User option to fail if model needs to be compiled (#2289)

* support "do not compile" for petab problems

* rewrite

documentation/ExampleJax.ipynb

@@ -572,7 +572,7 @@
    "source": [
     "from amici.petab.petab_import import import_petab_problem\n",
     "\n",
-    "amici_model = import_petab_problem(petab_problem, force_compile=True)"
+    "amici_model = import_petab_problem(petab_problem, compile_=True)"
    ]
   },
   {

python/examples/example_errors.ipynb

@@ -77,7 +77,7 @@
    "source": [
     "petab_problem = benchmark_models_petab.get_problem(\"Fujita_SciSignal2010\")\n",
     "amici_model = import_petab_problem(\n",
-    "    petab_problem, verbose=False, force_compile=False\n",
+    "    petab_problem, verbose=False, compile_=None\n",
     ")\n",
     "\n",
     "np.random.seed(2991)\n",
@@ -423,7 +423,7 @@
    "source": [
     "petab_problem = benchmark_models_petab.get_problem(\"Weber_BMC2015\")\n",
     "amici_model = import_petab_problem(\n",
-    "    petab_problem, verbose=False, force_compile=False\n",
+    "    petab_problem, verbose=False, compile_=None\n",
     ")\n",
     "\n",
     "np.random.seed(4)\n",
@@ -699,7 +699,7 @@
     "amici_model = import_petab_problem(\n",
     "    petab_problem,\n",
     "    verbose=False,\n",
-    "    force_compile=True,\n",
+    "    compile_=True,\n",
     "    model_name=\"Blasi_CellSystems2016_1\",\n",
     ")\n",
     "\n",
@@ -819,7 +819,7 @@
     "    # we need a different model name if we import the model again\n",
     "    # we cannot load a model with the same name as an already loaded model\n",
     "    model_name=\"Blasi_CellSystems2016_2\",\n",
-    "    force_compile=True,\n",
+    "    compile_=True,\n",
     ")\n",
     "del os.environ[\"AMICI_EXPERIMENTAL_SBML_NONCONST_CLS\"]\n",
     "\n",

python/examples/example_jax/ExampleJax.ipynb

@@ -265,7 +265,7 @@
     "from amici.petab.petab_import import import_petab_problem\n",
     "\n",
     "amici_model = import_petab_problem(\n",
-    "    petab_problem, force_compile=True, verbose=False\n",
+    "    petab_problem, compile_=True, verbose=False\n",
     ")"
    ]
   },

python/sdist/amici/petab/petab_import.py

@@ -35,7 +35,7 @@ def import_petab_problem(
     petab_problem: petab.Problem,
     model_output_dir: Union[str, Path, None] = None,
     model_name: str = None,
-    force_compile: bool = False,
+    compile_: bool = None,
     non_estimated_parameters_as_constants=True,
     **kwargs,
 ) -> "amici.Model":
@@ -53,9 +53,10 @@ def import_petab_problem(
         Name of the generated model module. Defaults to the ID of the model
         or the model file name without the extension.
 
-    :param force_compile:
-        Whether to compile the model even if the target folder is not empty,
-        or the model exists already.
+    :param compile_:
+        If ``True``, the model will be compiled. If ``False``, the model will
+        not be compiled. If ``None``, the model will be compiled if it cannot
+        be imported.
 
     :param non_estimated_parameters_as_constants:
         Whether parameters marked as non-estimated in PEtab should be
@@ -71,6 +72,16 @@ def import_petab_problem(
     :return:
         The imported model.
     """
+    if "force_compile" in kwargs:
+        if kwargs["force_compile"]:
+            compile_ = True
+        warn(
+            "The `force_compile` option is deprecated, please use the "
+            "new `compile_` option, which also supports 'do not compile'.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+
     if petab_problem.model.type_id not in (MODEL_TYPE_SBML, MODEL_TYPE_PYSB):
         raise NotImplementedError(
             "Unsupported model type " + petab_problem.model.type_id
@@ -107,12 +118,15 @@ def import_petab_problem(
         os.makedirs(model_output_dir)
 
     # check if compilation necessary
-    if force_compile or not _can_import_model(model_name, model_output_dir):
+    if compile_ or (
+        compile_ is None
+        and not _can_import_model(model_name, model_output_dir)
+    ):
         # check if folder exists
-        if os.listdir(model_output_dir) and not force_compile:
+        if os.listdir(model_output_dir) and not compile_:
             raise ValueError(
                 f"Cannot compile to {model_output_dir}: not empty. "
-                "Please assign a different target or set `force_compile`."
+                "Please assign a different target or set `compile_` to `True`."
             )
 
         # remove folder if exists

tests/petab_test_suite/test_petab_suite.py

@@ -62,7 +62,7 @@ def _test_case(case, model_type, version):
         petab_problem=problem,
         model_output_dir=model_output_dir,
         model_name=model_name,
-        force_compile=True,
+        compile_=True,
     )
     solver = model.getSolver()
     solver.setSteadyStateToleranceFactor(1.0)