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.
Start logging of messages to file and console.
The default logfile is named MDAnalysis.log and messages are logged with the tag MDAnalysis.
Stop logging to logfile and console.
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.
Set up the ProgressMeter
Arguments : |
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Keywords : |
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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.
Update the state of the ProgressMeter
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.
Simple string output that immediately prints to the console.