internlm/SWE-Fixer-Train-110K huggingface dataset:
Repository: canonical/microk8s

Issue:
hostname-override on master node creates problems on worker nodes.
<!--
   Thank you for submitting an issue. Please fill in the template below
   information about the bug you encountered.
-->

#### Summary
<!-- Please explain the bug in a few short sentences -->
If the `--hostname-override` option is used in the master node of a microk8s cluster and then a worker node joins the cluster, the same configuration will be added to the worker node as well.

#### What Should Happen Instead?
<!-- Please explain what the expected behavior is -->
When a master node uses the `--hostname-override` option it shouldn't have any side effects on the worker nodes joining the cluster.

#### Reproduction Steps
<!-- Are you able to consistently reproduce the issue? Please add a list of steps that lead to the bug. -->

1. `sudo snap install microk8s --classic`
2. `sudo microk8s enable dns ingress`
3. `sudo vi /var/snap/microk8s/current/args/kubelet` and add `--hostname-override=example`
4. `sudo snap stop microk8s && sudo snap start microk8s`
5. `sudo microk8s add-node` and copy the worker joining token.
6. Join the cluster from another node using the previous token.
7. `cat /var/snap/microk8s/current/args/kubelet` and you will see that the `--hostname-override=example` is added there.


#### Introspection Report
[inspection-report-20220909_082628.tar.gz](https://github.com/canonical/microk8s/files/9533752/inspection-report-20220909_082628.tar.gz)
<!-- Please run `microk8s inspect` and attach the generated tarball. -->


<!-- Thank you for making MicroK8s better -->



Discussion:

Resolving patch:
diff --git a/scripts/wrappers/join.py b/scripts/wrappers/join.py
--- a/scripts/wrappers/join.py
+++ b/scripts/wrappers/join.py
@@ -559,6 +559,16 @@ def update_kubelet_node_ip(args_string, hostname_override):
         set_arg("--node-ip", hostname_override, "kubelet")
 
 
+def update_kubelet_hostname_override(args_string):
+    """
+    Remove the kubelet --hostname-override argument if it was set on the node that we join.
+
+    :param args_string: the kubelet arguments
+    """
+    if "--hostname-override" in args_string:
+        set_arg("--hostname-override", None, "kubelet")
+
+
 def replace_admin_token(token):
     """
     Replaces the admin token in the known tokens
@@ -816,6 +826,7 @@ def join_dqlite_worker_node(info, master_ip, master_port, token):
 
     store_base_kubelet_args(info["kubelet_args"])
     update_kubelet_node_ip(info["kubelet_args"], hostname_override)
+    update_kubelet_hostname_override(info["kubelet_args"])
     update_cert_auth_kubeproxy(token, info["ca"], master_ip, master_port, hostname_override)
     update_cert_auth_kubelet(token, info["ca"], master_ip, master_port)
 


Test patch:
Repository: canonical/microk8s

Issue:
microk8s suggests command hiding error info
<!--
   Thank you for submitting an issue. Please fill in the template below
   information about the bug you encountered.
-->

#### Summary
<!-- Please explain the bug in a few short sentences -->

When you try to run microk8s with insufficient permissions, you get an error and suggestion:

```console
$ microk8s status
Insufficient permissions to access MicroK8s.
You can either try again with sudo or add the user runner to the 'snap_microk8s' group:

    sudo usermod -a -G snap_microk8s runner
    sudo chown -f -R runner ~/.kube

After this, reload the user groups either via a reboot or by running 'newgrp snap_microk8s'.
```

However, if you don't have a `~/.kube` file, the `chown` command will fail silently and suppress the error message. This can cause failures e.g. in GitHub runners / scripts with `set -e`, and the `-f` option will hide the error message. This makes it very hard to debug the failure as there are no log messages.

#### What Should Happen Instead?
<!-- Please explain what the expected behavior is -->

Suggest to the user not to use the `-f` flag in `chown`. There is no reason to suppress the error message.
```console
$ microk8s status
Insufficient permissions to access MicroK8s.
You can either try again with sudo or add the user runner to the 'snap_microk8s' group:

    sudo usermod -a -G snap_microk8s runner
    sudo chown -R runner ~/.kube

After this, reload the user groups either via a reboot or by running 'newgrp snap_microk8s'.
```


Discussion:
Hi, seems like a simple fix, contributions are welcome!

Resolving patch:
diff --git a/scripts/wrappers/common/utils.py b/scripts/wrappers/common/utils.py
--- a/scripts/wrappers/common/utils.py
+++ b/scripts/wrappers/common/utils.py
@@ -197,7 +197,7 @@ def exit_if_no_permission():
         )
         print("")
         print("    sudo usermod -a -G microk8s {}".format(user))
-        print("    sudo chown -f -R $USER ~/.kube")
+        print("    sudo chown -R $USER ~/.kube")
         print("")
         print(
             "After this, reload the user groups either via a reboot or by running 'newgrp microk8s'."


Test patch:
Repository: canonical/microk8s

Issue:
Non-HA single node, leaving node removes all pods


#### Summary
Iam running the microk8s in ubuntu in no high availability i.e. there is a single node onto the same machine where it is installed. I updated the certificates and then i issue following command:
`sudo microk8s leave`

It give following messages:

```
Generating new cluster certificates.
Waiting for node to start. 
```

and then i stopped microk8s and then started again, the node appeared  however all of my pods / namespaces are gone, how to recover?

#### What Should Happen Instead?
All the pods should retain

#### Reproduction Steps
Already described above

#### Introspection Report

#### Can you suggest a fix?
<!-- (This section is optional). How do you propose that the issue be fixed? -->
[https://wetransfer.com/downloads/ee891f9d62bd9ffd7fdac2f9597e638f20230529135310/bf5d38484b8a54a7107a5447153c884820230529135327/7b32a3](url)



Discussion:
Hey @khandg,

Thanks for reporting this issue. `microk8s leave` command is supposed to remove the node from a cluster and return it to a clean state. Although it does not sound right that a node that is not in a cluster acts the same way. Sorry about the trouble, I'll mark it as a bug and add it to our backlog.
Thanks @berkayoz for noting this issue. Is there any possible way i can have it recovered?

Resolving patch:
diff --git a/scripts/wrappers/remove_node.py b/scripts/wrappers/remove_node.py
--- a/scripts/wrappers/remove_node.py
+++ b/scripts/wrappers/remove_node.py
@@ -8,7 +8,7 @@
 import click
 import netifaces
 
-from ipaddress import ip_address, IPv4Address
+from ipaddress import ip_address
 
 from common.cluster.utils import (
     try_set_file_permissions,
@@ -26,7 +26,13 @@
 def remove_dqlite_node(node, force=False):
     try:
         # If node is an IP address, find the node name.
-        if type(ip_address(node)) is IPv4Address:
+        is_node_ip = True
+        try:
+            ip_address(node)
+        except ValueError:
+            is_node_ip = False
+
+        if is_node_ip:
             node_info = subprocess.check_output(
                 "{}/microk8s-kubectl.wrapper get no -o json".format(snap_path).split()
             )


Test patch:
Repository: canonical/microk8s

Issue:
update homebrew formula to newest microk8s version (1.27) and ubuntu version (22.04)- otherwise Mac Users can't use it. 
#### Summary
The latest present formula on homebrew  as of June 2023 point to ubuntu version 18.04 and microk8s version 1.26. This makes it near to impossible for mac users to use it.

#### Why is this important?
Lot has changed since that time. The instructions do not work in the present day, leading to newbies like myself wasting precious time, assuming the fault is theirs :)

#### Are you interested in contributing to this feature?
yep definitely.



Discussion:

Resolving patch:
diff --git a/installer/common/definitions.py b/installer/common/definitions.py
--- a/installer/common/definitions.py
+++ b/installer/common/definitions.py
@@ -28,8 +28,8 @@
 DEFAULT_MEMORY_GB: int = 4
 DEFAULT_DISK_GB: int = 50
 DEFAULT_ASSUME: bool = False
-DEFAULT_CHANNEL: str = "1.26/stable"
-DEFAULT_IMAGE: str = "18.04"
+DEFAULT_CHANNEL: str = "1.27/stable"
+DEFAULT_IMAGE: str = "22.04"
 
 MIN_CORES: int = 2
 MIN_MEMORY_GB: int = 2
diff --git a/installer/vm_providers/_multipass/_windows.py b/installer/vm_providers/_multipass/_windows.py
--- a/installer/vm_providers/_multipass/_windows.py
+++ b/installer/vm_providers/_multipass/_windows.py
@@ -39,12 +39,12 @@
 
 
 _MULTIPASS_RELEASES_API_URL = "https://api.github.com/repos/canonical/multipass/releases"
-_MULTIPASS_DL_VERSION = "1.11.1"
+_MULTIPASS_DL_VERSION = "1.12.0"
 _MULTIPASS_DL_NAME = "multipass-{version}+win-win64.exe".format(version=_MULTIPASS_DL_VERSION)
 
 # Download multipass installer and calculate hash:
 #   python3 -c "from installer.common.file_utils import calculate_sha3_384; print(calculate_sha3_384('$HOME/Downloads/multipass-1.11.1+win-win64.exe'))"  # noqa: E501
-_MULTIPASS_DL_SHA3_384 = "7691383eb0f4def0f9e2b5c77f04424756a63f222b3500bdc8fb25bf4725f1c0ce3bd0cb0b7cff7f79d8f489e199225b"  # noqa: E501
+_MULTIPASS_DL_SHA3_384 = "ddba66059052a67fa6a363729b75aca374591bc5a2531c938dd70d63f683c22108d5c2ab77025b818b31f69103228eee"  # noqa: E501
 
 
 def windows_reload_multipass_path_env():


Test patch:
Repository: canonical/microk8s

Issue:
update homebrew formula to newest microk8s version (1.28) - otherwise Mac Users can't use it. 
Summary
The latest present formula on homebrew as of October 2023 point to ubuntu version 22.04 and microk8s version 1.27. This makes it near to impossible for mac users to use it.

Why is this important?
Lot has changed since that time. The instructions do not work in the present day, leading to newbies like myself wasting precious time, assuming the fault is theirs :)

Are you interested in contributing to this feature?
yep definitely.


Discussion:

Resolving patch:
diff --git a/installer/common/definitions.py b/installer/common/definitions.py
--- a/installer/common/definitions.py
+++ b/installer/common/definitions.py
@@ -28,7 +28,7 @@
 DEFAULT_MEMORY_GB: int = 4
 DEFAULT_DISK_GB: int = 50
 DEFAULT_ASSUME: bool = False
-DEFAULT_CHANNEL: str = "1.27/stable"
+DEFAULT_CHANNEL: str = "1.28/stable"
 DEFAULT_IMAGE: str = "22.04"
 
 MIN_CORES: int = 2
diff --git a/installer/vm_providers/_multipass/_windows.py b/installer/vm_providers/_multipass/_windows.py
--- a/installer/vm_providers/_multipass/_windows.py
+++ b/installer/vm_providers/_multipass/_windows.py
@@ -39,12 +39,12 @@
 
 
 _MULTIPASS_RELEASES_API_URL = "https://api.github.com/repos/canonical/multipass/releases"
-_MULTIPASS_DL_VERSION = "1.12.0"
+_MULTIPASS_DL_VERSION = "1.12.2"
 _MULTIPASS_DL_NAME = "multipass-{version}+win-win64.exe".format(version=_MULTIPASS_DL_VERSION)
 
 # Download multipass installer and calculate hash:
 #   python3 -c "from installer.common.file_utils import calculate_sha3_384; print(calculate_sha3_384('$HOME/Downloads/multipass-1.11.1+win-win64.exe'))"  # noqa: E501
-_MULTIPASS_DL_SHA3_384 = "ddba66059052a67fa6a363729b75aca374591bc5a2531c938dd70d63f683c22108d5c2ab77025b818b31f69103228eee"  # noqa: E501
+_MULTIPASS_DL_SHA3_384 = "9031c8fc98b941df1094a832c356e12f281c70d0eb10bee15b5576c61af4c8a17ef32b833f0043c8df0e04897e69c8bc"  # noqa: E501
 
 
 def windows_reload_multipass_path_env():


Test patch:
Repository: canonical/microk8s

Issue:
Internet connectivity check fails if ICMP traffic is restricted
<!--
   Thank you for submitting an issue. Please fill in the template below
   information about the bug you encountered.
-->

#### Summary
<!-- Please explain the bug in a few short sentences -->
When trying to install on macOS I get a failure to connect to the internet, the check is done via a ping (ICMP) traffic which isn't allowed on my corp network. However http/https (which are the connections actually required) are fine. I can't see any other use of ping other than a test.

#### What Should Happen Instead?
<!-- Please explain what the expected behavior is -->
The internet check should check for http(s) connectivity instead of using ping.

#### Reproduction Steps
<!-- Are you able to consistently reproduce the issue? Please add a list of steps that lead to the bug. -->

1. be on network that disallows ICMP traffic
2. microk8s install

#### Introspection Report
<!-- Please run `microk8s inspect` and attach the generated tarball. -->
N/A

#### Can you suggest a fix?
<!-- (This section is optional). How do you propose that the issue be fixed? -->
https://github.com/canonical/microk8s/blob/master/installer/vm_providers/_base_provider.py#L131

`curl --fail --head https://snapcraft.io` instead perhaps?

#### Are you interested in contributing with a fix?
<!-- yes/no, or @mention maintainers. Community contributions are welcome. -->
Yes

<!-- Thank you for making MicroK8s better -->



Discussion:
Hi @asmithdt 

Thank you for raising this, this has also been discussed in the past, but I do agree that your proposal sounds quite sound.

We could even attempt both (try the ping, then fallback to curl if that does not work), and if any of the two works then proceed with the installation assuming that we have network connectivity.

Contirbutions are welcome! Otherwise we will work on this soon. Thanks for raising this!

Resolving patch:
diff --git a/installer/vm_providers/_base_provider.py b/installer/vm_providers/_base_provider.py
--- a/installer/vm_providers/_base_provider.py
+++ b/installer/vm_providers/_base_provider.py
@@ -18,6 +18,7 @@
 import logging
 import os
 import pathlib
+import requests
 import shlex
 import sys
 from typing import Dict
@@ -128,8 +129,8 @@ def launch_instance(self, specs: Dict) -> None:
     def _check_connectivity(self) -> None:
         """Check that the VM can access the internet."""
         try:
-            self.run("ping -c 1 snapcraft.io".split(), hide_output=True)
-        except errors.ProviderLaunchError:
+            requests.get("https://snapcraft.io")
+        except requests.exceptions.RequestException:
             self.destroy()
             url = None
             if sys.platform == "win32":


Test patch:
Repository: spacetelescope/jwql

Issue:
Make dev conda environment more general
We should make our `dev` `conda` environment more generalized so that it can be used on the new test server. 


Discussion:

Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
 AUTHORS = 'Matthew Bourque, Sara Ogaz, Joe Filippazzo, Bryan Hilbert, Misty Cracraft, Graham Kanarek'
 AUTHORS += 'Johannes Sahlmann, Lauren Chambers, Catherine Martlin'
 
-REQUIRES = ['astropy', 'astroquery', 'bokeh', 'django', 'matplotlib', 'numpy', 'python-dateutil', 'sphinx', 'sphinx-automodapi', 'sqlalchemy']
+REQUIRES = ['astropy', 'astroquery', 'bokeh==0.12.5', 'django', 'matplotlib', 'numpy', 'python-dateutil', 'sphinx', 'sphinx-automodapi', 'sqlalchemy']
 
 setup(
     name = 'jwql',


Test patch:
Repository: spacetelescope/jwql

Issue:
Update environment.yml to update Django version
When running the Django web server (on the `laurenmarietta/web-app-dev branch`) from the `jwql` environment on the VM, and I had to update Django from 1.11.8 to the latest version (2.0.5) to get rid of an error with Django.

The version of Django in `environment.yml` should be specified to >=2.0.5 in the environment file in the future.


Discussion:

Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
 AUTHORS = 'Matthew Bourque, Sara Ogaz, Joe Filippazzo, Bryan Hilbert, Misty Cracraft, Graham Kanarek'
 AUTHORS += 'Johannes Sahlmann, Lauren Chambers, Catherine Martlin'
 
-REQUIRES = ['astropy', 'astroquery', 'bokeh==0.12.5', 'django', 'matplotlib', 'numpy', 'python-dateutil', 'sphinx', 'sphinx-automodapi', 'sqlalchemy']
+REQUIRES = ['astropy', 'astroquery', 'bokeh==0.12.5', 'django==2.0.5', 'matplotlib', 'numpy', 'python-dateutil', 'sphinx', 'sphinx-automodapi', 'sqlalchemy']
 
 setup(
     name='jwql',


Test patch:
Repository: spacetelescope/jwql

Issue:
logging_functions should write logs from dev & test VMs to dev/
Currently `logging_functions.py` will write new log files to the `dev/` directory if the script being executed is not being executed from the admin account.  This should be extended to write to `dev/` when the script is run from personal accounts from the dev or test VMs. 

In other words, all logs should be written to `dev/` unless they are being run from the admin account on one of the production VMs. 


Discussion:

Resolving patch:
diff --git a/jwql/utils/logging_functions.py b/jwql/utils/logging_functions.py
--- a/jwql/utils/logging_functions.py
+++ b/jwql/utils/logging_functions.py
@@ -135,8 +135,7 @@ def make_log_file(module, production_mode=True, path='./'):
     admin_account = settings['admin_account']
     log_path = settings['log_dir']
 
-    exempt_modules = []
-    if user != admin_account and module not in exempt_modules and production_mode:
+    if user != admin_account or not production_mode:
         module = os.path.join('dev', module)
 
     if production_mode:


Test patch:
Repository: spacetelescope/jwql

Issue:
Add website API docs to Sphinx 
Now that the website code is part of the `jwql` package (#121), we can add appropriate `rst` files to get the web app API docs into our normal `sphinx` build. 


Discussion:

Resolving patch:
diff --git a/docs/source/conf.py b/docs/source/conf.py
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -172,7 +172,4 @@
     (master_doc, 'jwql', 'jwql Documentation',
      author, 'jwql', 'One line description of project.',
      'Miscellaneous'),
-]
-
-
-
+]
\ No newline at end of file
diff --git a/jwql/website/apps/jwql/views.py b/jwql/website/apps/jwql/views.py
--- a/jwql/website/apps/jwql/views.py
+++ b/jwql/website/apps/jwql/views.py
@@ -16,12 +16,11 @@
 ---
 
     This module is called in ``urls.py`` as such:
-
     ::
+
         from django.urls import path
         from . import views
-        urlpatterns = [path('web/path/to/view/',
-                             views.view_name, name='view_name')]
+        urlpatterns = [path('web/path/to/view/', views.view_name, name='view_name')]
 
 References
 ----------
diff --git a/jwql/website/manage.py b/jwql/website/manage.py
--- a/jwql/website/manage.py
+++ b/jwql/website/manage.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#! /usr/bin/env python
 
 """Utility module for administrative tasks.
 
@@ -14,14 +14,17 @@
 
     To run the web app server:
     ::
+
         python manage.py runserver
 
     To start the interactive shellL:
     ::
+
         python manage.py shell
 
     To run tests for all installed apps:
     ::
+
         python manage.py test
 
 References


Test patch:
Repository: spacetelescope/jwql

Issue:
Update generate_preview_images to use constants.py
It appears that we missed updating `generate_preview_images` to use the new `constants.py` module when we merged #253.  Per the `cron` error:

```
Traceback (most recent call last):
  File "/home/jwqladm/repositories/jwql/jwql/jwql_monitors/generate_preview_images.py", line 43, in <module>
    from jwql.utils.utils import NIRCAM_LONGWAVE_DETECTORS
ImportError: cannot import name 'NIRCAM_LONGWAVE_DETECTORS'
```

This probably would have been picked up by our test suite if it were currently working properly (#262).  We should probably solve #262 sooner than later. 


Discussion:

Resolving patch:
diff --git a/jwql/jwql_monitors/generate_preview_images.py b/jwql/jwql_monitors/generate_preview_images.py
--- a/jwql/jwql_monitors/generate_preview_images.py
+++ b/jwql/jwql_monitors/generate_preview_images.py
@@ -34,14 +34,10 @@
 import numpy as np
 
 from jwql.utils import permissions
-from jwql.utils.logging_functions import configure_logging
-from jwql.utils.logging_functions import log_info
-from jwql.utils.logging_functions import log_fail
+from jwql.utils.constants import NIRCAM_LONGWAVE_DETECTORS, NIRCAM_SHORTWAVE_DETECTORS
+from jwql.utils.logging_functions import configure_logging, log_info, log_fail
 from jwql.utils.preview_image import PreviewImage
-from jwql.utils.utils import get_config
-from jwql.utils.utils import filename_parser
-from jwql.utils.utils import NIRCAM_LONGWAVE_DETECTORS
-from jwql.utils.utils import NIRCAM_SHORTWAVE_DETECTORS
+from jwql.utils.utils import get_config, filename_parser
 
 # Size of NIRCam inter- and intra-module chip gaps
 SW_MOD_GAP = 1387  # pixels = int(43 arcsec / 0.031 arcsec/pixel)
@@ -637,8 +633,8 @@ def group_filenames(input_files):
         suffix = filename_parts['suffix']
 
         observation_base = 'jw{}{}{}_{}{}{}_{}_'.format(
-                        program, observation, visit, visit_group,
-                        parallel, activity, exposure)
+            program, observation, visit, visit_group,
+            parallel, activity, exposure)
 
         if detector in NIRCAM_SHORTWAVE_DETECTORS:
             detector_str = 'NRC[AB][1234]'


Test patch:
Repository: spacetelescope/jwql

Issue:
Update install_requires in setup.py
After some research on StackOverflow and discussion with @SaOgaz and @laurenmarietta on the subject of `setup.py` dependencies and `requirements.txt`/`environment.yml` dependencies (#261, #94), we should probably update the list of dependencies in `install_requires` in `setup.py` to better reflect what is actually needed to install and run our application.

In short: `setup.py` should _list the range of dependencies that allow a user to run any code in our repository_, while `environment.yml` should _list a set of specific dependencies that allow the application to operate on a specific architecture_ 


Discussion:
[This article](https://packaging.python.org/discussions/install-requires-vs-requirements/) from the Python docs sheds some more light on this.  In short:

- `install_requires` should contain what dependencies the project *minimally* needs to run
- `install_requires` ideally contain lower and upper bounds to dependency versions (e.g. `astropy>=1.0,<2.0`
- `requirements.txt` should contain an exhaustive list of pinned versions for the purpose of achieving repeatable installations of a complete environment.

Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -7,8 +7,22 @@
 AUTHORS = 'Matthew Bourque, Sara Ogaz, Joe Filippazzo, Bryan Hilbert, Misty Cracraft, '
 AUTHORS += 'Graham Kanarek, Johannes Sahlmann, Lauren Chambers, Catherine Martlin'
 
-REQUIRES = ['astroquery', 'bokeh==1.0.1', 'django==2.1.2', 'matplotlib', 'numpy',
-            'python-dateutil', 'sphinx', 'sphinx-automodapi', 'sqlalchemy']
+REQUIRES = ['astropy',
+            'astroquery>=0.3.9',
+            'authlib',
+            'bokeh>=1.0',
+            'django>=2.0',
+            'jinja2',
+            'jwst',
+            'matplotlib',
+            'numpy',
+            'numpydoc',
+            'pandas',
+            'psycopg2',
+            'pytest',
+            'sphinx',
+            'sqlalchemy',
+            'stsci_rtd_theme']
 
 setup(
     name='jwql',


Test patch: