Optional relative paths in generated YAML (#57)

* optional (default True) relative paths in generated YAML

Co-authored-by: Yannik Schälte <[email protected]>

Author: dilpath

petab/problem.py

@@ -271,7 +271,8 @@ def to_files(self,
                  parameter_file: Optional[str] = None,
                  visualization_file: Optional[str] = None,
                  observable_file: Optional[str] = None,
-                 yaml_file: Optional[str] = None) -> None:
+                 yaml_file: Optional[str] = None,
+                 relative_paths: bool = True,) -> None:
         """
         Write PEtab tables to files for this problem
 
@@ -289,6 +290,9 @@ def to_files(self,
             visualization_file: Visualization table destination
             observable_file: Observables table destination
             yaml_file: YAML file destination
+            relative_paths: whether all paths in the YAML file should be
+            relative to the location of the YAML file. If `False`, then paths
+            are left unchanged.
 
         Raises:
             ValueError:
@@ -344,7 +348,8 @@ def error(name: str) -> ValueError:
             yaml.create_problem_yaml(sbml_file, condition_file,
                                      measurement_file, parameter_file,
                                      observable_file, yaml_file,
-                                     visualization_file)
+                                     visualization_file,
+                                     relative_paths=relative_paths,)
 
     def get_optimization_parameters(self):
         """

petab/yaml.py

@@ -1,6 +1,7 @@
 """Code regarding the PEtab YAML config files"""
 
 import os
+from pathlib import Path
 from typing import Any, Dict, Union, Optional, List
 
 import jsonschema
@@ -172,14 +173,16 @@ def write_yaml(yaml_config: Dict[str, Any], filename: str) -> None:
                   sort_keys=False)
 
 
-def create_problem_yaml(sbml_files: Union[str, List[str]],
-                        condition_files: Union[str, List[str]],
-                        measurement_files: Union[str, List[str]],
-                        parameter_file: str,
-                        observable_files: Union[str, List[str]],
-                        yaml_file: str,
-                        visualization_files: Optional[Union[str, List[str]]]
-                        = None) -> None:
+def create_problem_yaml(
+        sbml_files: Union[str, List[str]],
+        condition_files: Union[str, List[str]],
+        measurement_files: Union[str, List[str]],
+        parameter_file: str,
+        observable_files: Union[str, List[str]],
+        yaml_file: str,
+        visualization_files: Optional[Union[str, List[str]]] = None,
+        relative_paths: bool = True,
+) -> None:
     """
     Create and write default YAML file for a single PEtab problem
 
@@ -192,6 +195,9 @@ def create_problem_yaml(sbml_files: Union[str, List[str]],
         yaml_file: Path to which YAML file should be written
         visualization_files: Optional Path to visualization file or list of
         such
+        relative_paths: whether all paths in the YAML file should be relative
+        to the location of the YAML file. If `False`, then paths are left
+        unchanged.
     """
     if isinstance(sbml_files, str):
         sbml_files = [sbml_files]
@@ -204,6 +210,25 @@ def create_problem_yaml(sbml_files: Union[str, List[str]],
     if isinstance(visualization_files, str):
         visualization_files = [visualization_files]
 
+    if relative_paths:
+        yaml_file_dir = Path(yaml_file).parent
+
+        def get_rel_to_yaml(paths: Union[List[str], None]):
+            if paths is None:
+                return paths
+            return [
+                os.path.relpath(path, start=yaml_file_dir)
+                for path in paths
+            ]
+
+        sbml_files = get_rel_to_yaml(sbml_files)
+        condition_files = get_rel_to_yaml(condition_files)
+        measurement_files = get_rel_to_yaml(measurement_files)
+        observable_files = get_rel_to_yaml(observable_files)
+        visualization_files = get_rel_to_yaml(visualization_files)
+
+        parameter_file = get_rel_to_yaml([parameter_file])[0]
+
     problem_dic = {CONDITION_FILES: condition_files,
                    MEASUREMENT_FILES: measurement_files,
                    SBML_FILES: sbml_files,