Merge pull request #759 from opencobra/feat-set-solver-early

feat: allow setting solver backend early

HISTORY.rst

@@ -4,6 +4,8 @@ History
 Next Release
 ------------
 
+* Set the solver backend earlier in the process, before a COBRApy model is created.
+
 0.16.0 (2023-11-19)
 -------------------
 * Allow the hybrid interface as a solver.

src/memote/suite/cli/reports.py

@@ -27,6 +27,7 @@
 from multiprocessing import Pool, cpu_count
 
 import click
+import cobra
 import git
 from libsbml import SBMLError
 from sqlalchemy.exc import ArgumentError
@@ -143,6 +144,10 @@ def snapshot(
     MODEL: Path to model file. Can also be supplied via the environment variable
     MEMOTE_MODEL or configured in 'setup.cfg' or 'memote.ini'.
     """
+    # Configure the chosen solver before attempting to load the model.
+    config = cobra.Configuration()
+    config.solver = solver
+
     model_obj, sbml_ver, notifications = api.validate_model(model)
     if model_obj is None:
         LOGGER.critical(
@@ -159,7 +164,6 @@ def snapshot(
     # Update the default test configuration with custom ones (if any).
     for custom in custom_config:
         config.merge(ReportConfiguration.load(custom))
-    model_obj.solver = solver
     _, results = api.test_model(
         model_obj,
         sbml_version=sbml_ver,
@@ -363,6 +367,10 @@ def diff(
 
     MODELS: List of paths to two or more model files.
     """
+    # Configure the chosen solver before attempting to load the model.
+    config = cobra.Configuration()
+    config.solver = solver
+
     if not any(a.startswith("--tb") for a in pytest_args):
         pytest_args = ["--tb", "no"] + pytest_args
     # Add further directories to search for tests.
@@ -390,7 +398,6 @@ def diff(
                     "reported in {}.".format(model_filename, report_path)
                 )
                 continue
-            model.solver = solver
             model_and_model_ver_tuple.append((model, model_ver))
         except (IOError, SBMLError):
             LOGGER.debug(exc_info=True)

src/memote/suite/cli/runner.py

@@ -31,6 +31,7 @@
 
 import click
 import click_log
+import cobra
 import git
 from cookiecutter.main import cookiecutter, get_user_config
 from github import Github
@@ -231,6 +232,11 @@ def is_verbose(arg):
             sys.exit(0)
     # Add further directories to search for tests.
     pytest_args.extend(custom_tests)
+
+    # Configure the chosen solver before attempting to load the model.
+    config = cobra.Configuration()
+    config.solver = solver
+
     # Check if the model can be loaded at all.
     model, sbml_ver, notifications = api.validate_model(model)
     if model is None:
@@ -239,7 +245,7 @@ def is_verbose(arg):
         )
         stdout_notifications(notifications)
         sys.exit(1)
-    model.solver = solver
+
     code, result = api.test_model(
         model=model,
         sbml_version=sbml_ver,
@@ -339,7 +345,6 @@ def _model_from_stream(stream, filename):
 def _test_history(
     model,
     sbml_ver,
-    solver,
     solver_timeout,
     manager,
     commit,
@@ -348,7 +353,6 @@ def _test_history(
     exclusive,
     experimental,
 ):
-    model.solver = solver
     # Load the experimental configuration using model information.
     if experimental is not None:
         experimental.load(model)
@@ -480,6 +484,9 @@ def history(
         previous = repo.active_branch
         LOGGER.info("Checking out deployment branch {}.".format(deployment))
         repo.git.checkout(deployment)
+    # Configure the chosen solver before attempting to load the model.
+    config = cobra.Configuration()
+    config.solver = solver
     # Temporarily move the results to a new location so that they are
     # available while checking out the various commits.
     engine = None
@@ -545,7 +552,6 @@ def history(
             args=(
                 model_obj,
                 sbml_ver,
-                solver,
                 solver_timeout,
                 manager,
                 commit,