improved package structure: utils and flux_analysis are now available as well

Author: SamiralVdB

src/PAModelpy/Enzyme.py

@@ -250,7 +250,7 @@ def change_kcat_values(self, rxn2kcat: Dict):
             else:
                 catalytic_event_id = f"CE_{CatalyticEvent._extract_reaction_id_from_catalytic_reaction_id(rxn_id, self.enzyme_id_regex)}"
             # change rxn2kcat dictionary
-            self.rxn2kcat[rxn_id] = {**self.rxn2kcat[rxn_id],**kcats}
+            self.rxn2kcat.setdefault(catalytic_event_id, {}).update(kcats)
             # is there already a link between enzyme and reaction?
             if catalytic_event_id not in self.catalytic_events:
                 warn(f"Reaction {rxn_id} is not associated with enzyme {self.id}. Skip")

src/PAModelpy/EnzymeSectors.py

@@ -380,9 +380,7 @@ def _get_model_genes_from_enzyme(self, enzyme_id: str, model: Model) -> list:
     def change_kcat_values(self, rxn_id:str, enzyme_id:str,
                            kcat_f_b:dict[Literal['f', 'b'], float]
                            ) -> None:
-        rxnid2protein = defaultdict(dict ,self.rxn2protein[rxn_id])
-        rxnid2protein[enzyme_id] = {**rxnid2protein[enzyme_id],**kcat_f_b}
-        self.rxn2protein[rxn_id] = dict(rxnid2protein)
+        self.rxn2protein.setdefault(rxn_id, {}).update(kcat_f_b)
 
     def __setstate__(self, state):
         # Restore state from the unpickled state

src/PAModelpy/__init__.py

@@ -1,4 +1,4 @@
-print('Loading PAModelpy modules version 0.0.4.1')
+print('Loading PAModelpy modules version 0.0.4.2')
 
 from .Enzyme import *
 from .EnzymeSectors import *

src/flux_analysis/__init__.py renamed to src/PAModelpy/flux_analysis/__init__.py

@@ -9,9 +9,9 @@
 from dataclasses import dataclass, field
 
 
-from src.PAModelpy.PAModel import PAModel
-from src.PAModelpy.EnzymeSectors import ActiveEnzymeSector, UnusedEnzymeSector, TransEnzymeSector
-from src.PAModelpy.configuration import Config
+from ..PAModel import PAModel
+from ..EnzymeSectors import ActiveEnzymeSector, UnusedEnzymeSector, TransEnzymeSector
+from ..configuration import Config
 
 DEFAULT_MOLMASS = 39959.4825 #kDa
 DEFAULT_KCAT = 11 #s-1
@@ -80,7 +80,7 @@ def parse_gpr_information(gpr_info:str,
                           gene2protein: dict[str, str] = None) -> tuple[list,list]:
     #filter out nan entries
     if not isinstance(gpr_info, str):
-        return None
+        return None, None
 
     # #only get the genes associated with this enzyme
     gpr_list = _parse_gpr(gpr_info)
@@ -191,11 +191,13 @@ def _check_if_all_model_reactions_are_in_rxn_info2protein(model: cobra.Model,
                                                           protein2gpr:defaultdict[str,list]
                                                           ) -> Tuple[dict[str, ReactionInformation],defaultdict[str,list]]:
     for rxn in model.reactions:
+        rxn_id = _extract_reaction_id(
+            rxn.id)  # some reactions ids are associated with copy numbers, only filter for the actual reaction id
         if not (
-                rxn.id not in rxn_info2protein.keys()
-                and 'EX'.lower() not in rxn.id.lower()#is the reaction an exchange with the environment?
-                and 'BIOMASS' not in rxn.id#is the reaction a pseudoreaction?
-                and len(rxn._genes) > 0 #is the reaction associated with enzymes?
+                rxn_id not in rxn_info2protein.keys()
+                and 'EX'.lower() not in rxn.id.lower()  # is the reaction an exchange with the environment?
+                and 'BIOMASS' not in rxn.id  # is the reaction a pseudoreaction?
+                and len(rxn._genes) > 0  # is the reaction associated with enzymes?
                 and list(rxn._genes)[0].id != 's0001'
         ): continue
 

src/flux_analysis/recombinant_protein_expression.py renamed to src/PAModelpy/flux_analysis/recombinant_protein_expression.py

@@ -1 +1,2 @@
-from PAModelpy import *
+from PAModelpy.src.PAModelpy.flux_analysis import *
+from PAModelpy.src.PAModelpy.utils import *

src/utils/__init__.py renamed to src/PAModelpy/utils/__init__.py

@@ -5,11 +5,11 @@ requires = [
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools.packages]
-find = {}  # Scan the project directory with the default parameters
+find = { where = ["src"] }  # Scan the project directory with the default parameters
 
 [project]
 name = 'PAModelpy'
-version = '0.0.4.1'
+version = '0.0.4.2'
 authors = [{name='Samira van den Bogaard', email = 'samira.vandenbogaard@rwth-aachen.de'}]
 description = 'Python framework for building and analysing protein allocation models'
 readme = 'README.md'