v2: Adapt to long conditions table

Update creation of PEtab problems, validation, conversion from v1 to v2,... to the new long condition table.

Author: dweindl

petab/v1/__init__.py

@@ -4,6 +4,7 @@
 """
 
 from ..version import __version__  # noqa: F401, E402
+from . import models  # noqa: F401, E402
 from .C import *  # noqa: F403, F401, E402
 from .calculate import *  # noqa: F403, F401, E402
 from .composite_problem import *  # noqa: F403, F401, E402
@@ -13,6 +14,7 @@
 from .lint import *  # noqa: F403, F401, E402
 from .mapping import *  # noqa: F403, F401, E402
 from .measurements import *  # noqa: F403, F401, E402
+from .models import Model  # noqa: F401, E402
 from .observables import *  # noqa: F403, F401, E402
 from .parameter_mapping import *  # noqa: F403, F401, E402
 from .parameters import *  # noqa: F403, F401, E402

petab/v1/lint.py

@@ -67,7 +67,7 @@ def _check_df(df: pd.DataFrame, req_cols: Iterable, name: str) -> None:
     """
     if missing_cols := set(req_cols) - set(df.columns.values):
         raise AssertionError(
-            f"DataFrame {name} requires the columns {missing_cols}."
+            f"{name.capitalize()} table requires the columns {missing_cols}."
         )
 
 

petab/v2/C.py

@@ -136,7 +136,6 @@
 # TODO: removed?
 #: Condition name column in the condition table
 CONDITION_NAME = "conditionName"
-
 #: Column in the condition table with the ID of an entity that is changed
 TARGET_ID = "targetId"
 #: Column in the condition table with the type of value that is changed
@@ -166,6 +165,8 @@
     TARGET_VALUE,
 ]
 
+CONDITION_DF_REQUIRED_COLS = CONDITION_DF_COLS
+
 # EXPERIMENTS
 EXPERIMENT_DF_REQUIRED_COLS = [
     EXPERIMENT_ID,

petab/v2/__init__.py

@@ -4,17 +4,35 @@
 """
 from warnings import warn
 
-from ..v1 import *  # noqa: F403, F401, E402
-from .experiments import (  # noqa: F401
-    get_experiment_df,
-    write_experiment_df,
-)
-
-# import after v1
-from .problem import Problem  # noqa: F401
+# 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,
 )
+
+# import after v1
+from ..version import __version__  # noqa: F401, E402
+from . import models  # noqa: F401, E402
+from .conditions import *  # noqa: F403, F401, E402
+from .experiments import (  # noqa: F401, E402
+    get_experiment_df,
+    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

petab/v2/_helpers.py

@@ -0,0 +1,2 @@
+"""Various internal helper functions."""
+from ..v1.core import to_float_if_float  # noqa: F401, E402

petab/v2/conditions.py

@@ -0,0 +1,67 @@
+"""Functions operating on the PEtab condition table"""
+from __future__ import annotations
+
+from pathlib import Path
+
+import pandas as pd
+import sympy as sp
+
+from .. import v2
+from ..v1.math import sympify_petab
+from .C import *
+from .lint import assert_no_leading_trailing_whitespace
+
+__all__ = [
+    "get_condition_df",
+    "write_condition_df",
+]
+
+
+def get_condition_df(
+    condition_file: str | pd.DataFrame | Path | None,
+) -> pd.DataFrame | None:
+    """Read the provided condition file into a ``pandas.Dataframe``.
+
+    Arguments:
+        condition_file: File name of PEtab condition file or pandas.Dataframe
+    """
+    if condition_file is None:
+        return condition_file
+
+    if isinstance(condition_file, str | Path):
+        condition_file = pd.read_csv(
+            condition_file, sep="\t", float_precision="round_trip"
+        )
+
+    assert_no_leading_trailing_whitespace(
+        condition_file.columns.values, "condition"
+    )
+
+    return condition_file
+
+
+def write_condition_df(df: pd.DataFrame, filename: str | Path) -> None:
+    """Write PEtab condition table
+
+    Arguments:
+        df: PEtab condition table
+        filename: Destination file name
+    """
+    df = get_condition_df(df)
+    df.to_csv(filename, sep="\t", index=False)
+
+
+def get_condition_table_free_symbols(problem: v2.Problem) -> set[sp.Basic]:
+    """Free symbols from condition table assignments.
+
+    Collects all free symbols from the condition table `targetValue` column.
+
+    :returns: Set of free symbols.
+    """
+    if problem.condition_df is None:
+        return set()
+
+    free_symbols = set()
+    for target_value in problem.condition_df[TARGET_VALUE]:
+        free_symbols |= sympify_petab(target_value).free_symbols
+    return free_symbols