Remaining refactoring

[snurk]

• TODO and FIXMes
• Rename Bin_ini/Merged_bin
• Create folder for the raw cog graph components
• Rename COGs_annotation.snake
• Check that tmp folders are cleaned
• Remove not up-to-date requirements files (e.g. requirements.txt)
• Move bins_to_merge to Merged_Bins

[Sebastien-Raguideau]

I started a new branch to look at that : refactoring_#64

• TODO and FIXMes : let's discuss them in the pull request.
• ~Rename Bin_ini/Merged_bin~ : Bin_ini/Merged_bin > bin_init, bin_merged
• ~Create folder for the raw cog graph components~ : subgraphs are now created at subgraphs/bin_init/raw_subgraphs
• ~Rename COGs_annotation.snake~ : --> cogs_annotation.snake
• Check that tmp folders are cleaned
• ~Remove not up-to-date requirements files (e.g. requirements.txt)~ done
• Move bins_to_merge to Merged_Bins : not sure but I think this is done? we have one in both bin_init and bin_merged.

[chrisquince]

OK but maybe start it from master after accepting my Debug pull request?

[chrisquince]

Otherwise it will just have a load of bugs in?

[Sebastien-Raguideau]

Too late, so I'll just copy (cherrypick) your commits to my branch.