm == pkg_rpm
+    assert rpm.epoch == '0'
+
+    rpm = InstalledRpm.from_package('bash-1:4.1.2-12.el7.x86_64')
+    assert rpm.epoch == '1'
+
 
 def test_from_line():
     rpms = InstalledRpms(context_wrap(RPMS_LINE))
Repository: RedHatInsights/insights-core

Issue:
DeprecationWarning from qemu_xml
A bunch of below warning are reported in the python3 test of insights-plugins:

~~~ 

 /Users/liuxc/work/insights/insights-core/insights/parsers/qemu_xml.py:149: DeprecationWarning: This method will be removed in future versions.  Use '
list(elem)' or iteration over elem instead.
  /Users/liuxc/work/insights/insights-core/insights/parsers/qemu_xml.py:149: DeprecationWarning: This method will be removed in future versions.  Use '
list(elem)' or iteration over elem instead.
~~~


Discussion:

Resolving patch:
diff --git a/insights/parsers/qemu_xml.py b/insights/parsers/qemu_xml.py
--- a/insights/parsers/qemu_xml.py
+++ b/insights/parsers/qemu_xml.py
@@ -146,10 +146,10 @@ def parse_dom(self):
         else:
             domain = {}
             for child in self.dom:
-                if not child.getchildren():
+                if len(child) == 0:
                     domain[child.tag] = child.text
                 else:
-                    domain[child.tag] = [c.items() for c in child.getchildren()]
+                    domain[child.tag] = [c.items() for c in child]
 
             return domain
 


Test patch: