Add petab.v2.Problem (#285)

Copy of v1.Problem with all deprecated functionality removed.

Loading PEtab 2.0 problems with petab.v1.Problem is now deprecated.

Author: dweindl

petab/v1/models/model.py

@@ -6,7 +6,7 @@
 from pathlib import Path
 from typing import Any
 
-__all__ = ["Model"]
+__all__ = ["Model", "model_factory"]
 
 
 class Model(abc.ABC):

petab/v1/problem.py

@@ -283,6 +283,12 @@ def from_yaml(yaml_config: dict | Path | str) -> Problem:
             )
         if yaml_config[FORMAT_VERSION] == "2.0.0":
             warn("Support for PEtab2.0 is experimental!", stacklevel=2)
+            warn(
+                "Using petab.v1.Problem with PEtab2.0 is deprecated. "
+                "Use petab.v2.Problem instead.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
 
         problem0 = yaml_config["problems"][0]
 

petab/v2/__init__.py

@@ -2,5 +2,15 @@
 
 Contains all functionality related to handling PEtab 2.0 problems.
 """
+from warnings import warn
 
 from ..v1 import *  # noqa: F403, F401, E402
+
+# import after v1
+from .problem import Problem  # noqa: F401
+
+warn(
+    "Support for PEtab2.0 and all of petab.v2 is experimental "
+    "and subject to changes!",
+    stacklevel=1,
+)