Execution of cobrawap init command from a non-interactive environment #96
Description
When executing Cobrawap in an environment which does allow the user to directly interact with the underlying shell, a few standard cobrawap commands may become cumbersome to deal with. A typical example is the execution of Cobrawap from a Jupyter Notebook, a situation becoming more and more frequent after the inclusion of Cobrawap within the EBRAINS Software Distribution (ESD).
In the specific case of cobrawap init command, for example:
cobrawap init --output_path "/path/to/output/folder" --config_path "/path/to/config/folder"
if at least one of the two paths above has already been set in the ~/.cobrawap/config file, or pipeline_path or stages list, then for each of them the prompt will ask the user if really wanting to overwrite the existing settings (default behavior is No).
In addition, if the linked path to the directory with config files already exists and is not empty, then the user is asked if wanting to overwrite the existing config files with the template ones (again, default behavior is No).
It would be useful to have this interaction with the user via the prompt to be switched off when needed, e.g. via the introduction of a --force-overwrite flag for the cobrawap init command, forcing the overwriting of the four settings above: output_path, config_path, pipeline_path, and stages.
However, caution should be posed at the behavior expected for config files: in this case, if the user linked config_path to a specific non-empty folder, then existing config files should not be replaced by template ones, as very likely that is not what the user meant. In my opinion, in this case the forced behavior should be 'No'.