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Resync #184

Merged
merged 52 commits into from
Nov 13, 2021
Merged

Resync #184

merged 52 commits into from
Nov 13, 2021

Commits on Nov 8, 2021

  1. README - add CI badge

    @tiborauer
    tiborauer committed Nov 8, 2021
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  2. tidy aamod_coreg_extended_2_epi.xml

    @ethanknights
    ethanknights committed Nov 8, 2021
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  3. Replace fileparts(strtok()) with a double fileparts 

    Fixes bug, the strtok gives unexpected results when the path contains a dot somewhere, which is a valid character in a directory name
    @AljenU
    AljenU committed Nov 8, 2021
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  4. Add fallback to SPM when FSL T1 template not available

    @AljenU
    AljenU committed Nov 8, 2021
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  5. Check for trailing filesep when constructing reqpath in aa_init

    @AljenU
    AljenU committed Nov 8, 2021
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  6. Partial fix aa_batch error in 2021b, use Task.RunningDuration when av… 

    …ailable
    @AljenU
    AljenU committed Nov 8, 2021
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  7. Fix validatepaths, check full chararray at once 

    Instead of passing through each character separately, check the full chararray. Only do indexing if the content of the field is a structarray or cellarray
    @AljenU
    AljenU committed Nov 8, 2021
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  8. Small refactor validatepaths 

    Use elseif where possible, to reduce nesting/indent

Also, consistent use of spaces around = and , characters. And use of braces with if and switch
    @AljenU
    AljenU committed Nov 8, 2021
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  9. Fix aas_checkpath allowcolon input effect 

    With wildcards, colon is now allowed when allowcolon is true, instead of when allowcolon is false

Without wildcards, colon is now only allowed when allowcolon is actually true
    @AljenU
    AljenU committed Nov 8, 2021
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  10. add bwt toolbox to CBSU default parameterlist

    @ethanknights
    ethanknights committed Nov 8, 2021
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Commits on Nov 9, 2021

  1. Fix capitalization of dvars and globalmean modules

    @AljenU
    AljenU committed Nov 9, 2021
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  2. TEST - diffusion BET

    @tiborauer
    tiborauer committed Nov 9, 2021
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  3. CI/TEST - scrubbing

    tiborauer committed Nov 9, 2021
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  4. CI/TEST - diffusion BET

    tiborauer committed Nov 9, 2021
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  5. Merge pull request #263 from AljenU/bugfixes_getting_started 

    Bugfixes related to Getting started
    @tiborauer
    tiborauer committed Nov 9, 2021
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  6. Merge pull request #268 from AljenU/bugfix-aas_checkpath-allowcolon 

    Fix aas_checkpath allowcolon input effect
    @tiborauer
    tiborauer committed Nov 9, 2021
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  7. Merge pull request #270 from AljenU/fix-validatepaths-chararray 

    Fix validatepaths chararray
    @tiborauer
    tiborauer committed Nov 9, 2021
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  8. Merge pull request #283 from ethanknights/tidy 

    tidy aamod_coreg_extended_2_epi.xml
    @tiborauer
    tiborauer committed Nov 9, 2021
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  9. Merge branch '5.7.0' into resync

    @tiborauer
    tiborauer committed Nov 9, 2021
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  10. Merge pull request #182 from automaticanalysis/resync 

    Resync
    @tiborauer
    tiborauer committed Nov 9, 2021
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  11. Merge branch 'automaticanalysis:master' into WASHU

    @tiborauer
    tiborauer committed Nov 9, 2021
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  12. FIX - CI: typo

    tiborauer committed Nov 9, 2021
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  13. ENH - AROMA (toolbox, CI)

    tiborauer committed Nov 9, 2021
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  14. FIX - AROMA (and test)

    tiborauer committed Nov 9, 2021
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  15. FIX - AROMA

    tiborauer committed Nov 9, 2021
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  16. FIX - AROMA

    tiborauer committed Nov 9, 2021
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  17. FIX - CI: AROMA

    tiborauer committed Nov 9, 2021
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  18. FIX - BWT and WLS toolboxes

    @tiborauer
    tiborauer committed Nov 9, 2021
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  19. FIX - AROMA

    tiborauer committed Nov 9, 2021
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  20. ENH - install tools

    tiborauer committed Nov 9, 2021
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  21. FIX - CI: python

    tiborauer committed Nov 9, 2021
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  22. FIX - CI: pip

    tiborauer committed Nov 9, 2021
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Commits on Nov 10, 2021

  1. FIX - AROMA

    tiborauer committed Nov 10, 2021
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  2. FIX - AROMA documentation

    tiborauer committed Nov 10, 2021
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  3. Fix aa_test_inittest, allow . in path and aa_demo being first in list 

    Fixes #290
    @AljenU
    AljenU committed Nov 10, 2021
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  4. Whitespace, formatting, code cleanup

    @AljenU
    AljenU committed Nov 10, 2021
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  5. Fix log messages containing a path 

    Escape backslash characters in the windows paths, to prevent them from being interpreted as special character identifiers in printf functions

Fixes for issue #276
    @AljenU
    AljenU committed Nov 10, 2021
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  6. Update aas_checkpath for windows compatibility 

    The path separator is platform dependent. Also, on Windows more character values are allowed, to allow drive letters in paths

Fix issue #277
    @AljenU
    AljenU committed Nov 10, 2021
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  7. Add is_absolute_path function, and use in aas_desc_outputs 

    Fix issue #278
    @AljenU
    AljenU committed Nov 10, 2021
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  8. Use getenv('HOME') instead of ~ 

    Fix issue #284
    @AljenU
    AljenU committed Nov 10, 2021
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  9. Fix aas_shell: do not try to stop colours on windows 

    Related to issue #279
    @AljenU
    AljenU committed Nov 10, 2021
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  10. Do not do aas_expandpathbyvars on windows 

    Related to issue #288 and issue #289
    @AljenU
    AljenU committed Nov 10, 2021
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  11. Adapt aa_init to use pathsep and filesep functions 

    Fix issue #266, fixes for issue #264
    @AljenU
    AljenU committed Nov 10, 2021
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Commits on Nov 11, 2021

  1. FIX - aaq SLURM/Torque with initialSubmitArguments

    @tiborauer
    tiborauer committed Nov 11, 2021
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  2. Merge pull request #292 from tiborauer/WASHU 

    New tests from WASHU
    @jones-michael-s
    jones-michael-s committed Nov 11, 2021
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  3. Merge branch '5.7.0' into resync

    @tiborauer
    tiborauer committed Nov 11, 2021
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  4. Merge pull request #183 from automaticanalysis/resync 

    Resync
    @tiborauer
    tiborauer committed Nov 11, 2021
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  5. FIX - update WASHU toolboxes

    @tiborauer
    tiborauer committed Nov 11, 2021
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  6. FIX - parametersets with partial toolboxes

    tiborauer committed Nov 11, 2021
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Commits on Nov 12, 2021

  1. Merge pull request #273 from tiborauer/5.7.0 

    5.7.0
    @jones-michael-s
    jones-michael-s committed Nov 12, 2021
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  2. Merge pull request #291 from AljenU/fixes_windows_helloworld 

    Fixes to be able to run example helloworld on windows
    @tiborauer
    tiborauer committed Nov 12, 2021
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Commits on Nov 13, 2021

  1. Merge branch 'master' into resync

    @tiborauer
    tiborauer committed Nov 13, 2021
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