snakefmt moves interspersed comments

[hepcat72]

I intentionally changed some triple quoted shell strings to separate concatenated strings so that I could intersperse comments, but even though the code works, snakefmt moved the comments to the beginning and end.

Desired (note the space between the + and the "):

    shell:
        # Concatenate all the files together
        "cat {input:q} 2> {log.cat:q} | "
        # Coordinate sort everything
        + "sortBed 2> {log.sort:q} | "
        # Merge overlapping coordinates into individual expanded records
        + "mergeBed 2> {log.merge:q} 1> {output:q}"

snakefmt's munge:

    shell:
        # Concatenate all the files together
        "cat {input:q} 2> {log.cat:q} | "

        +"sortBed 2> {log.sort:q} | "

        +"mergeBed 2> {log.merge:q} 1> {output:q}"
        # Coordinate sort everything
        # Merge overlapping coordinates into individual expanded records

It also requires that the + be at the beginning of the next line and won't let them be at the end. If they are at the end, it gived a confusing syntax error.

Desired:

    shell:
        # Concatenate all the files together
        "cat {input:q} 2> {log.cat:q} | " +
        # Coordinate sort everything
        "sortBed 2> {log.sort:q} | " +
        # Merge overlapping coordinates into individual expanded records
        "mergeBed 2> {log.merge:q} 1> {output:q}"

snakefmt error:

snakefmt.exceptions.InvalidPython: Black error:
Cannot parse: 17:35: "cat {input:q} 2> {log.cat:q} | " +

How can I intersperse comments in multi-line shell strings without snakefmt moving them?

[mbhall88]

This is related to #129

[mbhall88]

I am working on a fix for this at the moment but I wanted to say two things here first while they are fresh in my mind.

Firstly, the + at the beginning of the line, followed by the spaces being removed around it, is expected behaviour as this is a unary operator and thus PEP8 says there should not be a space between it and the value (see here for a discussion about this on the black github repo. You should just be able to remove the +).
Second, the second example fails as this is not valid python (as the error suggests).

Hopefully I will have a fix for the interspersed comments soon. Thanks for the very long patience/wait on this.