[feature] : Handle different configurations

[ns-rse]

Is your feature request related to a problem?

As I've started work on @LaiaPasquina AFMSlicer translation I would like the ability to write a configuration file for this particular workflow. That currently isn't possible with io.write_config_with_comments() it pulls the config_path from resources.files(__package__) / "[simple_config,default_config].yaml" which will always be TopoStats.

Describe the solution you would like.

We should add an additional option to io.write_config_with_comments() which indicates the type of pipeline we are running and in turn where the configuration is loaded from so that a configuration file is loaded from that package. A similar approach would benefit "PerovStats" and make TopoStats a more flexible package that others can build on.

Describe the alternatives you have considered.

Copying and pasting the functions into new/other packages.

Additional context

No response

[ns-rse]

Actually on-rereading we already have this in place partially but it expects the configuration file to live within TopoStats and not any other package.

This isn't optimal or useful for developers of packages which extend TopoStats so we should revised this.

Currently we have...

    if args.config is None or args.config == "default":
        if args.simple:
            config_path = resources.files(__package__) / "default_config.yaml"
        else:
            config_path = resources.files(__package__) / "default_config.yaml"
        config = config_path.read_text()
    elif args.config == "topostats.mplstyle":
        config = (resources.files(__package__) / "topostats.mplstyle").read_text()
        logger_msg = "A sample matplotlibrc parameters file has been written to"
    # Otherwise we have scope for loading different configs based on the argument, add future dictionaries to
    # topostats/<sample_type>_config.yaml
    else:
        try:
            config = (
                resources.files(__package__) / f"{args.config}_config.yaml"
            ).read_text()
        except FileNotFoundError as e:
            raise UserWarning(
                f"There is no configuration for samples of type : {args.config}"
            ) from e

What I envisage is something along the lines of...

import pkgutil
...
    if args.config is None or args.config == "default" or args.config == "topostats:
        if args.simple:
            config_path = resources.files(__package__) / "default_config.yaml"
        else:
            config_path = resources.files(__package__) / "default_config.yaml"
        config = config_path.read_text()
    elif args.config == "topostats.mplstyle":
        config = (resources.files(__package__) / "topostats.mplstyle").read_text()
        logger_msg = "A sample matplotlibrc parameters file has been written to"
    # Otherwise we have scope for loading different configs based on the argument, add future dictionaries to
    # topostats/<sample_type>_config.yaml
    else:
        try:
            config = pkgutil.get_data(package = args.config, resource="default_config.yaml")
        except FileNotFoundError as e:
            raise UserWarning(
                f"There is no configuration for samples of type : {args.config}"
            ) from e

Need to check what pkgutil.get_data() returns though but suspect it is the file contents that we can then write to disk.