Global configuration options

Global options are available to configure some of the library behaviour. Functions that depend on any of these options will be tagged with:

Note

Depends on option_class.option_id.

Currently available options

Option Class Option ID Description
system overwrite Allow overwriting already existing files
system output Default folder to output generated files
system cpu Available CPU for multiprocessing
rosetta path Path to the rosetta binaries
rosetta compilation Target binaries of rosetta

There are two ways of altering the values of these global options:

In Code

This approach can be taken during the development of a script. Has the advantages that:

  1. Allows to change the values of the global variables at different points of the script.
  2. Global option changes are visible for anyone checking the script.
  3. Transferred script will behave in the same manner.

On code changes can be called through set_option() to target individual options or by loading an option file with set_options_from_YAML() or set_options_from_JSON(). In these to cases, being yaml or json format, the structure is of a dictionary of dictionaries, being option_class the first level of keys and option_id the second.

Full description of all the functions that allow access to the global variables can be find in the libconfig API

Example: Allowing overwrite of previously generated files.

In [1]: import rstoolbox.core as rc
   ...: rc.set_option('system', 'overwrite', True)
   ...:

Globally

After the first execution of rstoolbox, a configuration file ~/.rstoolbox.cfg is generated in the user’s home folder.

Everytime the library is loaded after that, it checks on that file to see the user’s particular configuration. Thus, by changing the default parameters in that file, the user can set up global configurations.

Logically, this might change some behaviour between different users, but excludes the need of set up some options (like executable paths) every time.

Example: How a configuration file might look like (MacOS).

rosetta:
  compilation: macosclangrelease
  path: /Volumes/MiniTwo/bin/Rosetta/main/source/bin/
system:
  output: ./
  overwrite: false