From 33a8005f711434b7291f16c570199d9288f6d64b Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Wed, 22 Apr 2026 22:10:45 -0700
Subject: [PATCH 01/29] intial pseudocode

---
 package/MDAnalysis/lib/log.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index d63ec547828..64edef04198 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -93,15 +93,15 @@
 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)
+    create("MDAnalysis", stream=stream)
     logging.getLogger("MDAnalysis").info(
-        "MDAnalysis %s STARTED logging to %r", version, logfile
+        "MDAnalysis %s STARTED logging to %r", version, stream
     )
 
 
@@ -134,6 +134,14 @@ def create(logger_name="MDAnalysis", logfile="MDAnalysis.log"):
 
     logger.setLevel(logging.DEBUG)
 
+    ## TODO need logic for multiple handlers
+    # Pseudocode for create arguments and behavior 
+    # 1. input : str -> create new log_file
+    # 2. File objects (like file.open() and sys.stdout/sys.stderr) -> new file
+    # 3. Iterable (like [file, sys.stdout]) -> create file and print to console
+    ##
+
+
     # handler that writes to logfile
     logfile_handler = logging.FileHandler(logfile)
     logfile_formatter = logging.Formatter(

From 1bf0ee1e17fcd1665e7955d5683ee3dcf4389a58 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Wed, 22 Apr 2026 22:58:25 -0700
Subject: [PATCH 02/29] inital thought code (hadn't run it yet)

---
 package/MDAnalysis/lib/log.py | 37 +++++++++++++++++++++++++++++++++--
 1 file changed, 35 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index 64edef04198..f63d36e18b5 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -87,6 +87,7 @@
 import sys
 import logging
 import re
+from collections.abc import Iterable
 
 from tqdm.auto import tqdm
 
@@ -112,7 +113,7 @@ 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'):
     """Create a top level logger.
 
     - The file logger logs everything (including DEBUG).
@@ -132,7 +133,8 @@ def create(logger_name="MDAnalysis", logfile="MDAnalysis.log"):
 
     logger = logging.getLogger(logger_name)
 
-    logger.setLevel(logging.DEBUG)
+    #level parameter is from https://docs.python.org/3/library/logging.html#logging-levels
+    logger.setLevel(level.upper())
 
     ## TODO need logic for multiple handlers
     # Pseudocode for create arguments and behavior 
@@ -141,6 +143,37 @@ def create(logger_name="MDAnalysis", logfile="MDAnalysis.log"):
     # 3. Iterable (like [file, sys.stdout]) -> create file and print to console
     ##
 
+    # create a master logger, and attach handles to it?
+    # See https://docs.python.org/3/library/logging.handlers.html#
+    #
+    
+    # am borowwing this pattern from fetch module
+    if isinstance(stream, str):
+        streams = tuple(stream,)
+    # Want to allow ndarrays, tuple, and list but exclude strings
+    elif isinstance(stream, Iterable):
+        streams = stream
+    else:
+        raise Exception('foobar')
+    
+    for stream in streams:
+        # 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).
+        
+        # note this is looks gross and probably need to be written - invert the if and else case?
+        if (hasattr(streams, 'flush') and callable(getattr(streams, 'flush'))) and \
+            (hasattr(streams, 'write') and callable(getattr(streams, 'write'))):
+            handler = logging.StreamHandler(stream)
+        else:
+            handler = logging.FileHandler(stream)
+
+        logger.addHandler(handler)
+        
+    return logger
+
+    ## Old code
 
     # handler that writes to logfile
     logfile_handler = logging.FileHandler(logfile)

From 24a6c313592ffc41b2314909b685df595261a392 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 07:28:36 -0700
Subject: [PATCH 03/29] more comments

---
 package/MDAnalysis/lib/log.py | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index f63d36e18b5..5871e3e5ec7 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -87,6 +87,7 @@
 import sys
 import logging
 import re
+import io
 from collections.abc import Iterable
 
 from tqdm.auto import tqdm
@@ -138,19 +139,19 @@ def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level='DEBUG'):
 
     ## TODO need logic for multiple handlers
     # Pseudocode for create arguments and behavior 
-    # 1. input : str -> create new log_file
-    # 2. File objects (like file.open() and sys.stdout/sys.stderr) -> new file
-    # 3. Iterable (like [file, sys.stdout]) -> create file and print to console
+    # 1. input : file.log -> create file.log
+    # 2. File objects (like f = file.open() and sys.stdout/sys.stderr) -> log to stream
+    # 3. Iterable (like [file.log, sys.stdout]) -> create file.log and print to console
     ##
 
-    # create a master logger, and attach handles to it?
+    # create/call a master logger, and attach handles to it?
     # See https://docs.python.org/3/library/logging.handlers.html#
     #
     
     # am borowwing this pattern from fetch module
-    if isinstance(stream, str):
-        streams = tuple(stream,)
     # Want to allow ndarrays, tuple, and list but exclude strings
+    if isinstance(stream, str) or isinstance(stream, io.IOBase):
+        streams = (stream,)
     elif isinstance(stream, Iterable):
         streams = stream
     else:
@@ -163,8 +164,9 @@ def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level='DEBUG'):
         # any file-like object (or, more precisely, any object which supports write() and flush() methods).
         
         # note this is looks gross and probably need to be written - invert the if and else case?
-        if (hasattr(streams, 'flush') and callable(getattr(streams, 'flush'))) and \
-            (hasattr(streams, 'write') and callable(getattr(streams, 'write'))):
+        # Doesn't work since FileHandler inherits from Steam handler
+        if (hasattr(stream, 'flush') and callable(getattr(stream, 'flush'))) and \
+            (hasattr(stream, 'write') and callable(getattr(stream, 'write'))):
             handler = logging.StreamHandler(stream)
         else:
             handler = logging.FileHandler(stream)

From 7a5c0b3614af02571dc1c716e2a3fc65a9e6bf2d Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 07:49:33 -0700
Subject: [PATCH 04/29] general cleanup

---
 package/MDAnalysis/lib/log.py | 37 ++++++++---------------------------
 1 file changed, 8 insertions(+), 29 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index 5871e3e5ec7..6c57530e26e 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -87,7 +87,7 @@
 import sys
 import logging
 import re
-import io
+import io, os
 from collections.abc import Iterable
 
 from tqdm.auto import tqdm
@@ -149,8 +149,7 @@ def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level='DEBUG'):
     #
     
     # am borowwing this pattern from fetch module
-    # Want to allow ndarrays, tuple, and list but exclude strings
-    if isinstance(stream, str) or isinstance(stream, io.IOBase):
+    if isinstance(stream, (str, os.PathLike)) or isinstance(stream, io.IOBase):
         streams = (stream,)
     elif isinstance(stream, Iterable):
         streams = stream
@@ -163,38 +162,18 @@ def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level='DEBUG'):
         #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).
         
-        # note this is looks gross and probably need to be written - invert the if and else case?
-        # Doesn't work since FileHandler inherits from Steam handler
-        if (hasattr(stream, 'flush') and callable(getattr(stream, 'flush'))) and \
-            (hasattr(stream, 'write') and callable(getattr(stream, 'write'))):
+        # This only check the existance and not the functionality. Should be ok?
+        if hasattr(stream, "write") and hasattr(stream, "flush"):
             handler = logging.StreamHandler(stream)
-        else:
+        elif isinstance(stream, (str, os.PathLike)):
             handler = logging.FileHandler(stream)
-
+        else:
+            raise Exception('foobar')
+        
         logger.addHandler(handler)
         
     return logger
 
-    ## Old code
-
-    # 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)
-
-    return logger
-
 
 def clear_handlers(logger):
     """clean out handlers in the library top level logger

From f1be0df87a98430e2aeb675b78e00bd68f797340 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 07:52:04 -0700
Subject: [PATCH 05/29] Post black Need to add a fmt_string parameter if want
 to replicate earlier behavior

---
 package/MDAnalysis/lib/log.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index 6c57530e26e..3b368052834 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -114,7 +114,7 @@ def stop_logging():
     clear_handlers(logger)  # this _should_ do the job...
 
 
-def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level='DEBUG'):
+def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level="DEBUG"):
     """Create a top level logger.
 
     - The file logger logs everything (including DEBUG).
@@ -134,11 +134,11 @@ def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level='DEBUG'):
 
     logger = logging.getLogger(logger_name)
 
-    #level parameter is from https://docs.python.org/3/library/logging.html#logging-levels
+    # level parameter is from https://docs.python.org/3/library/logging.html#logging-levels
     logger.setLevel(level.upper())
 
     ## TODO need logic for multiple handlers
-    # Pseudocode for create arguments and behavior 
+    # Pseudocode for create arguments and behavior
     # 1. input : file.log -> create file.log
     # 2. File objects (like f = file.open() and sys.stdout/sys.stderr) -> log to stream
     # 3. Iterable (like [file.log, sys.stdout]) -> create file.log and print to console
@@ -147,31 +147,31 @@ def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level='DEBUG'):
     # create/call a master logger, and attach handles to it?
     # See https://docs.python.org/3/library/logging.handlers.html#
     #
-    
+
     # am borowwing this pattern from fetch module
     if isinstance(stream, (str, os.PathLike)) or isinstance(stream, io.IOBase):
         streams = (stream,)
     elif isinstance(stream, Iterable):
         streams = stream
     else:
-        raise Exception('foobar')
-    
+        raise Exception("foobar")
+
     for stream in streams:
         # 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
+        # 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 Exception('foobar')
-        
+            raise Exception("foobar")
+
         logger.addHandler(handler)
-        
+
     return logger
 
 

From dbcfb1c5287b5ba4de9c75a491767f017b92f6f2 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 11:28:07 -0700
Subject: [PATCH 06/29] removed loop based control

---
 package/MDAnalysis/lib/log.py | 50 +++++++++++------------------------
 1 file changed, 15 insertions(+), 35 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index 3b368052834..273338dbf10 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -87,7 +87,8 @@
 import sys
 import logging
 import re
-import io, os
+import io
+import os
 from collections.abc import Iterable
 
 from tqdm.auto import tqdm
@@ -134,43 +135,22 @@ def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level="DEBUG"):
 
     logger = logging.getLogger(logger_name)
 
-    # level parameter is from https://docs.python.org/3/library/logging.html#logging-levels
     logger.setLevel(level.upper())
 
-    ## TODO need logic for multiple handlers
-    # Pseudocode for create arguments and behavior
-    # 1. input : file.log -> create file.log
-    # 2. File objects (like f = file.open() and sys.stdout/sys.stderr) -> log to stream
-    # 3. Iterable (like [file.log, sys.stdout]) -> create file.log and print to console
-    ##
-
-    # create/call a master logger, and attach handles to it?
-    # See https://docs.python.org/3/library/logging.handlers.html#
-    #
-
-    # am borowwing this pattern from fetch module
-    if isinstance(stream, (str, os.PathLike)) or isinstance(stream, io.IOBase):
-        streams = (stream,)
-    elif isinstance(stream, Iterable):
-        streams = stream
+    # 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 Exception("foobar")
-
-    for stream in streams:
-        # 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 Exception("foobar")
-
-        logger.addHandler(handler)
+        raise TypeError("Input Stream is neither a file or a steam")
+        
+    logger.addHandler(handler)
 
     return logger
 

From 93966fbb56f87deeb2e9999b06aa2e73a96150f7 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 11:34:01 -0700
Subject: [PATCH 07/29] Added formatter to handler

---
 package/MDAnalysis/lib/log.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index 273338dbf10..63d44fed314 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -115,7 +115,7 @@ def stop_logging():
     clear_handlers(logger)  # this _should_ do the job...
 
 
-def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level="DEBUG"):
+def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level="DEBUG", fmt=None):
     """Create a top level logger.
 
     - The file logger logs everything (including DEBUG).
@@ -148,8 +148,9 @@ def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level="DEBUG"):
     elif isinstance(stream, (str, os.PathLike)):
         handler = logging.FileHandler(stream)
     else:
-        raise TypeError("Input Stream is neither a file or a steam")
-        
+        raise TypeError("Input Stream is neither a file or a stream")
+    
+    handler.setFormatter(logging.Formatter(fmt))
     logger.addHandler(handler)
 
     return logger

From c5f6133887499f557ecedd201acaf38ade5589c4 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 11:39:10 -0700
Subject: [PATCH 08/29] Added format to start_logging() to replicate old
 behavior

---
 package/MDAnalysis/lib/log.py | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index 63d44fed314..9da468c3e6a 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -102,7 +102,18 @@ def start_logging(stream="MDAnalysis.log", version=version.__version__):
     The default logfile is named `MDAnalysis.log` and messages are
     logged with the tag *MDAnalysis*.
     """
-    create("MDAnalysis", stream=stream)
+    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",
+    )
     logging.getLogger("MDAnalysis").info(
         "MDAnalysis %s STARTED logging to %r", version, stream
     )
@@ -115,7 +126,9 @@ def stop_logging():
     clear_handlers(logger)  # this _should_ do the job...
 
 
-def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level="DEBUG", fmt=None):
+def create(
+    logger_name="MDAnalysis", stream="MDAnalysis.log", level="DEBUG", fmt=None
+):
     """Create a top level logger.
 
     - The file logger logs everything (including DEBUG).
@@ -149,7 +162,7 @@ def create(logger_name="MDAnalysis", stream="MDAnalysis.log", level="DEBUG", fmt
         handler = logging.FileHandler(stream)
     else:
         raise TypeError("Input Stream is neither a file or a stream")
-    
+
     handler.setFormatter(logging.Formatter(fmt))
     logger.addHandler(handler)
 

From e30d0ab9351d4c73667e586c2e34b3dac500df0a Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 11:41:20 -0700
Subject: [PATCH 09/29] Applied flake8

---
 package/MDAnalysis/lib/log.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index 9da468c3e6a..1e4fdff7228 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -86,10 +86,7 @@
 """
 import sys
 import logging
-import re
-import io
 import os
-from collections.abc import Iterable
 
 from tqdm.auto import tqdm
 
@@ -151,9 +148,11 @@ def create(
     logger.setLevel(level.upper())
 
     # 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).
+    # 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"):

From 5a5906d0a84ed6bd719dd0f663aab33caa369ce7 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 12:11:55 -0700
Subject: [PATCH 10/29] notes for test later

---
 package/MDAnalysis/lib/log.py               | 5 ++---
 testsuite/MDAnalysisTests/utils/test_log.py | 2 ++
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index 1e4fdff7228..eef30ee1769 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -111,9 +111,6 @@ def start_logging(stream="MDAnalysis.log", version=version.__version__):
         level="INFO",
         fmt="%(name)-12s: %(levelname)-8s %(message)s",
     )
-    logging.getLogger("MDAnalysis").info(
-        "MDAnalysis %s STARTED logging to %r", version, stream
-    )
 
 
 def stop_logging():
@@ -165,6 +162,8 @@ def create(
     handler.setFormatter(logging.Formatter(fmt))
     logger.addHandler(handler)
 
+    logger.info(f"MDAnalysis {version} STARTED logging to {stream!r}")
+
     return logger
 
 
diff --git a/testsuite/MDAnalysisTests/utils/test_log.py b/testsuite/MDAnalysisTests/utils/test_log.py
index 0abaed2795d..cfb2194e7bd 100644
--- a/testsuite/MDAnalysisTests/utils/test_log.py
+++ b/testsuite/MDAnalysisTests/utils/test_log.py
@@ -40,6 +40,8 @@ def test_start_stop_logging():
     finally:
         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*.

From f679251e7bfc401c760f51e88151d97ed3b3ce31 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 12:19:06 -0700
Subject: [PATCH 11/29] fix linter

---
 testsuite/MDAnalysisTests/utils/test_log.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/utils/test_log.py b/testsuite/MDAnalysisTests/utils/test_log.py
index cfb2194e7bd..9c9f99153dc 100644
--- a/testsuite/MDAnalysisTests/utils/test_log.py
+++ b/testsuite/MDAnalysisTests/utils/test_log.py
@@ -40,9 +40,11 @@ def test_start_stop_logging():
     finally:
         MDAnalysis.log.stop_logging()
 
-# Write Tests here for later 
+
+# 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*.
 

From 2ba1c2e40a5e72582e7c81883597904be0f410b9 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 20:30:58 -0700
Subject: [PATCH 12/29] put logger back to start_logging()

---
 package/MDAnalysis/lib/log.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index eef30ee1769..04fd49c61fc 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -90,6 +90,8 @@
 
 from tqdm.auto import tqdm
 
+# from MDAnalysis.lib.util import deprecate
+
 from .. import version
 
 
@@ -111,6 +113,9 @@ def start_logging(stream="MDAnalysis.log", version=version.__version__):
         level="INFO",
         fmt="%(name)-12s: %(levelname)-8s %(message)s",
     )
+    logging.getLogger("MDAnalysis").info(
+        f"MDAnalysis {version} STARTED logging to {stream!r}"
+    )
 
 
 def stop_logging():
@@ -162,8 +167,6 @@ def create(
     handler.setFormatter(logging.Formatter(fmt))
     logger.addHandler(handler)
 
-    logger.info(f"MDAnalysis {version} STARTED logging to {stream!r}")
-
     return logger
 
 

From cca9258e7f8a5ac6938064c703ead801ac062fba Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 20:40:39 -0700
Subject: [PATCH 13/29] cleaned up create()

---
 package/MDAnalysis/lib/log.py | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index 04fd49c61fc..a3f099d6a54 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -126,7 +126,11 @@ def stop_logging():
 
 
 def create(
-    logger_name="MDAnalysis", stream="MDAnalysis.log", level="DEBUG", fmt=None
+    logger_name="MDAnalysis",
+    stream="MDAnalysis.log",
+    level="DEBUG",
+    fmt=None,
+    mode="a",
 ):
     """Create a top level logger.
 
@@ -146,23 +150,18 @@ def create(
     """
 
     logger = logging.getLogger(logger_name)
-
     logger.setLevel(level.upper())
 
+    # This checks for file-like object per duck typing
     # 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)
+        handler = logging.FileHandler(stream, mode=mode)
     else:
-        raise TypeError("Input Stream is neither a file or a stream")
+        raise TypeError(
+            "Input Stream is neither a string, PathLike object or a stream"
+        )
 
     handler.setFormatter(logging.Formatter(fmt))
     logger.addHandler(handler)

From 94f056f5ef168f814f12c6469d3407ef6cd48309 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 21:15:54 -0700
Subject: [PATCH 14/29] removed MDAnalysis NullHandler

---
 package/MDAnalysis/__init__.py |  3 +--
 package/MDAnalysis/lib/log.py  | 17 -----------------
 2 files changed, 1 insertion(+), 19 deletions(-)

diff --git a/package/MDAnalysis/__init__.py b/package/MDAnalysis/__init__.py
index 6843c3738ab..54388565846 100644
--- a/package/MDAnalysis/__init__.py
+++ b/package/MDAnalysis/__init__.py
@@ -197,10 +197,9 @@
     StreamWarning,
 )
 
-from .lib import log
 from .lib.log import start_logging, stop_logging
 
-logging.getLogger("MDAnalysis").addHandler(log.NullHandler())
+logging.getLogger("MDAnalysis").addHandler(logging.NullHandler())
 del logging
 
 # only MDAnalysis DeprecationWarnings are loud by default
diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index a3f099d6a54..4ccb74dc272 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -179,23 +179,6 @@ def clear_handlers(logger):
         logger.removeHandler(h)
 
 
-class NullHandler(logging.Handler):
-    """Silent Handler.
-
-    Useful as a default::
-
-      h = NullHandler()
-      logging.getLogger("MDAnalysis").addHandler(h)
-      del h
-
-    see the advice on logging and libraries in
-    http://docs.python.org/library/logging.html?#configuring-logging-for-a-library
-    """
-
-    def emit(self, record):
-        pass
-
-
 class ProgressBar(tqdm):
     r"""Display a visual progress bar and time estimate.
 

From 7f5812fa92f9ccb87cefc0b263bddf9a7790bd1b Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 21:36:06 -0700
Subject: [PATCH 15/29] readded top level import -- it broke some tests

---
 package/MDAnalysis/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/package/MDAnalysis/__init__.py b/package/MDAnalysis/__init__.py
index 54388565846..8b5db410db5 100644
--- a/package/MDAnalysis/__init__.py
+++ b/package/MDAnalysis/__init__.py
@@ -197,6 +197,7 @@
     StreamWarning,
 )
 
+from .lib import log
 from .lib.log import start_logging, stop_logging
 
 logging.getLogger("MDAnalysis").addHandler(logging.NullHandler())

From ba9315e379988e0a256791e184f62d2ab1c30a91 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 21:43:19 -0700
Subject: [PATCH 16/29] ported over tests

---
 testsuite/MDAnalysisTests/lib/test_log.py   | 14 +++-
 testsuite/MDAnalysisTests/utils/test_log.py | 79 ---------------------
 2 files changed, 12 insertions(+), 81 deletions(-)
 delete mode 100644 testsuite/MDAnalysisTests/utils/test_log.py

diff --git a/testsuite/MDAnalysisTests/lib/test_log.py b/testsuite/MDAnalysisTests/lib/test_log.py
index 541660ca4c7..6cd4ecffd26 100644
--- a/testsuite/MDAnalysisTests/lib/test_log.py
+++ b/testsuite/MDAnalysisTests/lib/test_log.py
@@ -20,11 +20,21 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
-import warnings
-import pytest
 
+import logging 
+
+import MDAnalysis
 from MDAnalysis.lib.log import ProgressBar
 
+def test_start_stop_logging():
+    try:
+        MDAnalysis.log.start_logging()
+        logger = logging.getLogger("MDAnalysis")
+        logger.info("Using the MDAnalysis logger works")
+    except Exception as err:
+        raise AssertionError("Problem with logger: {0}".format(err))
+    finally:
+        MDAnalysis.log.stop_logging()
 
 class TestProgressBar(object):
 
diff --git a/testsuite/MDAnalysisTests/utils/test_log.py b/testsuite/MDAnalysisTests/utils/test_log.py
deleted file mode 100644
index 9c9f99153dc..00000000000
--- a/testsuite/MDAnalysisTests/utils/test_log.py
+++ /dev/null
@@ -1,79 +0,0 @@
-# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
-#
-# MDAnalysis --- https://www.mdanalysis.org
-# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
-# (see the file AUTHORS for the full list of names)
-#
-# Released under the Lesser GNU Public Licence, v2.1 or any higher version
-#
-# Please cite your use of MDAnalysis in published work:
-#
-# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
-# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
-# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
-# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
-# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
-# doi: 10.25080/majora-629e541a-00e
-#
-# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
-# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
-# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
-#
-from io import StringIO
-
-import logging
-import sys
-
-import MDAnalysis
-import MDAnalysis.lib.log
-import pytest
-
-
-def test_start_stop_logging():
-    try:
-        MDAnalysis.log.start_logging()
-        logger = logging.getLogger("MDAnalysis")
-        logger.info("Using the MDAnalysis logger works")
-    except Exception as err:
-        raise AssertionError("Problem with logger: {0}".format(err))
-    finally:
-        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*.
-
-    Deals with cached stderr, see
-    http://stackoverflow.com/questions/6796492/temporarily-redirect-stdout-stderr
-    """
-
-    def __init__(self, stream=None):
-        self._stderr = sys.stderr
-        self.stream = stream or sys.stdout
-
-    def __enter__(self):
-        self.old_stderr = sys.stderr
-        self.old_stderr.flush()
-        sys.stderr = self.stream
-
-    def __exit__(self, exc_type, exc_value, traceback):
-        self._stderr.flush()
-        sys.stderr = self.old_stderr
-
-
-@pytest.fixture()
-def buffer():
-    return StringIO()
-
-
-def _assert_in(output, string):
-    assert (
-        string in output
-    ), "Output '{0}' does not match required format '{1}'.".format(
-        output.replace("\r", "\\r"), string.replace("\r", "\\r")
-    )

From 0e3623177a46c67384d4ff6ffcd29d4d0eaf78c3 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 21:45:56 -0700
Subject: [PATCH 17/29] Used black

---
 testsuite/MDAnalysisTests/lib/test_log.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/lib/test_log.py b/testsuite/MDAnalysisTests/lib/test_log.py
index 6cd4ecffd26..4efd69e1af0 100644
--- a/testsuite/MDAnalysisTests/lib/test_log.py
+++ b/testsuite/MDAnalysisTests/lib/test_log.py
@@ -21,11 +21,12 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 
-import logging 
+import logging
 
 import MDAnalysis
 from MDAnalysis.lib.log import ProgressBar
 
+
 def test_start_stop_logging():
     try:
         MDAnalysis.log.start_logging()
@@ -36,6 +37,7 @@ def test_start_stop_logging():
     finally:
         MDAnalysis.log.stop_logging()
 
+
 class TestProgressBar(object):
 
     def test_output(self, capsys):

From e63f5ef6a399dd06fc65656d314976851cf024d3 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 23:19:10 -0700
Subject: [PATCH 18/29] Added Tests for start_logging() and stop_logging()

---
 package/MDAnalysis/lib/log.py             |  4 +-
 testsuite/MDAnalysisTests/lib/test_log.py | 50 +++++++++++++++++++----
 2 files changed, 43 insertions(+), 11 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index 4ccb74dc272..ad3acaff484 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -150,7 +150,6 @@ def create(
     """
 
     logger = logging.getLogger(logger_name)
-    logger.setLevel(level.upper())
 
     # This checks for file-like object per duck typing
     # https://docs.python.org/3/library/logging.handlers.html#streamhandler
@@ -163,6 +162,7 @@ def create(
             "Input Stream is neither a string, PathLike object or a stream"
         )
 
+    handler.setLevel(level.upper())
     handler.setFormatter(logging.Formatter(fmt))
     logger.addHandler(handler)
 
@@ -175,7 +175,7 @@ def clear_handlers(logger):
     (only important for reload/debug cycles...)
 
     """
-    for h in logger.handlers:
+    for h in list(logger.handlers):
         logger.removeHandler(h)
 
 
diff --git a/testsuite/MDAnalysisTests/lib/test_log.py b/testsuite/MDAnalysisTests/lib/test_log.py
index 4efd69e1af0..672ed3ddd6e 100644
--- a/testsuite/MDAnalysisTests/lib/test_log.py
+++ b/testsuite/MDAnalysisTests/lib/test_log.py
@@ -21,21 +21,53 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 
+import sys
 import logging
+import MDAnalysis as mda
 
-import MDAnalysis
+from os.path import basename
 from MDAnalysis.lib.log import ProgressBar
 
 
-def test_start_stop_logging():
-    try:
-        MDAnalysis.log.start_logging()
+class TestConvenienceFunctions:
+    def test_start_logging(self, tmp_path):
+        mda.start_logging(tmp_path / "MDAnalysis.log")
         logger = logging.getLogger("MDAnalysis")
-        logger.info("Using the MDAnalysis logger works")
-    except Exception as err:
-        raise AssertionError("Problem with logger: {0}".format(err))
-    finally:
-        MDAnalysis.log.stop_logging()
+
+        # Test Handlers' presence and behavior
+        assert any(isinstance(h, logging.NullHandler) for h in logger.handlers)
+        any(
+            isinstance(h, logging.FileHandler)
+            and basename(h.stream.name) == "MDAnalysis.log"
+            and h.level == logging.DEBUG
+            for h in logger.handlers
+        )
+        assert any(
+            isinstance(h, logging.StreamHandler)
+            and h.stream is sys.stdout
+            and h.level == logging.INFO
+            for h in logger.handlers
+        )
+
+    def test_stop_logging(self, tmp_path):
+        mda.lib.log.start_logging(tmp_path / "MDAnalysis.log")
+        logger = logging.getLogger("MDAnalysis")
+        mda.lib.log.stop_logging()
+
+        assert len(logger.handlers) == 0
+
+
+# This doesn't test functionality at all
+# Need rewrite
+# def test_start_stop_logging():
+#     try:
+#         MDAnalysis.log.start_logging()
+#         logger = logging.getLogger("MDAnalysis")
+#         logger.info("Using the MDAnalysis logger works")
+#     except Exception as err:
+#         raise AssertionError("Problem with logger: {0}".format(err))
+#     finally:
+#         MDAnalysis.log.stop_logging()
 
 
 class TestProgressBar(object):

From a81e4adedfb217bd2ceae00f62ff0070fc2e5c9a Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 23:25:23 -0700
Subject: [PATCH 19/29] Added comment

---
 testsuite/MDAnalysisTests/lib/test_log.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/lib/test_log.py b/testsuite/MDAnalysisTests/lib/test_log.py
index 672ed3ddd6e..8b8c114e12b 100644
--- a/testsuite/MDAnalysisTests/lib/test_log.py
+++ b/testsuite/MDAnalysisTests/lib/test_log.py
@@ -34,7 +34,7 @@ def test_start_logging(self, tmp_path):
         mda.start_logging(tmp_path / "MDAnalysis.log")
         logger = logging.getLogger("MDAnalysis")
 
-        # Test Handlers' presence and behavior
+        # Test expected handlers' presence and behavior
         assert any(isinstance(h, logging.NullHandler) for h in logger.handlers)
         any(
             isinstance(h, logging.FileHandler)

From f25aec7440165fd0f0169d9d8c01dc6ef274db18 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 23:25:23 -0700
Subject: [PATCH 20/29] Added comment

---
 testsuite/MDAnalysisTests/lib/test_log.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/lib/test_log.py b/testsuite/MDAnalysisTests/lib/test_log.py
index 672ed3ddd6e..8b8c114e12b 100644
--- a/testsuite/MDAnalysisTests/lib/test_log.py
+++ b/testsuite/MDAnalysisTests/lib/test_log.py
@@ -34,7 +34,7 @@ def test_start_logging(self, tmp_path):
         mda.start_logging(tmp_path / "MDAnalysis.log")
         logger = logging.getLogger("MDAnalysis")
 
-        # Test Handlers' presence and behavior
+        # Test expected handlers' presence and behavior
         assert any(isinstance(h, logging.NullHandler) for h in logger.handlers)
         any(
             isinstance(h, logging.FileHandler)

From bdaf241e7ae621a4e71797e2b6c2f78440752e5a Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Thu, 23 Apr 2026 23:28:30 -0700
Subject: [PATCH 21/29] post black

---
 testsuite/MDAnalysisTests/lib/test_log.py | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/testsuite/MDAnalysisTests/lib/test_log.py b/testsuite/MDAnalysisTests/lib/test_log.py
index 8b8c114e12b..d8a0a6e9e21 100644
--- a/testsuite/MDAnalysisTests/lib/test_log.py
+++ b/testsuite/MDAnalysisTests/lib/test_log.py
@@ -57,19 +57,6 @@ def test_stop_logging(self, tmp_path):
         assert len(logger.handlers) == 0
 
 
-# This doesn't test functionality at all
-# Need rewrite
-# def test_start_stop_logging():
-#     try:
-#         MDAnalysis.log.start_logging()
-#         logger = logging.getLogger("MDAnalysis")
-#         logger.info("Using the MDAnalysis logger works")
-#     except Exception as err:
-#         raise AssertionError("Problem with logger: {0}".format(err))
-#     finally:
-#         MDAnalysis.log.stop_logging()
-
-
 class TestProgressBar(object):
 
     def test_output(self, capsys):

From d0b732f3ba78a9b8deaf2043a55f151d0b5fc749 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Fri, 24 Apr 2026 08:14:20 -0700
Subject: [PATCH 22/29] Added comments about deprecations

---
 package/MDAnalysis/__init__.py |  2 +-
 package/MDAnalysis/lib/log.py  | 20 ++++++++++++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/package/MDAnalysis/__init__.py b/package/MDAnalysis/__init__.py
index 8b5db410db5..fe9023f694a 100644
--- a/package/MDAnalysis/__init__.py
+++ b/package/MDAnalysis/__init__.py
@@ -200,7 +200,7 @@
 from .lib import log
 from .lib.log import start_logging, stop_logging
 
-logging.getLogger("MDAnalysis").addHandler(logging.NullHandler())
+logging.getLogger(__name__).addHandler(logging.NullHandler())
 del logging
 
 # only MDAnalysis DeprecationWarnings are loud by default
diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index ad3acaff484..a50399c83dc 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -94,6 +94,11 @@
 
 from .. import version
 
+# Things to deprecated:
+# logfile -> stream (bc it could be any stream like object)
+#
+# version? Why would any user want to modify version in the first place?
+# Just have the message logged it directly
 
 def start_logging(stream="MDAnalysis.log", version=version.__version__):
     """Start logging of messages to file and console.
@@ -124,7 +129,22 @@ def stop_logging():
     logger.info("MDAnalysis STOPPED logging")
     clear_handlers(logger)  # this _should_ do the job...
 
+# Things to deprecated overall:
+# log.NullHandler -> replace with logging.NullHandler() warning
+# create() -> add_handler() (confusing bc standard library has the same method)
+#             or create_handler()? 
+#
+# For create():
+# logger_name -> None (very dangerous to have user choose since all loggers share the same namespace)
+# logfile -> stream (bc it could be any stream like object, not just logfiles)
+
 
+# logger_name should be deprecated.
+# Standard library recommends constructing through
+# logging.getLogger(__name__) because ll loggers share the same namespace
+# __name__ is MDAnalysis
+#
+# 2nd paragraph: https://docs.python.org/3/library/logging.html#logger-objects
 def create(
     logger_name="MDAnalysis",
     stream="MDAnalysis.log",

From ec0ed2549c226d07606f2b81444393e6f1b5afb3 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Fri, 24 Apr 2026 08:22:59 -0700
Subject: [PATCH 23/29] Replaced logging.getLogger(MDAnalysis) with
 logging.getLogger(__name__)

---
 package/MDAnalysis/lib/log.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index a50399c83dc..2dbb17e3f24 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -118,14 +118,14 @@ def start_logging(stream="MDAnalysis.log", version=version.__version__):
         level="INFO",
         fmt="%(name)-12s: %(levelname)-8s %(message)s",
     )
-    logging.getLogger("MDAnalysis").info(
+    logging.getLogger(__name__).info(
         f"MDAnalysis {version} STARTED logging to {stream!r}"
     )
 
 
 def stop_logging():
     """Stop logging to logfile and console."""
-    logger = logging.getLogger("MDAnalysis")
+    logger = logging.getLogger(__name__)
     logger.info("MDAnalysis STOPPED logging")
     clear_handlers(logger)  # this _should_ do the job...
 

From 6d1a675884e34b3338b8f10fc045786ab976d4fd Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Fri, 24 Apr 2026 08:33:35 -0700
Subject: [PATCH 24/29] refined comments

---
 package/MDAnalysis/lib/log.py | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index 2dbb17e3f24..ab6e2c41288 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -100,6 +100,7 @@
 # version? Why would any user want to modify version in the first place?
 # Just have the message logged it directly
 
+
 def start_logging(stream="MDAnalysis.log", version=version.__version__):
     """Start logging of messages to file and console.
 
@@ -129,22 +130,24 @@ def stop_logging():
     logger.info("MDAnalysis STOPPED logging")
     clear_handlers(logger)  # this _should_ do the job...
 
+
 # Things to deprecated overall:
 # log.NullHandler -> replace with logging.NullHandler() warning
-# create() -> add_handler() (confusing bc standard library has the same method)
-#             or create_handler()? 
+# create() -> add_handler() (potentially confusing bc standard library
+#                            has the same method but in camelcase weirdly?)
+#                            or create_handler()?
 #
 # For create():
-# logger_name -> None (very dangerous to have user choose since all loggers share the same namespace)
 # logfile -> stream (bc it could be any stream like object, not just logfiles)
-
-
 # logger_name should be deprecated.
+#
 # Standard library recommends constructing through
-# logging.getLogger(__name__) because ll loggers share the same namespace
+# logging.getLogger(__name__) because all loggers share the same namespace
+# and this is a systemmatic way of defining loggers
+#
 # __name__ is MDAnalysis
+# See 2nd paragraph: https://docs.python.org/3/library/logging.html#logger-objects
 #
-# 2nd paragraph: https://docs.python.org/3/library/logging.html#logger-objects
 def create(
     logger_name="MDAnalysis",
     stream="MDAnalysis.log",
@@ -169,6 +172,7 @@ def create(
        http://docs.python.org/library/logging.html?#logging-to-multiple-destinations
     """
 
+    # replaced with logging.getLogger(__name__)
     logger = logging.getLogger(logger_name)
 
     # This checks for file-like object per duck typing

From 74bcc0300d5da5f2f5922f76a9549905ab49b7d9 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Fri, 24 Apr 2026 08:40:41 -0700
Subject: [PATCH 25/29] Updated tests

---
 testsuite/MDAnalysisTests/lib/test_log.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/testsuite/MDAnalysisTests/lib/test_log.py b/testsuite/MDAnalysisTests/lib/test_log.py
index d8a0a6e9e21..8d6eecac032 100644
--- a/testsuite/MDAnalysisTests/lib/test_log.py
+++ b/testsuite/MDAnalysisTests/lib/test_log.py
@@ -32,7 +32,7 @@
 class TestConvenienceFunctions:
     def test_start_logging(self, tmp_path):
         mda.start_logging(tmp_path / "MDAnalysis.log")
-        logger = logging.getLogger("MDAnalysis")
+        logger = logging.getLogger(__name__)
 
         # Test expected handlers' presence and behavior
         assert any(isinstance(h, logging.NullHandler) for h in logger.handlers)
@@ -51,7 +51,7 @@ def test_start_logging(self, tmp_path):
 
     def test_stop_logging(self, tmp_path):
         mda.lib.log.start_logging(tmp_path / "MDAnalysis.log")
-        logger = logging.getLogger("MDAnalysis")
+        logger = logging.getLogger(__name__)
         mda.lib.log.stop_logging()
 
         assert len(logger.handlers) == 0

From 0fdd02e17ab067fc003d976098a5ef61280fe661 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Fri, 24 Apr 2026 09:23:22 -0700
Subject: [PATCH 26/29] Change __name__ to MDAnalysis fix tests

---
 package/MDAnalysis/__init__.py            | 2 +-
 package/MDAnalysis/lib/log.py             | 2 +-
 testsuite/MDAnalysisTests/lib/test_log.py | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/__init__.py b/package/MDAnalysis/__init__.py
index fe9023f694a..8b5db410db5 100644
--- a/package/MDAnalysis/__init__.py
+++ b/package/MDAnalysis/__init__.py
@@ -200,7 +200,7 @@
 from .lib import log
 from .lib.log import start_logging, stop_logging
 
-logging.getLogger(__name__).addHandler(logging.NullHandler())
+logging.getLogger("MDAnalysis").addHandler(logging.NullHandler())
 del logging
 
 # only MDAnalysis DeprecationWarnings are loud by default
diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index ab6e2c41288..a060d7bcdd1 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -126,7 +126,7 @@ def start_logging(stream="MDAnalysis.log", version=version.__version__):
 
 def stop_logging():
     """Stop logging to logfile and console."""
-    logger = logging.getLogger(__name__)
+    logger = logging.getLogger("MDAnalysis")
     logger.info("MDAnalysis STOPPED logging")
     clear_handlers(logger)  # this _should_ do the job...
 
diff --git a/testsuite/MDAnalysisTests/lib/test_log.py b/testsuite/MDAnalysisTests/lib/test_log.py
index 8d6eecac032..d8a0a6e9e21 100644
--- a/testsuite/MDAnalysisTests/lib/test_log.py
+++ b/testsuite/MDAnalysisTests/lib/test_log.py
@@ -32,7 +32,7 @@
 class TestConvenienceFunctions:
     def test_start_logging(self, tmp_path):
         mda.start_logging(tmp_path / "MDAnalysis.log")
-        logger = logging.getLogger(__name__)
+        logger = logging.getLogger("MDAnalysis")
 
         # Test expected handlers' presence and behavior
         assert any(isinstance(h, logging.NullHandler) for h in logger.handlers)
@@ -51,7 +51,7 @@ def test_start_logging(self, tmp_path):
 
     def test_stop_logging(self, tmp_path):
         mda.lib.log.start_logging(tmp_path / "MDAnalysis.log")
-        logger = logging.getLogger(__name__)
+        logger = logging.getLogger("MDAnalysis")
         mda.lib.log.stop_logging()
 
         assert len(logger.handlers) == 0

From d952902bb45788f590d22358e971a656686cf522 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Fri, 24 Apr 2026 10:06:34 -0700
Subject: [PATCH 27/29] Updated Tests

---
 testsuite/MDAnalysisTests/lib/test_log.py | 32 +++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/testsuite/MDAnalysisTests/lib/test_log.py b/testsuite/MDAnalysisTests/lib/test_log.py
index d8a0a6e9e21..8b2faefea3c 100644
--- a/testsuite/MDAnalysisTests/lib/test_log.py
+++ b/testsuite/MDAnalysisTests/lib/test_log.py
@@ -21,6 +21,7 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 
+import pytest
 import sys
 import logging
 import MDAnalysis as mda
@@ -57,6 +58,37 @@ def test_stop_logging(self, tmp_path):
         assert len(logger.handlers) == 0
 
 
+# TODO need to make a fixture that can clear all handlers per test
+class TestCreateBehaviors:
+
+    def test_input_path(self, tmp_path):
+        mda.lib.log.create(stream=tmp_path / "foo.log")
+
+        assert (tmp_path / "foo.log").exists()
+
+    def test_input_string(self, tmp_path):
+        mda.lib.log.create(stream=str(tmp_path / "foo.log"))
+
+        assert (tmp_path / "foo.log").exists()
+
+    # NOTE Assert state could be cleaned up after clear_handlers() fixture is implemented
+    def test_input_stream(self):
+        mda.lib.log.create(stream=sys.stdout)
+
+        logger = logging.getLogger("MDAnalysis")
+        assert any(
+            isinstance(h, logging.StreamHandler) and h.stream is sys.stdout
+            for h in logger.handlers
+        )
+
+    def test_exception(tmp_path):
+        with pytest.raises(
+            TypeError,
+            match="Input Stream is neither a string, PathLike object or a stream",
+        ):
+            mda.lib.log.create(stream=2)
+
+
 class TestProgressBar(object):
 
     def test_output(self, capsys):

From c34eca5bcf67cd6a5245f8a561f57ba392434d7a Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Fri, 24 Apr 2026 12:52:20 -0700
Subject: [PATCH 28/29] Added future tests

---
 testsuite/MDAnalysisTests/lib/test_log.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/testsuite/MDAnalysisTests/lib/test_log.py b/testsuite/MDAnalysisTests/lib/test_log.py
index 8b2faefea3c..4bb434d9756 100644
--- a/testsuite/MDAnalysisTests/lib/test_log.py
+++ b/testsuite/MDAnalysisTests/lib/test_log.py
@@ -57,6 +57,11 @@ def test_stop_logging(self, tmp_path):
 
         assert len(logger.handlers) == 0
 
+def test_message_console(tmp_path):
+    pass
+
+def test_message_file(tmp_path):
+    pass
 
 # TODO need to make a fixture that can clear all handlers per test
 class TestCreateBehaviors:
@@ -88,6 +93,14 @@ def test_exception(tmp_path):
         ):
             mda.lib.log.create(stream=2)
 
+def test_level_parameter():
+    pass
+
+def test_fmt_parameter():
+    pass
+
+def test_mode_parameter():
+    pass
 
 class TestProgressBar(object):
 

From f9a4961adc4fc4cfbd189edccaec130d83ff37a6 Mon Sep 17 00:00:00 2001
From: Joshua Raphael Uy <jauy1@asu.edu>
Date: Fri, 1 May 2026 14:20:03 -0700
Subject: [PATCH 29/29] Finished tests for mda.start_logging() and
 mda.stop_logging()

---
 package/MDAnalysis/lib/log.py             |  5 +--
 testsuite/MDAnalysisTests/lib/test_log.py | 37 ++++++++++++++++++++---
 2 files changed, 36 insertions(+), 6 deletions(-)

diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py
index a060d7bcdd1..d93b9d4d74f 100644
--- a/package/MDAnalysis/lib/log.py
+++ b/package/MDAnalysis/lib/log.py
@@ -119,8 +119,8 @@ def start_logging(stream="MDAnalysis.log", version=version.__version__):
         level="INFO",
         fmt="%(name)-12s: %(levelname)-8s %(message)s",
     )
-    logging.getLogger(__name__).info(
-        f"MDAnalysis {version} STARTED logging to {stream!r}"
+    logging.getLogger("MDAnalysis").info(
+        f"MDAnalysis {version} STARTED logging to {stream}"
     )
 
 
@@ -174,6 +174,7 @@ def create(
 
     # replaced with logging.getLogger(__name__)
     logger = logging.getLogger(logger_name)
+    logger.setLevel(logging.DEBUG)
 
     # This checks for file-like object per duck typing
     # https://docs.python.org/3/library/logging.handlers.html#streamhandler
diff --git a/testsuite/MDAnalysisTests/lib/test_log.py b/testsuite/MDAnalysisTests/lib/test_log.py
index 4bb434d9756..f7eb16c58c7 100644
--- a/testsuite/MDAnalysisTests/lib/test_log.py
+++ b/testsuite/MDAnalysisTests/lib/test_log.py
@@ -24,12 +24,22 @@
 import pytest
 import sys
 import logging
+import time
 import MDAnalysis as mda
 
 from os.path import basename
 from MDAnalysis.lib.log import ProgressBar
 
 
+@pytest.fixture
+def fixed_log_time(monkeypatch):
+    """Pytest fixture which temporarily set the logging's t0 to the UNIX epoc"""
+    epoch = 0
+
+    monkeypatch.setattr(logging.time, "time", lambda: epoch)
+    monkeypatch.setattr(logging.Formatter, "converter", time.gmtime)
+
+
 class TestConvenienceFunctions:
     def test_start_logging(self, tmp_path):
         mda.start_logging(tmp_path / "MDAnalysis.log")
@@ -57,11 +67,26 @@ def test_stop_logging(self, tmp_path):
 
         assert len(logger.handlers) == 0
 
-def test_message_console(tmp_path):
-    pass
+    def test_message_file(self, tmp_path, fixed_log_time):
+
+        mda.start_logging(tmp_path / "MDAnalysis.log")
+
+        with open(tmp_path / "MDAnalysis.log") as f:
+
+            assert (
+                "1970-01-01 00:00:00,000 MDAnalysis   INFO     "
+                + f"MDAnalysis {mda.version.__version__} STARTED logging to {str(tmp_path)}"
+            )
+
+    def test_message_console(self, tmp_path, capsys):
+        mda.start_logging(tmp_path / "MDAnalysis.log")
+
+        assert (
+            "MDAnalysis  : INFO     "
+            + f"MDAnalysis {mda.version.__version__} STARTED logging to {str(tmp_path)}"
+            in capsys.readouterr().out
+        )
 
-def test_message_file(tmp_path):
-    pass
 
 # TODO need to make a fixture that can clear all handlers per test
 class TestCreateBehaviors:
@@ -93,15 +118,19 @@ def test_exception(tmp_path):
         ):
             mda.lib.log.create(stream=2)
 
+
 def test_level_parameter():
     pass
 
+
 def test_fmt_parameter():
     pass
 
+
 def test_mode_parameter():
     pass
 
+
 class TestProgressBar(object):
 
     def test_output(self, capsys):