9.4. Setting up logging — MDAnalysis.lib.log
¶
Configure logging for MDAnalysis. Import this module if logging is desired in application code.
Logging to a file and the console is set up by default as described under logging to multiple destinations.
The top level logger of the library is named MDAnalysis by
convention; a simple logger that writes to the console and logfile can
be created with the create()
function. This only has to be done
once. For convenience, the default MDAnalysis logger can be created
with MDAnalysis.start_logging()
:
import MDAnalysis
MDAnalysis.start_logging()
Once this has been done, MDAnalysis will write messages to the logfile
(named MDAnalysis.log by default but this can be changed with the
optional argument to start_logging()
).
Any code can log to the MDAnalysis logger by using
import logging
logger = logging.getLogger('MDAnalysis.MODULENAME')
# use the logger, for example at info level:
logger.info("Starting task ...")
The important point is that the name of the logger begins with “MDAnalysis.”.
See also
The logging
module in the standard library contains
in depth documentation about using logging.
9.4.1. Convenience functions¶
Two convenience functions at the top level make it easy to start and stop the default MDAnalysis logger.
9.4.2. Other functions and classes for logging purposes¶
-
class
MDAnalysis.lib.log.
NullHandler
(level=0)[source]¶ 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
Initializes the instance - basically setting the formatter to None and the filter list to empty.
-
class
MDAnalysis.lib.log.
ProgressMeter
(numsteps, format=None, interval=10, offset=0, quiet=False)[source]¶ Simple progress meter
Usage:
u = Universe(PSF, DCD) pm = ProgressMeter(u.trajectory.n_frames, interval=100) for ts in u.trajectory: pm.echo(ts.frame) ...
For a trajectory with 10000 frames this will produce output such as
Step 100/10000 [ 1.0%] Step 200/10000 [ 2.0%] ...
Because the default format string
"Step %(step)5d/%(numsteps)d [%(percentage)5.1f%%]\r"
ends with a carriage return
\r
and not a newline\n
, the lines will be printed on top of each other.It is possible to embed (almost) arbitrary additional data in the format string, for example a current RMSD value:
- pm = ProgressMeter(u.trajectory.n_frames, interval=100,
- “RMSD %(rmsd)5.2f at %(step)5d/%(numsteps)d [%(percentage)5.1f%%]r”)
- for ts in u.trajectory:
- pm.echo(ts.frame, rmsd=current_rmsd) ...
- This will print something like
- RMSD 1.02 at 100/10000 [ 1.0%] RMSD 1.89 at 200/10000 [ 2.0%] ...
Set up the ProgressMeter
Arguments: - numsteps
total number of steps
Keywords: - interval
only calculate progress every interval steps [10]
- format
a format string with Python variable interpolation. Allowed values:
- step: current step
- numsteps: total number of steps as supplied in numsteps
- percentage: percentage of total
The last call to
ProgressMeter.print()
will automatically issue a newline\n
if the last character is the carriage return\r
.If format is
None
then the default is used. [“Step %(step)5d/%(numsteps)d [%(percentage)5.1f%%]r”]- offset
number to add to step; e.g. if step is 0-based then one would set offset = 1 [0]
- quiet
If
True
, disable all output,False
print all messages as specified, [False
]
Changed in version 0.8: Keyword argument quiet was added.
-
echo
(step, **kwargs)[source]¶ Print the state to stderr, but only every interval steps.
- calls
update()
- writes step and percentage to stderr with
echo()
, using the format string (inProgressMeter.format
)
The last step is always shown, even if not on an interval, and a carriage return is replaced with a new line for a cleaner display.
kwargs are additional attributes that can be references in the format string.
Note
If quiet =
True
has been set in the constructor or ifProgressMeter.quiet
has been set toTrue
the no messages will be printed.- calls
-
MDAnalysis.lib.log.
clear_handlers
(logger)[source]¶ clean out handlers in the library top level logger
(only important for reload/debug cycles...)
-
MDAnalysis.lib.log.
create
(logger_name='MDAnalysis', logfile='MDAnalysis.log')[source]¶ Create a top level logger.
- The file logger logs everything (including DEBUG).
- The console logger only logs INFO and above.
Logging to a file and the console as described under logging to multiple destinations.
The top level logger of MDAnalysis is named MDAnalysis. Note that we are configuring this logger with console output. If a root logger also does this then we will get two output lines to the console.