Merge pull request #1761 from fabianegli/dirs-exist-ok

workaround for shutil.copytree's lack of dirs_exist_ok in Python3.7 + added tests for module patch

nf_core/modules/lint/module_changes.py

@@ -24,7 +24,8 @@ def module_changes(module_lint_object, module):
  if module.is_patched:
  # If the module is patched, we need to apply
  # the patch in reverse before comparing with the remote
- tempdir = Path(tempfile.mkdtemp())
+ tempdir_parent = Path(tempfile.mkdtemp())
+ tempdir = tempdir_parent / "tmp_module_dir"
  shutil.copytree(module.module_dir, tempdir)
  try:
  new_lines = ModulesDiffer.try_apply_patch(

tests/modules/lint.py

@@ -1,8 +1,11 @@
+import os
+
 import pytest
 
 import nf_core.modules
 
 from ..utils import GITLAB_URL
+from .patch import BISMARK_ALIGN, PATCH_BRANCH, setup_patch
 
 
 def test_modules_lint_trimgalore(self):
@@ -48,3 +51,26 @@ def test_modules_lint_gitlab_modules(self):
  assert len(module_lint.failed) == 0
  assert len(module_lint.passed) > 0
  assert len(module_lint.warned) >= 0
+
+
+def test_modules_lint_patched_modules(self):
+ """
+ Test creating a patch file and applying it to a new version of the the files
+ """
+ setup_patch(self.pipeline_dir, True)
+
+ # Create a patch file
+ patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+ patch_obj.patch(BISMARK_ALIGN)
+
+ # change temporarily working directory to the pipeline directory
+ # to avoid error from try_apply_patch() during linting
+ wd_old = os.getcwd()
+ os.chdir(self.pipeline_dir)
+ module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+ module_lint.lint(print_results=False, all_modules=True)
+ os.chdir(wd_old)
+
+ assert len(module_lint.failed) == 0
+ assert len(module_lint.passed) > 0
+ assert len(module_lint.warned) >= 0

tests/test_modules.py

@@ -115,6 +115,7 @@ def test_modulesrepo_class(self):
  test_modules_lint_gitlab_modules,
  test_modules_lint_new_modules,
  test_modules_lint_no_gitlab,
+ test_modules_lint_patched_modules,
  test_modules_lint_trimgalore,
  )
  from .modules.list import (