Runtime Configuration¶

You can change some runtime behaviour of PyEMMA by setting a configuration value in PyEMMAs config module. These can be persisted to hard disk to be permanent on every import of the package.

Examples¶

Change values¶

To access the config at runtime eg. if progress bars should be shown:

>>> from pyemma import config 
>>> print(config.show_progress_bars) 
True
>>> config.show_progress_bars = False 
>>> print(config.show_progress_bars) 
False

Store your changes / Create a configuration directory¶

To create an editable configuration file, use the pyemma.config.save() method:

>>> from pyemma import config 
>>> config.save('/tmp/pyemma_current.cfg') 

This will store the current runtime configuration values in the given file. Note that these settings will not be used on the next start of PyEMMA, because you first need to tell us, where you have stored this file. To do so, please set the environment variable “PYEMMA_CFG_DIR” to the directory, where you have stored the config file.

For Linux/OSX this thread thread may be helpful.
For Windows have a look at this.

For details have a look at the brief documentation: https://docs.python.org/2/howto/logging.html

Default configuration file¶

Default settings are stored in a provided pyemma.cfg file, which is included in the Python package:

################################################################################
# PyEMMA configuration file
#
# notes:
# - comments are not allowed in line, since they would be appended to the value!
################################################################################

[pyemma]
# configuration notice shown?
show_config_notification = False

# Source to logging configuration file (YAML).
# Special value: DEFAULT (use default config).
# If this is set to a filename, it will be red to configure logging. If it is a
# relative path, it is assumed to be located next to where you start your interpreter.
logging_config = DEFAULT

# show or hide progress bars globally?
show_progress_bars = True

# useful for trajectory formats, for which one has to read the whole file to get len
# eg. XTC format.
use_trajectory_lengths_cache = True
# maximum entries in database
traj_info_max_entries = 50000
# max size in MB
traj_info_max_size = 500

# check output of iterators in pyemma.coordinates for infinity and NaN, useful for debug purposes.
coordinates_check_output = False

# latest version check
check_version = True

# mute progressbars and logging events (only critical)
mute = False

Configuration files¶

To configure the runtime behavior such as the logging system or other parameters, the configuration module reads several config files to build its final set of settings. It searches for the file ‘pyemma.cfg’ in several locations with different priorities:

$CWD/pyemma.cfg
$HOME/.pyemma/pyemma.cfg
~/pyemma.cfg
$PYTHONPATH/pyemma/pyemma.cfg (always taken as default configuration file)

Note that you can also override the location of the configuration directory by setting an environment variable named “PYEMMA_CFG_DIR” to a writeable path to override the location of the config files.

The default values are stored in latter file to ensure these values are always defined.

If no configuration file could be found, the defaults from the shipped package will apply.

Load a configuration file¶

In order to load a pre-saved configuration file, use the load() method:

>>> from pyemma import config 
>>> config.load('pyemma_silent.cfg') 

Configuration values¶

class pyemma.util._config.Config¶

Methods

`keys`()	valid configuration keys
`load`([filename])	load runtime configuration from given filename.
`save`([filename])	Saves the runtime configuration to disk.

Attributes

`DEFAULT_CONFIG_DIR`
`DEFAULT_CONFIG_FILE_NAME`
`DEFAULT_LOGGING_FILE_NAME`
`cfg_dir`	PyEMMAs configuration directory (eg.
`check_version`	Check for the latest release online.
`coordinates_check_output`	Enabling this option will check for invalid output (NaN, Inf) in pyemma.coordinates
`default_config_file`	default config file living in PyEMMA package
`default_logging_file`	default logging configuration
`logging_config`	currently used logging configuration file. Can not be changed during runtime.
`mute`	Switch this to True, to tell PyEMMA not to use progress bars and logging to console.
`show_config_notification`
`show_progress_bars`	Show progress bars for heavy computations?
`traj_info_max_entries`	How many entries (files) the trajectory info cache can hold.
`traj_info_max_size`	Maximum trajectory info cache size in bytes.
`use_trajectory_lengths_cache`	Shall the trajectory info cache be used to remember attributes of trajectory files.
`used_filenames`	these filenames have been red to obtain basic configuration values.

DEFAULT_CONFIG_DIR = '/tmp/pyemma-doc-release/home/.pyemma'¶

DEFAULT_CONFIG_FILE_NAME = 'pyemma.cfg'¶

DEFAULT_LOGGING_FILE_NAME = 'logging.yml'¶

cfg_dir¶: PyEMMAs configuration directory (eg. ~/.pyemma)

check_version¶

Check for the latest release online.

Disable this if you have privacy concerns. We currently collect:

Python version

PyEMMA version

operating system

MAC address

See Legal Notices for further information.

coordinates_check_output¶: Enabling this option will check for invalid output (NaN, Inf) in pyemma.coordinates

default_config_file¶: default config file living in PyEMMA package

default_logging_file¶: default logging configuration

keys()¶: valid configuration keys

load(filename=None)¶: load runtime configuration from given filename. If filename is None try to read from default file from default location.

logging_config¶: currently used logging configuration file. Can not be changed during runtime.

mute¶: Switch this to True, to tell PyEMMA not to use progress bars and logging to console.

save(filename=None)¶

Saves the runtime configuration to disk.

Parameters:	filename (str or None, default=None) – writeable path to configuration filename. If None, use default location and filename.

show_config_notification¶

show_progress_bars¶: Show progress bars for heavy computations?

traj_info_max_entries¶: How many entries (files) the trajectory info cache can hold. The cache will forget the least recently used entries when this limit is hit.

traj_info_max_size¶: Maximum trajectory info cache size in bytes. The cache will forget the least recently used entries when this limit is hit.

use_trajectory_lengths_cache¶

Shall the trajectory info cache be used to remember attributes of trajectory files.

It is strongly recommended to use the cache especially for XTC files, because this will speed up reader creation a lot.

used_filenames¶: these filenames have been red to obtain basic configuration values.