Merge pull request #861 from KevinMenden/merge-markers

Add lint test for merge markers

CHANGELOG.md

@@ -40,6 +40,7 @@
 
 ### Linting
 
+* Added lint check for merge markers [[#321]](https://github.com/nf-core/tools/issues/321)
 * Added new option `--fix` to automatically correct some problems detected by linting
 * Added validation of default params to `nf-core schema lint` [[#823](https://github.com/nf-core/tools/issues/823)]
 * Added schema validation of GitHub action workflows to lint function [[#795](https://github.com/nf-core/tools/issues/795)]

docs/api/_src/lint_tests/merge_markers.rst

@@ -0,0 +1,4 @@
+merge_markers
+==============
+
+.. automethod:: nf_core.lint.PipelineLint.merge_markers

nf_core/lint/__init__.py

@@ -113,6 +113,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     from .schema_lint import schema_lint
     from .schema_params import schema_params
     from .actions_schema_validation import actions_schema_validation
+    from .merge_markers import merge_markers
 
     def __init__(self, wf_path, release_mode=False, fix=()):
         """ Initialise linting object """
@@ -144,6 +145,7 @@ def __init__(self, wf_path, release_mode=False, fix=()):
             "schema_lint",
             "schema_params",
             "actions_schema_validation",
+            "merge_markers",
         ]
         if self.release_mode:
             self.lint_tests.extend(["version_consistency"])

nf_core/lint/merge_markers.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+import logging
+import os
+import io
+import fnmatch
+
+log = logging.getLogger(__name__)
+
+
+def merge_markers(self):
+    """Check for remaining merge markers.
+
+    This test looks for remaining merge markers in the code, e.g.:
+    >>>>>>> or <<<<<<<
+
+
+    """
+    passed = []
+    failed = []
+
+    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:
+            for l in fh:
+                ignore.append(os.path.basename(l.strip().rstrip("/")))
+    for root, dirs, files in os.walk(self.wf_path):
+        # Ignore files
+        for i in ignore:
+            dirs = [d for d in dirs if not fnmatch.fnmatch(os.path.join(root, d), i)]
+            files = [f for f in files if not fnmatch.fnmatch(os.path.join(root, f), i)]
+        for fname in files:
+            try:
+                with io.open(os.path.join(root, fname), "rt", encoding="latin1") as fh:
+                    for l in fh:
+                        if ">>>>>>>" in l:
+                            failed.append(f"Merge marker in `{fname}`: {l}")
+                        if "<<<<<<<" in l:
+                            failed.append(f"Merge marker in `{fname}`: {l}")
+            except FileNotFoundError:
+                log.debug(f"Could not open file {fname} in merge_markers lint test")
+    if len(failed) == 0:
+        passed.append("No merge markers found in pipeline files")
+    return {"passed": passed, "failed": failed}

tests/lint/merge_markers.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+
+import os
+import yaml
+import nf_core.lint
+
+
+def test_merge_markers_found(self):
+    """Missing 'jobs' field should result in failure"""
+    new_pipeline = self._make_pipeline_copy()
+
+    with open(os.path.join(new_pipeline, "main.nf"), "r") as fh:
+        main_nf_content = fh.read()
+    main_nf_content = ">>>>>>>\n" + main_nf_content
+    with open(os.path.join(new_pipeline, "main.nf"), "w") as fh:
+        fh.write(main_nf_content)
+
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+
+    results = lint_obj.merge_markers()
+    assert len(results["failed"]) > 0
+    assert len(results["passed"]) == 0
+    assert "Merge marker in `main.nf`: >>>>>>>\n" == results["failed"][0]

tests/test_lint.py

@@ -200,6 +200,8 @@ def test_sphinx_rst_files(self):
         test_actions_schema_validation_missing_on,
     )
 
+    from lint.merge_markers import test_merge_markers_found
+
 
 #    def test_critical_missingfiles_example(self):
 #        """Tests for missing nextflow config and main.nf files"""