13.2.6. 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.”.

Note

The logging module in the standard library contains in depth documentation about using logging.

13.2.6.1. Convenience functions

Two convenience functions at the top level make it easy to start and stop the default MDAnalysis logger.

MDAnalysis.start_logging(logfile='MDAnalysis.log', version='1.0.1')[source]

Start logging of messages to file and console.

The default logfile is named MDAnalysis.log and messages are logged with the tag MDAnalysis.

MDAnalysis.stop_logging()[source]

Stop logging to logfile and console.

13.2.6.2. 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.

emit(record)[source]

Do whatever it takes to actually log the specified logging record.

This version is intended to be implemented by subclasses and so raises a NotImplementedError.

class MDAnalysis.lib.log.ProgressBar(*args, **kwargs)[source]

Display a visual progress bar and time estimate.

The ProgressBar decorates an iterable object, returning an iterator which acts exactly like the original iterable, but prints a dynamically updating progressbar every time a value is requested. See the example below for how to use it when iterating over the frames of a trajectory.

Parameters:
  • iterable (iterable, optional) – Iterable to decorate with a progressbar. Leave blank to manually manage the updates.
  • verbose (bool, optional) – If True (the default) then show the progress bar, unless the disable keyword is set to True (disable takes precedence over verbose). If verbose is set to None then the progress bar is displayed (like True), unless this is a non-TTY output device (see disable).
  • desc (str, optional) – Prefix for the progressbar.
  • total (int or float, optional) – The number of expected iterations. If unspecified, len(iterable) is used if possible. If float("inf") or as a last resort, only basic progress statistics are displayed (no ETA, no progressbar).
  • leave (bool, optional) – If [default: True], keeps all traces of the progressbar upon termination of iteration. If None, will leave only if position is 0.
  • file (io.TextIOWrapper or io.StringIO, optional) – Specifies where to output the progress messages (default: sys.stderr). Uses file.write() and file.flush() methods. For encoding, see write_bytes.
  • ncols (int, optional) – The width of the entire output message. If specified, dynamically resizes the progressbar to stay within this bound. If unspecified, attempts to use environment width. The fallback is a meter width of 10 and no limit for the counter and statistics. If 0, will not print any meter (only stats).
  • mininterval (float, optional) – Minimum progress display update interval [default: 0.1] seconds.
  • maxinterval (float, optional) – Maximum progress display update interval [default: 10] seconds. Automatically adjusts miniters to correspond to mininterval after long display update lag. Only works if dynamic_miniters or monitor thread is enabled.
  • miniters (int or float, optional) – Minimum progress display update interval, in iterations. If 0 and dynamic_miniters, will automatically adjust to equal mininterval (more CPU efficient, good for tight loops). If > 0, will skip display of specified number of iterations. Tweak this and mininterval to get very efficient loops. If your progress is erratic with both fast and slow iterations (network, skipping items, etc) you should set miniters=1.
  • ascii (bool or str, optional) – If unspecified or False, use unicode (smooth blocks) to fill the meter. The fallback is to use ASCII characters ” 123456789#”.
  • disable (bool, optional) – Whether to disable the entire progressbar wrapper [default: False]. If set to None, disable on non-TTY.
  • unit (str, optional) – String that will be used to define the unit of each iteration [default: it].
  • unit_scale (bool or int or float, optional) – If 1 or True, the number of iterations will be reduced/scaled automatically and a metric prefix following the International System of Units standard will be added (kilo, mega, etc.) [default: False]. If any other non-zero number, will scale total and n.
  • dynamic_ncols (bool, optional) – If set, constantly alters ncols and nrows to the environment (allowing for window resizes) [default: False].
  • smoothing (float, optional) – Exponential moving average smoothing factor for speed estimates (ignored in GUI mode). Ranges from 0 (average speed) to 1 (current/instantaneous speed) [default: 0.3].
  • bar_format (str, optional) –

    Specify a custom bar string formatting. May impact performance. [default: '{l_bar}{bar}{r_bar}'], where l_bar='{desc}: {percentage:3.0f}%|' and r_bar='| {n_fmt}/{total_fmt} [{elapsed}<{remaining}, {rate_fmt}{postfix}]'

    Possible vars: l_bar, bar, r_bar, n, n_fmt, total, total_fmt, percentage, elapsed, elapsed_s, ncols, nrows, desc, unit, rate, rate_fmt, rate_noinv, rate_noinv_fmt, rate_inv, rate_inv_fmt, postfix, unit_divisor, remaining, remaining_s.

    Note that a trailing “: ” is automatically removed after {desc} if the latter is empty.

  • initial (int or float, optional) – The initial counter value. Useful when restarting a progress bar [default: 0]. If using float, consider specifying {n:.3f} or similar in bar_format, or specifying unit_scale.
  • position (int, optional) – Specify the line offset to print this bar (starting from 0) Automatic if unspecified. Useful to manage multiple bars at once (e.g., from threads).
  • postfix (dict or *, optional) – Specify additional stats to display at the end of the bar. Calls set_postfix(**postfix) if possible (dict).
  • unit_divisor (float, optional) – [default: 1000], ignored unless unit_scale is True.
  • write_bytes (bool, optional) – If (default: None) and file is unspecified, bytes will be written in Python 2. If True will also write bytes. In all other cases will default to unicode.
  • lock_args (tuple, optional) – Passed to refresh for intermediate output (initialisation, iterating, and updating).
  • nrows (int, optional) – The screen height. If specified, hides nested bars outside this bound. If unspecified, attempts to use environment height. The fallback is 20.
Returns:

out
Return type:

decorated iterator.

Example

To get a progress bar when analyzing a trajectory:

from MDAnalysis.lib.log import ProgressBar

...

for ts in ProgressBar(u.trajectory):
   # perform analysis

will produce something similar to

30%|███████████                       | 3/10 [00:13<00:30,  4.42s/it]

in a terminal or Jupyter notebook.

See also

The ProgressBar is derived from tqdm.auto.tqdm; see the tqdm documentation for further details on how to use it.

class MDAnalysis.lib.log.ProgressMeter(numsteps, format=None, interval=10, offset=1, verbose=True, dynamic=True, format_handling='auto')[source]

Simple progress meter (Deprecated)

..Warning:
This class is deprecated and will be removed in version 2.0. Please use MDAnalysis.lib.log.ProgressBar instead.

The ProgressMeter class can be used to show running progress such as frames processed or percentage done to give the user feedback on the duration and progress of a task. It is structures as a class that is customized on instantation (e.g., using a custom format string and the expected total number of frames to be processed). Within a processing loop, call echo() with the current frame number to print the output to stderr.

Parameters:
  • numsteps (int) – total number of steps
  • interval (int) – only calculate and print progress every interval steps [10]
  • format (str) –

    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 format is None then the default is used:

    Step {step:5d}/{numsteps} [{percentage:5.1f}%]
  • offset (int) – number to add to step; e.g. if step is 0-based (as in MDAnalysis) then one should set offset = 1; for 1-based steps, choose 0. [1]
  • verbose (bool) – If False, disable all output, True print all messages as specified, [True]
  • dynamic (bool) – If True, each line will be printed on top of the previous one. This is done by prepedind the format with \r. [True]
  • format_handling (str) –

    how to handle the format string. Allowed values are:

    • new: the format string uses {}-based formating
    • legacy: the format string uses %-basedd formating
    • auto: default, try to guess how the format string should be handled

Examples

The typical use case is to show progress as frames of a trajectory are processed:

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%]
...

The default format string is:

Step {step:5d}/{numsteps} [{percentage:5.1f}%]

By default, each line of the progress meter is displayed on top of the previous one. To prevent this behaviour, set the dynamic keyword to False.

It is possible to embed (almost) arbitrary additional data in the format string, for example a current RMSD value:

format_line = "RMSD {rmsd:5.2f} at {step:5d}/{numsteps} [{percentage:5.1f}%]"
pm = ProgressMeter(u.trajectory.n_frames,
                   interval=100, format=format_line)
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%]
...

Changed in version 0.8: Keyword argument quiet was added.

Changed in version 0.16: Keyword argument dynamic replaces \r in the format.

Deprecated since version 0.16: Keyword argument quiet is deprecated in favor of verbose.

Deprecated since version 1.0: This class is deprecated in favor of ProgressBar.

echo(step, **kwargs)[source]

Print the state to stderr, but only every interval steps.

  1. calls update()
  2. writes step and percentage to stderr with echo(), using the format string (in ProgressMeter.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 verbose = False has been set in the constructor or if ProgressMeter.verbose has been set to False, then no messages will be printed.

update(step, **kwargs)[source]

Update the state of the ProgressMeter.

kwargs are additional attributes that can be references in the format string.

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.

MDAnalysis.lib.log.start_logging(logfile='MDAnalysis.log', version='1.0.1')[source]

Start logging of messages to file and console.

The default logfile is named MDAnalysis.log and messages are logged with the tag MDAnalysis.

MDAnalysis.lib.log.stop_logging()[source]

Stop logging to logfile and console.