New validation API (#288)

For petab.v2, refactor the current validation setup to 
* be more modular
* allow PEtab extensions to register additional validation steps in the future
* make validation messages accessible programmatically (previously, they were logged directly)

Also:
* Make `petablint` work with both v1 and v2 problems.
* Add first validation rules that are specific to v2

Author: dweindl

doc/modules.rst

@@ -28,3 +28,6 @@ API Reference
    petab.v1.simplify
    petab.v1.visualize
    petab.v1.yaml
+   petab.v2
+   petab.v2.lint
+   petab.v2.problem

petab/petablint.py

@@ -8,8 +8,13 @@
 
 from colorama import Fore
 from colorama import init as init_colorama
+from jsonschema.exceptions import ValidationError as SchemaValidationError
 
 import petab
+from petab.v1.C import FORMAT_VERSION
+from petab.v2.lint import lint_problem
+from petab.versions import get_major_version
+from petab.yaml import validate
 
 logger = logging.getLogger(__name__)
 
@@ -153,13 +158,9 @@ def main():
         ch.setLevel(logging.WARN)
 
     if args.yaml_file_name:
-        from jsonschema.exceptions import ValidationError
-
-        from petab.yaml import validate
-
         try:
             validate(args.yaml_file_name)
-        except ValidationError as e:
+        except SchemaValidationError as e:
             logger.error(
                 "Provided YAML file does not adhere to PEtab " f"schema: {e}"
             )
@@ -171,38 +172,54 @@ def main():
             #  problem = petab.CompositeProblem.from_yaml(args.yaml_file_name)
             return
 
-        problem = petab.Problem.from_yaml(args.yaml_file_name)
-
-    else:
-        # DEPRECATED
-        logger.debug("Looking for...")
-        if args.sbml_file_name:
-            logger.debug(f"\tSBML model: {args.sbml_file_name}")
-        if args.condition_file_name:
-            logger.debug(f"\tCondition table: {args.condition_file_name}")
-        if args.observable_file_name:
-            logger.debug(f"\tObservable table: {args.observable_file_name}")
-        if args.measurement_file_name:
-            logger.debug(f"\tMeasurement table: {args.measurement_file_name}")
-        if args.parameter_file_name:
-            logger.debug(f"\tParameter table: {args.parameter_file_name}")
-        if args.visualization_file_name:
-            logger.debug(
-                "\tVisualization table: " f"{args.visualization_file_name}"
-            )
+        match get_major_version(args.yaml_file_name):
+            case 1:
+                problem = petab.Problem.from_yaml(args.yaml_file_name)
+                ret = petab.lint.lint_problem(problem)
+                sys.exit(ret)
+            case 2:
+                validation_issues = lint_problem(args.yaml_file_name)
+                if validation_issues:
+                    validation_issues.log(logger=logger)
+                    sys.exit(1)
+                logger.info("PEtab format check completed successfully.")
+                sys.exit(0)
+            case _:
+                logger.error(
+                    "The provided PEtab files are of unsupported version "
+                    f"or the `{FORMAT_VERSION}` field is missing in the yaml "
+                    "file."
+                )
+
+    # DEPRECATED - only supported for v1
+    logger.debug("Looking for...")
+    if args.sbml_file_name:
+        logger.debug(f"\tSBML model: {args.sbml_file_name}")
+    if args.condition_file_name:
+        logger.debug(f"\tCondition table: {args.condition_file_name}")
+    if args.observable_file_name:
+        logger.debug(f"\tObservable table: {args.observable_file_name}")
+    if args.measurement_file_name:
+        logger.debug(f"\tMeasurement table: {args.measurement_file_name}")
+    if args.parameter_file_name:
+        logger.debug(f"\tParameter table: {args.parameter_file_name}")
+    if args.visualization_file_name:
+        logger.debug(
+            "\tVisualization table: " f"{args.visualization_file_name}"
+        )
 
-        try:
-            problem = petab.Problem.from_files(
-                sbml_file=args.sbml_file_name,
-                condition_file=args.condition_file_name,
-                measurement_file=args.measurement_file_name,
-                parameter_file=args.parameter_file_name,
-                observable_files=args.observable_file_name,
-                visualization_files=args.visualization_file_name,
-            )
-        except FileNotFoundError as e:
-            logger.error(e)
-            sys.exit(1)
+    try:
+        problem = petab.Problem.from_files(
+            sbml_file=args.sbml_file_name,
+            condition_file=args.condition_file_name,
+            measurement_file=args.measurement_file_name,
+            parameter_file=args.parameter_file_name,
+            observable_files=args.observable_file_name,
+            visualization_files=args.visualization_file_name,
+        )
+    except FileNotFoundError as e:
+        logger.error(e)
+        sys.exit(1)
 
     ret = petab.lint.lint_problem(problem)
     sys.exit(ret)