Version 0.1.0

[PedroBarbosa]

Significant improvements over the first stable version.

• Implementation of a grammar based on motifs represented as PWMs. As for now, only random perturbations were allowed throughout evolution. With the new grammar (which can be set via --which_grammar motif_based), perturbations are restricted to regions of motifs of known RNA-binding proteins. Closed Motif-based grammar  #2
• Added motif_ablation and motif_substitution to the motif_based grammar, which differs from motif_insertion of motif_deletion by the fact that sequence length remains unaltered with the perturbation.
• Motif scanning using FIMO, biopython utilities or just plain search is now implemented.
• Motif enrichment used STREME implemented.
• Added option --shuffle_input. Different shuffling modes were incorporated, which take into account specific regions of the search space, according to --acceptor_untouched_range, --donor_untouched_range and untouched_regions. This is very useful to do in silico experiments for model debugging.
• Modified the structure of a Dataset to include the original (wt) sequence in the first row.
• Additional tests were added, and a GitHub actions workflow was included for running pytest at each push and pull request at the main branch.