Refactoring the logging module

package/MDAnalysis/lib/log.py

@@ -86,22 +86,30 @@
 """
 import sys
 import logging
-import re
+import os
 
 from tqdm.auto import tqdm
 
 from .. import version
 
 
-def start_logging(logfile="MDAnalysis.log", version=version.__version__):
+def start_logging(stream="MDAnalysis.log", version=version.__version__):
     """Start logging of messages to file and console.
 
     The default logfile is named `MDAnalysis.log` and messages are
     logged with the tag *MDAnalysis*.
     """
-    create("MDAnalysis", logfile=logfile)
-    logging.getLogger("MDAnalysis").info(
-        "MDAnalysis %s STARTED logging to %r", version, logfile
+    create(
+        "MDAnalysis",
+        stream=stream,
+        level="DEBUG",
+        fmt="%(asctime)s %(name)-12s %(levelname)-8s %(message)s",
+    )
+    create(
+        "MDAnalysis",
+        stream=sys.stdout,
+        level="INFO",
+        fmt="%(name)-12s: %(levelname)-8s %(message)s",
     )
 
 
@@ -112,7 +120,9 @@ def stop_logging():
     clear_handlers(logger)  # this _should_ do the job...
 
 
-def create(logger_name="MDAnalysis", logfile="MDAnalysis.log"):
+def create(
+    logger_name="MDAnalysis", stream="MDAnalysis.log", level="DEBUG", fmt=None
+):
     """Create a top level logger.
 
     - The file logger logs everything (including DEBUG).
@@ -132,23 +142,27 @@ def create(logger_name="MDAnalysis", logfile="MDAnalysis.log"):
 
     logger = logging.getLogger(logger_name)
 
-    logger.setLevel(logging.DEBUG)
+    logger.setLevel(level.upper())
 
-    # handler that writes to logfile
-    logfile_handler = logging.FileHandler(logfile)
-    logfile_formatter = logging.Formatter(
-        "%(asctime)s %(name)-12s %(levelname)-8s %(message)s"
-    )
-    logfile_handler.setFormatter(logfile_formatter)
-    logger.addHandler(logfile_handler)
-
-    # define a Handler which writes INFO messages or higher to the sys.stderr
-    console_handler = logging.StreamHandler()
-    console_handler.setLevel(logging.INFO)
-    # set a format which is simpler for console use
-    formatter = logging.Formatter("%(name)-12s: %(levelname)-8s %(message)s")
-    console_handler.setFormatter(formatter)
-    logger.addHandler(console_handler)
+    # https://docs.python.org/3/library/logging.handlers.html#streamhandler
+    #
+    # The StreamHandler class, located in the core logging package,
+    # sends logging output to streams such as sys.stdout, sys.stderr or
+    # any file-like object (or, more precisely, any object which supports
+    # write() and flush() methods).
+
+    # This only check the existance and not the functionality. Should be ok?
+    if hasattr(stream, "write") and hasattr(stream, "flush"):
+        handler = logging.StreamHandler(stream)
+    elif isinstance(stream, (str, os.PathLike)):
+        handler = logging.FileHandler(stream)
+    else:
+        raise TypeError("Input Stream is neither a file or a stream")
+
+    handler.setFormatter(logging.Formatter(fmt))
+    logger.addHandler(handler)
+
+    logger.info(f"MDAnalysis {version} STARTED logging to {stream!r}")
 
     return logger
 

testsuite/MDAnalysisTests/utils/test_log.py

@@ -41,6 +41,10 @@ def test_start_stop_logging():
         MDAnalysis.log.stop_logging()
 
 
+# Write Tests here for later
+# Idk why there are two seperate tests files: lib/test_log.py and utils/test_log.py
+
+
 class RedirectedStderr(object):
     """Temporarily replaces sys.stderr with *stream*.