Include input-directory path option in argparser

[bobleesj]

Problem

All outputs are saved in the current working directory where the script is executed, making it difficult to tests via pytest (we want to use tmpdir)

Proposed solution

Like in diffpy.snmf , allow the user to set the output directory.

    parser.add_argument(
        "-o",
        "--output-directory",
        type=str,
        help="The directory where the results will be written. Defaults to '<input_directory>/snmf_results'.",
    )

[sbillinge]

sounds good. Please don't change any default behaviors because this is actually deployed in the cloud and we don't currently release this, though we could. Presumably any changes to the defaults will break the online deployment.

We originally thought that releasing it would compete with our online offering, but probably it doesn't....different people probably want to use it in different forms.

[bobleesj]

Fully noted - will maintain existing behaviors.