LIU-444: Add new Bash shell parsing approach.

[myxie]

JIRA Ticket

LIU-444

Type

• Feature (addition)
• Bug fix
• Refactor (change)
• Documentation

Problem/Issue

The current approach to managing BashShellApp command parsing is obfuscated and quite confusing. We both hard-code the port numbers of each in put in the bash command (e.g. "ls -l %i0 > %o0 ", where i0 is the 1st input/o0 is the 1st output) whilst also not having any knowledge of which port would be the first, second, third when translating.

It is also hard to understand how to perform redirection in the graph as we have a number of different redirection options. It would be great to replace this approach with a simplified way way of constructing the inputs/outputs, and the redirection.

Solution

This PR removes the redirection whilst replace all input/outputs with "%input_name%" options.

Here, %recursive% is a reference to the recursive parameter in the component (which is 'False').

Checklist

• Unittests added
  • Reason for not adding unittests (remove this line if added)
• Documentation added
  • Will be re-writing introductory documentation and will update accordingly soon.

Summary by Sourcery

Tests:

• Update tests to reflect changes in Bash shell application execution.

[coveralls]

coverage: 78.596%. remained the same
when pulling 80be514 on LIU-444
into 927717d on master.

[myxie]

Hi @awicenec, may you please review this PR when you have the time?

[myxie]

Set of instructions we discussed to produce replacement a la f-strings style:

>>> of = "my file" 
>>> s = "dd {of}"
>>> eval('f"'+s+'"')
>> 'dd my file'

I believe the issue with this approach is we do not have the actual variable names specified; they are keys in the dictionary, so we would have to construct variables dynamically and then perform the eval.

[myxie]

@awicenec to clarify - I think we can definitely replace the '%' with '{}' if you'd prefer that, so that it matches similar projects (e.g. Stimela); I just don't think we can do it with the eval.