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Updated standalone installation requirements #2009

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merged 5 commits into from
Mar 2, 2020

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bbfrederick
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Changes proposed in this pull request

This PR updates the external dependencies listed in installation.rst for standalone installation to match the packages and versions found in the Dockerfile.
There is also a typo fixed in CONTRIBUTING.md

This should close issue #2008, which I raised today.

The need for an updated version of ICA-AROMA is pretty clear, as fmriprep now uses a flag that doesn't exist in the older version. I used the version and download link used in the Dockerfile - if there's a more appropriate permalink that might be better.
The bids-validator version has been updated to match the Dockerfile.
I can't see any indication that c3d is installed in the Dockerfile, so I removed it as a dependency.

Documentation that should be reviewed

This is a documentation only fix, which modifies docs/installation.rst and CONTRIBUTING.md

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- FreeSurfer_ (version 6.0.1)
- `ICA-AROMA <https://github.com/rhr-pruim/ICA-AROMA/>`_ (version 0.4.1-beta)
- `bids-validator <https://github.com/bids-standard/bids-validator>`_ (version 1.1.0)
- `ICA-AROMA <https://github.com/oesteban/ICA-AROMA/archive/v0.4.5.tar.gz>`_ (version 0.4.5)
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Ugh. I didn't realize we have an unofficial release in here.

@oesteban I see @maartenmennes merged maartenmennes/ICA-AROMA#43. Perhaps we should pin:

Suggested change
- `ICA-AROMA <https://github.com/oesteban/ICA-AROMA/archive/v0.4.5.tar.gz>`_ (version 0.4.5)
- `ICA-AROMA <https://github.com/maartenmennes/ICA-AROMA/archive/e8d7a58.tar.gz>`_ (commit e8d7a58, post v0.4.4-beta)

WDYT?

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Seems reasonable to me.

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Well, my reading of the Dockerfile was not in fact as careful as I thought it was. C3D is installed when other packages are pulled from Neurodebian (as convert3d). So the line:

  • C3D <https://sourceforge.net/projects/c3d/>_ (version 1.0.0)

Should NOT be removed from the standalone dependencies. Should I open a new PR, or can this one be fixed?

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This one can be fixed. Just push to the same branch and it'll update.

@mgxd mgxd changed the base branch from master to maint/20.0.x March 2, 2020 16:26
@mgxd mgxd merged commit 1fa5a81 into nipreps:maint/20.0.x Mar 2, 2020
effigies added a commit that referenced this pull request Mar 11, 2020
Merge notes:

* Fix gh-2014 appears to have been made unnecessary by gh-2018.

Tag message:

20.0.2 (March 6, 2020)
======================
A bug squashing release in the 20.0.x series.

This release fixes the use of custom templates within the docker wrapper, remedies crashes
when FreeSurfer HOME was not set, and improves the documentation for local installations.

With thanks to Blaise Frederick for the contribution.

  * DOC: Update standalone installation requirements (#2009)
  * FIX: Crashes whenever FREESURFER_HOME is not set (#2014)
  * FIX: Local template mounting (wrapper) (#2020)
  * MAINT: Pin minor series of nipype, major series of nibabel (#2021)
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