Store problem configuration in v2.Problem (#338)

Introduces `v2.Problem.config` which contains the info from the PEtab yaml file.
The same as #326, but for `v2.Problem`.



---------

Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>

Author: dweindl

petab/v2/problem.py

@@ -12,6 +12,7 @@
 from typing import TYPE_CHECKING
 
 import pandas as pd
+from pydantic import AnyUrl, BaseModel, Field
 
 from ..v1 import (
     conditions,
@@ -25,6 +26,7 @@
     yaml,
 )
 from ..v1.models.model import Model, model_factory
+from ..v1.problem import ListOfFiles, VersionNumber
 from ..v1.yaml import get_path_prefix
 from ..v2.C import *  # noqa: F403
 from . import experiments
@@ -73,6 +75,7 @@ def __init__(
         observable_df: pd.DataFrame = None,
         mapping_df: pd.DataFrame = None,
         extensions_config: dict = None,
+        config: ProblemConfig = None,
     ):
         from ..v2.lint import default_validation_tasks
 
@@ -88,7 +91,7 @@ def __init__(
         self.validation_tasks: list[
             ValidationTask
         ] = default_validation_tasks.copy()
-
+        self.config = config
         if self.experiment_df is not None:
             warnings.warn(
                 "The experiment table is not yet supported and "
@@ -199,40 +202,37 @@ def get_path(filename):
                 "Consider using "
                 "petab.CompositeProblem.from_yaml() instead."
             )
+        config = ProblemConfig(
+            **yaml_config, base_path=base_path, filepath=yaml_file
+        )
+        problem0 = config.problems[0]
 
-        problem0 = yaml_config["problems"][0]
-
-        if isinstance(yaml_config[PARAMETER_FILE], list):
+        if isinstance(config.parameter_file, list):
             parameter_df = parameters.get_parameter_df(
-                [get_path(f) for f in yaml_config[PARAMETER_FILE]]
+                [get_path(f) for f in config.parameter_file]
             )
         else:
             parameter_df = (
-                parameters.get_parameter_df(
-                    get_path(yaml_config[PARAMETER_FILE])
-                )
-                if yaml_config[PARAMETER_FILE]
+                parameters.get_parameter_df(get_path(config.parameter_file))
+                if config.parameter_file
                 else None
             )
 
-        if len(problem0[MODEL_FILES] or []) > 1:
+        if len(problem0.model_files or []) > 1:
             # TODO https://github.com/PEtab-dev/libpetab-python/issues/6
             raise NotImplementedError(
                 "Support for multiple models is not yet implemented."
             )
-        if not problem0[MODEL_FILES]:
-            model = None
-        else:
-            model_id, model_info = next(iter(problem0[MODEL_FILES].items()))
+        model = None
+        if problem0.model_files:
+            model_id, model_info = next(iter(problem0.model_files.items()))
             model = model_factory(
-                get_path(model_info[MODEL_LOCATION]),
-                model_info[MODEL_LANGUAGE],
+                get_path(model_info.location),
+                model_info.language,
                 model_id=model_id,
             )
 
-        measurement_files = [
-            get_path(f) for f in problem0.get(MEASUREMENT_FILES, [])
-        ]
+        measurement_files = [get_path(f) for f in problem0.measurement_files]
         # If there are multiple tables, we will merge them
         measurement_df = (
             core.concat_tables(
@@ -242,19 +242,15 @@ def get_path(filename):
             else None
         )
 
-        condition_files = [
-            get_path(f) for f in problem0.get(CONDITION_FILES, [])
-        ]
+        condition_files = [get_path(f) for f in problem0.condition_files]
         # If there are multiple tables, we will merge them
         condition_df = (
             core.concat_tables(condition_files, conditions.get_condition_df)
             if condition_files
             else None
         )
 
-        experiment_files = [
-            get_path(f) for f in problem0.get(EXPERIMENT_FILES, [])
-        ]
+        experiment_files = [get_path(f) for f in problem0.experiment_files]
         # If there are multiple tables, we will merge them
         experiment_df = (
             core.concat_tables(experiment_files, experiments.get_experiment_df)
@@ -263,7 +259,7 @@ def get_path(filename):
         )
 
         visualization_files = [
-            get_path(f) for f in problem0.get(VISUALIZATION_FILES, [])
+            get_path(f) for f in problem0.visualization_files
         ]
         # If there are multiple tables, we will merge them
         visualization_df = (
@@ -272,17 +268,15 @@ def get_path(filename):
             else None
         )
 
-        observable_files = [
-            get_path(f) for f in problem0.get(OBSERVABLE_FILES, [])
-        ]
+        observable_files = [get_path(f) for f in problem0.observable_files]
         # If there are multiple tables, we will merge them
         observable_df = (
             core.concat_tables(observable_files, observables.get_observable_df)
             if observable_files
             else None
         )
 
-        mapping_files = [get_path(f) for f in problem0.get(MAPPING_FILES, [])]
+        mapping_files = [get_path(f) for f in problem0.mapping_files]
         # If there are multiple tables, we will merge them
         mapping_df = (
             core.concat_tables(mapping_files, mapping.get_mapping_df)
@@ -299,7 +293,7 @@ def get_path(filename):
             model=model,
             visualization_df=visualization_df,
             mapping_df=mapping_df,
-            extensions_config=yaml_config.get(EXTENSIONS, {}),
+            extensions_config=config.extensions,
         )
 
     @staticmethod
@@ -981,3 +975,49 @@ def add_experiment(self, id_: str, *args):
             if self.experiment_df is not None
             else tmp_df
         )
+
+
+class ModelFile(BaseModel):
+    """A file in the PEtab problem configuration."""
+
+    location: str | AnyUrl
+    language: str
+
+
+class SubProblem(BaseModel):
+    """A `problems` object in the PEtab problem configuration."""
+
+    model_files: dict[str, ModelFile] | None = {}
+    measurement_files: ListOfFiles = []
+    condition_files: ListOfFiles = []
+    experiment_files: ListOfFiles = []
+    observable_files: ListOfFiles = []
+    visualization_files: ListOfFiles = []
+    mapping_files: ListOfFiles = []
+
+
+class ExtensionConfig(BaseModel):
+    """The configuration of a PEtab extension."""
+
+    name: str
+    version: str
+    config: dict
+
+
+class ProblemConfig(BaseModel):
+    """The PEtab problem configuration."""
+
+    filepath: str | AnyUrl | None = Field(
+        None,
+        description="The path to the PEtab problem configuration.",
+        exclude=True,
+    )
+    base_path: str | AnyUrl | None = Field(
+        None,
+        description="The base path to resolve relative paths.",
+        exclude=True,
+    )
+    format_version: VersionNumber = "2.0.0"
+    parameter_file: str | AnyUrl | None = None
+    problems: list[SubProblem] = []
+    extensions: list[ExtensionConfig] = []