Simplify PEtab v2 schema (#658)

Be less repetitive.

And add pre-commit hook for schema validation.

Author: dweindl

.pre-commit-config.yaml

@@ -1,10 +1,16 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.36.0
+    hooks:
+      - id: check-metaschema
+        files: ^.*schema.*\.(yaml|json)$

doc/v2/_static/petab_schema_v2.yaml

@@ -1,17 +1,28 @@
 # For syntax see: https://json-schema.org/understanding-json-schema
 $schema: "https://json-schema.org/draft/2020-12/schema"
-description: PEtab parameter estimation problem config file schema
+description: PEtab 2.0 parameter estimation problem configuration schema.
+
+definitions:
+  list_of_files:
+    type: array
+    description: List of files.
+    items:
+      type: string
+      description: |
+        File name or URL, absolute or relative to the location of the PEtab
+        problem configuration file.
+  version_number:
+    type: string
+    pattern: ^([1-9][0-9]*!)?(0|[1-9][0-9]*)(\.(0|[1-9][0-9]*))*((a|b|rc)(0|[1-9][0-9]*))?(\.post(0|[1-9][0-9]*))?(\.dev(0|[1-9][0-9]*))?$
+    description: Version number.
 
 properties:
 
   format_version:
     anyOf:
-      - type: string
-        #  (corresponding to PEP 440).
-        pattern: ^([1-9][0-9]*!)?(0|[1-9][0-9]*)(\.(0|[1-9][0-9]*))*((a|b|rc)(0|[1-9][0-9]*))?(\.post(0|[1-9][0-9]*))?(\.dev(0|[1-9][0-9]*))?$
+      - $ref: "#/definitions/version_number"
       - type: integer
-
-    description: Version of the PEtab format
+    description: Version of the PEtab format.
 
   id:
     type: string
@@ -22,18 +33,12 @@ properties:
     pattern: "^[a-zA-Z_]\\w*$"
 
   parameter_files:
-    type: array
-    description: |
-      List of PEtab parameter files.
-
-    items:
-        type: string
-        description: |
-          File name (absolute or relative) or URL to a PEtab parameter table.
+    description: List of PEtab parameter files.
+    $ref: "#/definitions/list_of_files"
 
   model_files:
     type: object
-    description: One or multiple models
+    description: One or multiple models.
 
     # the model ID
     patternProperties:
@@ -42,7 +47,9 @@ properties:
         properties:
           location:
             type: string
-            description: Model file name or URL
+            description: |
+              Model file name or URL, absolute or relative to the location of
+              the PEtab problem configuration file.
           language:
             type: string
             description: |
@@ -53,44 +60,24 @@ properties:
     additionalProperties: false
 
   measurement_files:
-    type: array
     description: List of PEtab measurement files.
-
-    items:
-      type: string
-      description: PEtab measurement file name or URL.
+    $ref: "#/definitions/list_of_files"
 
   condition_files:
-    type: array
     description: List of PEtab condition files.
-
-    items:
-      type: string
-      description: PEtab condition file name or URL.
+    $ref: "#/definitions/list_of_files"
 
   experiment_files:
-    type: array
-    description: List of PEtab experiment files
-
-    items:
-      type: string
-      description: PEtab experiment file name or URL.
+    description: List of PEtab experiment files.
+    $ref: "#/definitions/list_of_files"
 
   observable_files:
-    type: array
     description: List of PEtab observable files.
-
-    items:
-      type: string
-      description: PEtab observable file name or URL.
+    $ref: "#/definitions/list_of_files"
 
   mapping_files:
-    type: array
     description: List of PEtab mapping files.
-
-    items:
-      type: string
-      description: PEtab mapping file name or URL.
+    $ref: "#/definitions/list_of_files"
 
   extensions:
     type: object
@@ -104,8 +91,7 @@ properties:
           Information on a specific extension
         properties:
           version:
-            type: string
-            pattern: ^([1-9][0-9]*!)?(0|[1-9][0-9]*)(\.(0|[1-9][0-9]*))*((a|b|rc)(0|[1-9][0-9]*))?(\.post(0|[1-9][0-9]*))?(\.dev(0|[1-9][0-9]*))?$
+            $ref: "#/definitions/version_number"
           required:
             type: boolean
             description: |