internlm/SWE-Fixer-Train-110K huggingface dataset:
Repository: sosreport/sos

Issue:
containerd plugin does not enable when containerd is installed from docker repo
The Fedora/RHEL RPM follows the naming conventions [found at containerd.io](https://containerd.io/downloads/), and an rpm name of `containerd`. However, when containerd is installed [from docker repositories](https://download.docker.com/linux/centos/8/x86_64/stable/Packages/) on EL8 distributions the RPM is actually named `containerd.io`, resulting in the plugin not enabling itself even though containerd is installed.



Discussion:

Resolving patch:
diff --git a/sos/report/plugins/containerd.py b/sos/report/plugins/containerd.py
--- a/sos/report/plugins/containerd.py
+++ b/sos/report/plugins/containerd.py
@@ -14,7 +14,7 @@ class Containerd(Plugin, RedHatPlugin, UbuntuPlugin, CosPlugin):
     short_desc = 'Containerd containers'
     plugin_name = 'containerd'
     profiles = ('container',)
-    packages = ('containerd',)
+    packages = ('containerd', 'containerd.io',)
 
     def setup(self):
         self.add_copy_spec([


Test patch:
Repository: sosreport/sos

Issue:
[hpssm] controller collection misses Gen10+ controllers and above slot 9.
1. Gen10+ controllers changed the naming from **Smart Array** for at least some controllers.
   * `HPE SR932i-p Gen10+ in Slot 3`
2. Controllers are showing up above slot 9 even when there is only 1 or two total controllers.
   * `HPE Smart Array P816i-a SR Gen10 in Slot 12`

This system had no controller in slot 0, a new naming style in slot 3, and the old naming style in slot 12. 
The `ssacli ctrl all show status` still lists them, and `ssacli ctrl all show config detail` still gets the config details of each. The current pattern fails to identify the slots in both cases, leading to not executing individual slot based commands or executing on the wrong slot.




Discussion:

Resolving patch:
diff --git a/sos/report/plugins/hpssm.py b/sos/report/plugins/hpssm.py
--- a/sos/report/plugins/hpssm.py
+++ b/sos/report/plugins/hpssm.py
@@ -45,7 +45,7 @@ def setup(self):
             ["%s %s" % (cmd, subcmd) for subcmd in subcmds]
         )
 
-        pattern = re.compile("^HP.*Smart Array (.*) in Slot ([0123456789])")
+        pattern = re.compile("^HP[E] (.*) in Slot ([0123456789]+)")
         config_detail_cmd = cmd + ' ctrl all show config detail'
         config_detail = self.collect_cmd_output(config_detail_cmd)
         ctrl_slots = []


Test patch:
Repository: sosreport/sos

Issue:
[transport] saltstack causes a final error trying to parse the package list from down nodes
Down nodes for saltstack transport cause a final error for each down host after not being able to connect early on.

Similar to the control_persist transport error:
```
[store-2:__init__] Unable to open remote session: Timeout expires while trying to connect
```
The saltstack transport errors slightly differently for nodes that are down:
```
[store-2:read_file] Exception while reading /etc/os-release: Timeout expired executing salt --out json --static --no-color store-2 cmd.shell  'cat /etc/os-release'
```

Then one additional error via `sys.stderr.write()` in `redhat.py` occurs for each down node:
```
Could not obtain installed package list[root@EL8_supervisor ~]#
```

_Originally posted by @TrevorBenson in https://github.com/sosreport/sos/issues/3456#issuecomment-1870554310_

----

I'll try to diagnose why it differs from control_persist transport.


Discussion:

Resolving patch:
diff --git a/sos/collector/transports/saltstack.py b/sos/collector/transports/saltstack.py
--- a/sos/collector/transports/saltstack.py
+++ b/sos/collector/transports/saltstack.py
@@ -106,6 +106,8 @@ def _connect(self, password=None):
         self.log_info("Transport is locally supported and service running. ")
         cmd = "echo Connected"
         result = self.run_command(cmd, timeout=180)
+        if result['status'] == 1:
+            raise ConnectionException(self.address)
         return result['status'] == 0
 
     def _disconnect(self):


Test patch:
Repository: sosreport/sos

Issue:
Obtain CNI files for containerd
Containerd uses the CNI configuration present in the defined folders by the configuration

```
   [plugins."io.containerd.grpc.v1.cri".cni]
      conf_dir = "/etc/cni/net.d
```

It will be very useful to obtain the cni configurations present on the folder for debugging networking related problems 


https://github.com/sosreport/sos/blob/b94ced8370824bd62f3c7573ae33fcb96c5da531/sos/report/plugins/containerd.py#L12-L28


Discussion:
For reference files at the default folder are already listed by another plugin, but not copied:

https://github.com/sosreport/sos/blob/b94ced8370824bd62f3c7573ae33fcb96c5da531/sos/report/plugins/crio.py#L49

Resolving patch:
diff --git a/sos/report/plugins/containerd.py b/sos/report/plugins/containerd.py
--- a/sos/report/plugins/containerd.py
+++ b/sos/report/plugins/containerd.py
@@ -19,6 +19,7 @@ class Containerd(Plugin, RedHatPlugin, UbuntuPlugin, CosPlugin):
     def setup(self):
         self.add_copy_spec([
             "/etc/containerd/",
+            "/etc/cni/net.d/",
         ])
 
         self.add_cmd_output('containerd config dump')


Test patch:
Repository: xonsh/xonsh

Issue:
Path auto complition for vim returns error
Hi, thanks for this new cool shell, I realy like it! The only problem I've got so far is when I type 'vim ' and then press tab button it prints error message "/usr/share/bash-completion/bash_completion: line 1856: compopt: not currently executing completion function" instead of list of files in a directory. If I press tab again, it shows files as usual, but the error message is still printed to command line, so path becomes unreadable. Example:

```
pablo@alien /some/path branch $ vim /usr/share/bash-completion/bash_completion: line 1856: compopt: not currently executing completion function
/usr/share/bash-completion/bash_completion: line 1856: compopt: not currently executing completion function

.git/                 AUTHORS               GPATH                 MinSizeRel/           benchmark/            dependencies/
```



Discussion:

Resolving patch:
diff --git a/xonsh/completer.py b/xonsh/completer.py
--- a/xonsh/completer.py
+++ b/xonsh/completer.py
@@ -119,7 +119,7 @@ def bash_complete(self, prefix, line, begidx, endidx):
         script = BASH_COMPLETE_SCRIPT.format(filename=fnme, line=line, n=n,
                     func=func, cmd=cmd, end=endidx+1, prefix=prefix, prev=prev)
         out = subprocess.check_output(['bash'], input=script, 
-                                      universal_newlines=True)
+                                      universal_newlines=True, stderr=subprocess.PIPE)
         space = ' '
         rtn = {s+space if s[-1:].isalnum() else s for s in out.splitlines()}
         return rtn


Test patch:
Repository: xonsh/xonsh

Issue:
setup.py install fails if working directory not location of setup.py
C:\Python34>.\python.exe \temp\xonsh-0.1.2\setup.py install
...
Traceback (most recent call last):
  File "\temp\xonsh-0.1.2\setup.py", line 114, in <module>
    main()
  File "\temp\xonsh-0.1.2\setup.py", line 50, in main
    with open('README.rst', 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: 'README.rst'



Discussion:

Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -49,7 +49,7 @@ def main():
     if sys.version_info[0] < 3:
         sys.exit('xonsh currently requires Python 3.4+')
     print(logo)
-    with open('README.rst', 'r') as f:
+    with open(os.path.join(os.path.dirname(__file__), 'README.rst'), 'r') as f:
         readme = f.read()
     skw = dict(
         name='xonsh',


Test patch:
Repository: xonsh/xonsh

Issue:
In .xonshrc, import does not create a global name
xonsh: git checkout f44013b31756ba5491f2a7e1dffb7ad64513b28e
python: 3.4.1
OS: Fedora 21

With this as your .xonshrc:

``` python
import subprocess

def get_tty():
    tty = subprocess.check_output('tty').decode().strip()
    segments = tty.split('/')
    return '/'.join(segments[-2:])

$PROMPT='{tty}@{{hostname}}$ '.format(tty=get_tty())
```

Trying to start .xonshrc yields a traceback:

```
Traceback (most recent call last):
  File "scripts/xonsh", line 3, in <module>
    main()
  File "/srv/git/wishlist/xonsh/xonsh/main.py", line 36, in main
    shell = Shell()
  File "/srv/git/wishlist/xonsh/xonsh/shell.py", line 94, in __init__
    execer=self.execer)
  File "/srv/git/wishlist/xonsh/xonsh/environ.py", line 168, in xonshrc_context
    execer.exec(rc, glbs={}, locs=env)
  File "/srv/git/wishlist/xonsh/xonsh/execer.py", line 110, in exec
    return exec(code, glbs, locs)
  File "/home/badger/.xonshrc", line 7, in <module>

  File "/home/badger/.xonshrc", line 259, in get_tty
NameError: name 'subprocess' is not defined
Exception ignored in: <bound method Shell.__del__ of <xonsh.shell.Shell object at 0x7f383127e4e0>>
Traceback (most recent call last):
  File "/srv/git/wishlist/xonsh/xonsh/shell.py", line 102, in __del__
    teardown_readline()
  File "/srv/git/wishlist/xonsh/xonsh/shell.py", line 65, in teardown_readline
    import readline
  File "<frozen importlib._bootstrap>", line 2237, in _find_and_load
  File "<frozen importlib._bootstrap>", line 2222, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 2164, in _find_spec
  File "<frozen importlib._bootstrap>", line 1940, in find_spec
  File "<frozen importlib._bootstrap>", line 1908, in _get_spec
TypeError: 'NoneType' object is not iterable
```

If I change .xonshrc to have the subprocess import inside of the function then it starts up fine.  So it seems like importing does not create a globally available name.  The other things I tried such as:

``` python
import subprocess as subprocess
subprocess = __import__('subprocess')
```

also lead to the same traceback.



Discussion:

Resolving patch:
diff --git a/xonsh/environ.py b/xonsh/environ.py
--- a/xonsh/environ.py
+++ b/xonsh/environ.py
@@ -165,7 +165,7 @@ def xonshrc_context(rcfile=None, execer=None):
     env = {}
     try:
         execer.filename = rcfile
-        execer.exec(rc, glbs={}, locs=env)
+        execer.exec(rc, glbs=env)
     except SyntaxError as err:
         msg = 'syntax error in xonsh run control file {0!r}: {1!s}'
         warn(msg.format(rcfile, err), RuntimeWarning)


Test patch:
Repository: xonsh/xonsh

Issue:
Parser error on import *
Well, that is one way to prevent bad behaviour :)

``` console
scopatz@athenaie ~ $ from sys import *
Traceback (most recent call last):
  File "/home/scopatz/.local/bin/xonsh", line 3, in <module>
    main()
  File "/home/scopatz/.local/lib/python3.4/site-packages/xonsh/main.py", line 69, in main
    shell.cmdloop()
  File "/home/scopatz/.local/lib/python3.4/site-packages/xonsh/shell.py", line 167, in cmdloop
    super(Shell, self).cmdloop(intro=intro)
  File "/home/scopatz/miniconda3/lib/python3.4/cmd.py", line 138, in cmdloop
    stop = self.onecmd(line)
  File "/home/scopatz/miniconda3/lib/python3.4/cmd.py", line 211, in onecmd
    return self.default(line)
  File "/home/scopatz/.local/lib/python3.4/site-packages/xonsh/shell.py", line 119, in default
    code = self.push(line)
  File "/home/scopatz/.local/lib/python3.4/site-packages/xonsh/shell.py", line 140, in push
    locs=self.ctx)
  File "/home/scopatz/.local/lib/python3.4/site-packages/xonsh/execer.py", line 85, in compile
    tree = self.parse(input, ctx, mode=mode)
  File "/home/scopatz/.local/lib/python3.4/site-packages/xonsh/execer.py", line 73, in parse
    tree = self.ctxtransformer.ctxvisit(tree, input, ctx, mode=mode)
  File "/home/scopatz/.local/lib/python3.4/site-packages/xonsh/ast.py", line 80, in ctxvisit
    node = self.visit(node)
  File "/home/scopatz/miniconda3/lib/python3.4/ast.py", line 245, in visit
    return visitor(node)
  File "/home/scopatz/miniconda3/lib/python3.4/ast.py", line 301, in generic_visit
    value = self.visit(value)
  File "/home/scopatz/miniconda3/lib/python3.4/ast.py", line 245, in visit
    return visitor(node)
  File "/home/scopatz/.local/lib/python3.4/site-packages/xonsh/ast.py", line 169, in visit_ImportFrom
    if name.asname is None:
AttributeError: 'str' object has no attribute 'asname'
```



Discussion:

Resolving patch:
diff --git a/xonsh/parser.py b/xonsh/parser.py
--- a/xonsh/parser.py
+++ b/xonsh/parser.py
@@ -947,6 +947,8 @@ def p_import_from_post(self, p):
                             | import_as_names
         """
         if len(p) == 2:
+            if p[1] == '*':
+                p[1] = [ast.alias(name='*', asname=None)]
             p0 = p[1]
         elif len(p) == 4:
             p0 = p[2]


Test patch:
Repository: xonsh/xonsh

Issue:
File-redirect and `&` aren't compatible
``` bash
ls > file &
```

The above doesn't create `file`. The reason for the bug is in `built_ins.run_subproc`. When it's a background job it doesn't wait, and consequently doesn't write to the file at the end.

Maybe the fix would be send the object created by `open` as the `stdout` argument to `Popen`? Then, presumably, the process will begin writing to the file before all the output is computed, which is more standard behavior.



Discussion:
Yep.  This is an issue.  Thanks for reporting @SmartViking 


Resolving patch:
diff --git a/xonsh/built_ins.py b/xonsh/built_ins.py
--- a/xonsh/built_ins.py
+++ b/xonsh/built_ins.py
@@ -427,7 +427,15 @@ def run_subproc(cmds, captured=True):
         write_target = cmds[-1][0]
         write_mode = WRITER_MODES[cmds[-2]]
         cmds = cmds[:-2]
-        last_stdout = PIPE
+        if write_target is not None:
+            try:
+                last_stdout = open(write_target, write_mode)
+            except FileNotFoundError:
+                e = 'xonsh: {0}: no such file or directory'
+                print(e.format(write_target))
+                return
+        else:
+            last_stdout = PIPE
     last_cmd = cmds[-1]
     prev = None
     procs = []
@@ -503,20 +511,16 @@ def run_subproc(cmds, captured=True):
         print_one_job(num)
         return
     wait_for_active_job()
-    # get output
-    if isinstance(prev_proc, ProcProxy):
-        output = prev_proc.stdout
-    elif prev_proc.stdout is not None:
-        output = prev_proc.stdout.read()
-    # write the output if we should
-    if write_target is not None:
-        try:
-            with open(write_target, write_mode) as f:
-                f.write(output)
-        except FileNotFoundError:
-            print('xonsh: {0}: no such file or directory'.format(write_target))
-    if captured:
-        return output
+    if write_target is None:
+        # get output
+        if isinstance(prev_proc, ProcProxy):
+            output = prev_proc.stdout
+        elif prev_proc.stdout is not None:
+            output = prev_proc.stdout.read()
+        if captured:
+            return output
+    elif last_stdout not in (PIPE, None):
+        last_stdout.close()
 
 
 def subproc_captured(*cmds):


Test patch:
Repository: xonsh/xonsh

Issue:
inconsistent tilde (~) handling
On Windows, handling of tilde (`~`) expansion is inconsistent.  xonsh seems to expand tilde correctly (to the user's home directory) for its builtin functions such as `cd ~`.

Windows commands perform no tilde expansion, so for example, doing `move foobar.txt ~` results in renaming the file `foobar.txt` to a file named `~` in the current directory.

Unix commands ported to Windows in the msysGit suite (e.g. `cp`, `mv`) perform their own tilde expansion.  Unfortunately, they expand tilde to the location where msysGit is installed.

To summarize: on windows there are currently 3 different behaviors of tilde expansion.  It seems like this could be cleaned up if on Windows xonsh always performed tilde expansion of all arguments in subprocess mode.  Does this seem like a valid way to proceed?



Discussion:
This seems to happen on GNU/Linux as well, so I don't think it is specific to Windows.  I think your suggestion is the right way.  Right now, the expansion is happening at a weird time, so that single characters never get expanded (`cd` only works because it also handles the `~` character itself (it never gets expanded to the user's home)).

That expansion is currently happening [here](https://github.com/scopatz/xonsh/blob/master/xonsh/parser.py#L2299-2309), but it should probably be moved someplace else, after we have the full `subproc_atom` (maybe in `p_subproc_atom`, [here](https://github.com/scopatz/xonsh/blob/master/xonsh/parser.py#L2262-2263)?).  I'm happy to make the change myself, or to help if you want to tackle it.

I haven't looked into the parser at all yet so it's probably best if you take this one.


Resolving patch:
diff --git a/xonsh/parser.py b/xonsh/parser.py
--- a/xonsh/parser.py
+++ b/xonsh/parser.py
@@ -2260,6 +2260,7 @@ def p_subproc_atom(self, p):
                                     col=self.col)
                     p0._cliarg_action = 'extend'
                 else:
+                    p0.s = os.path.expanduser(p0.s)
                     p0._cliarg_action = 'append'
             elif isinstance(p1, ast.AST):
                 p0 = p1
@@ -2305,7 +2306,7 @@ def p_subproc_arg(self, p):
         if len(p) == 2:
             p0 = p1
         else:
-            p0 = os.path.expanduser(p1 + p[2])
+            p0 = p1 + p[2]
         p[0] = p0
 
     def p_subproc_arg_part(self, p):


Test patch:
Repository: xonsh/xonsh

Issue:
Vim refuses to come back to foreground with fg
https://asciinema.org/a/0qa0ncj2izljo0oyr9wn3pi2u

When inside of vim, CTRL+Z works fine, however running the `fg` command fails, giving me the following output : 

```
*[1] running: vim (15707)

*[1] stopped: vim & (15707)
```

Running on archlinux.
Xonsh version : 0.1.6
Vim version : 7.4.729



Discussion:
Thanks for reporting this, @roblabla!

Not sure exactly what's going on, but I am able to reproduce this here.  I'll take a look when I have a chance.

I haven't had a chance to look too deeply into this yet, but this also happens with emacs (for those who are on the other side), though I haven't noticed this behavior with any programs aside from those two.

By now, I know a couple of "almost" fixes, but I am still working on something robust.


Resolving patch:
diff --git a/xonsh/jobs.py b/xonsh/jobs.py
--- a/xonsh/jobs.py
+++ b/xonsh/jobs.py
@@ -19,7 +19,7 @@
 
 if ON_WINDOWS:
     def _continue(obj):
-        pass
+        return None
 
 
     def _kill(obj):
@@ -33,7 +33,7 @@ def ignore_sigtstp():
     def _set_pgrp(info):
         pass
 
-    def wait_for_active_job():
+    def wait_for_active_job(signal_to_send=None):
         """
         Wait for the active job to finish, to be killed by SIGINT, or to be
         suspended by ctrl-z.
@@ -58,7 +58,7 @@ def wait_for_active_job():
 
 else:
     def _continue(obj):
-        os.kill(obj.pid, signal.SIGCONT)
+        return signal.SIGCONT
 
 
     def _kill(obj):
@@ -91,7 +91,7 @@ def _give_terminal_to(pgid):
             signal.pthread_sigmask(signal.SIG_SETMASK, oldmask)
 
 
-    def wait_for_active_job():
+    def wait_for_active_job(signal_to_send=None):
         """
         Wait for the active job to finish, to be killed by SIGINT, or to be
         suspended by ctrl-z.
@@ -107,7 +107,13 @@ def wait_for_active_job():
         pgrp = job['pgrp']
         obj.done = False
 
-        _give_terminal_to(pgrp)  # give the terminal over to the fg process
+        # give the terminal over to the fg process
+        _give_terminal_to(pgrp)
+        # if necessary, send the specified signal to this process
+        # (this hook  was added because vim, emacs, etc, seem to need to have
+        # the terminal when they receive SIGCONT from the "fg" command)
+        if signal_to_send is not None:
+            os.kill(obj.pid, signal_to_send)
         _, s = os.waitpid(obj.pid, os.WUNTRACED)
         if os.WIFSTOPPED(s):
             obj.done = True
@@ -235,7 +241,7 @@ def fg(args, stdin=None):
     job['bg'] = False
     job['status'] = 'running'
     print_one_job(act)
-    _continue(job['obj'])
+    wait_for_active_job(_continue(job['obj']))
 
 
 def bg(args, stdin=None):
@@ -265,4 +271,4 @@ def bg(args, stdin=None):
     job['bg'] = True
     job['status'] = 'running'
     print_one_job(act)
-    _continue(job['obj'])
+    wait_for_active_job(_continue(job['obj']))


Test patch:
Repository: xonsh/xonsh

Issue:
xonsh dies if the prompt raises an exception
If a function in the prompt raises an exception, it kills xonsh. I would expect the error to be displayed, but not kill the shell. 



Discussion:
Yup, agreed.  This should be an easy fix.


Resolving patch:
diff --git a/xonsh/base_shell.py b/xonsh/base_shell.py
--- a/xonsh/base_shell.py
+++ b/xonsh/base_shell.py
@@ -102,12 +102,19 @@ def prompt(self):
         """Obtains the current prompt string."""
         if self.need_more_lines:
             if self.mlprompt is None:
-                self.mlprompt = multiline_prompt()
+                try:
+                    self.mlprompt = multiline_prompt()
+                except Exception:
+                    _print_exception()
+                    self.mlprompt =  '<multiline prompt error> '
             return self.mlprompt
         env = builtins.__xonsh_env__
         if 'PROMPT' in env:
             p = env['PROMPT']
-            p = format_prompt(p)
+            try:
+                p = format_prompt(p)
+            except Exception:
+                _print_exception()
         else:
             p = "set '$PROMPT = ...' $ "
         self.settitle()


Test patch:
Repository: xonsh/xonsh

Issue:
Can't type literal tab with prompt_toolkit
In bash or zsh I would typically type `Ctl-V TAB` to insert a literal tab, however, when using prompt_tookitas my shell type this simply tries to do tab completion and there doesn't seem to be a way to create a literal tab.



Discussion:
I forgot to mention that I'm running Python 3.5.0 on Manjaro LInux
`Linux kommandcenter 3.19.8.7-1-MANJARO #1 SMP PREEMPT Fri Sep 25 18:20:07 UTC 2015 x86_64 GNU/Linux`

With readline, you can type Shift+Tab to get a literal tab.  Not sure about prompt-toolkit, though it seems like there definitely should be a way to do this.


Resolving patch:
diff --git a/xonsh/prompt_toolkit_key_bindings.py b/xonsh/prompt_toolkit_key_bindings.py
--- a/xonsh/prompt_toolkit_key_bindings.py
+++ b/xonsh/prompt_toolkit_key_bindings.py
@@ -32,3 +32,11 @@ def _(event):
         indent instead of autocompleting.
         """
         event.cli.current_buffer.insert_text(env.get('INDENT'))
+
+    @handle(Keys.BackTab)
+    def insert_literal_tab(event):
+        """
+        Insert literal tab on Shift+Tab instead of autocompleting
+        """
+        event.cli.current_buffer.insert_text(env.get('INDENT'))
+


Test patch: