Fix test cases and ensure test is run. Make sure label linting method…

… is called
nf-core · Apr 26, 2023 · d593f86 · d593f86
1 parent ee0b95b
commit d593f86
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Showing 3 changed files with 18 additions and 13 deletions.
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
@@ -235,6 +235,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
         self.failed.append(("process_capitals", "Process name is not in capital letters", self.main_nf))
 
     # Check that process labels are correct
+    check_process_labels(self, lines)
 
     # Deprecated enable_conda
     for i, l in enumerate(lines):
@@ -393,13 +394,13 @@ def check_process_section(self, lines, fix_version, progress_bar):
 
 def check_process_labels(self, lines):
     correct_process_labels = ["process_single", "process_low", "process_medium", "process_high", "process_long"]
-    all_labels = [l for l in lines if l.lstrip().startswith("label ")]
+    all_labels = [l.strip() for l in lines if l.lstrip().startswith("label ")]
     bad_labels = []
     good_labels = []
     if len(all_labels) > 0:
         for label in all_labels:
             try:
-                label = re.match("^label\s+([a-zA-Z0-9_-]+)", label).group(1)
+                label = re.match("^label\s+([a-zA-Z0-9_-]+)$", label).group(1)
             except AttributeError:
                 self.warned.append(
                     (
@@ -427,7 +428,7 @@ def check_process_labels(self, lines):
             self.warned.append(("process_standard_label", "Standard process label not found", self.main_nf))
         if len(bad_labels) > 0:
             self.warned.append(
-                ("process_standard_label", f"Non-standard labels found: `{'`,`'.join(good_labels)}`", self.main_nf)
+                ("process_standard_label", f"Non-standard labels found: `{'`,`'.join(bad_labels)}`", self.main_nf)
             )
         if len(all_labels) > len(set(all_labels)):
             self.warned.append(

diff --git a/tests/modules/lint.py b/tests/modules/lint.py
@@ -117,6 +117,8 @@ def __init__(self):
         self.warned = []
         self.failed = []
 
+        self.main_nf = "main_nf"
+
 
 PROCESS_LABEL_GOOD = (
     """
@@ -133,7 +135,7 @@ def __init__(self):
     cpus 12
     """,
     0,
-    1,
+    2,
     0,
 )
 PROCESS_LABEL_GOOD_CONFLICTING = (
@@ -163,7 +165,7 @@ def __init__(self):
     cpus 12
     """,
     1,
-    2,
+    1,
     0,
 )
 PROCESS_LABEL_NONSTANDARD = (
@@ -172,7 +174,7 @@ def __init__(self):
     cpus 12
     """,
     0,
-    1,
+    2,
     0,
 )
 PROCESS_LABEL_NONSTANDARD_DUPLICATES = (
@@ -206,10 +208,11 @@ def __init__(self):
 ]
 
 
-@pytest.mark.parametrize("lines,passed,warned,failed", PROCESS_LABEL_TEST_CASES)
-def test_modules_lint_check_process_labels(self, lines, passed, warned, failed):
-    mocked_ModuleLint = MockModuleLint()
-    main_nf.check_process_labels(mocked_ModuleLint, lines)
-    assert len(mocked_ModuleLint.passed) == passed
-    assert len(mocked_ModuleLint.warned) == warned
-    assert len(mocked_ModuleLint.failed) == failed
+def test_modules_lint_check_process_labels(self):
+    for test_case in PROCESS_LABEL_TEST_CASES:
+        process, passed, warned, failed = test_case
+        mocked_ModuleLint = MockModuleLint()
+        main_nf.check_process_labels(mocked_ModuleLint, process.splitlines())
+        assert len(mocked_ModuleLint.passed) == passed
+        assert len(mocked_ModuleLint.warned) == warned
+        assert len(mocked_ModuleLint.failed) == failed
diff --git a/tests/test_modules.py b/tests/test_modules.py
@@ -162,6 +162,7 @@ def test_modulesrepo_class(self):
         test_modules_install_trimgalore_twice,
     )
     from .modules.lint import (
+        test_modules_lint_check_process_labels,
         test_modules_lint_empty,
         test_modules_lint_gitlab_modules,
         test_modules_lint_multiple_remotes,