Merge pull request #2722 from mashehu/fix-files-unchanged-parital

fix ignoring changes in partial template files

CHANGELOG.md

@@ -13,6 +13,7 @@
 
 ### General
 
+- fix ignoring changes in partially templated files (e.g. `.gitignore`) ([#2722](https://github.com/nf-core/tools/pull/2722))
 - update ruff to 0.2.0 and add it to pre-commit step ([#2725](https://github.com/nf-core/tools/pull/2725))
 - Update codecov/codecov-action digest to e0b68c6 ([#2728](https://github.com/nf-core/tools/pull/2728))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.1 ([#2730](https://github.com/nf-core/tools/pull/2730))

nf_core/lint/files_exist.py

@@ -236,7 +236,7 @@ def pf(file_path: Union[str, Path]) -> Path:
 
     # Files that cause an error if they exist
     for file in files_fail_ifexists:
-        if file in ignore_files:
+        if str(file) in ignore_files:
             continue
         if pf(file).is_file():
             failed.append(f"File must be removed: {self._wrap_quotes(file)}")

nf_core/lint/files_unchanged.py

@@ -176,7 +176,7 @@ def _tf(file_path: Union[str, Path]) -> Path:
     # Files that can be added to, but that must contain the template contents
     for files in files_partial:
         # Ignore if file specified in linting config
-        if any([f in ignore_files for f in files]):
+        if any([str(f) in ignore_files for f in files]):
             ignored.append(f"File ignored due to lint config: {self._wrap_quotes(files)}")
 
         # Ignore if we can't find the file