The reason I have files end in _file and directories end in _directory is that this way the output .yml of every stage / of the entire pipeline has either paths where the keys end in _file or _directory, otherwise values.
This potentially facilitates IO at the end, e.g. in the webserver.
For the above case, I would change from model_file_X to model_X_file
I noticed we have this: https://github.com/sacdallago/bio_embeddings/blob/develop/bio_embeddings/utilities/defaults.yml#L63 which slipped my attention at the review stage.
The reason I have files end in _file and directories end in _directory is that this way the output .yml of every stage / of the entire pipeline has either paths where the keys end in _file or _directory, otherwise values.
This potentially facilitates IO at the end, e.g. in the webserver.
For the above case, I would change from
model_file_Xtomodel_X_file