v2: Adapt to updated yaml schema (#394)

Basically, the `problems` list is disolved and its contents moved one level up.

See https://github.com/PEtab-dev/PEtab/pull/622/files

Related to #392.

Closes #391.

Author: dweindl

petab/petablint.py

@@ -179,14 +179,14 @@ def main():
             logger.error(e)
             sys.exit(1)
 
-        if petab.is_composite_problem(args.yaml_file_name):
-            # TODO: further checking:
-            #  https://github.com/ICB-DCM/PEtab/issues/191
-            #  problem = petab.CompositeProblem.from_yaml(args.yaml_file_name)
-            return
-
         match get_major_version(args.yaml_file_name):
             case 1:
+                if petab.is_composite_problem(args.yaml_file_name):
+                    # TODO: further checking:
+                    #  https://github.com/ICB-DCM/PEtab/issues/191
+                    #  petab.CompositeProblem.from_yaml(args.yaml_file_name)
+                    return
+
                 problem = petab.Problem.from_yaml(args.yaml_file_name)
                 ret = petab.lint.lint_problem(problem)
                 sys.exit(ret)

petab/schemas/petab_schema.v2.0.0.yaml

@@ -31,71 +31,47 @@ properties:
       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.
-  problems:
-    type: array
-    description: |
-      One or multiple PEtab problems (sets of model, condition, observable
-      and measurement files). If different model and data files are
-      independent, they can be specified as separate PEtab problems, which
-      may allow more efficient handling. Files in one problem cannot refer
-      to models entities or data specified inside another problem.
-    items:
 
-      type: object
-      description: |
-        A set of PEtab model, condition, observable and measurement
-        files and optional visualization files.
-      properties:
-
-        model_files:
-          type: object
-          description: One or multiple models
-
-          # the model ID
-          patternProperties:
-            "^[a-zA-Z_]\\w*$":
-              type: object
-              properties:
-                location:
-                  type: string
-                  description: Model file name or URL
-                language:
-                  type: string
-                  description: |
-                    Model language, e.g., 'sbml', 'cellml', 'bngl', 'pysb'
-              required:
-                - location
-                - language
-          additionalProperties: false
-
-        measurement_files:
-          description: List of PEtab measurement files.
-          $ref: "#/definitions/list_of_files"
-
-        condition_files:
-          description: List of PEtab condition files.
-          $ref: "#/definitions/list_of_files"
-
-        experiment_files:
-          description: List of PEtab experiment files.
-          $ref: "#/definitions/list_of_files"
-
-        observable_files:
-          description: List of PEtab observable files.
-          $ref: "#/definitions/list_of_files"
-
-        visualization_files:
-          description: List of PEtab visualization files.
-          $ref: "#/definitions/list_of_files"
-
-        mapping_file:
+  model_files:
+    type: object
+    description: One or multiple models
+
+    # the model ID
+    patternProperties:
+      "^[a-zA-Z_]\\w*$":
+        type: object
+        properties:
+          location:
             type: string
-            description: Optional PEtab mapping file name or URL.
+            description: Model file name or URL
+          language:
+            type: string
+            description: |
+              Model language, e.g., 'sbml', 'cellml', 'bngl', 'pysb'
+        required:
+          - location
+          - language
+    additionalProperties: false
+
+  measurement_files:
+    description: List of PEtab measurement files.
+    $ref: "#/definitions/list_of_files"
+
+  condition_files:
+    description: List of PEtab condition files.
+    $ref: "#/definitions/list_of_files"
+
+  experiment_files:
+    description: List of PEtab experiment files.
+    $ref: "#/definitions/list_of_files"
+
+  observable_files:
+    description: List of PEtab observable files.
+    $ref: "#/definitions/list_of_files"
 
-      required:
-        - model_files
-        - observable_files
-        - measurement_files
+  mapping_files:
+    description: List of PEtab mapping files.
+    $ref: "#/definitions/list_of_files"
 
   extensions:
     type: object
@@ -120,4 +96,6 @@ properties:
 required:
   - format_version
   - parameter_file
-  - problems
+  - model_files
+  - observable_files
+  - measurement_files

petab/v2/lint.py

@@ -216,13 +216,13 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         # TODO: we need some option for validating partial vs full problems
         # check for unset but required files
         missing_files = []
-        if not config.parameter_file:
+        if not config.parameter_files:
             missing_files.append("parameters")
 
-        if not [p.measurement_files for p in config.problems]:
+        if not config.measurement_files:
             missing_files.append("measurements")
 
-        if not [p.observable_files for p in config.problems]:
+        if not config.observable_files:
             missing_files.append("observables")
 
         if missing_files: