Apply ruff/pygrep-hooks rule PGH003 (#708)

Use specific rule codes when ignoring type issues

Author: DimitriPapadopoulos

.github/workflows/create_workflows.py

@@ -27,7 +27,7 @@
 import argparse
 from pathlib import Path
 
-import yaml  # type: ignore
+import yaml
 from jinja2 import Environment, FileSystemLoader, select_autoescape
 
 apt_based = [

neurodocker/reproenv/renderers.py

@@ -660,8 +660,7 @@ def copy(
 
     @_log_instruction
     def env(self, **kwds: str) -> SingularityRenderer:
-        # TODO: why does this raise a type error?
-        self._environment.extend(kwds.items())  # type: ignore
+        self._environment.extend(kwds.items())
         return self
 
     @_log_instruction
@@ -695,10 +694,7 @@ def install(self, pkgs: list[str], opts=None) -> SingularityRenderer:
 
     @_log_instruction
     def label(self, **kwds: str) -> SingularityRenderer:
-        # TODO: why are we getting this error?
-        # Argument 1 to "update" of "dict" has incompatible type
-        # "Dict[str, Mapping[str, str]]"; expected "Mapping[str, str]"
-        self._labels.update(kwds)  # type: ignore
+        self._labels.update(kwds)
         return self
 
     @_log_instruction

neurodocker/reproenv/state.py

@@ -16,7 +16,7 @@
 try:
     from yaml import CSafeLoader as SafeLoader
 except ImportError:  # pragma: no cover
-    from yaml import SafeLoader  # type: ignore  # pragma: no cover
+    from yaml import SafeLoader  # type: ignore[assignment]  # pragma: no cover
 
 from neurodocker.reproenv.exceptions import (
     RendererError,

neurodocker/reproenv/template.py

@@ -220,7 +220,7 @@ def versions(self) -> set[str]:
     def dependencies(self, pkg_manager: str) -> list[str]:
         deps_dict = self._template.get("dependencies", {})
         # TODO: not sure why the following line raises a type error in mypy.
-        return deps_dict.get(pkg_manager, [])  # type: ignore
+        return deps_dict.get(pkg_manager, [])  # type: ignore[return-value]
 
     def install(self, pkgs: list[str], opts: str = None) -> str:
         raise NotImplementedError(