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In this PR

  1. start converting paths in opt into absolute path (might still be necessary for opt.model.file)

Mostly for the opt.dataDir and opt.derivativeDir.
This relies on an abspath standalone function added as dependency in lib.

  1. some quick fix to getAnatFile to make sure it throws an helpful error message if it can't find a file and that it is "smart" enough to find an anat file by itself even if the user did not specify anything.

fixes #196

@Remi-Gau Remi-Gau linked an issue Nov 29, 2020 that may be closed by this pull request
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getAnatFile: tests to write

add tests to check:

  • errors when the requested file is not in the correct session
  • that the fucntion is smart enough to find an anat even when user has not
    specified a session

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codecov bot commented Nov 29, 2020

Codecov Report

Merging #200 (39a599a) into dev (d17b773) will increase coverage by 0.02%.
The diff coverage is 66.66%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #200      +/-   ##
==========================================
+ Coverage   45.15%   45.18%   +0.02%     
==========================================
  Files          96       96              
  Lines        1694     1702       +8     
==========================================
+ Hits          765      769       +4     
- Misses        929      933       +4     
Impacted Files Coverage Δ
src/getAnatFilename.m 69.23% <50.00%> (-30.77%) ⬇️
src/defaults/checkOptions.m 100.00% <100.00%> (ø)
src/setDerivativesDir.m 83.33% <100.00%> (+0.98%) ⬆️

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@Remi-Gau Remi-Gau merged commit c41d478 into dev Nov 29, 2020
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make getAnatFilename error message more informative

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