Enable passing the base path to Problem.from_yaml

When passing the problem configuration as `dict` to
`Problem.from_yaml`, one should be able to specify
the base path for resolving relative paths. See #324.

Closes #324

Author: dweindl

petab/v1/problem.py

@@ -251,21 +251,28 @@ def from_files(
         )
 
     @staticmethod
-    def from_yaml(yaml_config: dict | Path | str) -> Problem:
+    def from_yaml(
+        yaml_config: dict | Path | str, base_path: str | Path = None
+    ) -> Problem:
         """
         Factory method to load model and tables as specified by YAML file.
 
         Arguments:
             yaml_config: PEtab configuration as dictionary or YAML file name
+            base_path: Base directory or URL to resolve relative paths
         """
         if isinstance(yaml_config, Path):
             yaml_config = str(yaml_config)
 
-        get_path = lambda filename: filename  # noqa: E731
         if isinstance(yaml_config, str):
-            path_prefix = get_path_prefix(yaml_config)
+            if base_path is None:
+                base_path = get_path_prefix(yaml_config)
             yaml_config = yaml.load_yaml(yaml_config)
-            get_path = lambda filename: f"{path_prefix}/{filename}"  # noqa: E731
+
+        def get_path(filename):
+            if base_path is None:
+                return filename
+            return f"{base_path}/{filename}"
 
         if yaml.is_composite_problem(yaml_config):
             raise ValueError(

tests/v1/test_petab.py

@@ -862,11 +862,16 @@ def test_problem_from_yaml_v1_multiple_files():
                 observables_df, Path(tmpdir, f"observables{i}.tsv")
             )
 
-        petab_problem = petab.Problem.from_yaml(yaml_path)
+        petab_problem1 = petab.Problem.from_yaml(yaml_path)
 
-    assert petab_problem.measurement_df.shape[0] == 2
-    assert petab_problem.observable_df.shape[0] == 2
-    assert petab_problem.condition_df.shape[0] == 2
+        # test that we can load the problem from a dict with a custom base path
+        yaml_config = petab.v1.load_yaml(yaml_path)
+        petab_problem2 = petab.Problem.from_yaml(yaml_config, base_path=tmpdir)
+
+    for petab_problem in (petab_problem1, petab_problem2):
+        assert petab_problem.measurement_df.shape[0] == 2
+        assert petab_problem.observable_df.shape[0] == 2
+        assert petab_problem.condition_df.shape[0] == 2
 
 
 def test_get_required_parameters_for_parameter_table(petab_problem):