Mrtpipelines update

[kaitj]

Proposed changes

A number of quality changes (primarily to mrtpipelines.smk) to try to bring this up-to-date as of snakebids==0.6.2. Includes updates to:

• pybids_inputs
• Use of variables instead of grabbing from config for every rule
• Renamed rules to reflect similar naming of mrtrix functions
• Update mrtrix container to 3.0.3.
• Make use of functools.partial

See the commit notes for full details.

Types of changes

What types of changes does your code introduce? Put an x in the boxes that apply

• [ ] Bugfix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionalitiy)
• [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [x] Other (if none of the other choices apply)

Checklist

Put an x in the boxes that apply. You can also fill these out after creating the PR. If you are unsure about any of the choices, don't hesitate to ask!

• [ ] Changes have been tested to ensure that fix is effective or that a feature works.
• [ ] Changes pass the unit tests
• [x] Code has been run through the poe quality task
• [x] I have included necessary documentation or comments (as necessary)
• [ ] Any dependent changes have been merged and published

Notes

All PRs will undergo the unit testing before being reviewed. You may be requested to explain or make additional changes before the PR is accepted.

[kaitj]

I just went through and replaced any use of expand for the old outputs to make use of functools.partial as of d80dbe2