Moved the printing of input variables from dockonsurf.py to dos_input.py
Created specific module for the reading of command-line arguments and transferred the relevant commands into it
Included tests to the implemented functions to check new commits don't mess things up
Refactor file dos_input.py, every option is read and checked its value with a specific function for the purpose.Included the possibility to run the file as standalone program.
Added empty init file to ease importing modules
Increase of the input errors that get caught by the program, change how the logger is setup, its message format and how it is organized internally.
Reformat files and extend documentation
Moved the input file option from 'Global' to each relative section and changed the values of options to non-default ones.
Include errors in the log, improved error handling by catching new errors.
Written the docstrings to document the code following the PEP 257 conventions
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