From 883bd8a0fd779e3d8cbfa7b76b4933a8553d06d4 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jun 2026 11:34:16 +0200 Subject: [PATCH 1/4] fix sphinx breaking bug --- docs/api/_src/api/nf_core_yml.md | 1 + nf_core/pipelines/create/utils.py | 8 +++++--- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/docs/api/_src/api/nf_core_yml.md b/docs/api/_src/api/nf_core_yml.md index d264948f4b..ab03b23304 100644 --- a/docs/api/_src/api/nf_core_yml.md +++ b/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: ``` diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index 5751ddbd77..d7609126ac 100644 --- a/nf_core/pipelines/create/utils.py +++ b/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() From c170a767280c41fb6e81384f4e07451932500b28 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 10 Jun 2026 10:32:27 +0200 Subject: [PATCH 2/4] rename pipelines/utils to correct pipelines/lint_utils --- docs/api/_src/api/pipelines/{utils.md => lint_utils.md} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename docs/api/_src/api/pipelines/{utils.md => lint_utils.md} (73%) diff --git a/docs/api/_src/api/pipelines/utils.md b/docs/api/_src/api/pipelines/lint_utils.md similarity index 73% rename from docs/api/_src/api/pipelines/utils.md rename to docs/api/_src/api/pipelines/lint_utils.md index 36c2ecca4d..f74c103ad3 100644 --- a/docs/api/_src/api/pipelines/utils.md +++ b/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: From 863168a8138d0de2cc227512155786c5d51e3dad Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 10 Jun 2026 10:45:10 +0200 Subject: [PATCH 3/4] fix path for PipelineLint in API docs --- docs/api/_src/api/pipelines/lint.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/api/_src/api/pipelines/lint.md b/docs/api/_src/api/pipelines/lint.md index 91b37c26f6..9fdfba0812 100644 --- a/docs/api/_src/api/pipelines/lint.md +++ b/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: From d8351f20504bb2c52271144d81c8b35966864cda Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 11 Jun 2026 08:22:25 +0000 Subject: [PATCH 4/4] [automated] Update CHANGELOG.md [skip ci] --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 584ff96191..7ebe6ba66d 100644 --- a/CHANGELOG.md +++ b/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