Merge branch 'main' into v2_rm_vis

Author: dweindl

petab/schemas/petab_schema.v2.0.0.yaml

@@ -23,14 +23,14 @@ properties:
       - type: integer
     description: Version of the PEtab format
 
-  parameter_file:
-    oneOf:
-    - type: string
-    - type: array
+  parameter_files:
+    type: array
     description: |
-      File name (absolute or relative) or URL to PEtab parameter table
-      containing parameters of all models listed in `problems`. A single
-      table may be split into multiple files and described as an array here.
+      List of PEtab parameter files.
+    items:
+      type: string
+      description: |
+        File name (absolute or relative) or URL to a PEtab parameter table.
 
   model_files:
     type: object
@@ -95,7 +95,7 @@ properties:
 
 required:
   - format_version
-  - parameter_file
+  - parameter_files
   - model_files
   - observable_files
   - measurement_files

petab/v2/C.py

@@ -236,8 +236,8 @@
 # YAML
 #: PEtab version key in the YAML file
 FORMAT_VERSION = "format_version"
-#: Parameter file key in the YAML file
-PARAMETER_FILE = "parameter_file"
+#: Parameter files key in the YAML file
+PARAMETER_FILES = "parameter_files"
 #: Problems key in the YAML file
 PROBLEMS = "problems"
 #: Model files key in the YAML file

petab/v2/petab1to2.py

@@ -95,8 +95,9 @@ def petab_files_1to2(yaml_config: Path | str, output_dir: Path | str):
 
     # parameter table
     parameter_df = v1v2_parameter_df(petab_problem.parameter_df.copy())
-    file = yaml_config[v2.C.PARAMETER_FILE]
-    v2.write_parameter_df(parameter_df, get_dest_path(file))
+    v2.write_parameter_df(
+        parameter_df, get_dest_path(new_yaml_config.parameter_files[0])
+    )
 
     # copy files that don't need conversion: models
     for file in (
@@ -290,6 +291,15 @@ def _update_yaml(yaml_config: dict) -> dict:
             if file_type in problem:
                 yaml_config[file_type] = problem[file_type]
                 del problem[file_type]
+    del yaml_config[v1.C.PROBLEMS]
+
+    # parameter_file -> parameter_files
+    if not isinstance(
+        (par_files := yaml_config.pop(v1.C.PARAMETER_FILE, [])), list
+    ):
+        par_files = [par_files]
+    yaml_config[v2.C.PARAMETER_FILES] = par_files
+
     return yaml_config
 
 

petab/v2/problem.py

@@ -1277,7 +1277,7 @@ class ProblemConfig(BaseModel):
     #  rename to parameter_files in yaml for consistency with other files?
     #   always a list?
     parameter_files: list[str | AnyUrl] = Field(
-        default=[], alias=PARAMETER_FILE
+        default=[], alias=PARAMETER_FILES
     )
 
     # TODO: consider changing str to Path

tests/v2/test_problem.py

@@ -67,7 +67,7 @@ def test_problem_from_yaml_multiple_files():
     """
     yaml_config = """
     format_version: 2.0.0
-    parameter_file: []
+    parameter_files: []
     condition_files: [conditions1.tsv, conditions2.tsv]
     measurement_files: [measurements1.tsv, measurements2.tsv]
     observable_files: [observables1.tsv, observables2.tsv]