take into account alternate sysroot for /bin/bash used by run_cmd

[casparvl]

EasyBuild's run_cmd runs commands in a subshell. The shell used is defined in the exec_cmd. However, in context where the use of a sysroot is configured, one would want to use <sysroot>/bin/bash instead. This PR implements that change. Note that since run_cmd is also called a few times before set_up_configuration is called, we need to be able to disable the check for the build_option('sysroot') for those instances (similar to how this is already don for build_option('hooks')).

Solves this issue.

Edit: hmmm, I made this PR, and then realized, this is probably one of the components that is very different in EB 5.0. And it seems to be indeed...

Someone with more EB 5.0 knowledge needs to give me a pointer of how to fix this for EB 5.0 :)

[casparvl]

Ok, this issue actually does not exist for EB 5.0: the whole run_cmd is now replaced by run_shell_cmd, and that has a different way of determining the shell command. See this piece of code:

    # use bash as shell instead of the default /bin/sh used by subprocess.run
    # (which could be dash instead of bash, like on Ubuntu, see https://wiki.ubuntu.com/DashAsBinSh)
    # stick to None (default value) when not running command via a shell
    if use_bash:
        bash = shutil.which('bash')
        _log.info(f"Path to bash that will be used to run shell commands: {bash}")
        executable, shell = bash, True
    else:
        executable, shell = None, False

at least for EESSI, the result is that the bash from the prefix is used. That means our issue no longer exists. I'm closing this PR, as it is not relevant.

[boegel]

@casparvl As discussed, I think it's worth considering this to be merged into develop, since there's a (small) window of opportunity to get this included in EasyBuild v4.9.4 (which we'll be releasing because of a bug that was introduced in the GCC easyblock, see here).

I'll take a thorough look into this right now...

[boegel]

lgtm