Merge pull request #853 from ewels/lint-validation

Lint validation
nf-core · Feb 16, 2021 · 95b9d6f · 95b9d6f
2 parents 3f44a18 + daca4be
commit 95b9d6f
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Showing 2 changed files with 18 additions and 10 deletions.
diff --git a/nf_core/lint/files_exist.py b/nf_core/lint/files_exist.py
@@ -27,7 +27,9 @@ def files_exist(self):
         'docs/usage.md',
         '.github/workflows/branch.yml',
         '.github/workflows/ci.yml',
-        '.github/workflows/linting.yml'
+        '.github/workflows/linting.yml',
+        'lib/NfcoreSchema.groovy',
+        'lib/nfcore_external_java_deps.jar'
 
     Files that *should* be present::
 
@@ -71,6 +73,8 @@ def files_exist(self):
         [os.path.join(".github", "workflows", "branch.yml")],
         [os.path.join(".github", "workflows", "ci.yml")],
         [os.path.join(".github", "workflows", "linting.yml")],
+        [os.path.join("lib", "NfcoreSchema.groovy")],
+        [os.path.join("lib", "nfcore_external_java_deps.jar")],
     ]
     files_warn = [
         ["main.nf"],

diff --git a/nf_core/lint/files_unchanged.py b/nf_core/lint/files_unchanged.py
@@ -38,7 +38,9 @@ def files_unchanged(self):
         'bin/markdown_to_html.py',
         'conf/charliecloud.config',
         'docs/README.md',
-        'docs/images/nf-core-PIPELINE_logo.png'
+        'docs/images/nf-core-PIPELINE_logo.png',
+        'lib/NfcoreSchema.groovy',
+        'lib/nfcore_external_java_deps.jar'
 
     Files that can have additional content but must include the template contents::
 
@@ -97,6 +99,8 @@ def files_unchanged(self):
         [os.path.join("conf", "charliecloud.config")],
         [os.path.join("docs", "README.md")],
         [os.path.join("docs", "images", "nf-core-{}_logo.png".format(short_name))],
+        [os.path.join("lib", "NfcoreSchema.groovy")],
+        [os.path.join("lib", "nfcore_external_java_deps.jar")],
     ]
     files_partial = [
         [".gitignore", "foo"],
@@ -144,15 +148,15 @@ def _tf(file_path):
             for f in files:
                 try:
                     if filecmp.cmp(_pf(f), _tf(f), shallow=True):
-                        passed.append(f"'{f}' matches the template")
+                        passed.append(f"`{f}` matches the template")
                     else:
                         if "files_unchanged" in self.fix:
                             # Try to fix the problem by overwriting the pipeline file
                             shutil.copy(_tf(f), _pf(f))
-                            passed.append(f"'{f}' matches the template")
-                            fixed.append(f"'{f}' overwritten with template file")
+                            passed.append(f"`{f}` matches the template")
+                            fixed.append(f"`{f}` overwritten with template file")
                         else:
-                            failed.append(f"'{f}' does not match the template")
+                            failed.append(f"`{f}` does not match the template")
                             could_fix = True
                 except FileNotFoundError:
                     pass
@@ -178,18 +182,18 @@ def _tf(file_path):
                     with open(_tf(f), "r") as fh:
                         template_file = fh.read()
                     if template_file in pipeline_file:
-                        passed.append(f"'{f}' matches the template")
+                        passed.append(f"`{f}` matches the template")
                     else:
                         if "files_unchanged" in self.fix:
                             # Try to fix the problem by overwriting the pipeline file
                             with open(_tf(f), "r") as fh:
                                 template_file = fh.read()
                             with open(_pf(f), "w") as fh:
                                 fh.write(template_file)
-                            passed.append(f"'{f}' matches the template")
-                            fixed.append(f"'{f}' overwritten with template file")
+                            passed.append(f"`{f}` matches the template")
+                            fixed.append(f"`{f}` overwritten with template file")
                         else:
-                            failed.append(f"'{f}' does not match the template")
+                            failed.append(f"`{f}` does not match the template")
                             could_fix = True
                 except FileNotFoundError:
                     pass