fix linting

Author: nvnieuwk

nf_core/components/nfcore_component.py

@@ -299,7 +299,7 @@ def get_topics_from_main_nf(self) -> None:
         with open(self.main_nf) as f:
             data = f.read()
         if self.component_type == "modules":
-            topics = {}
+            topics: dict[str, list[dict[str, dict] | list[dict[str, dict[str, str]]]]] = {}
             # get topic name from main.nf after "output:". the names are always after "topic:"
             if "output:" not in data:
                 log.debug(f"Could not find any outputs in {self.main_nf}")
@@ -313,7 +313,7 @@ def get_topics_from_main_nf(self) -> None:
                 matches_elements = re.finditer(regex_elements, line)
                 if not match_topic:
                     continue
-                channel_elements = []
+                channel_elements: list[dict[str, dict]] = []
                 topic_name = match_topic.group(1)
                 if topic_name in topics:
                     continue

nf_core/modules/lint/main_nf.py

@@ -720,7 +720,7 @@ def _parse_input(self, line_raw):
     return inputs
 
 
-def _parse_output_emits(self, line:str) -> list[str]:
+def _parse_output_emits(self, line: str) -> list[str]:
     output = []
     if "meta" in line:
         output.append("meta")
@@ -732,7 +732,7 @@ def _parse_output_emits(self, line:str) -> list[str]:
     return output
 
 
-def _parse_output_topics(self, line:str) -> list[str]:
+def _parse_output_topics(self, line: str) -> list[str]:
     output = []
     if "meta" in line:
         output.append("meta")

tests/modules/lint/test_main_nf.py

@@ -115,7 +115,6 @@ def setUp(self):
         if not self.mods_install.install("bamstats/generalstats"):
             self.skipTest("Could not install samtools/sort module")
 
-
     def test_main_nf_lint_with_alternative_registry(self):
         """Test main.nf linting with alternative container registry"""
         # Test with alternative registry - should warn/fail when containers don't match the registry
@@ -142,12 +141,16 @@ def test_topics_and_emits_version_check(self):
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
         module_lint.lint(print_results=False, module="samtools/sort")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-        assert len(module_lint.warned) == 2, f"Linting warned with {[x.__dict__ for x in module_lint.warned]}, expected 2 warnings"
+        assert len(module_lint.warned) == 2, (
+            f"Linting warned with {[x.__dict__ for x in module_lint.warned]}, expected 2 warnings"
+        )
         assert len(module_lint.passed) > 0
-        
+
         # Lint a module known to have topics as output in main.nf
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
         module_lint.lint(print_results=False, module="bamstats/generalstats")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-        assert len(module_lint.warned) == 0, f"Linting warned with {[x.__dict__ for x in module_lint.warned]}, expected 1 warning"
-        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) == 0, (
+            f"Linting warned with {[x.__dict__ for x in module_lint.warned]}, expected 1 warning"
+        )
+        assert len(module_lint.passed) > 0