Contains SLiMSuite and Sequite General Objects
Copyright © 2005 Richard J. Edwards - See source code for GNU License Notice
General module containing Classes used by all SLiMSuite and Sequite programs plus a number of miscellaneous methods. Controls output to screen, commandline parameters and Log files.
General SLiMSuite Options
Common Options (most programs)
Forking Options (Some programs only)
Program-Specific Commands (Some programs only)
History Module Version History
# 0.0 - Initial Compilation based on RJE_General01.plx. Simplified Class Names # 0.1 - Added comments and changed capitilisation etc. # 0.2 - Added RJE_Object class and 'No Log' concept # 0.3 - Updated RJE_Object to not need Out object (restrict Out Object to Log object?) # 1.0 - Better Documentation to go with GASP V:1.2 # 1.1 - Added make Path and sorted ErrorLog # 1.1 - def errorLog(self, text='Missing text for errorLog() call!',quitchoice=False,printerror=True): # 1.2 - Added Norman's error-tracking and 'basefile/outfile' options as Object defaults # 2.0 - Major Overhaul of Module. Out, Log and RJE_Object will now inherit RJE_Object_Shell (see also changes below) # 2.1 - Added X="Y" options # 2.2 - Added confirm=T/F option to choice() # 2.3 - Added more delimited text functions # 2.4 - Added listFromCommand() function # 2.5 - Added Force opt # 3.0 - Added self.list and self.dict dictionaries to RJE_Object. Added 'list', 'clist' and 'glist' to cmdRead. # 3.1 - Added object save and load methods # 3.2 - Added more refined path options # 3.3 - Added general delimitedFileOut() method based on slim_pickings.py compileOut() # 3.4 - Added cmdReadList for handling lists of "standard" options # 3.5 - Added getFileName for interactive input of file names with confirmation/existence options and checkInputFiles() # 3.6 - Added dataDict() method for extracting data from delimited file into dictionary # 3.7 - Added extra dictionary methods for storage and retrieval of results in a dict['Data'] dictionary # 3.8 - Gave module a general tidy up. # 3.9 - Added RunPath to control where program is run. # 3.10- Added errorlog=FILE option to redirect errors to an additional error file. # 3.11- Added dictionary ranking method. # 3.12- Added more list methods. # 4.0 - Added RJE_ObjectLite for data storage objects with minimal generic methods and attributes. # 4.1 - Added a bioware_server switch for reading iniServer/ ini files on bioware. # 4.2 - Modified INI reading across the board to look in ../settings/ and look for defaults.ini as well as rje.ini. # 4.2 - Enabled handing on -ini FILE in addition to ini=FILE. # 4.3 - Added ilist and nlist types to cmdRead for objects. (Lists of integers and floats). Add ratio() function. # 4.4 - Added lineFromIndex(target,file,re_index='^(\S+)\s',sortunique=False,xreplace=True). # 4.5 - Modified randomString() and added stringShuffle() methods. # 4.6 - Added dev and warn options. Fixed -h lack of help. # 4.7 - Added self.warn list and self.warnLog() functions to Log object. Modified i=-1 quitchoice to raise not quit. # 4.8 - Added perc cmdtype = float that is multiplied by 100.0 if < 1.0. Removed server option from iniCmds(). # 4.9 - Added rje.slimsuite, which determines the slimsuite home directory from rje.py file path. # 4.10- Added osx=T/F option for Mac-specific running options. # 4.11- Enabled '\t#' comments in ini files. Modified getStrLC to return '' for 'none' by default. Added listMax(). # 4.11- Added self.name() to basic object class. # 4.12- Added 'bool' and 'str' to _cmdRead() to ease switchover to new RJE_Objects. # 4.13.0 - Added new built-in attributes/options for REST services. # 4.13.1 - Fixed MemSaver typo in WarnLog output. Modified mkDir() to avoid clashes raising errors. # 4.13.2 - Removed excess REST HTML methods. # 4.13.3 - Added uselower=False to dataDict() method. # 4.13.4 - Added maxrep=X to listCombos() method. # 4.14.0 - Added listToDict() method. # 4.14.1 - Fixed matchExp method to be able to handline multilines. (Shame re.DOTALL doesn't work!) # 4.14.2 - Modified integer commands to read/convert floats. # 4.15.0 - Added intList() and numList() functions. # 4.15.1 - Fixed rare errorlog printlog error vicious cycle. # 4.16.0 - Added list2dict(inlist,inkeys) and dict2list(indict,inkeys) functions. # 4.16.1 - Improved handling of integer parameters when given bad commands. # 4.17.0 - Added extra functions to randomList() # 4.18.0 - Added Roman numeral functions. # 4.18.1 - Updated error handling for full REST output. # 4.18.2 - Fixed rje module call bug. # 4.19.0 - Tweaked Docstring. Added extra parameter catching. Added report of INI loading. # 4.19.1 - Added code for catching non-ASCII log filenames. # 4.20.0 - Added quiet mode to log object and output of errors to stderr. Fixed rankList(unique=True) # 4.21.0 - Added hashlib MD% functions. # 4.21.1 - Fixed bug where silent=T wasn't running silent. # 4.22.0 - Added flist command type that reads file lines as a list, ignoring commas. # 4.22.1 - Reformatting for Python3 compatibility. # 4.22.3 - Added highest tied ranking. # 4.22.4 - Added some Python 2.6 back-compatbility for the server. # 4.22.5 - Added checking of glist inputs. # 4.23.0 - Added rje_py2 and rje_py3 code divergence for Python3 compatibility development. # 4.23.1 - Added HPC etc. warning for i>=0.
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