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Major improvements to loops, misc other fixes (#789)
* DRR - Use forward declares. * DRR - Split ControlBlock class stuff from the Control file. * DRR - Add missing file. * DRR - Start trying to split out the various for loop types. * DRR - Add mask for loop type * DRR - Most of VarType only needed for mask type loop * DRR - Have SetVarName prepend the $ automatically * DRR - Add list for loop type * DRR - Add begin and end functions. * DRR - Add ForLoop files, update depends * DRR - Try to use new ForLoop class. Doesnt appear to work yet... * DRR - Need to account for prepended $ * DRR - Fix variable name and 'in' for list for loop * DRR - Add GetVariable function * DRR - Have loop start use CurrentVars * DRR - Have BeginFor return the number of iterations. * DRR - Number of iterations is now determined when loop starts. * DRR - Allow end argument to be a variable. More informative messages on how many iterations loop will execute. * DRR - Hide debug and change warning to info * DRR - Hide some debug info * DRR - Add MemUsageInBytes to template * DRR - Add StringVar data set * DRR - Add STRINGVAR to DataSet * DRR - Add Add and append functions * DRR - Add Exec version of the Set command * DRR - Exec version of show command * DRR - Start massive changes to move VariableArray functionality to DataSetList * DRR - More work replacing VariableArray with DataSetList. Add some functions to DataSetList * DRR - Add another check * DRR - Add UpdateStringVar routine and make ForLoop_integer use it. * DRR - Use DataSetList in remaining for loops. * DRR - DSL can be const& for CheckDone * DRR - Add list string variables function * DRR - Finish up show exec. Still not quite working. * DRR - Add comment * DRR - Ensure loop variable is set up as a dataset * DRR - Loop variable cannot be the same as DataSet name anymore * DRR - Give vectors a name * DRR - Give RMS sets a name * DRR - Give distance sets a name * DRR - Name sets * DRR - Name sets * DRR - Ensure final value of integer loops is updated to make behavior consistent with all common integer for loops * DRR - Make 0 iteration loops a warning instead of an error. Ensure all integer for loops are properly integrated on loop end. Add >= and <= end ops. * DRR - Make start and end values that will result in no iterations a warning, not an error * DRR - No such thing as CTL objects anymore * DRR - Fix help. * DRR - More fixing up of help * DRR - Add a check that for loop variable was properly set up. Hide some debug info * DRR - Hide some more debug info * DRR - Start adding data set blocks loop * DRR - Exit if error occurrs setting up loop var * DRR - More loop setup * DRR - Make blocksize an unsigned int * DRR - Start splitting for loop components into separate argument lists * DRR - Better way of handling individual for loop components; should be no cross-contamination between multiple for loop components of the same type * DRR - Change index vars to long int; refactor so that data set does not need to exist until loop is actually executed. * DRR - Add missing file * DRR - Finish initial loop - still need to actually create the sets * DRR - Add test of nested loop vars and <= loop operator * DRR - Enabled dataSetBlocks for loop * DRR - DataSetList needs to be passed in non-const so that data sets can be created each iteration * DRR - New class for abstracting data set copies * DRR - Improve error message when no valid file type can be found for a given data set * DRR - Use DataSetBlock * DRR - No need to abstract to DataBlock, just require that DataSet of same type be used in function (now called CopyBlock); this will make it easier to make universal. * DRR - Add MemAlloc and CopyBlock for mesh * DRR - Fix up dependencies * DRR - Start attempt to split DataSet_Vector into two sets, 1 with origins and 1 without * DRR - Fix up Sync routines, update dependencies * DRR - Fix shadowed variables * DRR - Accidentally duplicated a function * DRR - Add new vector types and group * DRR - Enable new types in the DataSetList * DRR - Ensure MemAlloc routine is declared * DRR - Start converting to use new types * DRR - More updates for new vector types * DRR - prototype test for loop over datasetblocks * DRR - More changes for new set types * DRR - Finish fixing up vector action * DRR - More VECTOR_1D changes * DRR - More updates for new vector types * DRR - Finish up vector changes. Still needs testing. * DRR - Origin is no longer stored when not needed * DRR - Vector origin no longer included when not needed * DRR - Handle append of vector data sets inside DataIO_Std to handle case where data being read in type does not match existing set type * DRR - Add reverse append test * DRR - Ensure old memory is freed * DRR - Add MemAlloc and CopyBlock for vector sets * DRR - Add CopyBlock and MemAlloc routines to float and integer data sets * DRR - Add initial test for data set blocks loop * DRR - Improve error message * DRR - Minor version bump; vector output for vectors with no origin data is different. * DRR - Add a cumulative mode for datasetblocks * DRR - Hide some debug info. Use CheckForSet to avoid spurious warnings. * DRR - Add 'firstblock' keyword to cumulative datasetblocks to set size of first block * DRR - Fix calculation of number of iterations. * DRR - Allow 'show' to only show specified string vars * DRR - If variables are replaced in a command, re-parse the Argument list in case new spaces have been introduced etc. May want to eventually have the ExecuteCommand function just take a string. * DRR - Add test for cumulative blocks * DRR - Hide some debug info * DRR - Improve output message * DRR - Allow multiple variables to be passed to show * DRR - Fix loop descriptions * DRR - Dont write unneeded temp files during test * DRR - Fix manual entries * DRR - Start adding advanced help for for loops * DRR - Fix up for loop help * DRR - Fix up for loop help in manual. * DRR - Remove extra whitespace * DRR - Give created datasetblocks sets an aspect to reduce the chances of collision. Set legend to be more descriptive. * DRR - Updated set legends. * DRR - Data set index +1 to be consistent with set legend * DRR - Fix up for loop manual entry * DRR - First check if string variable with name exists. This allows string variables to be used in data set name expressions, e.g. $i[phi] * DRR - Implement data set copying for sets that support CopyBlock - otherwise revert to old behavior of renaming. * DRR - Add data set copy test * DRR - Minor version bump, vector output is different. * DRR - Improve math help and manual entry * DRR - Use forward declares. When processing expression, first remove all whitespace to make parsing easier. * DRR - expression has already had all whitespace removed * DRR - Add array that can be used to ID functions. * DRR - Add function to identify functions in expression * DRR - Use new function to look for function names. Should address #744 * DRR - Add test with function names * DRR - More forward declares. * DRR - More forward declares * DRR - Add missing header guard * DRR - Protect datasetblocks in parallel * DRR - Allow wildcard expansion in 'for in' loop to fail with a warning. * DRR - Add for loop over data sets. * DRR - Enable oversets loop * DRR - Test loop filename wildcards and oversets loop * DRR - Add for oversets manual entry * DRR - Add missing argument to printf. * DRR - Add missing include. * DRR - Make it so that list for loops can access script variables. * DRR - Allow oversets loop to access script variables. * DRR - Enable label print for grace xydy. Update help. * DRR - Update manual * DRR - I give up for now. Reverting DataSet_Vector changes so that pytraj will build and pass tests. I want the rest of the stuff committed before the amber meeting. * DRR - Revert to DataSet_Vector * DRR - Add MemAlloc and CopyBlock * DRR - Reorganize routine order to separate vector and vector with origin functions. Cleanup. * DRR - Revert to DataSet_Vector * DRR - Cpptraj: Revert to DataSet_Vector * DRR - Revert to DataSet_Vector * DRR - Revert to DataSet_Vector * DRR - Revert to DataSet_Vector * DRR - Revert to DataSet_Vector * DRR - Revert to DataSet_Vector..... * DRR - Add missing include due to new forward declare * DRR - Add missing include due to forward declare * DRR - Revert to DataSet_Vector * DRR - Revert to DataSet_Vector * DRR - Make sure vector set is in VECTOR_1D group * DRR - Revert to DataSet_Vector * DRR - Revert to DataSet_Vector * DRR - Update dependencies * DRR - Add missing ref operator * DRR - Revert tests, origins still printed for non-origin vector sets * DRR - Decrement minor version; revision bump insteead, vector output now unchanged.
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