Fix #1160: Replace broad except Exception with specific exception typ…

[khushthecoder]

Fix #1160: Replace broad except Exception with specific exception types in phenotypes.py

Fixes: #1160

Summary

phenotypes.py had 5 instances of except Exception that silently converted real bugs (TypeError, KeyError, AttributeError, etc.) into warnings, returning empty or partial data. This is dangerous for scientific analysis where data correctness is critical.

Changes

Site	Fix
_load_phenotype_data() outer loop	Narrowed to (KeyError, FileNotFoundError, IOError)
_create_phenotype_dataset() variant merge	Removed redundant catch-all — KeyError and ValueError already caught above
phenotype_data() metadata fetch	Removed try/except — let sample_metadata() errors propagate naturally
phenotype_data() query evaluation	Narrowed to (pd.errors.UndefinedVariableError, SyntaxError)
phenotype_sample_sets() path check	Narrowed to (KeyError, FileNotFoundError)

Design rationale

• Fail loudly on unexpected errors — a TypeError or AttributeError is a real bug that should crash with a traceback, not get silently converted into a warning
• Keep expected error handling — FileNotFoundError when a sample set has no phenotype data, KeyError when a sample set has no release mapping, and UndefinedVariableError for bad user queries are all expected and still handled gracefully
• Net negative lines — the fix removes more code than it adds (6 insertions, 17 deletions)

[jonbrenas]

Thanks @khushthecoder, phenotypes.py is a work in progress (or maybe dead code) as the phenotypic data doesn't exist yet. Making it work better is thus not a priority but I will look at your PR as it may come in handy later if the code actually gets used.

[khushthecoder]

Thank you for the review and approval @jonbrenas! Really appreciate it. Feel free to merge whenever convenient.