fix API docs bug in pydantic autodoc

CHANGELOG.md

@@ -8,6 +8,7 @@
 - container configs: use correct key for conda configs ([#4269](https://github.com/nf-core/tools/pull/4269))
 - Coerce launch params_out to Path to fix AttributeError (#4299) ([#4317](https://github.com/nf-core/tools/pull/4317))
 - generate valid Markdown when piping schema docs to file ([#4319](https://github.com/nf-core/tools/pull/4319))
+- fix API docs bug in pydantic autodoc ([#4320](https://github.com/nf-core/tools/pull/4320))
 
 ### Linting
 

docs/api/_src/api/nf_core_yml.md

@@ -64,4 +64,5 @@ container-registry:
     :model-show-validator-members: false
     :model-show-field-summary: true
     :field-show-alias: true
+    :no-index:
 ```

docs/api/_src/api/pipelines/lint.md

@@ -12,7 +12,7 @@ See the [Lint Tests](/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests)
 ```
 
 ```{eval-rst}
-.. autoclass:: nf_core.lint.PipelineLint
+.. autoclass:: nf_core.pipelines.lint.PipelineLint
     :members: _lint_pipeline
     :private-members: _print_results, _get_results_md, _save_json_results, _wrap_quotes
     :show-inheritance:

docs/api/_src/api/pipelines/utils.md → docs/api/_src/api/pipelines/lint_utils.md

@@ -1,7 +1,7 @@
 # nf_core.pipelines.utils
 
 ```{eval-rst}
-.. automodule:: nf_core.pipelines.utils
+.. automodule:: nf_core.pipelines.lint_utils
     :members:
     :undoc-members:
     :show-inheritance:

nf_core/pipelines/create/utils.py

@@ -6,7 +6,7 @@
 from typing import Any
 
 import yaml
-from pydantic import ConfigDict, ValidationError, ValidationInfo, field_validator
+from pydantic import ValidationError, ValidationInfo, field_validator
 from textual import on
 from textual.app import ComposeResult
 from textual.containers import Grid, HorizontalScroll
@@ -18,6 +18,10 @@
 import nf_core
 from nf_core.utils import NFCoreTemplateConfig
 
+# Sphinx/autodoc triggers Pydantic model rebuilds which require `Dict` in this module's namespace.
+# Using the builtin dict (not typing.Dict) because Pydantic v2 only accepts the lowercase form.
+Dict = dict
+
 # Use ContextVar to define a context on the model initialization
 _init_context_var: ContextVar = ContextVar("_init_context_var", default=None)
 
@@ -41,8 +45,6 @@ def init_context(value: dict[str, Any]) -> Iterator[None]:
 class CreateConfig(NFCoreTemplateConfig):
     """Pydantic model for the nf-core create config."""
 
-    model_config = ConfigDict(extra="allow")
-
     def __init__(self, /, **data: Any) -> None:
         """Custom init method to allow using a context on the model initialization."""
         context = _init_context_var.get()