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Major improvements to loops, misc other fixes #789

Merged
merged 167 commits into from
Jan 31, 2020
Merged

Major improvements to loops, misc other fixes #789

merged 167 commits into from
Jan 31, 2020

Commits on Dec 17, 2019

  1. DRR - Use forward declares.

    Daniel R. Roe committed Dec 17, 2019
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  2. DRR - Split ControlBlock class stuff from the Control file.

    Daniel R. Roe committed Dec 17, 2019
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Commits on Dec 18, 2019

  1. DRR - Add missing file.

    Daniel R. Roe committed Dec 18, 2019
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  2. DRR - Start trying to split out the various for loop types.

    @drroe
    drroe committed Dec 18, 2019
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  3. DRR - Add mask for loop type

    @drroe
    drroe committed Dec 18, 2019
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  4. DRR - Most of VarType only needed for mask type loop

    @drroe
    drroe committed Dec 18, 2019
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  5. DRR - Have SetVarName prepend the $ automatically

    @drroe
    drroe committed Dec 18, 2019
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  6. DRR - Add list for loop type

    @drroe
    drroe committed Dec 18, 2019
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  7. DRR - Add begin and end functions.

    @drroe
    drroe committed Dec 18, 2019
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  8. DRR - Add ForLoop files, update depends

    @drroe
    drroe committed Dec 18, 2019
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  9. DRR - Try to use new ForLoop class. Doesnt appear to work yet...

    @drroe
    drroe committed Dec 18, 2019
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  10. DRR - Need to account for prepended $

    @drroe
    drroe committed Dec 18, 2019
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  11. DRR - Fix variable name and 'in' for list for loop

    @drroe
    drroe committed Dec 18, 2019
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Commits on Dec 19, 2019

  1. DRR - Add GetVariable function

    @drroe
    drroe committed Dec 19, 2019
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  2. DRR - Have loop start use CurrentVars

    @drroe
    drroe committed Dec 19, 2019
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  3. DRR - Have BeginFor return the number of iterations.

    @drroe
    drroe committed Dec 19, 2019
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  4. DRR - Number of iterations is now determined when loop starts.

    @drroe
    drroe committed Dec 19, 2019
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  5. DRR - Allow end argument to be a variable. More informative messages … 

    …on how many iterations loop will execute.
    @drroe
    drroe committed Dec 19, 2019
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  6. DRR - Hide debug and change warning to info

    @drroe
    drroe committed Dec 19, 2019
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  7. DRR - Hide some debug info

    @drroe
    drroe committed Dec 19, 2019
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  8. DRR - Add MemUsageInBytes to template

    Daniel R. Roe committed Dec 19, 2019
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  9. DRR - Add StringVar data set

    Daniel R. Roe committed Dec 19, 2019
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  10. DRR - Add STRINGVAR to DataSet

    Daniel R. Roe committed Dec 19, 2019
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  11. DRR - Add Add and append functions

    Daniel R. Roe committed Dec 19, 2019
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  12. DRR - Add Exec version of the Set command

    Daniel R. Roe committed Dec 19, 2019
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  13. DRR - Exec version of show command

    Daniel R. Roe committed Dec 19, 2019
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  14. DRR - Start massive changes to move VariableArray functionality to Da… 

    …taSetList
    Daniel R. Roe committed Dec 19, 2019
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Commits on Dec 20, 2019

  1. DRR - More work replacing VariableArray with DataSetList. Add some fu… 

    …nctions to DataSetList
    @drroe
    drroe committed Dec 20, 2019
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  2. DRR - Add another check

    @drroe
    drroe committed Dec 20, 2019
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  3. DRR - Add UpdateStringVar routine and make ForLoop_integer use it.

    @drroe
    drroe committed Dec 20, 2019
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  4. DRR - Use DataSetList in remaining for loops.

    @drroe
    drroe committed Dec 20, 2019
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  5. DRR - DSL can be const& for CheckDone

    @drroe
    drroe committed Dec 20, 2019
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  6. DRR - Add list string variables function

    @drroe
    drroe committed Dec 20, 2019
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  7. DRR - Finish up show exec. Still not quite working.

    @drroe
    drroe committed Dec 20, 2019
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  8. DRR - Add comment

    @drroe
    drroe committed Dec 20, 2019
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Commits on Dec 21, 2019

  1. DRR - Ensure loop variable is set up as a dataset

    @drroe
    drroe committed Dec 21, 2019
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  2. DRR - Loop variable cannot be the same as DataSet name anymore

    @drroe
    drroe committed Dec 21, 2019
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  3. DRR - Give vectors a name

    @drroe
    drroe committed Dec 21, 2019
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  4. DRR - Give RMS sets a name

    @drroe
    drroe committed Dec 21, 2019
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  5. DRR - Give distance sets a name

    @drroe
    drroe committed Dec 21, 2019
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Commits on Dec 22, 2019

  1. DRR - Name sets

    @drroe
    drroe committed Dec 22, 2019
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  2. DRR - Name sets

    @drroe
    drroe committed Dec 22, 2019
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Commits on Dec 23, 2019

  1. Merge branch 'master' into forloops

    @drroe
    drroe committed Dec 23, 2019
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  2. Merge branch 'master' into forloops

    @drroe
    drroe committed Dec 23, 2019
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  3. DRR - Ensure final value of integer loops is updated to make behavior… 

    … consistent with all common integer for loops
    @drroe
    drroe committed Dec 23, 2019
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  4. DRR - Make 0 iteration loops a warning instead of an error. Ensure al… 

    …l integer for loops are properly integrated on loop end. Add >= and <= end ops.
    @drroe
    drroe committed Dec 23, 2019
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  5. DRR - Make start and end values that will result in no iterations a w… 

    …arning, not an error
    @drroe
    drroe committed Dec 23, 2019
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  6. DRR - No such thing as CTL objects anymore

    @drroe
    drroe committed Dec 23, 2019
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  7. DRR - Fix help.

    @drroe
    drroe committed Dec 23, 2019
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  8. DRR - More fixing up of help

    @drroe
    drroe committed Dec 23, 2019
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  9. DRR - Add a check that for loop variable was properly set up. Hide so… 

    …me debug info
    @drroe
    drroe committed Dec 23, 2019
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  10. DRR - Hide some more debug info

    @drroe
    drroe committed Dec 23, 2019
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Commits on Dec 30, 2019

  1. DRR - Start adding data set blocks loop

    @drroe
    drroe committed Dec 30, 2019
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Commits on Dec 31, 2019

  1. DRR - Exit if error occurrs setting up loop var

    @drroe
    drroe committed Dec 31, 2019
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  2. DRR - More loop setup

    @drroe
    drroe committed Dec 31, 2019
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  3. DRR - Make blocksize an unsigned int

    @drroe
    drroe committed Dec 31, 2019
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Commits on Jan 1, 2020

  1. DRR - Start splitting for loop components into separate argument lists

    @drroe
    drroe committed Jan 1, 2020
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  2. DRR - Better way of handling individual for loop components; should b… 

    …e no cross-contamination between multiple for loop components of the same type
    @drroe
    drroe committed Jan 1, 2020
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  3. DRR - Change index vars to long int; refactor so that data set does n… 

    …ot need to exist until loop is actually executed.
    @drroe
    drroe committed Jan 1, 2020
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Commits on Jan 2, 2020

  1. DRR - Add missing file

    @drroe
    drroe committed Jan 2, 2020
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  2. DRR - Finish initial loop - still need to actually create the sets

    @drroe
    drroe committed Jan 2, 2020
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  3. DRR - Add test of nested loop vars and <= loop operator

    @drroe
    drroe committed Jan 2, 2020
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  4. DRR - Enabled dataSetBlocks for loop

    @drroe
    drroe committed Jan 2, 2020
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  5. DRR - DataSetList needs to be passed in non-const so that data sets c… 

    …an be created each iteration
    @drroe
    drroe committed Jan 2, 2020
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Commits on Jan 3, 2020

  1. DRR - New class for abstracting data set copies

    Daniel R. Roe committed Jan 3, 2020
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  2. DRR - Improve error message when no valid file type can be found for … 

    …a given data set
    Daniel R. Roe committed Jan 3, 2020
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  3. DRR - Use DataSetBlock

    Daniel R. Roe committed Jan 3, 2020
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  4. 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.
    Daniel R. Roe committed Jan 3, 2020
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  5. DRR - Add MemAlloc and CopyBlock for mesh

    Daniel R. Roe committed Jan 3, 2020
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  6. DRR - Fix up dependencies

    Daniel R. Roe committed Jan 3, 2020
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  7. DRR - Start attempt to split DataSet_Vector into two sets, 1 with ori… 

    …gins and 1 without
    Daniel R. Roe committed Jan 3, 2020
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  8. DRR - Fix up Sync routines, update dependencies

    Daniel R. Roe committed Jan 3, 2020
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  9. DRR - Fix shadowed variables

    Daniel R. Roe committed Jan 3, 2020
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  10. DRR - Accidentally duplicated a function

    Daniel R. Roe committed Jan 3, 2020
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  11. DRR - Add new vector types and group

    Daniel R. Roe committed Jan 3, 2020
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  12. DRR - Enable new types in the DataSetList

    Daniel R. Roe committed Jan 3, 2020
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  13. DRR - Ensure MemAlloc routine is declared

    Daniel R. Roe committed Jan 3, 2020
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  14. DRR - Start converting to use new types

    Daniel R. Roe committed Jan 3, 2020
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  15. DRR - More updates for new vector types

    Daniel R. Roe committed Jan 3, 2020
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  16. DRR - prototype test for loop over datasetblocks

    Daniel R. Roe committed Jan 3, 2020
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  17. DRR - More changes for new set types

    @drroe
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Commits on Jan 4, 2020

  1. DRR - Finish fixing up vector action

    @drroe
    drroe committed Jan 4, 2020
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  2. DRR - More VECTOR_1D changes

    @drroe
    drroe committed Jan 4, 2020
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Commits on Jan 5, 2020

  1. DRR - More updates for new vector types

    @drroe
    drroe committed Jan 5, 2020
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  2. DRR - Finish up vector changes. Still needs testing.

    @drroe
    drroe committed Jan 5, 2020
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Commits on Jan 6, 2020

  1. DRR - Origin is no longer stored when not needed

    @drroe
    drroe committed Jan 6, 2020
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  2. DRR - Vector origin no longer included when not needed

    @drroe
    drroe committed Jan 6, 2020
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  3. DRR - Handle append of vector data sets inside DataIO_Std to handle c… 

    …ase where data being read in type does not match existing set type
    @drroe
    drroe committed Jan 6, 2020
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  4. DRR - Add reverse append test

    @drroe
    drroe committed Jan 6, 2020
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  5. DRR - Ensure old memory is freed

    @drroe
    drroe committed Jan 6, 2020
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  6. DRR - Add MemAlloc and CopyBlock for vector sets

    @drroe
    drroe committed Jan 6, 2020
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  7. DRR - Add CopyBlock and MemAlloc routines to float and integer data sets

    @drroe
    drroe committed Jan 6, 2020
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  8. DRR - Add initial test for data set blocks loop

    @drroe
    drroe committed Jan 6, 2020
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  9. DRR - Improve error message

    @drroe
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  10. DRR - Minor version bump; vector output for vectors with no origin da… 

    …ta is different.
    @drroe
    drroe committed Jan 6, 2020
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  11. DRR - Add a cumulative mode for datasetblocks

    @drroe
    drroe committed Jan 6, 2020
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  12. DRR - Hide some debug info. Use CheckForSet to avoid spurious warnings.

    @drroe
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Commits on Jan 7, 2020

  1. DRR - Add 'firstblock' keyword to cumulative datasetblocks to set siz… 

    …e of first block
    @drroe
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  2. DRR - Fix calculation of number of iterations.

    @drroe
    drroe committed Jan 7, 2020
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  3. DRR - Allow 'show' to only show specified string vars

    @drroe
    drroe committed Jan 7, 2020
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  4. DRR - If variables are replaced in a command, re-parse the Argument l… 

    …ist in case new spaces have been introduced etc. May want to eventually have the ExecuteCommand function just take a string.
    @drroe
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  5. DRR - Add test for cumulative blocks

    @drroe
    drroe committed Jan 7, 2020
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  6. DRR - Hide some debug info

    @drroe
    drroe committed Jan 7, 2020
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  7. DRR - Improve output message

    @drroe
    drroe committed Jan 7, 2020
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  8. DRR - Allow multiple variables to be passed to show

    @drroe
    drroe committed Jan 7, 2020
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  9. DRR - Fix loop descriptions

    @drroe
    drroe committed Jan 7, 2020
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  10. DRR - Dont write unneeded temp files during test

    @drroe
    drroe committed Jan 7, 2020
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  11. DRR - Fix manual entries

    @drroe
    drroe committed Jan 7, 2020
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  12. DRR - Start adding advanced help for for loops

    @drroe
    drroe committed Jan 7, 2020
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  13. DRR - Fix up for loop help

    @drroe
    drroe committed Jan 7, 2020
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  14. DRR - Fix up for loop help in manual.

    @drroe
    drroe committed Jan 7, 2020
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  15. DRR - Remove extra whitespace

    @drroe
    drroe committed Jan 7, 2020
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Commits on Jan 8, 2020

  1. DRR - Give created datasetblocks sets an aspect to reduce the chances… 

    … of collision. Set legend to be more descriptive.
    @drroe
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  2. DRR - Updated set legends.

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    drroe committed Jan 8, 2020
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  3. DRR - Data set index +1 to be consistent with set legend

    @drroe
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  4. DRR - Fix up for loop manual entry

    @drroe
    drroe committed Jan 8, 2020
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  5. DRR - First check if string variable with name exists. This allows st… 

    …ring variables to be used in data set name expressions, e.g. $i[phi]
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Commits on Jan 9, 2020

  1. DRR - Implement data set copying for sets that support CopyBlock - ot… 

    …herwise revert to old behavior of renaming.
    Daniel R. Roe committed Jan 9, 2020
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  2. DRR - Add data set copy test

    Daniel R. Roe committed Jan 9, 2020
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  3. Merge branch 'master' into forloops

    Daniel R. Roe committed Jan 9, 2020
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  4. DRR - Minor version bump, vector output is different.

    Daniel R. Roe committed Jan 9, 2020
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Commits on Jan 10, 2020

  1. DRR - Improve math help and manual entry

    Daniel R. Roe committed Jan 10, 2020
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  2. DRR - Use forward declares. When processing expression, first remove … 

    …all whitespace to make parsing easier.
    Daniel R. Roe committed Jan 10, 2020
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  3. DRR - expression has already had all whitespace removed

    Daniel R. Roe committed Jan 10, 2020
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  4. DRR - Add array that can be used to ID functions.

    Daniel R. Roe committed Jan 10, 2020
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  5. DRR - Add function to identify functions in expression

    Daniel R. Roe committed Jan 10, 2020
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  6. DRR - Use new function to look for function names. Should address Amb… 

    …er-MD#744
    Daniel R. Roe committed Jan 10, 2020
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  7. DRR - Add test with function names

    Daniel R. Roe committed Jan 10, 2020
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  8. DRR - More forward declares.

    Daniel R. Roe committed Jan 10, 2020
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  9. DRR - More forward declares

    Daniel R. Roe committed Jan 10, 2020
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  10. DRR - Add missing header guard

    Daniel R. Roe committed Jan 10, 2020
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  11. DRR - Protect datasetblocks in parallel

    Daniel R. Roe committed Jan 10, 2020
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Commits on Jan 15, 2020

  1. DRR - Allow wildcard expansion in 'for in' loop to fail with a warning.

    @drroe
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  2. DRR - Add for loop over data sets.

    @drroe
    drroe committed Jan 15, 2020
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  3. DRR - Enable oversets loop

    @drroe
    drroe committed Jan 15, 2020
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  4. DRR - Test loop filename wildcards and oversets loop

    @drroe
    drroe committed Jan 15, 2020
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  5. DRR - Add for oversets manual entry

    @drroe
    drroe committed Jan 15, 2020
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  6. Merge branch 'master' into forloops

    @drroe
    drroe committed Jan 15, 2020
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  7. DRR - Add missing argument to printf.

    @drroe
    drroe committed Jan 15, 2020
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  8. DRR - Add missing include.

    @drroe
    drroe committed Jan 15, 2020
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Commits on Jan 16, 2020

  1. DRR - Make it so that list for loops can access script variables.

    Daniel R. Roe committed Jan 16, 2020
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  2. DRR - Allow oversets loop to access script variables.

    Daniel R. Roe committed Jan 16, 2020
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Commits on Jan 17, 2020

  1. DRR - Enable label print for grace xydy. Update help.

    Daniel R. Roe committed Jan 17, 2020
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  2. DRR - Update manual

    Daniel R. Roe committed Jan 17, 2020
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Commits on Jan 28, 2020

  1. Merge branch 'master' into forloops

    @drroe
    drroe committed Jan 28, 2020
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Commits on Jan 31, 2020

  1. DRR - I give up for now. Reverting DataSet_Vector changes so that pyt… 

    …raj will build and pass tests. I want the rest of the stuff committed before the amber meeting.
    Daniel R. Roe committed Jan 31, 2020
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  2. DRR - Revert to DataSet_Vector

    Daniel R. Roe committed Jan 31, 2020
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  3. DRR - Add MemAlloc and CopyBlock

    Daniel R. Roe committed Jan 31, 2020
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  4. DRR - Reorganize routine order to separate vector and vector with ori… 

    …gin functions. Cleanup.
    Daniel R. Roe committed Jan 31, 2020
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  5. DRR - Revert to DataSet_Vector

    Daniel R. Roe committed Jan 31, 2020
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  6. DRR - Cpptraj: Revert to DataSet_Vector

    Daniel R. Roe committed Jan 31, 2020
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  7. DRR - Revert to DataSet_Vector

    Daniel R. Roe committed Jan 31, 2020
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  8. DRR - Revert to DataSet_Vector

    Daniel R. Roe committed Jan 31, 2020
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  9. DRR - Revert to DataSet_Vector

    Daniel R. Roe committed Jan 31, 2020
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  10. DRR - Revert to DataSet_Vector

    Daniel R. Roe committed Jan 31, 2020
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  11. DRR - Revert to DataSet_Vector.....

    Daniel R. Roe committed Jan 31, 2020
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  12. DRR - Add missing include due to new forward declare

    Daniel R. Roe committed Jan 31, 2020
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  13. DRR - Add missing include due to forward declare

    Daniel R. Roe committed Jan 31, 2020
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  14. DRR - Revert to DataSet_Vector

    Daniel R. Roe committed Jan 31, 2020
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  15. DRR - Revert to DataSet_Vector

    Daniel R. Roe committed Jan 31, 2020
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  16. DRR - Make sure vector set is in VECTOR_1D group

    Daniel R. Roe committed Jan 31, 2020
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  17. DRR - Revert to DataSet_Vector

    Daniel R. Roe committed Jan 31, 2020
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  18. DRR - Revert to DataSet_Vector

    Daniel R. Roe committed Jan 31, 2020
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  19. DRR - Update dependencies

    Daniel R. Roe committed Jan 31, 2020
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  20. DRR - Add missing ref operator

    Daniel R. Roe committed Jan 31, 2020
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  21. DRR - Revert tests, origins still printed for non-origin vector sets

    Daniel R. Roe committed Jan 31, 2020
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  22. DRR - Decrement minor version; revision bump insteead, vector output … 

    …now unchanged.
    Daniel R. Roe committed Jan 31, 2020
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