Fix pydantic dump

CHANGELOG.md

@@ -19,6 +19,7 @@
 
 - Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220))
 - create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226))
+- Fix pydantic dump ([#3227](https://github.com/nf-core/tools/pull/3227))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 

nf_core/utils.py

@@ -19,7 +19,7 @@
 import time
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union
+from typing import Any, Callable, Dict, Generator, List, Literal, Optional, Tuple, Union
 
 import git
 import prompt_toolkit.styles
@@ -30,7 +30,7 @@
 import rich.markup
 import yaml
 from packaging.version import Version
-from pydantic import BaseModel, ValidationError, field_validator
+from pydantic import BaseModel, Field, ValidationError, field_validator
 from rich.live import Live
 from rich.spinner import Spinner
 
@@ -1094,27 +1094,52 @@ def get(self, item: str, default: Any = None) -> Any:
 class NFCoreYamlConfig(BaseModel):
     """.nf-core.yml configuration file schema"""
 
-    repository_type: str
-    """ Type of repository: pipeline or modules """
-    nf_core_version: Optional[str] = None
-    """ Version of nf-core/tools used to create/update the pipeline"""
-    org_path: Optional[str] = None
-    """ Path to the organisation's modules repository (used for modules repo_type only) """
-    lint: Optional[LintConfigType] = None
-    """ Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation """
-    template: Optional[NFCoreTemplateConfig] = None
-    """ Pipeline template configuration """
-    bump_version: Optional[Dict[str, bool]] = None
-    """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information."""
-    update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = None
-    """ Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information."""
+    repository_type: Literal["pipeline", "modules"] = Field(..., description="Type of repository")
+    nf_core_version: Optional[str] = Field(
+        None, description="Version of nf-core/tools used to create/update the pipeline"
+    )
+    org_path: Optional[str] = Field(
+        None, description="Path to the organisation's modules repository (used for modules repo_type only)"
+    )
+    lint: Optional[LintConfigType] = Field(
+        None,
+        description="Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation",
+    )
+    template: Optional[NFCoreTemplateConfig] = Field(
+        None, description="Pipeline template configuration", exclude=repository_type == "modules"
+    )
+    bump_version: Optional[Dict[str, bool]] = Field(
+        None,
+        description="Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information.",
+    )
+    update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = Field(
+        None,
+        description="Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information.",
+    )
 
     def __getitem__(self, item: str) -> Any:
         return getattr(self, item)
 
     def get(self, item: str, default: Any = None) -> Any:
         return getattr(self, item, default)
 
+    def model_dump(self, **kwargs) -> Dict[str, Any]:
+        # Get the initial data
+        config = super().model_dump(**kwargs)
+
+        if self.repository_type == "modules":
+            # Fields to exclude for modules
+            fields_to_exclude = ["template", "update"]
+        else:  # pipeline
+            # Fields to exclude for pipeline
+            fields_to_exclude = ["bump_version"]
+
+        # Remove the fields based on repository_type
+        for field in fields_to_exclude:
+            config.pop(field, None)
+
+        return config
+
 
 def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path], Optional[NFCoreYamlConfig]]:
     """

tests/pipelines/lint/test_nfcore_yml.py

@@ -33,7 +33,9 @@ def test_nfcore_yml_fail_repo_type(self):
         with open(self.nf_core_yml, "w") as fh:
             fh.write(new_content)
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
+        # assert that it raises assertion error
+        with self.assertRaises(AssertionError):
+            lint_obj._load()
         results = lint_obj.nfcore_yml()
         assert "Repository type in `.nf-core.yml` is not valid." in str(results["failed"])
         assert len(results.get("warned", [])) == 0