gsrap 0.9.0__py3-none-any.whl → 0.10.1__py3-none-any.whl

gsrap/parsedb/parsedb.py

@@ -1,6 +1,7 @@
 import os
 import pickle
 from importlib import resources
+import shutil
 
 
 import cobra
@@ -15,7 +16,6 @@ from ..commons import introduce_universal_biomass
 from ..commons import write_excel_model
 from ..commons import show_contributions
 from ..commons import adjust_biomass_precursors
-from ..commons import count_undrawn_rids
 from ..commons import count_undrawn_rids_focus
 
 from ..commons import format_expansion
@@ -49,13 +49,20 @@ from .cycles import verify_egc_all
 def main(args, logger):
     
     
-    ###### FORMAT ARGS NOT REQUIRING RESOURCES
+    
+    ###### PRE-PARSING
+    
     # adjust out folder path                      
     while args.outdir.endswith('/'):              
         args.outdir = args.outdir[:-1]
     os.makedirs(f'{args.outdir}/', exist_ok=True)
     
     
+    # prepare empty logs folder
+    shutil.rmtree(f'{args.outdir}/logs', ignore_errors=True)
+    os.makedirs(f'{args.outdir}/logs', exist_ok=True)
+    
+    
     # check compatibility of input parameters
     if args.progress==False and args.module==True: 
         logger.error(f"You cannot ask --module without --progress (see --help).")
@@ -81,8 +88,6 @@ def main(args, logger):
     if args.onlyauthor == '-': args.onlyauthor = None
     
     
-    
-    ###### LOAD LOCAL RESOURCES
     # check and extract the required 'gsrap.maps' file
     if os.path.exists(f'{args.inmaps}') == False:
         logger.error(f"File 'gsrap.maps' not found at {args.inmaps}.")
@@ -105,152 +110,157 @@ def main(args, logger):
         with open(asset_path, 'rb') as handle:
             kegg_reaction_to_others = pickle.load(handle) 
             
-            
-            
-    ###### FORMAT/CHECK FOCUSING ARGS
+                        
     # format the --eggnog param
     args.eggnog = format_expansion(logger, args.eggnog)  # now 'args.eggnog' could still be '-'
     
+    
     # check the --taxon param
     if args.taxon != '-':
         response = check_taxon(logger, args.taxon, idcollection_dict)
         if response == 1: return 1
     
+    
     # get the kegg organism if requested
     if args.keggorg != '-':
         response = download_keggorg(logger, args.keggorg, args.outdir)
         if response == 1: return 1
     
     
-    
-    # DOWNLOAD ONLINE RESOURCES
-    # get dbuni and dbexp:
-    logger.info("Downloading gsrap database...")
-    response = get_databases(logger)
+    # download dbuni, dbexp and lastmap:
+    logger.info("Downloading updated gsrap assets...")
+    response = get_databases(logger, map_id=args.focus)
     if type(response)==int: return 1
     else: dbuni, dbexp, lastmap = response
     
+    
+    
+    ###### PARSING
 
     # show simple statistics of contributions
     response = show_contributions(logger, dbuni, args.goodbefore)
     if response == 1: return 1
-                                    
-        
     
-    ###### RECONSTRUCTION
+    
     # create the model
     universe = cobra.Model('universe')   
-    logger.info("Parsing gsrap database...")
     
-    # introduce M / R / T
-    universe = introduce_metabolites(logger, dbuni, universe, idcollection_dict, kegg_compound_to_others, args.goodbefore[0], args.onlyauthor)
+    
+    # introduce M 
+    universe = introduce_metabolites(logger, dbuni, universe, idcollection_dict, kegg_compound_to_others, args.outdir, args.goodbefore[0], args.onlyauthor)
     if type(universe)==int: return 1
-    universe = introduce_reactions(logger, dbuni, universe, idcollection_dict, kegg_reaction_to_others, args.goodbefore[1], args.onlyauthor)
+
+
+    # introduce R
+    universe = introduce_reactions(logger, dbuni, universe, idcollection_dict, kegg_reaction_to_others, args.outdir, args.goodbefore[1], args.onlyauthor)
     if type(universe)==int: return 1
-    universe = introduce_transporters(logger, dbuni, universe, idcollection_dict, kegg_reaction_to_others, args.goodbefore[2], args.onlyauthor)
+
+
+    # introduce T
+    universe = introduce_transporters(logger, dbuni, universe, idcollection_dict, kegg_reaction_to_others, args.outdir, args.goodbefore[2], args.onlyauthor)
     if type(universe)==int: return 1
 
+
     # introduce sinks / demands (exchanges where included during T)
     universe = introduce_sinks_demands(logger, universe)
     if type(universe)==int: return 1
 
-    # introducce biomass
+
+    # introducce universal biomass
     universe = introduce_universal_biomass(logger, dbexp, universe)
     if type(universe)==int: return 1
 
 
-
-    ###### ANNOTATION
     # translate Gs to symbols and annotate them (EC, COG, GO, ...)
     universe = translate_annotate_genes(logger, universe, idcollection_dict)
     if type(universe)==int: return 1
 
-    # introduce collectionas (groups of Rs as maps/modules)
+
+    # introduce collections (groups of Rs as maps/modules)
     universe = set_up_groups(logger, universe, idcollection_dict)
     if type(universe)==int: return 1
 
 
     
-    # # # # #   PARSING ENDS HERE   # # # # #
+    ###### POST-PARSING
+    
+    # log metrics
     log_metrics(logger, universe)
+    
+    
+    # check absence of unbalancing above the threshold
     log_unbalances(logger, universe)
 
     
-    
-    ###### CHECKS 1
     # check universe completness
     df_C = check_completeness(logger, universe, args.progress, args.module, args.focus, args.taxon, args.eggnog, args.keggorg, idcollection_dict, summary_dict, args.outdir)
     if type(df_C)==int: return 1
 
 
-
-    ###### POLISHING 1
     # remove disconnected metabolites
     if args.keepdisconn == False:
         universe = remove_disconnected(logger, universe)   # can be commented when using booster.py
 
     
-    
-    ###### CHECKS 2
-    # check erroneous EGCs
-    verify_egc_all(logger, universe, args.outdir)
-    
+    # avoid time-consuming activities
+    if not args.justparse:
     
     
-    if not args.justparse:
+        # check erroneous EGCs
+        verify_egc_all(logger, universe, args.outdir)
+
         
-        ###### CHECKS 3
         # check growth on minmal media
-        df_G = grow_on_media(logger, universe, dbexp, args.media, '-', True)
+        df_G = grow_on_media(logger, universe, dbexp, args.media, fva=False, universe_in_parsedb=True)
         if type(df_G)==int: return 1
 
+    
         # check blocked biomass precursors
         cond_col_dict = adjust_biomass_precursors(logger, universe, universe, 1.0)
         df_E = precursors_on_media(logger, universe, universe, dbexp, args.media, cond_col_dict, args.precursors)
         if type(df_E)==int: return 1
 
+    
         # check blocked metabolites / dead-ends
         df_S = biosynthesis_on_media(logger, universe, dbexp, args.media, args.biosynth)
         if type(df_S)==int: return 1
 
 
-    
-        ###### POLISHING 2
-        # reset growth environment befor saving the model
+        # reset growth environment befor saving the model (changed during growth sims)
         gempipe.reset_growth_env(universe)
 
+        
         # initialize model
         response = initialize_model(logger, universe, dbexp, args.initialize, args.media)
         if response==1: return 1
 
 
-
-        ###### CHECKS 4
         # compute Memote metrics
         memote_results_dict = get_memote_results_dict(logger, universe)
 
 
-
-    # output the universe (even when --justparse)
+    # write JSON 
     logger.info("Writing universal model...")
     cobra.io.save_json_model(universe, f'{args.outdir}/universe.json')
     logger.info(f"'{args.outdir}/universe.json' created!")
     
     
+    # avoid time-consuming activities
     if not args.justparse:
         
-        # outptu in the remaining formats:
+        
+        # write XML
         cobra.io.write_sbml_model(universe, f'{args.outdir}/universe.xml')   # groups are saved only to SBML 
         logger.info(f"'{args.outdir}/universe.xml' created!")
         force_id_on_sbml(f'{args.outdir}/universe.xml', 'universe')   # force introduction of the 'id=""' field
+        
+        
+        # write XLSX
         sheets_dict = write_excel_model(universe, f'{args.outdir}/universe.parsedb.xlsx', args.nofigs, memote_results_dict, df_E, None, None, df_S, df_C)  
         logger.info(f"'{args.outdir}/universe.parsedb.xlsx' created!")
 
-
     
-    ###### CHECKS 4
-    # check if universal escher map is updated:
-    count_undrawn_rids(logger, universe, lastmap, args.focus)
+    # check if escher map is updated:
     if args.focus != '-':
         count_undrawn_rids_focus(logger, universe, lastmap, args.focus, args.outdir)
     

gsrap/parsedb/repeating.py

@@ -8,9 +8,13 @@ from .manual import get_rids_with_mancheck_balancing
 
 
 
-def check_gpr(logger, rid, row, kr_ids, idcollection_dict, addtype='R'): 
+def check_gpr(logger, rid, row, kr_ids, idcollection_dict, addtype, outdir): 
     
-    itemtype = 'Reaction' if addtype=='R' else 'Transporter'
+    
+    # define the itemtype:
+    if addtype=='R':
+        itemtype = 'Reaction' 
+    else: itemtype = 'Transporter'
     
     
     # check presence of the GPR
@@ -53,7 +57,8 @@ def check_gpr(logger, rid, row, kr_ids, idcollection_dict, addtype='R'):
             if ko_id not in ko_for_rid and ko_id != 'spontaneous' and ko_id != 'orphan':
                 if kr_id != 'RXXXXX':
                     if rid not in get_rids_with_mancheck_gpr():
-                        logger.debug(f"Ortholog '{ko_id}' should not be linked to reaction '{rid}' (available for {kr_ids}: {ko_for_rid}).")
+                        with open(f"{outdir}/logs/R.orthlink.txt", 'a') as f:
+                            print(f"Ortholog '{ko_id}' should not be linked to reaction '{rid}' (available for {kr_ids}: {ko_for_rid}).", file=f)
             
     
     # check if some ko_ids are missing from this reaction:
@@ -68,12 +73,79 @@ def check_gpr(logger, rid, row, kr_ids, idcollection_dict, addtype='R'):
                 
 
 
-def add_reaction(logger, model, rid, row, kr_ids, kegg_reaction_to_others, addtype='R'):
-    
+def check_rstring_arrow(logger, rid, row, addtype='R'):
     
     itemtype = 'Reaction' if addtype=='R' else 'Transporter'
     
     
+    if pnd.isna(row['rstring']): 
+        logger.error(f"{itemtype} '{rid}' has no definition (rstring).")
+        return 1
+    if ' --> ' not in row['rstring'] and ' <=> ' not in row['rstring']:
+        logger.error(f"{itemtype} '{rid}' has invalid arrow: '{row['rstring']}'.")
+        return 1
+        
+        
+    return 0
+
+
+
+def check_author(logger, mrid, row, db, addtype='R'): 
+    
+    
+    # define itemtype:
+    if addtype=='M':
+        itemtype = 'Metabolite'
+    elif  addtype=='R' :
+        itemtype = 'Reaction'
+    else: itemtype = 'Transporter'
+    
+    
+    # check if author was indicated:
+    if pnd.isna(row['curator']): 
+        logger.error(f"{itemtype} '{mrid}' has no curator.")
+        return 1
+    
+    
+    # check if the are valid authors
+    authors = set()
+    for author in row['curator'].split(';'):
+        author = author.strip()
+        authors.add(author)
+        if author not in db['curators']['username'].to_list(): 
+            logger.error(f"{itemtype} '{mrid}' has invalid curator: '{author}'.")
+            return 1
+    
+    
+    return list(authors)
+    
+    
+    
+def get_curator_notes(logger, row):
+    
+    
+    # notes are separated by ';'
+    notes = []
+    if pnd.isna(row['notes']) == False:
+        for i in row['notes'].strip().split(';'):
+            notes.append(i.strip())
+        if notes == ['-']:
+            notes = []
+        
+        
+    return notes
+    
+    
+    
+def add_reaction(logger, model, rid, authors, row, kr_ids, kegg_reaction_to_others, addtype, outdir):
+    
+    
+    # define the itemtype:
+    if addtype=='R':
+        itemtype = 'Reaction' 
+    else: itemtype = 'Transporter'
+    
+    
     # create a frash reaction
     r = cobra.Reaction(rid)
     model.add_reactions([r])
@@ -95,7 +167,8 @@ def add_reaction(logger, model, rid, row, kr_ids, kegg_reaction_to_others, addty
     # handle GPR
     r.gene_reaction_rule = row['gpr_manual'].strip()
     if r.gene_reaction_rule == 'orphan': 
-        r.gene_reaction_rule = ''    # don't want 'orphan' as artificial gene in adition to 'spontaneous'!
+        # don't want 'orphan' as artificial gene in adition to 'spontaneous'!
+        r.gene_reaction_rule = ''    
     r.update_genes_from_gpr()
     
     
@@ -105,22 +178,29 @@ def add_reaction(logger, model, rid, row, kr_ids, kegg_reaction_to_others, addty
             logger.error(f"Metabolite '{m.id}' appears in '{r.id}' but was not previously defined.")
             return 1
         
+        
+    # write curators as annotations
+    r.annotation['curator_codes'] = authors
+        
     
     # add annotations to model (same order of Memote)
     ankeys = [
         'rhea', 'kegg.reaction', 'seed.reaction', 'metanetx.reaction', 
         'bigg.reaction', 'reactome', 'ec-code', 'brenda', 'biocyc',         
     ]
+    #
     # initialize sets:
     for ankey in ankeys:
         if ankey == 'kegg.reaction': r.annotation[ankey] = set(kr_ids) - set(['RXXXXX'])
         else: r.annotation[ankey] = set()
+    #
     # populate sets:
     for kr_id in kr_ids:
         if kr_id != 'RXXXXX':
             if kr_id in kegg_reaction_to_others.keys():
                 for ankey in ankeys:
                     r.annotation[ankey].update(kegg_reaction_to_others[kr_id][ankey])
+    #
     # save as list: 
     for ankey in ankeys:
         r.annotation[ankey] = list(r.annotation[ankey])
@@ -133,6 +213,10 @@ def add_reaction(logger, model, rid, row, kr_ids, kegg_reaction_to_others, addty
         r.annotation['sbo'] = ['SBO:0000185']  # transport reaction
         
         
+    # add curator notes
+    r.annotation['curator_notes'] = get_curator_notes(logger, row)
+        
+        
     # check if unbalanced
     if r.check_mass_balance() != {}: 
         logger.error(f"{itemtype} '{r.id}' is unbalanced: {r.check_mass_balance()}.")
@@ -148,50 +232,3 @@ def add_reaction(logger, model, rid, row, kr_ids, kegg_reaction_to_others, addty
     
     
     return 0
-
-
-
-def check_rstring_arrow(logger, rid, row, addtype='R'):
-    
-    itemtype = 'Reaction' if addtype=='R' else 'Transporter'
-    
-    
-    if pnd.isna(row['rstring']): 
-        logger.error(f"{itemtype} '{rid}' has no definition (rstring).")
-        return 1
-    if ' --> ' not in row['rstring'] and ' <=> ' not in row['rstring']:
-        logger.error(f"{itemtype} '{rid}' has invalid arrow: '{row['rstring']}'.")
-        return 1
-        
-        
-    return 0
-
-
-
-def check_author(logger, mrid, row, db, addtype='R'): 
-    
-    
-    if addtype=='M':
-        itemtype = 'Metabolite'
-    elif  addtype=='R' :
-        itemtype = 'Reaction'
-    else: itemtype = 'Transporter'
-    
-    
-    if pnd.isna(row['author']): 
-        logger.error(f"{itemtype} '{mrid}' has no author.")
-        return 1
-    
-    authors = set()
-    for author in row['author'].split(';'):
-        author = author.strip()
-        authors.add(author)
-        if author not in db['authors']['username'].to_list(): 
-            logger.error(f"{itemtype} '{mrid}' has invalid author: '{author}'.")
-            return 1
-    
-    
-    return list(authors)
-    
-    
-    

gsrap/runsims/.ipynb_checkpoints/runsims-checkpoint.py

@@ -15,7 +15,8 @@ def main(args, logger):
     
     
     # get dbuni and dbexp:
-    response = get_databases(logger)
+    logger.info("Downloading updated gsrap assets...")
+    response = get_databases(logger, map_id=None)
     if type(response)==int: return 1
     else: dbuni, dbexp = response
 

gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py

@@ -44,7 +44,6 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
             continue
         # create dedicated column con the excel output
         df_G[f'{medium}'] = '/'
-        logger.debug(f"Growing on medium '{medium}'...")
                     
         
         # apply medium

gsrap/runsims/runsims.py

@@ -15,7 +15,8 @@ def main(args, logger):
     
     
     # get dbuni and dbexp:
-    response = get_databases(logger)
+    logger.info("Downloading updated gsrap assets...")
+    response = get_databases(logger, map_id=None)
     if type(response)==int: return 1
     else: dbuni, dbexp = response
 

gsrap/runsims/simplegrowth.py

@@ -44,7 +44,6 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
             continue
         # create dedicated column con the excel output
         df_G[f'{medium}'] = '/'
-        logger.debug(f"Growing on medium '{medium}'...")
                     
         
         # apply medium

{gsrap-0.9.0.dist-info → gsrap-0.10.1.dist-info}/METADATA

@@ -1,8 +1,9 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: gsrap
-Version: 0.9.0
+Version: 0.10.1
 Summary: 
 License: GNU General Public License v3.0
+License-File: LICENSE.txt
 Author: Gioele Lazzari
 Requires-Python: >=3.9
 Classifier: License :: Other/Proprietary License
@@ -12,9 +13,11 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Requires-Dist: biopython (>=1.80)
 Requires-Dist: cobra (>=0.29)
 Requires-Dist: colorlog (>=6.9.0)
+Requires-Dist: escher (>=1.8.1)
 Requires-Dist: gdown (>=5.2.0)
 Requires-Dist: gempipe (>=1.38.1)
 Requires-Dist: matplotlib (>=3.9.0)

{gsrap-0.9.0.dist-info → gsrap-0.10.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
-gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=8or3yeJRjjuaKUSWD5w3-I27LWKUF5hz9ECtzdQ_PKU,15583
-gsrap/__init__.py,sha256=8or3yeJRjjuaKUSWD5w3-I27LWKUF5hz9ECtzdQ_PKU,15583
+gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=OIblfpgppQI7PgC7Or9D4AmLsihTRdiuMUsGs2iiJ_A,15624
+gsrap/__init__.py,sha256=OIblfpgppQI7PgC7Or9D4AmLsihTRdiuMUsGs2iiJ_A,15624
 gsrap/assets/.ipynb_checkpoints/PM1-checkpoint.csv,sha256=0qjaMVG_t9aFxbHbxON6ecmEUnWPwN9nhmxc61QFeCU,8761
 gsrap/assets/.ipynb_checkpoints/PM2A-checkpoint.csv,sha256=rjYTdwe8lpRS552BYiUP3J71juG2ywVdR5Sux6fjZTY,8816
 gsrap/assets/.ipynb_checkpoints/PM3B-checkpoint.csv,sha256=42IGX_2O5bRYSiHoMuVKT-T-bzVj0cSRZBvGOrbnQMA,8130
@@ -9,35 +9,35 @@ gsrap/assets/PM2A.csv,sha256=rjYTdwe8lpRS552BYiUP3J71juG2ywVdR5Sux6fjZTY,8816
 gsrap/assets/PM3B.csv,sha256=42IGX_2O5bRYSiHoMuVKT-T-bzVj0cSRZBvGOrbnQMA,8130
 gsrap/assets/PM4A.csv,sha256=f_5__0Ap_T0KYje5h9veW29I2qB4yU0h7Hr7WpaHjSc,9081
 gsrap/assets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-gsrap/assets/kegg_compound_to_others.pickle,sha256=ddo1bdFSQOSmXJBuvsWWKSsFDWT_XOfV6ZG1BBj4-ew,8498114
-gsrap/assets/kegg_reaction_to_others.pickle,sha256=x53Ch8GjNWXHeqCF5wCPdANmi0ZxmhusYGNfDlk2ZpQ,1582568
+gsrap/assets/kegg_compound_to_others.pickle,sha256=BPjrr8Gmlqqj1ufCT_lWLmDJaZ0Iu8f_XS7KJU_gLck,8498114
+gsrap/assets/kegg_reaction_to_others.pickle,sha256=Gh4ANppTm_ZW-Hn-YE8EG87fMPt3EIVXk2YMZBerKqA,1763940
 gsrap/commons/.ipynb_checkpoints/__init__-checkpoint.py,sha256=9lrb0sBFSWEgV_e5FYzSgjTbam8b959rW_8VuxQHt1M,268
-gsrap/commons/.ipynb_checkpoints/biomass-checkpoint.py,sha256=4u7WBaUgo42tBoXDU1D0VUjICatb44e0jfswZrBeHYs,17987
+gsrap/commons/.ipynb_checkpoints/biomass-checkpoint.py,sha256=eJ2lej72mjDAibS7lQCFfN-L4inkaQ3lERe7K6-1E5o,18059
 gsrap/commons/.ipynb_checkpoints/coeffs-checkpoint.py,sha256=qI3_GuqHkeA2KbK9pYdkqJaFwYemAVZJGLRR4QtHt6w,19182
-gsrap/commons/.ipynb_checkpoints/downloads-checkpoint.py,sha256=JrVk-UbQzelefGvOz5k4j8Ofib58u_KD_zlUzTcuv6g,11170
-gsrap/commons/.ipynb_checkpoints/escherutils-checkpoint.py,sha256=VQ1FXyby6Cbfw3UNHzRoePH8M8owJ8E2rzB-11vBweA,3732
-gsrap/commons/.ipynb_checkpoints/excelhub-checkpoint.py,sha256=_LtaWripY_D99f14Yk-3v9VIov2cUGzJ53AXgmNFpUk,11457
+gsrap/commons/.ipynb_checkpoints/downloads-checkpoint.py,sha256=UKgFSPkxuxVWXoqrtZXEF42RR_KUjyoo_9wpCL-19X8,15908
+gsrap/commons/.ipynb_checkpoints/escherutils-checkpoint.py,sha256=4xtFsR-DDFsrYoDC6FIGZuLxQPLfNHoaE92RlnilunI,3747
+gsrap/commons/.ipynb_checkpoints/excelhub-checkpoint.py,sha256=h0TNzbjUiUQfXQrl7GRZlSc16GRzSRg3GJuwz9cXK78,11735
 gsrap/commons/.ipynb_checkpoints/figures-checkpoint.py,sha256=IRHSQXrCi4SQoISEfNB0rDhvUzbjcgsPi9zUSefsRto,4316
 gsrap/commons/.ipynb_checkpoints/fluxbal-checkpoint.py,sha256=jgC3-vI9Tbjvqohh2mJwFra4rl_pbUzHWrSa_QAxVO4,1262
 gsrap/commons/.ipynb_checkpoints/keggutils-checkpoint.py,sha256=M2nhHRiNH_xObHSxOIdt7ix59MrPdl9q3HNICC8X36M,4514
 gsrap/commons/.ipynb_checkpoints/logutils-checkpoint.py,sha256=VsnrkIsUftS3MOOwAd0n0peQ7a2X5ZEx930eCtzmW7g,1317
 gsrap/commons/.ipynb_checkpoints/medium-checkpoint.py,sha256=AMj95IvyWpbqKAYW5QdG_pyFXHDllUZ-b8dAsPR7tvU,3859
 gsrap/commons/.ipynb_checkpoints/memoteutils-checkpoint.py,sha256=rulJFSVX4I-XGi4uHXloL0eGIkC5zhpuJYWJn9zCDbY,4981
-gsrap/commons/.ipynb_checkpoints/metrics-checkpoint.py,sha256=gvqF2c0e31m5qQWQ11JF4-eMqxtuONy_7lUiC7uaXX4,3291
+gsrap/commons/.ipynb_checkpoints/metrics-checkpoint.py,sha256=yosbgX_EWUujN3AT6joY4xNxxJI97Qk3C0aKwko_mXs,3297
 gsrap/commons/.ipynb_checkpoints/sbmlutils-checkpoint.py,sha256=gkY02qbGXrbYStn2F8J0KM0fmqati2Nbvi128EF7coI,365
 gsrap/commons/__init__.py,sha256=9lrb0sBFSWEgV_e5FYzSgjTbam8b959rW_8VuxQHt1M,268
-gsrap/commons/biomass.py,sha256=4u7WBaUgo42tBoXDU1D0VUjICatb44e0jfswZrBeHYs,17987
+gsrap/commons/biomass.py,sha256=eJ2lej72mjDAibS7lQCFfN-L4inkaQ3lERe7K6-1E5o,18059
 gsrap/commons/coeffs.py,sha256=qI3_GuqHkeA2KbK9pYdkqJaFwYemAVZJGLRR4QtHt6w,19182
-gsrap/commons/downloads.py,sha256=JrVk-UbQzelefGvOz5k4j8Ofib58u_KD_zlUzTcuv6g,11170
-gsrap/commons/escherutils.py,sha256=VQ1FXyby6Cbfw3UNHzRoePH8M8owJ8E2rzB-11vBweA,3732
-gsrap/commons/excelhub.py,sha256=_LtaWripY_D99f14Yk-3v9VIov2cUGzJ53AXgmNFpUk,11457
+gsrap/commons/downloads.py,sha256=UKgFSPkxuxVWXoqrtZXEF42RR_KUjyoo_9wpCL-19X8,15908
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 gsrap/commons/figures.py,sha256=IRHSQXrCi4SQoISEfNB0rDhvUzbjcgsPi9zUSefsRto,4316
 gsrap/commons/fluxbal.py,sha256=jgC3-vI9Tbjvqohh2mJwFra4rl_pbUzHWrSa_QAxVO4,1262
 gsrap/commons/keggutils.py,sha256=M2nhHRiNH_xObHSxOIdt7ix59MrPdl9q3HNICC8X36M,4514
 gsrap/commons/logutils.py,sha256=VsnrkIsUftS3MOOwAd0n0peQ7a2X5ZEx930eCtzmW7g,1317
 gsrap/commons/medium.py,sha256=AMj95IvyWpbqKAYW5QdG_pyFXHDllUZ-b8dAsPR7tvU,3859
 gsrap/commons/memoteutils.py,sha256=rulJFSVX4I-XGi4uHXloL0eGIkC5zhpuJYWJn9zCDbY,4981
-gsrap/commons/metrics.py,sha256=gvqF2c0e31m5qQWQ11JF4-eMqxtuONy_7lUiC7uaXX4,3291
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 gsrap/commons/sbmlutils.py,sha256=gkY02qbGXrbYStn2F8J0KM0fmqati2Nbvi128EF7coI,365
 gsrap/getmaps/.ipynb_checkpoints/__init__-checkpoint.py,sha256=L4gLwk1vgnPlQuIP-FPnvy9uXnmGVQ4Rvjv3uyciDfk,92
 gsrap/getmaps/.ipynb_checkpoints/getmaps-checkpoint.py,sha256=5Odf2PS1PmPZqQyKoLPYHYgNvYsp6IxrTy5HEQ5LNEM,2943
@@ -49,40 +49,40 @@ gsrap/mkmodel/.ipynb_checkpoints/__init__-checkpoint.py,sha256=PNze-26HMOwfdJ92K
 gsrap/mkmodel/.ipynb_checkpoints/biologcuration-checkpoint.py,sha256=Nn7z-js-mzzeO23kVM2L7sJ5PNle7AkCUeBcEAYjlFU,15378
 gsrap/mkmodel/.ipynb_checkpoints/gapfill-checkpoint.py,sha256=BPZw4sszlBhAYfHnV0pA7EpG0b2ePwS6kUfFt0Ww-ss,5159
 gsrap/mkmodel/.ipynb_checkpoints/gapfillutils-checkpoint.py,sha256=S6nFUZ1Bbdf13nVJhGK2S5C_V3hd5zwTg2o5nzejngg,3123
-gsrap/mkmodel/.ipynb_checkpoints/mkmodel-checkpoint.py,sha256=zm-JA2sXwqTLalCc0L5POw2iRI56QK0UJMUgorHQrLw,10830
+gsrap/mkmodel/.ipynb_checkpoints/mkmodel-checkpoint.py,sha256=k_HZMmFTaJnXxjjk9nWCX5m1VyAXyNAM0S5h69wi-PM,10840
 gsrap/mkmodel/.ipynb_checkpoints/polishing-checkpoint.py,sha256=R1UdFPxN8N27Iu0jsYW2N_1BkWEbBHaMYW6NkCYZK_k,3256
 gsrap/mkmodel/.ipynb_checkpoints/pruner-checkpoint.py,sha256=FAZid-0H6j66wR2dVKRAaMaDREVt1edflmZXbX7blXg,9836
 gsrap/mkmodel/__init__.py,sha256=PNze-26HMOwfdJ92KiXpr--VV1ftVfo3CAxBZgeokp8,92
 gsrap/mkmodel/biologcuration.py,sha256=Nn7z-js-mzzeO23kVM2L7sJ5PNle7AkCUeBcEAYjlFU,15378
 gsrap/mkmodel/gapfill.py,sha256=BPZw4sszlBhAYfHnV0pA7EpG0b2ePwS6kUfFt0Ww-ss,5159
 gsrap/mkmodel/gapfillutils.py,sha256=S6nFUZ1Bbdf13nVJhGK2S5C_V3hd5zwTg2o5nzejngg,3123
-gsrap/mkmodel/mkmodel.py,sha256=zm-JA2sXwqTLalCc0L5POw2iRI56QK0UJMUgorHQrLw,10830
+gsrap/mkmodel/mkmodel.py,sha256=k_HZMmFTaJnXxjjk9nWCX5m1VyAXyNAM0S5h69wi-PM,10840
 gsrap/mkmodel/polishing.py,sha256=R1UdFPxN8N27Iu0jsYW2N_1BkWEbBHaMYW6NkCYZK_k,3256
 gsrap/mkmodel/pruner.py,sha256=FAZid-0H6j66wR2dVKRAaMaDREVt1edflmZXbX7blXg,9836
 gsrap/parsedb/.ipynb_checkpoints/__init__-checkpoint.py,sha256=1k2K1gz4lIdXAwHEdJ0OhdkPu83woGv0Z4TpT1kGrTk,97
-gsrap/parsedb/.ipynb_checkpoints/annotation-checkpoint.py,sha256=r0sYkSqA6b8mZOGD1tgk7I__ZFkH8r4aqxVA6EUspEY,5205
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 gsrap/parsedb/.ipynb_checkpoints/cycles-checkpoint.py,sha256=HJ58LcHQseQ1eploysfXd5Y8Rip8n62qhje4pmL22VM,4761
-gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py,sha256=UuwGWGB2saG9VDMoboumeRBWhHOO68bs5_1r2RSkyVo,17145
-gsrap/parsedb/.ipynb_checkpoints/manual-checkpoint.py,sha256=sDux5CFNC8v2YJ3oDMV0vXsQrvSG6gov1f4hftc4nyo,3874
-gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py,sha256=HbjkcWRI916_pvKVwTruNUbRWrHRlT__200wocLSOMY,8860
-gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py,sha256=ph1gC-84SyBnBuM7s0A9jTJBJmBlRzq0lk4FYG70228,6215
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 gsrap/parsedb/__init__.py,sha256=1k2K1gz4lIdXAwHEdJ0OhdkPu83woGv0Z4TpT1kGrTk,97
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 gsrap/parsedb/cycles.py,sha256=HJ58LcHQseQ1eploysfXd5Y8Rip8n62qhje4pmL22VM,4761
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 gsrap/runsims/.ipynb_checkpoints/__init__-checkpoint.py,sha256=6E6E1gWgH0V7ls4Omx4mxxC85gMJ_27YqhjugJzlZtY,97
 gsrap/runsims/.ipynb_checkpoints/biosynth-checkpoint.py,sha256=fUlHUo4CfB4rGX9Dth87B1p5E5sz7i6spR7ZoqDDGaI,2836
 gsrap/runsims/.ipynb_checkpoints/cnps-checkpoint.py,sha256=A0U8QPqW_uyrtHs99F286aEDEC6eukHXeMWrmnd0efA,5636
 gsrap/runsims/.ipynb_checkpoints/essentialgenes-checkpoint.py,sha256=MzHiuaU1gwiPdjZAgG7tkdYzkTTvoNCLp5tkezZhzxE,2247
 gsrap/runsims/.ipynb_checkpoints/growthfactors-checkpoint.py,sha256=r_W4idtOSJBDh7HURRsU8s1TqfOZ3TfeVw2HHDxmnGU,2265
 gsrap/runsims/.ipynb_checkpoints/precursors-checkpoint.py,sha256=1RNt_Rxs0L1lolDmYh4_CiZgiwHfU5B_AcomJO6vJ28,2219
-gsrap/runsims/.ipynb_checkpoints/runsims-checkpoint.py,sha256=2FC5Gs8oSYyZTjHF3A7aXB_O6myVfcn3bCxQfLJlZTk,2842
-gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py,sha256=tCQHTMUqum1YwlBKRTNaQoag2co_yQlCaKmISOARAlE,2353
+gsrap/runsims/.ipynb_checkpoints/runsims-checkpoint.py,sha256=aVELI1re1Dlm1_Lh7t1DwSoA8AcxQw0JKNnjV9w5F20,2910
+gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py,sha256=rVN69v4B-DdxOJDsJ_JOVzbnWsDYafMq43QD_GJIpjs,2296
 gsrap/runsims/.ipynb_checkpoints/singleomission-checkpoint.py,sha256=jMuKAi0pINP8Jlrm-yI-tX7D110VzttR3YfTSnDRe4I,2847
 gsrap/runsims/__init__.py,sha256=6E6E1gWgH0V7ls4Omx4mxxC85gMJ_27YqhjugJzlZtY,97
 gsrap/runsims/biosynth.py,sha256=fUlHUo4CfB4rGX9Dth87B1p5E5sz7i6spR7ZoqDDGaI,2836
@@ -90,11 +90,11 @@ gsrap/runsims/cnps.py,sha256=A0U8QPqW_uyrtHs99F286aEDEC6eukHXeMWrmnd0efA,5636
 gsrap/runsims/essentialgenes.py,sha256=MzHiuaU1gwiPdjZAgG7tkdYzkTTvoNCLp5tkezZhzxE,2247
 gsrap/runsims/growthfactors.py,sha256=r_W4idtOSJBDh7HURRsU8s1TqfOZ3TfeVw2HHDxmnGU,2265
 gsrap/runsims/precursors.py,sha256=1RNt_Rxs0L1lolDmYh4_CiZgiwHfU5B_AcomJO6vJ28,2219
-gsrap/runsims/runsims.py,sha256=2FC5Gs8oSYyZTjHF3A7aXB_O6myVfcn3bCxQfLJlZTk,2842
-gsrap/runsims/simplegrowth.py,sha256=tCQHTMUqum1YwlBKRTNaQoag2co_yQlCaKmISOARAlE,2353
+gsrap/runsims/runsims.py,sha256=aVELI1re1Dlm1_Lh7t1DwSoA8AcxQw0JKNnjV9w5F20,2910
+gsrap/runsims/simplegrowth.py,sha256=rVN69v4B-DdxOJDsJ_JOVzbnWsDYafMq43QD_GJIpjs,2296
 gsrap/runsims/singleomission.py,sha256=jMuKAi0pINP8Jlrm-yI-tX7D110VzttR3YfTSnDRe4I,2847
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-gsrap-0.9.0.dist-info/METADATA,sha256=Zd_nRZYHhrKBle7mzTBWnQQ1KdMWlHPuKqH9-YU5IHA,898
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-gsrap-0.9.0.dist-info/RECORD,,
+gsrap-0.10.1.dist-info/METADATA,sha256=AGbAQL3AEB3s3o9-jmWHZoVsjZQXRyUKVfQQlbWUitA,1008
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+gsrap-0.10.1.dist-info/licenses/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gsrap-0.10.1.dist-info/RECORD,,

{gsrap-0.9.0.dist-info → gsrap-0.10.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
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+Generator: poetry-core 2.3.0
 Root-Is-Purelib: true
 Tag: py3-none-any