WIP: filenames to tables

Author: dweindl

petab/v2/core.py

@@ -279,6 +279,7 @@ class ObservableTable(BaseModel):
 
     #: List of observables.
     observables: list[Observable]
+    relpath: Path or None = Field(exclude=True)
 
     def __getitem__(self, observable_id: str) -> Observable:
         """Get an observable by ID."""
@@ -433,6 +434,7 @@ class ConditionTable(BaseModel):
 
     #: List of conditions.
     conditions: list[Condition] = []
+    relpath: Path or None = Field(exclude=True)
 
     def __getitem__(self, condition_id: str) -> Condition:
         """Get a condition by ID."""
@@ -607,6 +609,7 @@ class ExperimentTable(BaseModel):
 
     #: List of experiments.
     experiments: list[Experiment]
+    relpath: Path or None = Field(exclude=True)
 
     @classmethod
     def from_df(cls, df: pd.DataFrame) -> ExperimentTable:
@@ -767,6 +770,7 @@ class MeasurementTable(BaseModel):
 
     #: List of measurements.
     measurements: list[Measurement]
+    relpath: Path or None = Field(exclude=True)
 
     @classmethod
     def from_df(
@@ -851,6 +855,7 @@ class MappingTable(BaseModel):
 
     #: List of mappings.
     mappings: list[Mapping]
+    relpath: Path or None = Field(exclude=True)
 
     @classmethod
     def from_df(cls, df: pd.DataFrame) -> MappingTable:
@@ -1081,6 +1086,7 @@ class ParameterTable(BaseModel):
 
     #: List of parameters.
     parameters: list[Parameter]
+    relpath: Path or None = Field(exclude=True)
 
     @classmethod
     def from_df(cls, df: pd.DataFrame) -> ParameterTable:
@@ -1138,9 +1144,6 @@ def n_estimated(self) -> int:
         return sum(p.estimate for p in self.parameters)
 
 
-"""PEtab v2 problems."""
-
-
 class Problem:
     """
     PEtab parameter estimation problem
@@ -1267,11 +1270,6 @@ def from_yaml(
 
         validate_yaml_syntax(yaml_config)
 
-        def get_path(filename):
-            if base_path is None:
-                return filename
-            return f"{base_path}/{filename}"
-
         if (format_version := parse_version(yaml_config[C.FORMAT_VERSION]))[
             0
         ] != 2:
@@ -1311,27 +1309,28 @@ def get_path(filename):
             **yaml_config, base_path=base_path, filepath=yaml_file
         )
         parameter_tables = [
-            ParameterTable.from_tsv(get_path(f))
+            ParameterTable.from_tsv(f, base_path=base_path)
             for f in config.parameter_files
         ]
 
         if len(config.model_files or []) > 1:
-            # TODO https://github.com/PEtab-dev/libpetab-python/issues/6
+            # TODO https://github.com/PEtab-dev/libpetab-python/issues/392
             raise NotImplementedError(
                 "Support for multiple models is not yet implemented."
             )
         model = None
         if config.model_files:
             model_id, model_info = next(iter(config.model_files.items()))
             model = model_factory(
+                # TODO: store path
                 get_path(model_info.location),
                 model_info.language,
                 model_id=model_id,
             )
 
         measurement_tables = (
             [
-                MeasurementTable.from_tsv(get_path(f))
+                MeasurementTable.from_tsv(f, base_path)
                 for f in config.measurement_files
             ]
             if config.measurement_files
@@ -1340,7 +1339,7 @@ def get_path(filename):
 
         condition_tables = (
             [
-                ConditionTable.from_tsv(get_path(f))
+                ConditionTable.from_tsv(f, base_path)
                 for f in config.condition_files
             ]
             if config.condition_files
@@ -1349,7 +1348,7 @@ def get_path(filename):
 
         experiment_tables = (
             [
-                ExperimentTable.from_tsv(get_path(f))
+                ExperimentTable.from_tsv(f, base_path)
                 for f in config.experiment_files
             ]
             if config.experiment_files
@@ -1358,15 +1357,15 @@ def get_path(filename):
 
         observable_tables = (
             [
-                ObservableTable.from_tsv(get_path(f))
+                ObservableTable.from_tsv(f, base_path)
                 for f in config.observable_files
             ]
             if config.observable_files
             else None
         )
 
         mapping_tables = (
-            [MappingTable.from_tsv(get_path(f)) for f in config.mapping_files]
+            [MappingTable.from_tsv(f, base_path) for f in config.mapping_files]
             if config.mapping_files
             else None
         )