Merge pull request #2478 from fa2k/add-test-for-test-profile

Add lint test to check existence of test profile

nf_core/lint/nextflow_config.py

@@ -108,6 +108,11 @@ def nextflow_config(self):
 
                 lint:
                     nextflow_config: False
+
+    **The configuration should contain the following or the test will fail:**
+
+    * A ``test`` configuration profile should exist.
+
     """
     passed = []
     warned = []
@@ -312,4 +317,32 @@ def nextflow_config(self):
                 )
             )
 
+    # Check for the availability of the "test" configuration profile by parsing nextflow.config
+    with open(os.path.join(self.wf_path, "nextflow.config"), "r") as f:
+        content = f.read()
+
+        # Remove comments
+        cleaned_content = re.sub(r"//.*", "", content)
+        cleaned_content = re.sub(r"/\*.*?\*/", "", content, flags=re.DOTALL)
+
+        match = re.search(r"\bprofiles\s*{", cleaned_content)
+        if not match:
+            failed.append("nextflow.config does not contain `profiles` scope, but `test` profile is required")
+        else:
+            # Extract profiles scope content and check for test profile
+            start = match.end()
+            end = start
+            brace_count = 1
+            while brace_count > 0 and end < len(content):
+                if cleaned_content[end] == "{":
+                    brace_count += 1
+                elif cleaned_content[end] == "}":
+                    brace_count -= 1
+                end += 1
+            profiles_content = cleaned_content[start : end - 1].strip()
+            if re.search(r"\btest\s*{", profiles_content):
+                passed.append("nextflow.config contains configuration profile `test`")
+            else:
+                failed.append("nextflow.config does not contain configuration profile `test`")
+
     return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored}

tests/lint/nextflow_config.py

@@ -1,3 +1,6 @@
+import os
+import re
+
 import nf_core.create
 import nf_core.lint
 
@@ -33,3 +36,20 @@ def test_nextflow_config_dev_in_release_mode_failed(self):
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) > 0
     assert len(result["warned"]) == 0
+
+
+def test_nextflow_config_missing_test_profile_failed(self):
+    """Test failure if config file does not contain `test` profile."""
+    new_pipeline = self._make_pipeline_copy()
+    # Change the name of the test profile so there is no such profile
+    nf_conf_file = os.path.join(new_pipeline, "nextflow.config")
+    with open(nf_conf_file, "r") as f:
+        content = f.read()
+        fail_content = re.sub(r"\btest\b", "testfail", content)
+    with open(nf_conf_file, "w") as f:
+        f.write(fail_content)
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) > 0
+    assert len(result["warned"]) == 0

tests/test_lint.py

@@ -213,6 +213,7 @@ def test_sphinx_md_files(self):
         test_nextflow_config_bad_name_fail,
         test_nextflow_config_dev_in_release_mode_failed,
         test_nextflow_config_example_pass,
+        test_nextflow_config_missing_test_profile_failed,
     )
     from .lint.version_consistency import test_version_consistency