Merge pull request #203 from HelikarLab/hotfix

hotfix: allow setting solvers through troppo; update actions

Author: JoshLoecker

.github/workflows/continuous_integration.yml

@@ -14,7 +14,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v3
+        uses: astral-sh/setup-uv@v4
 
       - name: Create Virtual Environment
         run: uv venv
@@ -26,17 +26,17 @@ jobs:
         run: uv run jupyter nbconvert --clear-output --inplace "main/COMO.ipynb"
 
       - name: Format Python Imports
-        uses: astral-sh/ruff-action@v1
+        uses: astral-sh/ruff-action@v2
         with:
           args: "check --fix --select I"
 
       - name: Format code
-        uses: astral-sh/ruff-action@v1
+        uses: astral-sh/ruff-action@v2
         with:
           args: "format"
 
       - name: Format Notebook
-        uses: astral-sh/ruff-action@v1
+        uses: astral-sh/ruff-action@v2
         with:
           args: "format main/COMO.ipynb"
 
@@ -54,7 +54,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Check Lint
-        uses: astral-sh/ruff-action@v1
+        uses: astral-sh/ruff-action@v2
         with:
           args: "check --no-fix --verbose"
 

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]
@@ -626,10 +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)
@@ -662,7 +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,
     )

pyproject.toml

@@ -17,8 +17,8 @@ dependencies = [
     "openpyxl>=3.1.5",
     "aiofiles>=24.1.0",
     "aioftp>=0.23.1",
-    "troppo",
-    "cobamp",
+    "troppo@git+https://github.com/JoshLoecker/troppo@master",
+    "cobamp@git+https://github.com/JoshLoecker/cobamp@master",
 ]
 
 [build-system]
@@ -46,7 +46,3 @@ dev-dependencies = [
     "hypothesis>=6.122.1",
     "pytest-cov>=6.0.0",
 ]
-
-[tool.uv.sources]
-troppo = { git = "https://github.com/JoshLoecker/troppo", rev = "update_dependencies" }
-cobamp = { git = "https://github.com/JoshLoecker/cobamp", rev = "update_packages" }