Metakernel not instantiating because of shell magic.

[fred441a]

Hi, I have an issue with metakernel in Octave kernel.

when i run

$ python -m octave_kernel.check

it stalls when instantiating the octave kernel.
output:

Octave kernel v0.36.0
Metakernel v0.30.2
Python v3.12.7 (main, Oct  1 2024, 02:05:46) [GCC 13.3.0]
Python path: /nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/bin/python3.12

Connecting to Octave...

When i then interrupt the process it always throws the same error.

^CTraceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/octave_kernel/check.py", line 14, in <module>
    o = OctaveKernel()
        ^^^^^^^^^^^^^^
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/metakernel/process_metakernel.py", line 53, in __init__
    MetaKernel.__init__(self, *args, **kwargs)
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/metakernel/_metakernel.py", line 167, in __init__
    self.reload_magics()
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/metakernel/_metakernel.py", line 766, in reload_magics
    module.register_magics(self)
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/metakernel/magics/shell_magic.py", line 114, in register_magics
    kernel.register_magics(ShellMagic)
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/metakernel/_metakernel.py", line 772, in register_magics
    magic = magic_klass(self)
            ^^^^^^^^^^^^^^^^^
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/metakernel/magics/shell_magic.py", line 16, in __init__
    self.start_process()
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/metakernel/magics/shell_magic.py", line 64, in start_process
    self.repl = bash()
                ^^^^^^
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/metakernel/replwrap.py", line 317, in bash
    return REPLWrapper(child, prompt_regex, prompt_change_cmd,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/metakernel/replwrap.py", line 99, in __init__
    self._expect_prompt()
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/metakernel/replwrap.py", line 131, in _expect_prompt
    pos = self.child.expect(expects, timeout=timeout)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/pexpect/spawnbase.py", line 354, in expect
    return self.expect_list(compiled_pattern_list,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/pexpect/spawnbase.py", line 383, in expect_list
    return exp.expect_loop(timeout)
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/pexpect/expect.py", line 169, in expect_loop
    incoming = spawn.read_nonblocking(spawn.maxread, timeout)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/pexpect/pty_spawn.py", line 500, in read_nonblocking
    if (timeout != 0) and select(timeout):
                          ^^^^^^^^^^^^^^^
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/pexpect/pty_spawn.py", line 450, in select
    return select_ignore_interrupts([self.child_fd], [], [], timeout)[0]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/03shgnhh9yynhqdqlyqpn6aac962aisa-python3-3.12.7-env/lib/python3.12/site-packages/pexpect/utils.py", line 143, in select_ignore_interrupts
    return select.select(iwtd, owtd, ewtd, timeout)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
KeyboardInterrupt

I thought this might be due to Nix putting my binaries in weird directories so i soft linked ( copied ) my bash binary to /bin/bash and /usr/bin/bash. This did not work or change anything. However, bypassing all magic by adding

def register_magics(self, magic_klass):
    return []

to the OctaveKernel class in kernel.py in octave kernel "fixed" the issue, by removing all the magic :(.

I can see the metakernel uses the which() function to find the correct paths to bash from the user environment, so now i am at a little bit of a loss as to how I could fix this issue (or even where/what the issue is). Any help hints or comments would be appreciated.

to reproduce

1. install nix

sh <(curl -L https://nixos.org/nix/install) --daemon

2. enable flakes

echo experimental-features = nix-command flakes >> /etc/nix/nix.conf

or

echo experimental-features = nix-command flakes >> ~/.config/nix/nix.conf

3. Enter my development environment

nix develop github:fred441a/octave_kernel

4. run the python check

python -m octave_kernel.check

[fred441a]

Sorry, fixed it by installing bashInteractiveFHS