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.
Two convenience functions at the top level make it easy to start and stop the default MDAnalysis logger.
Silent Handler.
Useful as a default:
h = NullHandler()
logging.getLogger("MDAnalysis").addHandler(h)
del h
Initializes the instance - basically setting the formatter to None and the filter list to empty.
Simple progress meter
Usage:
u = Universe(PSF, DCD)
pm = ProgressMeter(u.trajectory.numframes, 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.numframes, 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) ...
Set up the ProgressMeter
Arguments : |
|
---|---|
Keywords : |
|
Changed in version 0.8: Keyword argument quiet was added.
Print the state to stderr, but only every interval steps.
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 if ProgressMeter.quiet has been set to True the no messages will be printed.
clean out handlers in the library top level logger
(only important for reload/debug cycles...)
Create a top level logger.
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.