Linting checks test files for TODO statements as well as the main m…

…odule code

Closes nf-core#1271

CHANGELOG.md

@@ -52,6 +52,7 @@
 * Tweak handling of empty files when generating the test YAML ([#1376](https://github.com/nf-core/tools/issues/1376))
     * Fail linting if a md5sum for an empty file is found (instead of a warning)
     * Don't skip the md5 when generating a test file if an empty file is found (so that linting fails and can be manually checked)
+* Linting checks test files for `TODO` statements as well as the main module code ([#1271](https://github.com/nf-core/tools/issues/1271))
 
 ## [v2.2 - Lead Liger](https://github.com/nf-core/tools/releases/tag/2.2) - [2021-12-14]
 

nf_core/lint/pipeline_todos.py

@@ -8,7 +8,7 @@
 log = logging.getLogger(__name__)
 
 
-def pipeline_todos(self):
+def pipeline_todos(self, root_dir = None):
     """Check for nf-core *TODO* lines.
 
     The nf-core workflow template contains a number of comment lines to help developers
@@ -34,15 +34,19 @@ def pipeline_todos(self):
     """
     passed = []
     warned = []
-    failed = []
     file_paths = []
 
+    # Pipelines don't provide a path, so use the workflow path.
+    # Modules run this function twice and provide a string path
+    if root_dir is None:
+        root_dir = self.wf_path
+
     ignore = [".git"]
-    if os.path.isfile(os.path.join(self.wf_path, ".gitignore")):
-        with io.open(os.path.join(self.wf_path, ".gitignore"), "rt", encoding="latin1") as fh:
+    if os.path.isfile(os.path.join(root_dir, ".gitignore")):
+        with io.open(os.path.join(root_dir, ".gitignore"), "rt", encoding="latin1") as fh:
             for l in fh:
                 ignore.append(os.path.basename(l.strip().rstrip("/")))
-    for root, dirs, files in os.walk(self.wf_path, topdown=True):
+    for root, dirs, files in os.walk(root_dir, topdown=True):
         # Ignore files
         for i_base in ignore:
             i = os.path.join(root, i_base)
@@ -65,6 +69,10 @@ def pipeline_todos(self):
                             file_paths.append(os.path.join(root, fname))
             except FileNotFoundError:
                 log.debug(f"Could not open file {fname} in pipeline_todos lint test")
+
+    if len(warned) == 0:
+        passed.append("No TODO strings found")
+
     # HACK file paths are returned to allow usage of this function in modules/lint.py
     # Needs to be refactored!
-    return {"passed": passed, "warned": warned, "failed": failed, "file_paths": file_paths}
+    return {"passed": passed, "warned": warned, "file_paths": file_paths}

nf_core/modules/lint/module_todos.py

@@ -11,7 +11,17 @@ def module_todos(module_lint_object, module):
     Slight modification of the "nf_core.lint.pipeline_todos" function to make it work
     for a single module
     """
-    module.wf_path = module.module_dir
-    results = pipeline_todos(module)
-    for i, warning in enumerate(results["warned"]):
-        module.warned.append(("module_todo", warning, results["file_paths"][i]))
+
+    # Main module directory
+    mod_results = pipeline_todos(None, root_dir=module.module_dir)
+    for i, warning in enumerate(mod_results["warned"]):
+        module.warned.append(("module_todo", warning, mod_results["file_paths"][i]))
+    for i, passed in enumerate(mod_results["passed"]):
+        module.passed.append(("module_todo", passed, module.module_dir))
+
+    # Module tests directory
+    test_results = pipeline_todos(None, root_dir=module.test_dir)
+    for i, warning in enumerate(test_results["warned"]):
+        module.warned.append(("module_todo", warning, test_results["file_paths"][i]))
+    for i, passed in enumerate(test_results["passed"]):
+        module.passed.append(("module_todo", passed, module.test_dir))