Merge pull request #3189 from mashehu/sync-modules

add API docs for .nf-core.yml

docs/api/_src/api/utils.md

@@ -0,0 +1,9 @@
+# nf_core.utils
+
+```{eval-rst}
+.. automodule:: nf_core.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:
+```

docs/api/_src/conf.py

@@ -40,7 +40,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ["myst_parser", "sphinx.ext.autodoc", "sphinx.ext.napoleon"]
+extensions = ["myst_parser", "sphinx.ext.autodoc", "sphinx.ext.napoleon", "sphinxcontrib.autodoc_pydantic"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["./_templates"]

docs/api/requirements.txt

@@ -1,3 +1,4 @@
+autodoc_pydantic
 Sphinx>=3.3.1
 sphinxcontrib-napoleon
 sphinx-markdown-builder

nf_core/modules/modules_json.py

@@ -432,7 +432,7 @@ def move_component_to_local(self, component_type: str, component: str, repo_name
             to_name += f"-{datetime.datetime.now().strftime('%y%m%d%H%M%S')}"
         shutil.move(str(current_path), local_dir / to_name)
 
-    def unsynced_components(self) -> Tuple[List[str], List[str], dict]:
+    def unsynced_components(self) -> Tuple[List[str], List[str], Dict]:
         """
         Compute the difference between the modules/subworkflows in the directory and the
         modules/subworkflows in the 'modules.json' file. This is done by looking at all

nf_core/utils.py

@@ -1050,15 +1050,26 @@ def get_repo_releases_branches(pipeline, wfs):
 
 
 class NFCoreTemplateConfig(BaseModel):
+    """Template configuration schema"""
+
     org: Optional[str] = None
+    """ Organisation name """
     name: Optional[str] = None
+    """ Pipeline name """
     description: Optional[str] = None
+    """ Pipeline description """
     author: Optional[str] = None
+    """ Pipeline author """
     version: Optional[str] = None
+    """ Pipeline version """
     force: Optional[bool] = True
+    """ Force overwrite of existing files """
     outdir: Optional[Union[str, Path]] = None
+    """ Output directory """
     skip_features: Optional[list] = None
+    """ Skip features. See https://nf-co.re/docs/nf-core-tools/pipelines/create for a list of features. """
     is_nfcore: Optional[bool] = None
+    """ Whether the pipeline is an nf-core pipeline. """
 
     # convert outdir to str
     @field_validator("outdir")
@@ -1081,13 +1092,22 @@ 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."""
 
     def __getitem__(self, item: str) -> Any:
         return getattr(self, item)