add types, include review comments, add pydantic mypy plugin

.pre-commit-config.yaml

@@ -28,3 +28,4 @@ repos:
           - types-jsonschema
           - types-Markdown
           - types-setuptools
+          - pydantic

mypy.ini

@@ -1,3 +1,4 @@
 [mypy]
 warn_unused_configs = True
 ignore_missing_imports = true
+plugins = pydantic.mypy

nf_core/components/components_command.py

@@ -254,7 +254,11 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
                 # Update path in modules.json if the file is in the correct format
                 modules_json = ModulesJson(self.directory)
                 modules_json.load()
-                if modules_json.has_git_url_and_modules() and modules_json.modules_json is not None:
+                if (
+                    modules_json.has_git_url_and_modules()
+                    and self.modules_repo.repo_path is not None
+                    and modules_json.modules_json is not None
+                ):
                     modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][
                         self.modules_repo.repo_path
                     ][module_name]["patch"] = str(patch_path.relative_to(Path(self.directory).resolve()))

nf_core/components/components_utils.py

@@ -77,7 +77,7 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P
             ).unsafe_ask()
             log.info("To avoid this prompt in the future, add the 'org_path' key to a root '%s' file.", config_fn.name)
             if rich.prompt.Confirm.ask("[bold][blue]?[/] Would you like me to add this config now?", default=True):
-                with open(str(config_fn), "a+") as fh:
+                with open(config_fn, "a+") as fh:
                     fh.write(f"org_path: {org}\n")
                     log.info(f"Config added to '{config_fn.name}'")
 

nf_core/components/info.py

@@ -107,7 +107,7 @@ def init_mod_name(self, component):
                 elif self.repo_type == "pipeline":
                     assert self.modules_json is not None  # mypy
                     all_components = self.modules_json.get_all_components(self.component_type).get(
-                        self.modules_repo.remote_url, []
+                        self.modules_repo.remote_url, {}
                     )
                     components = [
                         component if directory == self.modules_repo.repo_path else f"{directory}/{component}"

nf_core/components/lint/__init__.py

@@ -22,6 +22,7 @@
 from nf_core.components.nfcore_component import NFCoreComponent
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.pipelines.lint_utils import console
+from nf_core.utils import LintConfigType
 from nf_core.utils import plural_s as _s
 
 log = logging.getLogger(__name__)
@@ -77,8 +78,8 @@ def __init__(
         self.failed: List[LintResult] = []
         self.all_local_components: List[NFCoreComponent] = []
 
-        self.lint_config = None
-        self.modules_json = None
+        self.lint_config: Optional[LintConfigType] = None
+        self.modules_json: Optional[ModulesJson] = None
 
         if self.component_type == "modules":
             self.lint_tests = self.get_all_module_lint_tests(self.repo_type == "pipeline")