False positive merge marker failures due to .venv directory

[heuermh]

Description of the bug

If nf-core is installed via pip and venv, nf-core pipelines lint will find merge markers in the .venv directory and report these as errors

$ nf-core pipelines lint
...
╭─ [✗] 16 Pipeline Tests Failed ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                               │
│ merge_markers: Merge marker '>>>>>>>' in .venv/lib/python3.12/site-packages/tests/pipelines/lint/test_merge_markers.py:         main_nf_content = ">>>                                                        │
│ merge_markers: Merge marker '>>>>>>>' in .venv/lib/python3.12/site-packages/tests/pipelines/lint/test_merge_markers.py:         assert "Merge marker '                                                        │
│ merge_markers: Merge marker '>>>>>>>' in .venv/lib/python3.12/site-packages/ruamel/yaml/constructor.py:         # print('>>>>>>>> here                                                                        │
│ merge_markers: Merge marker '>>>>>>>' in .venv/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-x86_64-linux-gnu.so: ���<<<<<<<<<<<<<<<<<<<<<<<<<<<                                     │
│ merge_markers: Merge marker '<<<<<<<' in .venv/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-x86_64-linux-gnu.so: ���<<<<<<<<<<<<<<<<<<<<<<<<<<<                                     │
│ merge_markers: Merge marker '>>>>>>>' in .venv/lib/python3.12/site-packages/nf_core/pipelines/lint/merge_markers.py:     >>>>>>> or <<<<<<<                                                                   │
│ merge_markers: Merge marker '<<<<<<<' in .venv/lib/python3.12/site-packages/nf_core/pipelines/lint/merge_markers.py:     >>>>>>> or <<<<<<<                                                                   │
│ merge_markers: Merge marker '>>>>>>>' in .venv/lib/python3.12/site-packages/nf_core/pipelines/lint/merge_markers.py:                         if ">>                                                           │
│ merge_markers: Merge marker '>>>>>>>' in .venv/lib/python3.12/site-packages/nf_core/pipelines/lint/merge_markers.py:                             fa                                                           │
│ merge_markers: Merge marker '<<<<<<<' in .venv/lib/python3.12/site-packages/nf_core/pipelines/lint/merge_markers.py:                         if "<<                                                           │
│ merge_markers: Merge marker '<<<<<<<' in .venv/lib/python3.12/site-packages/nf_core/pipelines/lint/merge_markers.py:                             fa                                                           │
│ merge_markers: Merge marker '>>>>>>>' in .venv/lib/python3.12/site-packages/pillow.libs/libharfbuzz-07d0ad17.so.0.61010.0:                                                                                    │
│ merge_markers: Merge marker '<<<<<<<' in .venv/lib/python3.12/site-packages/pillow.libs/libharfbuzz-07d0ad17.so.0.61010.0: ///<<<<<<<<<<<����                                                                 │
│ merge_markers: Merge marker '<<<<<<<' in .venv/lib/python3.12/site-packages/pillow.libs/libharfbuzz-07d0ad17.so.0.61010.0:  │
│ merge_markers: Merge marker '>>>>>>>' in .venv/lib/python3.12/site-packages/pillow.libs/libharfbuzz-07d0ad17.so.0.61010.0:                                                                                    │
│ merge_markers: Merge marker '<<<<<<<' in .venv/lib/python3.12/site-packages/pillow.libs/libharfbuzz-07d0ad17.so.0.61010.0: ����                                                                               │
│                                                                                                                                                                                                               │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔] 230 Tests Passed  │
│ [?]   3 Tests Ignored │
│ [!]  89 Test Warnings │
│ [✗]  16 Tests Failed  │
╰───────────────────────╯

Command used and terminal output

System information

No response

[awgymer]

Looking at the code, if .venv is in your .gitignore then it should be being ignored from this test.

Can you confirm whether you have .venv in your .gitignore?