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MNT: Update Ubuntu, FreeSurfer, AFNI and Convert3D #2931

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merged 7 commits into from
Jan 20, 2023
Merged

MNT: Update Ubuntu, FreeSurfer, AFNI and Convert3D #2931

merged 7 commits into from
Jan 20, 2023

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effigies
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@effigies effigies commented Jan 11, 2023 •
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Changes proposed in this pull request

  • Update Ubuntu to 22.04 LTS
  • Update FreeSurfer to 7.3.2
  • Update FSL to 6.0.6.2, download only needed packages from conda
  • Update AFNI installation to work on 22.04
  • Update ANTs to 2.4.3
  • Update Convert3D to 1.3.0, from conda-forge

@effigies effigies force-pushed the mnt/update_deps branch 2 times, most recently from b9afdb5 to 5c9acb9 Compare January 11, 2023 19:26
@effigies effigies changed the title MNT: Update Ubuntu, FreeSurfer, FSL, AFNI, ANTs and Convert3D MNT: Update Ubuntu, FreeSurfer, FSL, AFNI and Convert3D Jan 11, 2023
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Removing ANTs bump for now. AFAIK there are no outstanding issues we've been waiting on a new ANTs for.

@effigies effigies added this to the 23.0.0 milestone Jan 12, 2023
@effigies effigies force-pushed the mnt/update_deps branch 3 times, most recently from a4a0922 to 4d4b775 Compare January 17, 2023 02:18
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ICA-AROMA is the only thing stopping us from upgrading FSL: #2936.

effigies
effigies commented Jan 18, 2023
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@effigies effigies force-pushed the mnt/update_deps branch 2 times, most recently from 0c3e03f to 7b8dd0c Compare January 18, 2023 16:21
@effigies effigies changed the title MNT: Update Ubuntu, FreeSurfer, FSL, AFNI and Convert3D MNT: Update Ubuntu, FreeSurfer, AFNI and Convert3D Jan 19, 2023
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@mgxd I would appreciate a review on this one today, if possible. It would be good to do all local testing on updated dependencies.

mgxd
mgxd reviewed Jan 19, 2023
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Looks good, have you tested on any non-CI datasets? I can test with one of mine.

PS - I think having a FreeSurfer include file, rather than exclude, will lessen the burden of these migrations.

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have you tested on any non-CI datasets?

I have tested on one. It will be good to do some more, but the changes relative to 7.2 were not massive.

I think having a FreeSurfer include file, rather than exclude,

The majority of the change was just running sort on the file. I think an include would be more brittle. Here, a name change means we are over-inclusive, while an include file would reverse that.

mgxd
mgxd approved these changes Jan 20, 2023
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Local tests didn't raise any red flags, LGTM

@effigies effigies merged commit 50a8bd9 into nipreps:master Jan 20, 2023
@effigies effigies mentioned this pull request Apr 4, 2023
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@effigies effigies deleted the mnt/update_deps branch August 24, 2023 03:43
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Status: Done (To be released)
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