Merge branch 'develop' into remove-hardcoded-paths/rnaseq-gen

# Conflicts:
#	main/como/rnaseq_gen.py

Author: JoshLoecker

main/como/__init__.py

@@ -4,7 +4,7 @@
 from como.utils import stringlist_to_list
 
 __all__ = ["stringlist_to_list", "Config"]
-__version__ = "1.10.0"
+__version__ = "1.11.1"
 
 
 def return_placeholder_data() -> pd.DataFrame:

main/como/create_context_specific_model.py

@@ -308,9 +308,16 @@ def _build_with_imat(
     expr_vector: npt.NDArray,
     expr_thesh: tuple[float, float],
     force_gene_ids: Sequence[int],
+    solver: str,
 ) -> (cobra.Model, pd.DataFrame):
     expr_vector = np.array(expr_vector)
-    properties = IMATProperties(exp_vector=expr_vector, exp_thresholds=expr_thesh, core=force_gene_ids, epsilon=0.01)
+    properties = IMATProperties(
+        exp_vector=expr_vector,
+        exp_thresholds=expr_thesh,
+        core=force_gene_ids,
+        epsilon=0.01,
+        solver=solver.upper(),
+    )
     algorithm = IMAT(s_matrix, np.array(lb), np.array(ub), properties)
     context_rxns: npt.NDArray = algorithm.run()
     fluxes: pd.Series = algorithm.sol.to_series()
@@ -507,7 +514,14 @@ def _build_model(  # noqa: C901
     elif recon_algorithm == Algorithm.IMAT:
         context_model_cobra: cobra.Model
         context_model_cobra, flux_df = _build_with_imat(
-            reference_model, s_matrix, lb, ub, expr_vector, exp_thresh, idx_force
+            reference_model,
+            s_matrix,
+            lb,
+            ub,
+            expr_vector,
+            exp_thresh,
+            idx_force,
+            solver=solver,
         )
         imat_reactions = flux_df.rxn
         model_reactions = [reaction.id for reaction in context_model_cobra.reactions]
@@ -550,6 +564,7 @@ def _collect_boundary_reactions(path: Path) -> _BoundaryReactions:
     df = _create_df(path)
     for column in df.columns:
         if column not in [
+            "boundary",
             "reaction",
             "abbreviation",
             "compartment",
@@ -561,31 +576,25 @@ def _collect_boundary_reactions(path: Path) -> _BoundaryReactions:
                 f"'Minimum Reaction Rate', and 'Maximum Reaction Rate'. Found: {column}"
             )
 
-    reactions: list[str] = []
+    reactions: list[str] = [""] * len(df)
     boundary_type: list[str] = df["reaction"].tolist()
     reaction_abbreviation: list[str] = df["abbreviation"].tolist()
     reaction_compartment: list[str] = df["compartment"].tolist()
-    lower_bounds = df["minimum reaction rate"].tolist()
-    upper_bounds = df["maximum reaction rate"].tolist()
+    lower_bound = df["minimum reaction rate"].tolist()
+    upper_bound = df["maximum reaction rate"].tolist()
+    boundary_map = {"exchange": "EX", "demand": "DM", "sink": "SK"}
     for i in range(len(boundary_type)):
-        current_type: str = boundary_type[i]
-        temp_reaction: str = ""
-
-        match current_type.lower():
-            case "exchange":
-                temp_reaction += "EX_"
-            case "demand":
-                temp_reaction += "DM_"
-            case "sink":
-                temp_reaction += "SK_"
+        boundary: str = boundary_type[i].lower()
+        if boundary not in boundary_map:
+            raise ValueError(f"Boundary reaction type must be 'Exchange', 'Demand', or 'Sink'. Found: {boundary[i]}")
 
         shorthand_compartment = Compartments.get(reaction_compartment[i])
-        temp_reaction += f"{reaction_abbreviation[i]}[{shorthand_compartment}]"
-        reactions.append(temp_reaction)
+        reactions[i] = f"{boundary_map.get(boundary)}_{reaction_abbreviation[i]}[{shorthand_compartment}]"
+
     return _BoundaryReactions(
         reactions=reactions,
-        lower_bounds=lower_bounds,
-        upper_bounds=upper_bounds,
+        lower_bounds=lower_bound,
+        upper_bounds=upper_bound,
     )
 
 
@@ -631,10 +640,10 @@ def create_context_specific_model(  # noqa: C901
             raise ValueError(f"Output file type {output_type} not recognized. Must be one of: 'xml', 'mat', 'json'")
 
     if algorithm not in Algorithm:
-        raise ValueError(f"Algorithm {algorithm} not supported. Please use one of: GIMME, FASTCORE, or IMAT")
+        raise ValueError(f"Algorithm {algorithm} not supported. Use one of {', '.join(a.value for a in Algorithm)}")
 
     if solver not in Solver:
-        raise ValueError(f"Solver '{solver}' not supported. Use 'GLPK' or 'GUROBI'")
+        raise ValueError(f"Solver '{solver}' not supported. Use one of {', '.join(s.value for s in Solver)}")
 
     if boundary_rxns_filepath:
         boundary_reactions = _collect_boundary_reactions(boundary_rxns_filepath)
@@ -667,7 +676,7 @@ def create_context_specific_model(  # noqa: C901
         bound_ub=boundary_reactions.upper_bounds,
         exclude_rxns=exclude_rxns,
         force_rxns=force_rxns,
-        solver=solver.value,
+        solver=solver.value.lower(),
         low_thresh=low_threshold,
         high_thresh=high_threshold,
     )

main/data/boundary_rxns/naiveB_boundary_rxns.csv

@@ -1,4 +1,4 @@
-Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
+Boundary,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
 Exchange,glc_D,Extracellular,-100,1000
 Exchange,fe2,Extracellular,-1000,1000
 Exchange,gal,Extracellular,0,1000

main/data/boundary_rxns/smB_boundary_rxns.csv

@@ -1,4 +1,4 @@
-Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
+Boundary,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate
 Exchange,glc_D,Extracellular,-100,1000
 Exchange,fe2,Extracellular,-1000,1000
 Exchange,gal,Extracellular,0,1000
@@ -67,4 +67,4 @@ Exchange,orn,Extracellular,-1,1000
 Exchange,orn_D,Extracellular,-1,1000
 Exchange,so4,Extracellular,-1000,1000
 Exchange,ribflv,Extracellular,-1,1000
-Exchange,Lcystin,Extracellular,-1,1000
+Exchange,Lcystin,Extracellular,-1,1000

pyproject.toml

@@ -5,7 +5,7 @@ requires-python = ">=3.10,<3.13"
 dependencies = [
     "aiofiles>=24.1.0",
     "aioftp>=0.23.1",
-    "cobamp",
+    "cobamp@git+https://github.com/JoshLoecker/cobamp@master",
     "cobra>=0.28.0",
     "fast-bioservices>=0.3.9",
     "gurobipy>=11.0",
@@ -20,7 +20,7 @@ dependencies = [
     "scikit-learn>=1.5.2",
     "scipy>=1.7.3",
     "setuptools<60.0",
-    "troppo",
+    "troppo@git+https://github.com/JoshLoecker/troppo@master",
 ]
 
 [project.optional-dependencies]
@@ -57,14 +57,9 @@ dev-dependencies = [
     "cz-conventional-gitmoji>=0.6.1",
 ]
 
-[tool.uv.sources]
-troppo = { git = "https://github.com/JoshLoecker/troppo", rev = "update_dependencies" }
-cobamp = { git = "https://github.com/JoshLoecker/cobamp", rev = "update_packages" }
-pydantic-settings = { git = "https://github.com/pydantic/pydantic-settings" }
-
 [tool.commitizen]
 name = "cz_conventional_commits"
 tag_format = "$version"
 version_scheme = "semver2"
 version_provider = "pep621"
-update_changelog_on_bump = true
+update_changelog_on_bump = true