config.yaml in small walkthrough example about casanovo HOT 5 CLOSED

Currently, when no config file is given, the code tries to find a default config file in the same directory as the script. If we don't package a (fully functional) config file with Casanovo, this doesn't make a lot of sense imo.

We could:

• Include a default config file. It might be a bit challenging to come up with sensible default values for all options, but it's probably possible.
• Change the code so that it gives a more informative error message, rather than look for a non-existing file.
• In each case, update the documentation accordingly so that this is more clearly described.

from casanovo.

I updated the tutorial to tell the user how to make their own config file. However, a default already exists and it is supposed to be accessed with these lines:

if config_path == None:
        abs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'config.yaml')
        with open(abs_path) as f:
            config = yaml.safe_load(f)

You can see the file here: https://github.com/Noble-Lab/casanovo/blob/main/casanovo/config.yaml

from casanovo.

There are two problems with the default config file:

• It's not packaged along with the source code, so will not be available by default after installing with pip.
• It does not always work out of the box (i.e. fails if you don't have a GPU). Especially when the config file is hidden in some internal package directory, this is challenging for people to find and modify.

from casanovo.

How can I modify the repo so that the config.yaml is packaged and placed in its proper place with a pip install? I'll also update the default values.

from casanovo.

You have to specify non-Python files you want included using a MANIFEST.in file.

from casanovo.