finished conflict resolution and dependency updates

freiburgermsu · Jul 19, 2023 · 525c245 · 525c245
1 parent 332672b
commit 525c245
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Showing 3 changed files with 5 additions and 44 deletions.
diff --git a/modelseedpy/core/msatpcorrection.py b/modelseedpy/core/msatpcorrection.py
@@ -344,21 +344,15 @@ def determine_growth_media(self, max_gapfilling=None):
         self.selected_media = []
         best_score = inf
         for media in self.media_gapfill_stats:
-<<<<<<< HEAD
-=======
             atp_att["core_atp_gapfilling"][media.id] = {
                 "score": 0,
                 "new": {},
                 "reversed": {},
             }
->>>>>>> b08f8f38362c3a9140571f5ade10f8d00ab10ae6
             if self.media_gapfill_stats[media]:
                 atp_att["core_atp_gapfilling"][media.id]["score"] = len(
                     self.media_gapfill_stats[media]["new"].keys()
                 ) + 0.5 * len(self.media_gapfill_stats[media]["reversed"].keys())
-<<<<<<< HEAD
-            best_score = min(best_score, gfscore)
-=======
                 atp_att["core_atp_gapfilling"][media.id][
                     "new"
                 ] = self.media_gapfill_stats[media]["new"]
@@ -370,13 +364,8 @@ def determine_growth_media(self, max_gapfilling=None):
                     "score": 1000,
                     "failed": True,
                 }
-            if (
-                best_score is None
-                or atp_att["core_atp_gapfilling"][media.id]["score"] < best_score
-            ):
-                best_score = atp_att["core_atp_gapfilling"][media.id]["score"]
+            best_score = min(best_score, atp_att["core_atp_gapfilling"][media.id]["score"])
 
->>>>>>> b08f8f38362c3a9140571f5ade10f8d00ab10ae6
         if self.max_gapfilling is None:
             self.max_gapfilling = best_score
 

diff --git a/modelseedpy/core/mstemplate.py b/modelseedpy/core/mstemplate.py
@@ -802,17 +802,6 @@ def build_biomass(self, model, index="0", classic=False, GC=0.5, add_to_model=Tr
                     coef = comp.coefficient
                 elif comp.coefficient_type == "AT":
                     coef = (
-<<<<<<< HEAD
-                            comp.coefficient
-                            * (1 - GC)
-                            * (type_abundances[type] / bio_type_hash[type]["total_mw"])
-                    )
-                elif comp.coefficient_type == "GC":
-                    coef = (
-                            comp.coefficient
-                            * GC
-                            * (type_abundances[type] / bio_type_hash[type]["total_mw"])
-=======
                         2
                         * comp.coefficient
                         * (1 - GC)
@@ -824,7 +813,6 @@ def build_biomass(self, model, index="0", classic=False, GC=0.5, add_to_model=Tr
                         * comp.coefficient
                         * GC
                         * (type_abundances[type] / bio_type_hash[type]["total_mw"])
->>>>>>> b08f8f38362c3a9140571f5ade10f8d00ab10ae6
                     )
                 if coef:
                     met = model.metabolites.get_by_id(comp.metabolite.id + index)
@@ -848,20 +836,9 @@ def build_biomass(self, model, index="0", classic=False, GC=0.5, add_to_model=Tr
                             else:
                                 metabolites[met] = coef * comp.linked_metabolites[l_met]
                         elif not classic:
-<<<<<<< HEAD
-                            if met in metabolites:
-                                specific_reactions[type].metabolites[met] += (
-                                        coef * comp.linked_metabolites[l_met]
-                                )
-                            else:
-                                specific_reactions[type].metabolites[met] = (
-                                        coef * comp.linked_metabolites[l_met]
-                                )
-=======
                             specific_reactions[type].add_metabolites(
                                 {met: coef * comp.linked_metabolites[l_met]}
                             )
->>>>>>> b08f8f38362c3a9140571f5ade10f8d00ab10ae6
         biorxn.annotation[SBO_ANNOTATION] = "SBO:0000629"
         biorxn.add_metabolites(metabolites)
         if add_to_model:
@@ -1282,16 +1259,9 @@ def add_reactions(self, reaction_list: list):
                 if cpx.id not in self.complexes:
                     self.add_complexes([cpx])
                 complex_replace.add(self.complexes.get_by_id(cpx.id))
-<<<<<<< HEAD
             rxn._metabolites = metabolites_replace
+            rxn._update_awareness()
             rxn.complexes = complex_replace
-=======
-
-            x._metabolites = metabolites_replace
-            x._update_awareness()
-            x.complexes = complex_replace
-
->>>>>>> b08f8f38362c3a9140571f5ade10f8d00ab10ae6
         self.reactions += reaction_list
 
     def get_role_sources(self):

diff --git a/setup.py b/setup.py
@@ -47,7 +47,9 @@
         "deepdiff",
         "openpyxl",
         "jinja2",
-        "multiprocess"
+        "multiprocess",
+        "h5py",
+        "graphviz"
     ],
     tests_require=[
         "pytest",