revert logging changes

jcvi/apps/base.py

@@ -27,7 +27,7 @@
 from typing import Any, Collection, List, Optional, Union
 
 from natsort import natsorted
-from rich.logging import RichHandler
+from rich.logging import Console, RichHandler
 
 from jcvi import __copyright__, __version__
 
@@ -38,6 +38,21 @@
 JCVIHELP = "JCVI utility libraries {} [{}]\n".format(__version__, __copyright__)
 
 
+def debug(level=logging.DEBUG):
+    """
+    Turn on the debugging
+    """
+    logging.basicConfig(
+        level=level,
+        format="%(message)s",
+        datefmt="[%X]",
+        handlers=[RichHandler(console=Console(stderr=True))],
+    )
+
+
+debug()
+
+
 def get_logger(name: str):
     """Return a logger with a default ColoredFormatter."""
     logger = logging.getLogger(name)

jcvi/graphics/base.py

@@ -7,6 +7,11 @@
 import sys
 import logging
 
+logging.getLogger("matplotlib").setLevel(logging.WARNING)
+logging.getLogger("numexpr").setLevel(logging.WARNING)
+logging.getLogger("PIL").setLevel(logging.INFO)
+
+
 from functools import partial
 
 import numpy as np
@@ -32,12 +37,9 @@
 from matplotlib.path import Path
 from typing import Optional
 
-from ..apps.base import datadir, get_logger, glob, listify, logger, sample_N, which
+from ..apps.base import datadir, glob, listify, logger, sample_N, which
 from ..formats.base import LineFile
 
-get_logger("matplotlib").setLevel(logging.WARNING)
-get_logger("numexpr").setLevel(logging.WARNING)
-logging.getLogger("PIL").setLevel(logging.INFO)
 
 CHARS = {
     "&": r"\&",