[ENH] [DOC] Add matlab to python file conversion functions, add docs for custom tractography integration

[36000]

Closes #549

• Add matlab to pyhton converters from pyAFQ-scripts
• Add tests for converters
• Add docs for m2p converter
• add docs for custom tractography

[36000]

@arokem is there a small matlab file I could use to unit test these new functions?

[36000]

Try this: https://github.com/yeatmanlab/AFQ-Browser/blob/master/afqbrowser/site/client/data/afq.mat

[pep8speaks]

Hello @36000! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file AFQ/utils/conversion.py:

Line 57:63: W291 trailing whitespace

Comment last updated at 2020-11-25 17:32:10 UTC

[36000]

@arokem where should I put the mat files I use for testing here?

[arokem]

You can put them in a tests/data/ folder, but you'll have to make sure to provide metadata that will tell Python to install the data as part of the package. See: https://github.com/nipy/nibabel/blob/master/setup.cfg#L84

[36000]

I believe thats being used already for some s3 tests. I may have to modify those tests to use that folder.

For example, it looks like test_get_matching_s3_keys expects everything in that folder to be the same as whats in the test bucket.

@richford anything you would like to add to this discussion about how AFQ/tests/data is used?

[36000]

I ended up moving the mock s3 data into a "mocks3" folder in data to separate it from the rest.

Anyways, this is ready for review / merge @arokem .

[arokem]

Overall, looks good! Just a few minor comments/suggestions.

[36000]

@arokem I tried using squeeze_me but I got confused by what it was returning. The current system works for the files I have encountered, so I don't know if it would be useful to re-figure it out with squeeze_me.

Other than that, this is ready for review / merge.