openvax / topiary / 36324211746-1

93%

master: 93%

Pull #418

github

Exit 1 with one line for runtime CLI errors; check paths first (5.81.0)

Every failure main() caught went through argparse's error, printing the
whole usage block and exiting 2, and write_outputs ran outside the
handler. A malformed command line now keeps that (CommandLineError for
the flag checks argparse can't express); anything found afterwards
exits 1 with one line. ImportError and mhcgnomes' allele ParseError are
caught. Output paths and --mhc-predictor-path are checked before
predicting, inputs are read before predictors load, --output-csv-sep
must be one character, and unknown output columns are errors.

Fixes #310, fixes #324. Part of #326.

Claude-Session: https://claude.ai/code/session_016qyxwku965ujmfSRxnmDb7

63 of 66 new or added lines in 4 files covered. (95.45%)

8365 of 8975 relevant lines covered (93.2%)

0.93 hits per line