Capture stdout/stderr in run_command's timeout path so BNG2.pl errors reach callers#83
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wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
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Capture stdout/stderr in run_command's timeout path so BNG2.pl errors reach callers#83wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
run_command's timeout path so BNG2.pl errors reach callers#83wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
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… reach callers `run_command(suppress=True, timeout=set)` was redirecting stdout/stderr to `DEVNULL`, so when `BNGCLI` raised `BNGRunError` on a failing BNG2.pl invocation, the actual diagnostic message (e.g. `Missing end parentheses ... at and(...)`) never reached the user. Always capture instead. With a timeout set, `subprocess.run` buffers all output anyway, so the `suppress` distinction was already a no-op for the user during the run — what it did do was discard the bytes needed to build a useful error message after the fact. After this, the `_run.log` for a failing BNG2.pl call shows the real ABORT message, which makes round-trip / regenerated-BNGL bugs trivial to localize.
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Summary
`run_command(suppress=True, timeout=set)` in `bionetgen/core/utils/utils.py` redirects stdout/stderr to `DEVNULL`, so when `BNGCLI` raises `BNGRunError` on a failing BNG2.pl invocation, the actual diagnostic message (e.g. `Missing end parentheses ... at and(...)`) never reaches the user.
Fix
Always capture stdout/stderr. With a timeout set, `subprocess.run` buffers all output anyway, so the `suppress` distinction is already a no-op for the user during the run — what it does do is discard the bytes needed to build a useful error message after the fact.
After this, the `_run.log` for a failing BNG2.pl call shows the real ABORT message, which makes round-trip / regenerated-BNGL bugs trivial to localize.
Test plan