feat(1929): allow missing files when linting local modules

CHANGELOG.md

@@ -18,9 +18,12 @@
 ### Modules
 
 - add a panel around diff previews when updating ([#3246](https://github.com/nf-core/tools/pull/3246))
+- Modules created in pipelines "local" dir now use the full template ([#3256](https://github.com/nf-core/tools/pull/3256))
 
 ### Subworkflows
 
+- Subworkflows created in pipelines "local" dir now use the full template ([#3256](https://github.com/nf-core/tools/pull/3256))
+
 ### General
 
 - Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220))
@@ -33,7 +36,6 @@
 - Update GitHub Actions ([#3237](https://github.com/nf-core/tools/pull/3237))
 - add `--dir/-d` option to schema commands ([#3247](https://github.com/nf-core/tools/pull/3247))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1 ([#3250](https://github.com/nf-core/tools/pull/3250))
-- fix(1929): more type-gating ([#3256](https://github.com/nf-core/tools/pull/3256))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 

nf_core/components/lint/__init__.py

@@ -162,6 +162,10 @@ def _set_registry(self, registry) -> None:
             self.registry = registry
         log.debug(f"Registry set to {self.registry}")
 
+    @property
+    def local_module_exclude_tests(self):
+        return ["module_version", "module_changes", "modules_patch"]
+
     @staticmethod
     def get_all_module_lint_tests(is_pipeline):
         if is_pipeline:

nf_core/modules/lint/__init__.py

@@ -234,13 +234,31 @@ def lint_module(
         # TODO: consider unifying modules and subworkflows lint_module() function and add it to the ComponentLint class
         # Only check the main script in case of a local module
         if local:
+            mod.get_inputs_from_main_nf()
+            mod.get_outputs_from_main_nf()
+            # Update meta.yml file if requested
+            if self.fix and mod.meta_yml is not None:
+                self.update_meta_yml_file(mod)
+
+            for test_name in self.lint_tests:
+                if test_name in self.local_module_exclude_tests:
+                    continue
+                if test_name == "main_nf":
+                    getattr(self, test_name)(mod, fix_version, self.registry, progress_bar)
+                elif test_name in ["meta_yml", "environment_yml"]:
+                    # Allow files to be missing for local
+                    getattr(self, test_name)(mod, allow_missing=True)
+            """
             self.main_nf(mod, fix_version, self.registry, progress_bar)
+            """
+
             self.passed += [LintResult(mod, *m) for m in mod.passed]
             warned = [LintResult(mod, *m) for m in (mod.warned + mod.failed)]
             if not self.fail_warned:
                 self.warned += warned
             else:
                 self.failed += warned
+            self.failed += [LintResult(mod, *m) for m in mod.failed]
 
         # Otherwise run all the lint tests
         else:

nf_core/modules/lint/environment_yml.py

@@ -12,7 +12,7 @@
 log = logging.getLogger(__name__)
 
 
-def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None:
+def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_missing: bool = False) -> None:
     """
     Lint an ``environment.yml`` file.
 
@@ -23,6 +23,15 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
     env_yml = None
     #  load the environment.yml file
     if module.environment_yml is None:
+        if allow_missing:
+            module.warned.append(
+                (
+                    "environment_yml_exists",
+                    "Module's `environment.yml` does not exist",
+                    Path(module.component_dir, "environment.yml"),
+                ),
+            )
+            return
         raise LintExceptionError("Module does not have an `environment.yml` file")
     try:
         with open(module.environment_yml) as fh:

nf_core/modules/lint/meta_yml.py

@@ -13,7 +13,7 @@
 log = logging.getLogger(__name__)
 
 
-def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None:
+def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_missing: bool = False) -> None:
     """
     Lint a ``meta.yml`` file
 
@@ -42,7 +42,13 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
         module (NFCoreComponent): The module to lint
 
     """
-
+    if module.meta_yml is None:
+        if allow_missing:
+            module.warned.append(
+                ("meta_yml_exists", "Module `meta.yml` does not exist", Path(module.component_dir, "meta.yml"))
+            )
+            return
+        raise LintExceptionError("Module does not have a `meta.yml` file")
     # Check if we have a patch file, get original file in that case
     meta_yaml = read_meta_yml(module_lint_object, module)
     if module.is_patched and module_lint_object.modules_repo.repo_path is not None:
@@ -56,8 +62,6 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
         if lines is not None:
             yaml = ruamel.yaml.YAML()
             meta_yaml = yaml.safe_load("".join(lines))
-    if module.meta_yml is None:
-        raise LintExceptionError("Module does not have a `meta.yml` file")
     if meta_yaml is None:
         module.failed.append(("meta_yml_exists", "Module `meta.yml` does not exist", module.meta_yml))
         return

nf_core/modules/lint/module_tests.py

@@ -9,21 +9,44 @@
 
 import yaml
 
+from nf_core.components.lint import LintExceptionError
 from nf_core.components.nfcore_component import NFCoreComponent
 
 log = logging.getLogger(__name__)
 
 
-def module_tests(_, module: NFCoreComponent):
+def module_tests(_, module: NFCoreComponent, allow_missing: bool = False):
     """
     Lint the tests of a module in ``nf-core/modules``
 
     It verifies that the test directory exists
     and contains a ``main.nf.test`` and a ``main.nf.test.snap``
 
     """
-    if module.nftest_testdir is None or module.nftest_main_nf is None:
-        raise ValueError()
+    if module.nftest_testdir is None:
+        if allow_missing:
+            module.warned.append(
+                (
+                    "test_dir_exists",
+                    "nf-test directory is missing",
+                    Path(module.component_dir, "tests"),
+                )
+            )
+            return
+        raise LintExceptionError("Module does not have a `tests` dir")
+
+    if module.nftest_main_nf is None:
+        if allow_missing:
+            module.warned.append(
+                (
+                    "test_main_nf_exists",
+                    "test `main.nf.test` does not exist",
+                    Path(module.component_dir, "tests", "main.nf.test"),
+                )
+            )
+            return
+        raise LintExceptionError("Module does not have a `tests` dir")
+
     repo_dir = module.component_dir.parts[: module.component_dir.parts.index(module.component_name.split("/")[0])][-1]
     test_dir = Path(module.base_dir, "tests", "modules", repo_dir, module.component_name)
     pytest_main_nf = Path(test_dir, "main.nf")