scipion.scripts.config module

Check the local configuration files, and/or create them if requested or if they do not exist.

scipion.scripts.config.addPluginsVariables(cf)[source]
scipion.scripts.config.addPyworkflowVariables(cf)[source]
scipion.scripts.config.addVariablesToSection(cf, section, vars, exclude=[])[source]

Add all the variables in vars to the config “cf” at the section passed it cleans the path to avoid long absolute repetitive paths

scipion.scripts.config.ansi(n)[source]

Return function that escapes text with ANSI color n.

scipion.scripts.config.black(txt)
scipion.scripts.config.blue(txt)
scipion.scripts.config.checkConf(fpath, ftemplate, update=False, unattended=False, compare=False)[source]

Check that all the variables in the template are in the config file too :parameter fpath: path to the config file :parameter ftemplate, template file to compare. Only used for protocols and hosts :parameter update: flag, default to false. if true, values from the template will be written to the config file :parameter unattended: avoid questions, default to false. :parameter compare: make a comparison with the template

scipion.scripts.config.checkNotify(config, configfile, unattended)[source]

Check if protocol statistics should be collected.

scipion.scripts.config.checkPaths(conf)[source]

Check that some paths in the config file actually make sense

scipion.scripts.config.compareConfig(cf, ct, fPath, fTemplate)[source]

Compare configuration against template values

scipion.scripts.config.compareConfigVariable(section, variableName, valueInConfig, valueInTemplate)[source]
scipion.scripts.config.createConf(fpath, ftemplate, unattended=False)[source]

Create config file in fpath following the template in ftemplate

scipion.scripts.config.cyan(txt)
scipion.scripts.config.getConfigPathFromConfigFile(scipionConfigFile, configFile)[source]

:param scipionConfigFile path to the config file to derive the folder name from :param configFile: name of the template: protocols or hosts so far :return theoretical path for the template at the same path as the config file

scipion.scripts.config.getConfigVariable(config, section, variableName)[source]
scipion.scripts.config.getTemplateName(template)[source]
scipion.scripts.config.green(txt)
scipion.scripts.config.guessJava()[source]

Guess the system’s Java installation, return a dict with the Java keys

scipion.scripts.config.guessMPI()[source]

Guess the system’s MPI installation, return a dict with MPI keys

scipion.scripts.config.magenta(txt)
scipion.scripts.config.main(args=None)[source]
scipion.scripts.config.red(txt)
scipion.scripts.config.white(txt)
scipion.scripts.config.yellow(txt)