Move logging setup out of __init__.py

bedboss/__init__.py

@@ -1,10 +1,7 @@
 """Package-level data"""
 
-import logging
 from importlib.metadata import version
 
-import coloredlogs
-
 __version__ = version(__package__)
 __package_name__ = "bedboss"
 
@@ -23,51 +20,3 @@
     "__package_name__",
     "__author__",
 ]
-
-_LOGGER = logging.getLogger("bedboss")
-_LOGGER.propagate = False
-coloredlogs.install(
-    logger=_LOGGER,
-    datefmt="%H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] [BEDBOSS] %(message)s",
-)
-
-_LOGGER_PIPESTAT = logging.getLogger("pipestat")
-_LOGGER_PIPESTAT.propagate = False
-coloredlogs.install(
-    logger=_LOGGER_PIPESTAT,
-    datefmt="%H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] [PIPESTAT] %(message)s",
-)
-
-_LOGGER_GENIML = logging.getLogger("geniml")
-_LOGGER_GENIML.propagate = False
-coloredlogs.install(
-    logger=_LOGGER_GENIML,
-    datefmt="%H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] [GENIML] %(message)s",
-)
-
-_LOGGER_BBCONF = logging.getLogger("bbconf")
-_LOGGER_BBCONF.propagate = False
-coloredlogs.install(
-    logger=_LOGGER_BBCONF,
-    datefmt="%H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] [BBCONF] %(message)s",
-)
-
-_LOGGER_PHC = logging.getLogger("pephubclient")
-_LOGGER_PHC.propagate = False
-coloredlogs.install(
-    logger=_LOGGER_PHC,
-    datefmt="%H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] [PEPHUBCLIENT] %(message)s",
-)
-
-_LOGGER_REF_CONF = logging.getLogger("refgenconf")
-_LOGGER_REF_CONF.propagate = False
-coloredlogs.install(
-    logger=_LOGGER_PHC,
-    datefmt="%H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] [REFGENCONF] %(message)s",
-)

bedboss/bbuploader/__init__.py

@@ -1,13 +1 @@
 """Package-level data"""
-
-import coloredlogs
-import logmuse
-
-from bedboss.bbuploader.constants import PKG_NAME
-
-_LOGGER = logmuse.init_logger(PKG_NAME)
-coloredlogs.install(
-    logger=_LOGGER,
-    datefmt="%H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] [BBUPLOADER] %(message)s",
-)

bedboss/cli.py

@@ -1,6 +1,7 @@
 import os
 from importlib.metadata import version as _pkg_version
 
+import logmuse
 import typer
 
 __version__ = _pkg_version("bedboss")
@@ -900,8 +901,22 @@ def common(
     version: bool = typer.Option(
         None, "--version", "-v", callback=version_callback, help="App version"
     ),
+    verbosity: int = typer.Option(
+        None, "--verbosity", help="Set logging level: 1 (CRITICAL) to 5 (DEBUG)"
+    ),
+    logdev: bool = typer.Option(False, "--logdev", help="Use developer logging format"),
+    silent: bool = typer.Option(False, "--silent", help="Silence logging"),
 ):
-    pass
+    # This callback runs before any command, so it is where logging gets
+    # configured. Don't move this into `__init__.py`.
+    #
+    # Configure the root logger so that bedboss and its dependencies (pipestat,
+    # geniml, bbconf, pephubclient, refgenconf, bbuploader) all log through one
+    # handler. Each line is tagged with its logger name, so there is no need to
+    # attach a per-package handler to identify the source.
+    logmuse.init_logger(
+        "", make_root=True, verbosity=verbosity, devmode=logdev, silent=silent
+    )
 
 
 app.add_typer(app_bbuploader, name="geo")

pyproject.toml

@@ -24,7 +24,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dependencies = [
-    "logmuse>=0.2.7",
+    "logmuse>=0.3.1",
     "coloredlogs>=15.0.1",
     "eido>=0.2.5",
     "peppy>=0.40.7",