openvax / pyensembl / 28954107378

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Pull #363

github

Fix #362: don't reconfigure root logger when importing pyensembl.shell

pyensembl/shell.py called logging.config.fileConfig() at module top-level.
fileConfig defaults to disable_existing_loggers=True, so importing the
module (a) attached pyensembl's console handlers to the root logger and set
its level to INFO, and (b) disabled every logger the host application had
created before the import. A library must not configure the root logger or
disable other loggers as an import side effect.

Following the Python logging HOWTO ("Configuring Logging for a Library"):

- Move the fileConfig() call into a configure_logging() helper that is only
  invoked from the CLI entrypoint (run()), and pass
  disable_existing_loggers=False so it never disables application loggers.
- Attach a NullHandler to the "pyensembl" package logger in __init__.py so
  library use emits nothing by default and never warns about missing
  handlers, while leaving the root logger untouched.

Adds regression tests covering the import side-effects and the CLI logging
setup.

Claude-Session: https://claude.ai/code/session_016pKPSmCAts4cacC3CQ9qsL

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