v2: Store path info in *Table objects

Store path info in *Table and Model objects to make it easier to read, modify, write complete PEtab problem.

Add `Problem.to_files()`.

Closes #412.

Author: dweindl

petab/_utils.py

@@ -0,0 +1,35 @@
+"""Private, version-independent utility functions for PEtab."""
+
+from pathlib import Path
+
+from pydantic import AnyUrl, TypeAdapter
+
+PathOrUrlAdapter = TypeAdapter(AnyUrl | Path)
+
+
+def _generate_path(
+    file_path: str | Path | AnyUrl,
+    base_path: Path | str | AnyUrl | None = None,
+) -> str:
+    """
+    Generate a local path or URL from a file path and an optional base path.
+
+    :return: A string representing the relative or absolute path or URL.
+        Absolute if `file_path` or `base_path` is an absolute path or URL,
+        relative otherwise.
+    """
+    if base_path is None:
+        return str(file_path)
+
+    file_path = PathOrUrlAdapter.validate_python(file_path)
+    if isinstance(file_path, AnyUrl):
+        # if URL, this is absolute
+        return str(file_path)
+
+    base_path = PathOrUrlAdapter.validate_python(base_path)
+    if isinstance(base_path, Path):
+        # if file_path is absolute, base_path will be ignored
+        return str(base_path / file_path)
+
+    # combine URL parts
+    return f"{base_path}/{file_path}"

petab/v1/models/model.py

@@ -21,17 +21,22 @@ def __repr__(self):
 
     @staticmethod
     @abc.abstractmethod
-    def from_file(filepath_or_buffer: Any, model_id: str) -> Model:
+    def from_file(
+        filepath_or_buffer: Any, model_id: str, base_path: str | Path = None
+    ) -> Model:
         """Load the model from the given path/URL
 
-        :param filepath_or_buffer: URL or path of the model
+        :param filepath_or_buffer:
+            Absolute or relative path/URL to the model file.
+            If relative, it is interpreted relative to `base_path` if given.
+        :param base_path: Base path for relative paths in the model file.
         :param model_id: Model ID
         :returns: A ``Model`` instance holding the given model
         """
         ...
 
     @abc.abstractmethod
-    def to_file(self, filename: [str, Path]):
+    def to_file(self, filename: str | Path | None = None):
         """Save the model to the given file
 
         :param filename: Destination filename
@@ -131,11 +136,16 @@ def is_state_variable(self, id_: str) -> bool:
 
 
 def model_factory(
-    filepath_or_buffer: Any, model_language: str, model_id: str = None
+    filepath_or_buffer: Any,
+    model_language: str,
+    model_id: str = None,
+    base_path: str | Path = None,
 ) -> Model:
     """Create a PEtab model instance from the given model
 
-    :param filepath_or_buffer: Path/URL of the model
+    :param filepath_or_buffer: Path/URL of the model.
+        Absolute or relative to `base_path` if given.
+    :param base_path: Base path for relative paths in the model file.
     :param model_language: PEtab model language ID for the given model
     :param model_id: PEtab model ID for the given model
     :returns: A :py:class:`Model` instance representing the given model
@@ -145,12 +155,16 @@ def model_factory(
     if model_language == MODEL_TYPE_SBML:
         from .sbml_model import SbmlModel
 
-        return SbmlModel.from_file(filepath_or_buffer, model_id=model_id)
+        return SbmlModel.from_file(
+            filepath_or_buffer, model_id=model_id, base_path=base_path
+        )
 
     if model_language == MODEL_TYPE_PYSB:
         from .pysb_model import PySBModel
 
-        return PySBModel.from_file(filepath_or_buffer, model_id=model_id)
+        return PySBModel.from_file(
+            filepath_or_buffer, model_id=model_id, base_path=base_path
+        )
 
     if model_language in known_model_types:
         raise NotImplementedError(

petab/v1/models/pysb_model.py

@@ -1,5 +1,7 @@
 """Functions for handling PySB models"""
 
+from __future__ import annotations
+
 import itertools
 import re
 import sys
@@ -9,6 +11,7 @@
 
 import pysb
 
+from ..._utils import _generate_path
 from .. import is_valid_identifier
 from . import MODEL_TYPE_PYSB
 from .model import Model
@@ -54,9 +57,18 @@ class PySBModel(Model):
 
     type_id = MODEL_TYPE_PYSB
 
-    def __init__(self, model: pysb.Model, model_id: str = None):
+    def __init__(
+        self,
+        model: pysb.Model,
+        model_id: str = None,
+        rel_path: Path | str | None = None,
+        base_path: str | Path | None = None,
+    ):
         super().__init__()
 
+        self.rel_path = rel_path
+        self.base_path = base_path
+
         self.model = model
         self._model_id = model_id or self.model.name
 
@@ -68,16 +80,25 @@ def __init__(self, model: pysb.Model, model_id: str = None):
             )
 
     @staticmethod
-    def from_file(filepath_or_buffer, model_id: str = None):
+    def from_file(
+        filepath_or_buffer, model_id: str = None, base_path: str | Path = None
+    ) -> PySBModel:
         return PySBModel(
-            model=_pysb_model_from_path(filepath_or_buffer), model_id=model_id
+            model=_pysb_model_from_path(
+                _generate_path(filepath_or_buffer, base_path)
+            ),
+            model_id=model_id,
+            rel_path=filepath_or_buffer,
+            base_path=base_path,
         )
 
-    def to_file(self, filename: [str, Path]):
+    def to_file(self, filename: str | Path | None = None) -> None:
         from pysb.export import export
 
         model_source = export(self.model, "pysb_flat")
-        with open(filename, "w") as f:
+        with open(
+            filename or _generate_path(self.rel_path, self.base_path), "w"
+        ) as f:
             f.write(model_source)
 
     @property

petab/v1/models/sbml_model.py

@@ -10,6 +10,7 @@
 import sympy as sp
 from sympy.abc import _clash
 
+from ..._utils import _generate_path
 from ..sbml import (
     get_sbml_model,
     is_sbml_consistent,
@@ -33,6 +34,8 @@ def __init__(
         sbml_reader: libsbml.SBMLReader = None,
         sbml_document: libsbml.SBMLDocument = None,
         model_id: str = None,
+        rel_path: Path | str | None = None,
+        base_path: str | Path | None = None,
     ):
         """Constructor.
 
@@ -42,6 +45,9 @@ def __init__(
         :param model_id: Model ID. Defaults to the SBML model ID."""
         super().__init__()
 
+        self.rel_path = rel_path
+        self.base_path = base_path
+
         if sbml_model is None and sbml_document is None:
             raise ValueError(
                 "Either sbml_model or sbml_document must be given."
@@ -87,15 +93,19 @@ def __setstate__(self, state):
         self.__dict__.update(state)
 
     @staticmethod
-    def from_file(filepath_or_buffer, model_id: str = None) -> SbmlModel:
+    def from_file(
+        filepath_or_buffer, model_id: str = None, base_path: str | Path = None
+    ) -> SbmlModel:
         sbml_reader, sbml_document, sbml_model = get_sbml_model(
-            filepath_or_buffer
+            _generate_path(filepath_or_buffer, base_path=base_path)
         )
         return SbmlModel(
             sbml_model=sbml_model,
             sbml_reader=sbml_reader,
             sbml_document=sbml_document,
             model_id=model_id,
+            rel_path=filepath_or_buffer,
+            base_path=base_path,
         )
 
     @staticmethod
@@ -159,9 +169,10 @@ def model_id(self):
     def model_id(self, model_id):
         self._model_id = model_id
 
-    def to_file(self, filename: [str, Path]):
+    def to_file(self, filename: str | Path | None = None) -> None:
         write_sbml(
-            self.sbml_document or self.sbml_model.getSBMLDocument(), filename
+            self.sbml_document or self.sbml_model.getSBMLDocument(),
+            filename or _generate_path(self.rel_path, self.base_path),
         )
 
     def get_parameter_value(self, id_: str) -> float: