..

Author: dweindl

petab/v2/__init__.py

@@ -5,27 +5,27 @@
 
 from warnings import warn
 
-# TODO: remove v1 star imports
-from ..v1.calculate import *  # noqa: F403, F401, E402
-from ..v1.composite_problem import *  # noqa: F403, F401, E402
-from ..v1.core import *  # noqa: F403, F401, E402
-from ..v1.format_version import __format_version__  # noqa: F401, E402
-from ..v1.mapping import *  # noqa: F403, F401, E402
-from ..v1.measurements import *  # noqa: F403, F401, E402
-from ..v1.observables import *  # noqa: F403, F401, E402
-from ..v1.parameter_mapping import *  # noqa: F403, F401, E402
-from ..v1.parameters import *  # noqa: F403, F401, E402
-from ..v1.sampling import *  # noqa: F403, F401, E402
-from ..v1.sbml import *  # noqa: F403, F401, E402
-from ..v1.simulate import *  # noqa: F403, F401, E402
-from ..v1.yaml import *  # noqa: F403, F401, E402
-
 warn(
     "Support for PEtab2.0 and all of petab.v2 is experimental "
     "and subject to changes!",
     stacklevel=1,
 )
 
+# TODO: move this module to v2
+from petab.v1.mapping import (  # noqa: F403, F401, E402
+    get_mapping_df,
+    write_mapping_df,
+)
+from petab.v1.measurements import (  # noqa: F401, E402
+    get_measurement_df,
+    write_measurement_df,
+)
+from petab.v1.observables import (  # noqa: F401, E402
+    get_observable_df,
+    write_observable_df,
+)
+from petab.v1.yaml import load_yaml  # noqa: F401, E402
+
 # import after v1
 from ..version import __version__  # noqa: F401, E402
 from . import (  # noqa: F401, E402
@@ -38,5 +38,5 @@
     write_experiment_df,
 )
 from .lint import lint_problem  # noqa: F401, E402
-from .models import Model  # noqa: F401, E402
-from .problem import Problem  # noqa: F401, E402
+from .models import MODEL_TYPE_PYSB, MODEL_TYPE_SBML, Model  # noqa: F401, E402
+from .problem import Problem, ProblemConfig  # noqa: F401, E402

petab/v2/petab1to2.py

@@ -1,5 +1,7 @@
 """Convert PEtab version 1 problems to version 2."""
 
+from __future__ import annotations
+
 import shutil
 from contextlib import suppress
 from itertools import chain
@@ -14,12 +16,13 @@
 from ..v1.yaml import get_path_prefix, load_yaml, validate
 from ..versions import get_major_version
 from .models import MODEL_TYPE_SBML
-from .problem import ProblemConfig
 
 __all__ = ["petab1to2"]
 
 
-def petab1to2(yaml_config: Path | str, output_dir: Path | str = None):
+def petab1to2(
+    yaml_config: Path | str, output_dir: Path | str = None
+) -> v2.Problem | None:
     """Convert from PEtab 1.0 to PEtab 2.0 format.
 
     Convert a PEtab problem from PEtab 1.0 to PEtab 2.0 format.
@@ -56,7 +59,7 @@ def petab1to2(yaml_config: Path | str, output_dir: Path | str = None):
 
     get_dest_path = lambda filename: f"{output_dir}/{filename}"  # noqa: E731
 
-    # Validate original PEtab problem
+    # Validate the original PEtab problem
     validate(yaml_config, path_prefix=path_prefix)
     if get_major_version(yaml_config) != 1:
         raise ValueError("PEtab problem is not version 1.")
@@ -72,7 +75,7 @@ def petab1to2(yaml_config: Path | str, output_dir: Path | str = None):
 
     # Update YAML file
     new_yaml_config = _update_yaml(yaml_config)
-    new_yaml_config = ProblemConfig(**new_yaml_config)
+    new_yaml_config = v2.ProblemConfig(**new_yaml_config)
 
     # Update tables
     # condition tables, observable tables, SBML files, parameter table:
@@ -218,7 +221,7 @@ def create_experiment_id(sim_cond_id: str, preeq_cond_id: str) -> str:
                 measurement_df, get_dest_path(measurement_file)
             )
 
-    # Write new YAML file
+    # Write the new YAML file
     new_yaml_file = output_dir / Path(yaml_file).name
     new_yaml_config.to_yaml(new_yaml_file)