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FIX the run log printing to the terminal as well as the file - #8
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pyranges calls logging.basicConfig on import, which puts a handler on the root logger, so every INFO record the pipelines write propagated there and was printed to stderr. The log belongs in the file; the command's own summary is what goes to the terminal. Each pipeline now clears propagate while its file handler is attached, so no library's root handler can pick the records up. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
The reversed-library test read the warning through caplog, which captures by propagation and so could not see it any more. It now reads the run's own log file, which is what the fix actually promises, and a new test fails if a record ever reaches a root handler again. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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import pyranges1callslogging.basicConfig(level=logging.INFO), whichattaches a
StreamHandlerto the root logger and lowers its level. EveryINFO record the pipelines write then propagated to it and was printed to
stderr, so
cau guide-annotation runandcau element-mapping rundumpedtheir internal log on the terminal next to their summary.
Each pipeline now clears
propagatewhile its file handler is attached. Thelog goes to the file, the summary to stdout, and nothing a library does to
the root logger can change that.
Before: 1.6 kB of stderr for a normal run. After: 0 bytes.
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