17 merge tesia and victors changes into concerto

[djinnome]

This adds vtcode and victor_files_n_codes. The most recent version is vtcode. We will clean this up before merging into main.

vtcodes needs to be merged with victor_files_n_codes first, but because these are notebooks, merging will be challenging.

[djinnome]

• biolog_files : carbon_biolog.csv does not exist/unclear what information it's suppose to contain, but otherwise successfully runs locally
• check-if to files... : relative filepaths (..\victor_files_n_codes\Check_if_two_files_contain_same_metabolites\PreBiologFile_Rep1_M2.csv) generating FileNotFound Error
  • tried [import os, current_dir = os.getcwd()] solution from saturncloud, but otherwise successfully runs locally

[tiekneeshrimp]

• create_community_model... ; we never went over this together because gapfill model was still being worked on for this
• generate_carveme ; ^ same as above
• generate_rich_media ; relative filepaths to model (../victor_files_n_codes/Generation_of_rich_media_csv_file/updated_modelcsc031FixedCompartments.xml) generates FileNotFound error, otherwise runs locally
• CarveMe_Codes ; new to me but relative filepaths to model (csc031/data/growth/biolog_carbon_microbacterium.csv) won't work. From what I understand, this data doesn't get updated thought. .csv file in github csc031-gem folder
• PSAMM_reaction_count : also new to me, but I think it's less relevant than CarveMe?