handle dicts during dependency sorting correctly

Author: mashehu

nf_core/modules/lint/environment_yml.py

@@ -83,7 +83,28 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
 
         if valid_env_yml:
             # Check that the dependencies section is sorted alphabetically
-            if sorted(env_yml["dependencies"]) == env_yml["dependencies"]:
+            def sort_recursively(obj):
+                """Simple recursive sort for nested structures."""
+                if isinstance(obj, list):
+
+                    def get_key(x):
+                        if isinstance(x, dict):
+                            # For dicts like {"pip": [...]}, use the key "pip"
+                            return (list(x.keys())[0], 1)
+                        else:
+                            # For strings like "pip=23.3.1", use "pip" and for bioconda::samtools=1.15.1, use "bioconda::samtools"
+                            return (str(x).split("=")[0], 0)
+
+                    return sorted([sort_recursively(item) for item in obj], key=get_key)
+                elif isinstance(obj, dict):
+                    return {k: sort_recursively(v) for k, v in obj.items()}
+                else:
+                    return obj
+
+            sorted_dependencies = sort_recursively(env_yml["dependencies"])
+
+            # Direct comparison of sorted vs original dependencies
+            if sorted_dependencies == env_yml["dependencies"]:
                 module.passed.append(
                     (
                         "environment_yml_sorted",
@@ -96,6 +117,6 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
                 log.info(
                     f"Dependencies in {module.component_name}'s environment.yml were not sorted alphabetically. Sorting them now."
                 )
-                env_yml["dependencies"].sort()
+                env_yml["dependencies"] = sorted_dependencies
                 with open(Path(module.component_dir, "environment.yml"), "w") as fh:
                     yaml.dump(env_yml, fh, Dumper=custom_yaml_dumper())

requirements.txt

@@ -7,7 +7,6 @@ jsonschema>=4.0
 markdown>=3.3
 packaging
 pillow
-pdiff
 pre-commit
 prompt_toolkit<=3.0.51
 pydantic>=2.2.1

tests/modules/test_lint.py

@@ -505,6 +505,71 @@ def test_modules_environment_yml_file_not_array(self):
         assert len(module_lint.warned) >= 0
         assert module_lint.failed[0].lint_test == "environment_yml_valid"
 
+    def test_modules_environment_yml_file_mixed_dependencies(self):
+        """Test linting a module with mixed-type dependencies (strings and pip dict)"""
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            )
+        ) as fh:
+            yaml_content = yaml.safe_load(fh)
+
+        # Create mixed dependencies with strings and pip dict in wrong order
+        yaml_content["dependencies"] = [
+            "python=3.8",
+            {"pip": ["zzz-package==1.0.0", "aaa-package==2.0.0"]},
+            "bioconda::samtools=1.15.1",
+            "bioconda::fastqc=0.12.1",
+            "pip=23.3.1",
+        ]
+
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            ),
+            "w",
+        ) as fh:
+            fh.write(yaml.dump(yaml_content))
+
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+
+        # Check that the dependencies were sorted correctly
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            )
+        ) as fh:
+            sorted_yaml = yaml.safe_load(fh)
+
+        expected_deps = [
+            "bioconda::fastqc=0.12.1",
+            "bioconda::samtools=1.15.1",
+            "pip=23.3.1",
+            {"pip": ["aaa-package==2.0.0", "zzz-package==1.0.0"]},
+            "python=3.8",
+        ]
+
+        assert sorted_yaml["dependencies"] == expected_deps
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
     def test_modules_meta_yml_incorrect_licence_field(self):
         """Test linting a module with an incorrect Licence field in meta.yml"""
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh: