From 3d4cda5e32550dd321662298733c822446140001 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de>
Date: Thu, 5 May 2022 13:22:57 +0200
Subject: [PATCH] Model.to_file

---
 petab/models/model.py      | 10 ++++++++++
 petab/models/sbml_model.py |  6 ++++++
 petab/problem.py           | 18 +++++++++++++-----
 3 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/petab/models/model.py b/petab/models/model.py
index cfc94ab4..00270204 100644
--- a/petab/models/model.py
+++ b/petab/models/model.py
@@ -2,7 +2,9 @@
 from __future__ import annotations
 
 import abc
+from pathlib import Path
 from typing import Any, Iterable, Tuple
+
 from . import MODEL_TYPE_SBML, known_model_types
 
 
@@ -25,6 +27,14 @@ def from_file(filepath_or_buffer: Any) -> Model:
         """
         ...
 
+    @abc.abstractmethod
+    def to_file(self, filename: [str, Path]):
+        """Save the model to the given file
+
+        :param filename: Destination filename
+        """
+        ...
+
     @classmethod
     @property
     @abc.abstractmethod
diff --git a/petab/models/sbml_model.py b/petab/models/sbml_model.py
index 62aa887d..bac5c675 100644
--- a/petab/models/sbml_model.py
+++ b/petab/models/sbml_model.py
@@ -1,6 +1,7 @@
 """Functions for handling SBML models"""
 
 import itertools
+from pathlib import Path
 from typing import Iterable, Optional, Tuple
 
 import libsbml
@@ -64,6 +65,11 @@ def from_file(filepath_or_buffer):
             sbml_document=sbml_document,
         )
 
+    def to_file(self, filename: [str, Path]):
+        from ..sbml import write_sbml
+        write_sbml(self.sbml_document or self.sbml_model.getSBMLDocument(),
+                   filename)
+
     def get_parameter_ids(self) -> Iterable[str]:
         return (
             p.getId() for p in self.sbml_model.getListOfParameters()
diff --git a/petab/problem.py b/petab/problem.py
index faed0cf2..d9549a13 100644
--- a/petab/problem.py
+++ b/petab/problem.py
@@ -356,6 +356,7 @@ def to_files(self,
                  yaml_file: Union[None, str, Path] = None,
                  prefix_path: Union[None, str, Path] = None,
                  relative_paths: bool = True,
+                 model_file: Union[None, str, Path] = None,
                  ) -> None:
         """
         Write PEtab tables to files for this problem
@@ -404,11 +405,18 @@ def add_prefix(path0: Union[None, str, Path]) -> str:
             yaml_file = add_prefix(yaml_file)
 
         if sbml_file:
-            if self.sbml_document is not None:
-                sbml.write_sbml(self.sbml_document, sbml_file)
-            else:
-                raise ValueError("Unable to save SBML model with no "
-                                 "sbml_doc set.")
+            warn("The `sbml_file` argument is deprecated and will be "
+                 "removed in a future version. Use `model_file` instead.",
+                 DeprecationWarning, stacklevel=2)
+
+            if model_file:
+                raise ValueError("Must provide either `sbml_file` or "
+                                 "`model_file` argument, but not both.")
+
+            model_file = sbml_file
+
+        if model_file:
+            self.model.to_file(model_file)
 
         def error(name: str) -> ValueError:
             return ValueError(f"Unable to save non-existent {name} table")