pyworkflow.config module
- class pyworkflow.config.Config[source]
Bases:
object
Main Config for pyworkflow. It contains the main Scipion configuration variables providing default values or, if present, taking them from the environment. Necessary value is SCIPION_HOME and has to be present in the environment
- NO_COLOR = ''
//no-color.org/ iniative. Set it to something different than ‘’ to deactivate colors in the output.
- Type
Complain with https
- SCIPION_CANCEL_FASTCOPY = None
Cancel fast copy done by shutil (copying files) when it fails. Has happened in GPFS environments.
- SCIPION_CONFIG = 'scipion.conf'
Path to the scipion configuration file where all this variables could be defined.
- SCIPION_CWD = '/tmp/tmp6zh7_6g7/7adc389a21502317587912afe444b43d9a1a9e29'
- SCIPION_DOMAIN = None
- SCIPION_FONT_NAME = 'Helvetica'
Name of the font to use in Scipion GUI. Defaults to Helvetica.
- SCIPION_FONT_SIZE = 10
Size of the ‘normal’ font to be used in Scipion GUI. Defaults to 10.
- SCIPION_GUI_REFRESH_IN_THREAD = 'False'
- SCIPION_HOME = '/home/buildbot/devel/scipion'
Path where Scipion is installed. Other paths are based on this like SCIPION_SOFTWARE, SCIPION_TESTS,… unless specified
- SCIPION_HOSTS = 'hosts.conf'
Path to the host.cof file to allow scipion to use queue engines and run in HPC environments.
- SCIPION_LOCAL_CONFIG = '/home/buildbot/.config/scipion/scipion_devel.conf'
Path to an optional/extra/user configuration file meant to overwrite default variables.
- SCIPION_LOG = '/home/buildbot/ScipionUserData/logs/scipion.log'
Path to the file where scipion will write GUI logging messages. Defaults to SCIPION_LOGS/scipion.log
- SCIPION_LOGO = 'scipion_logo.gif'
- SCIPION_LOGS = '/home/buildbot/ScipionUserData/logs'
Path for Scipion logs folder used by the GUI. Defaults to SCIPION_USER_DATA/logs.
- SCIPION_LOG_CONFIG = None
Optional. Path to a python logging configuration file fine tune the logging.
- SCIPION_LOG_LEVEL = 'INFO'
Default logging level. String among CRITICAL, ERROR, WARNING, INFO, DEBUG, NOTSET. Default value is INFO.
- SCIPION_NOTES_ARGS = None
- SCIPION_NOTES_FILE = 'notes.txt'
Name of the file where to write per project notes.
- SCIPION_NOTES_PROGRAM = None
Command or program to use to open the notes file. Otherwise system will extension association will take place.
- SCIPION_NOTIFY = 'True'
If set to False, Scipion developers will know almost nothing about Scipion usage and will have less information to improve it.
- SCIPION_PLUGIN_JSON = 'plugins.json'
Optional. Path to get the json file with all the plugins available for Scipion.
- SCIPION_PLUGIN_REPO_URL = 'http://scipion.i2pc.es/getplugins/'
Url from where to get the list of plugins.
- SCIPION_PRIORITY_PACKAGE_LIST = None
- SCIPION_PROTOCOLS = 'protocols.conf'
- SCIPION_SCRATCH = None
Optional. Path to a location mounted in a scratch drive (SSD,…)
- SCIPION_SOFTWARE = '/home/buildbot/devel/scipion/software'
Path where Scipion will install the software. Defaults to SCIPION_HOME/software.
- SCIPION_STEPS_CHECK_SEC = 5
Number of seconds to wait before checking if new input is available in streamified protocols.
- SCIPION_SUPPORT_EMAIL = 'scipion@cnb.csic.es'
- SCIPION_TESTS = '/home/buildbot/devel/scipion/data/tests'
Path where to find/download test data. Defaults to SCIPION_HOME/data/tests.
- SCIPION_TESTS_CMD = '/home/buildbot/devel/scipion/scipion-pyworkflow/pyworkflow/apps/pw_run_tests.py'
- SCIPION_TESTS_OUTPUT = '/home/buildbot/ScipionUserData/Tests'
Path to a folder Where the output of the tests will be written. Defaults to SCIPION_USER_DATA/Tests.
- SCIPION_TMP = '/home/buildbot/ScipionUserData/tmp'
General purpose scipion tmp folder. Defaults to SCIPION_USER_DATA/tmp
- SCIPION_UPDATE_SET_ATTEMPTS = 3
Number of attempts to modify the protocol output before failing. The default value is 3
- SCIPION_UPDATE_SET_ATTEMPT_WAIT = 2
Time in seconds to wait until the next attempt when checking new outputs. The default value is 2 seconds
- SCIPION_URL = 'http://scipion.cnb.csic.es/downloads/scipion'
- SCIPION_URL_SOFTWARE = 'http://scipion.cnb.csic.es/downloads/scipion/software'
- SCIPION_URL_TESTDATA = 'http://scipion.cnb.csic.es/downloads/scipion/data/tests'
- SCIPION_USER_DATA = '/home/buildbot/ScipionUserData'
Path where Scipion projects are or will be created. Defaults to ~/ScipionUserData
- VIEWERS = {}
- WIZARD_MASK_COLOR = '[0.125, 0.909, 0.972]'
Color to use in some wizards.
- classmethod colorsInTerminal()[source]
Returns true if colors are allowed. Based on NO_COLOR variable. Undefined or ‘’ colors are enabled
- classmethod getBindingsFolder()[source]
Folder where bindings must be placed. This folder is added to sys.path at launching time. If the binding depends on a dynamic libraries, those must be placed at cls.getLibFolder() :return: The bindings folder
- classmethod getLibFolder()[source]
- Returns
Folder where libraries must be placed in case a binding needs them