Prep 0.1.3

[johaGL]

• args: multiple modifications:
  • change: no more positional argument --> -cf
  • change: type_of_file --> -tf
  • change: targetedMetabo_path --> -lm
  • changed default of --alternative_div_amount_material, to True
  • NEW: --div_isotopologues_by_amount_material
  • NEW: --fractions_stomp_values
  • NEW: -ox (the extension of the output files (csv|tsv|txt))
  • deleted: isosprop_stomp_values
  • deleted: meanenrich_or_fracfontrib_stomp_values
  • deleted: auto_drop_metabolite_LOD_based
• add logger
• refactored code: class CompositeData (new)
• refactored functions in tidy and utils (solves repeated code/functions #9 )
• new: supports style of input: variableMetadata + isotopologues_dataMatrix (both in .tsv), solves support dataMatrix + variableMetadata as input for TraceGroomer #10
• automatically imports samples metadata with .tsv and .csv extensions
• add unittests (solves only one unitary test? #11 )

Note: new examples in Zenodo: new link in Wiki

[johaGL]

Also added new arg -ox for handling the output file extension, hopefully this will solve the issue 7, this will need verification from the Galaxy devs with the new release 0.1.3 to check if the issue gets solved or not.