fix: replace 5 bare excepts with except Exception in bio-research scripts#82
Open
haosenwang1018 wants to merge 1 commit intoanthropics:mainfrom
Open
fix: replace 5 bare excepts with except Exception in bio-research scripts#82haosenwang1018 wants to merge 1 commit intoanthropics:mainfrom
haosenwang1018 wants to merge 1 commit intoanthropics:mainfrom
Conversation
…ipts Bare `except:` clauses catch `KeyboardInterrupt` and `SystemExit`, which can mask real errors and make debugging harder. Replace with `except Exception:` to preserve the intended error-suppression behavior while allowing system-level exceptions to propagate normally. Files changed: - bio-research/skills/nextflow-development/scripts/check_environment.py (4 sites) - bio-research/skills/nextflow-development/scripts/detect_data_type.py (1 site)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Replace 5 bare
except:clauses withexcept Exception:in the bio-research nextflow-development scripts.Why
Bare
except:catchesKeyboardInterruptandSystemExit, which can mask real errors and prevent clean process termination.except Exception:preserves the error-suppression behavior while allowing system-level exceptions to propagate.Changes
check_environment.py: 4 sites (memory detection, disk space, Docker Hub check, nf-core check)detect_data_type.py: 1 site (file size calculation)All changes are minimal and behavior-preserving — only the exception base class changes.