Linting: allow ignoring specific files when linting template_strings

CHANGELOG.md

@@ -21,6 +21,7 @@
 - Fix linting of a pipeline with patched custom module ([#2669](https://github.com/nf-core/tools/pull/2669))
 - linting a pipeline also lints the installed subworkflows ([#2677](https://github.com/nf-core/tools/pull/2677))
 - environment.yml name must be lowercase ([#2676](https://github.com/nf-core/tools/pull/2676))
+- allow ignoring specific files when template_strings ([#2686](https://github.com/nf-core/tools/pull/2686))
 - lint `nextflow.config` default values match the ones specified in `nextflow_schema.json` ([#2684](https://github.com/nf-core/tools/pull/2684))
 
 ### Modules

nf_core/lint/merge_markers.py

@@ -13,6 +13,17 @@ def merge_markers(self):
     This test looks for remaining merge markers in the code, e.g.:
     >>>>>>> or <<<<<<<
 
+    .. tip:: You can choose to ignore this lint tests by editing the file called
+        ``.nf-core.yml`` in the root of your pipeline and setting the test to false:
+        .. code-block:: yaml
+            lint:
+                merge_markers: False
+        To disable this test only for specific files, you can specify a list of file paths to ignore.
+        For example, to ignore a pdf you added to the docs:
+        .. code-block:: yaml
+            lint:
+                merge_markers:
+                    - docs/my_pdf.pdf
     """
     passed = []
     failed = []

nf_core/lint/template_strings.py

@@ -16,13 +16,36 @@ def template_strings(self):
 
     This test ignores any double-brackets prefixed with a dollar sign, such as
     ``${{ secrets.AWS_ACCESS_KEY_ID }}`` as these placeholders are used in GitHub Actions workflows.
+
+    .. tip:: You can choose to ignore lint test tests by editing the file called
+        ``.nf-core.yml`` in the root of your pipeline and setting the test to false:
+
+        .. code-block:: yaml
+
+            lint:
+                template_strings: False
+
+        To disable this test only for specific files, you can specify a list of file paths to ignore.
+        For example, to ignore a pdf you added to the docs:
+
+        .. code-block:: yaml
+
+            lint:
+                template_strings:
+                    - docs/my_pdf.pdf
     """
     passed = []
     failed = []
+    ignored = []
+    # Files that should be ignored according to the linting config
+    ignore_files = self.lint_config.get("template_strings", [])
 
     # Loop through files, searching for string
     num_matches = 0
     for fn in self.files:
+        if str(fn.relative_to(self.wf_path)) in ignore_files:
+            ignored.append(f"Ignoring Jinja template strings in file `{fn}`")
+            continue
         # Skip binary files
         binary_ftypes = ["image", "application/java-archive"]
         (ftype, encoding) = mimetypes.guess_type(fn)
@@ -41,4 +64,4 @@ def template_strings(self):
     if num_matches == 0:
         passed.append(f"Did not find any Jinja template strings ({len(self.files)} files)")
 
-    return {"passed": passed, "failed": failed}
+    return {"passed": passed, "failed": failed, "ignored": ignored}

nf_core/utils.py

@@ -159,8 +159,8 @@ def _list_files(self):
             git_ls_files = subprocess.check_output(["git", "ls-files"], cwd=self.wf_path).splitlines()
             self.files = []
             for fn in git_ls_files:
-                full_fn = os.path.join(self.wf_path, fn.decode("utf-8"))
-                if os.path.isfile(full_fn):
+                full_fn = Path(self.wf_path) / fn.decode("utf-8")
+                if full_fn.is_file():
                     self.files.append(full_fn)
                 else:
                     log.debug(f"`git ls-files` returned '{full_fn}' but could not open it!")
@@ -170,7 +170,7 @@ def _list_files(self):
             self.files = []
             for subdir, _, files in os.walk(self.wf_path):
                 for fn in files:
-                    self.files.append(os.path.join(subdir, fn))
+                    self.files.append(Path(subdir) / fn)
 
     def _load_pipeline_config(self):
         """Get the nextflow config for this pipeline

tests/lint/template_strings.py

@@ -0,0 +1,54 @@
+import subprocess
+from pathlib import Path
+
+import nf_core.create
+import nf_core.lint
+
+
+def test_template_strings(self):
+    """Tests finding a template string in a file fails linting."""
+    new_pipeline = self._make_pipeline_copy()
+    # Add template string to a file
+    txt_file = Path(new_pipeline) / "docs" / "test.txt"
+    with open(txt_file, "w") as f:
+        f.write("my {{ template_string }}")
+    subprocess.check_output(["git", "add", "docs"], cwd=new_pipeline)
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+    result = lint_obj.template_strings()
+    print(result["failed"])
+    assert len(result["failed"]) == 1
+    assert len(result["ignored"]) == 0
+
+
+def test_template_strings_ignored(self):
+    """Tests ignoring template_strings"""
+    new_pipeline = self._make_pipeline_copy()
+    # Ignore template_strings test
+    nf_core_yml = Path(new_pipeline) / ".nf-core.yml"
+    with open(nf_core_yml, "w") as f:
+        f.write("repository_type: pipeline\nlint:\n  template_strings: False")
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+    lint_obj._lint_pipeline()
+    assert len(lint_obj.failed) == 0
+    assert len(lint_obj.ignored) == 1
+
+
+def test_template_strings_ignore_file(self):
+    """Tests ignoring template_strings file"""
+    new_pipeline = self._make_pipeline_copy()
+    # Add template string to a file
+    txt_file = Path(new_pipeline) / "docs" / "test.txt"
+    with open(txt_file, "w") as f:
+        f.write("my {{ template_string }}")
+    subprocess.check_output(["git", "add", "docs"], cwd=new_pipeline)
+    # Ignore template_strings test
+    nf_core_yml = Path(new_pipeline) / ".nf-core.yml"
+    with open(nf_core_yml, "w") as f:
+        f.write("repository_type: pipeline\nlint:\n  template_strings:\n    - docs/test.txt")
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+    result = lint_obj.template_strings()
+    assert len(result["failed"]) == 0
+    assert len(result["ignored"]) == 1

tests/test_lint.py

@@ -227,6 +227,11 @@ def test_sphinx_md_files(self):
         test_nextflow_config_example_pass,
         test_nextflow_config_missing_test_profile_failed,
     )
+    from .lint.template_strings import (  # type: ignore[misc]
+        test_template_strings,
+        test_template_strings_ignore_file,
+        test_template_strings_ignored,
+    )
     from .lint.version_consistency import test_version_consistency  # type: ignore[misc]
 
 

tests/test_utils.py

@@ -112,14 +112,14 @@ def test_load_pipeline_config(self):
     def test_list_files_git(self):
         """Test listing pipeline files using `git ls`"""
         self.pipeline_obj._list_files()
-        assert os.path.join(self.test_pipeline_dir, "main.nf") in self.pipeline_obj.files
+        assert Path(self.test_pipeline_dir, "main.nf") in self.pipeline_obj.files
 
     @with_temporary_folder
     def test_list_files_no_git(self, tmpdir):
         """Test listing pipeline files without `git-ls`"""
         # Create a test file in a temporary directory
-        tmp_fn = os.path.join(tmpdir, "testfile")
-        Path(tmp_fn).touch()
+        tmp_fn = Path(tmpdir, "testfile")
+        tmp_fn.touch()
         pipeline_obj = nf_core.utils.Pipeline(tmpdir)
         pipeline_obj._list_files()
         assert tmp_fn in pipeline_obj.files