RF - Direction getters naming

[gabknight]

Change direction getter naming in preparation of new direction getters based on peaks object (PR in prep).

• class BaseDirectionGetter -> BasePmfDirectionGetter
• file peak_direction_getter.pyx -> eudx_direction_getter.pyx
• file test_peak_dg.py -> test_eudx_dg.py

[codecov]

Codecov Report

Merging #2033 into master will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #2033      +/-   ##
==========================================
+ Coverage   91.21%   91.22%   +0.01%     
==========================================
  Files         250      252       +2     
  Lines       31803    31832      +29     
  Branches     3340     3340              
==========================================
+ Hits        29009    29039      +30     
  Misses       2074     2074              
+ Partials      720      719       -1     

Impacted Files	Coverage Δ
dipy/segment/tests/test_bundles.py	89.52% <0.00%> (-0.96%)	⬇️
...ection/tests/test_closest_peak_direction_getter.py	100.00% <0.00%> (ø)
dipy/reconst/peak_direction_getter.py	100.00% <0.00%> (ø)
dipy/viz/app.py	77.25% <0.00%> (+0.50%)	⬆️

[skoudoro]

Hi @gabknight,

Thank you for this update. If this naming conventions change is really necessary, we will need to set up a deprecation cycle for at least 2 releases and keep the old system (release 1.0.0 was an exception for breaking without any deprecation cycle)
So we need:

• to keep the old file and create a new one
• In the old file, add a deprecation warning and call the new one.

Let me know if you need help with that and I will create a PR on local branch/dipy repo.

[gabknight]

Hi @skoudoro, thanks for your response. I wasn't sure how to do the deprecation for a class. Let me know if you would do it differently. Maybe instead of defining a function, I should just do
EuDXDirectionGetter = dipy.reconst.eudx_direction_getter.EuDXDirectionGetter ?

The warning is in peak_direction_getter .py rather than .pyx. Do you think this is an issue?

[skoudoro]

Hi @gabknight,

I think it is good the way you do it!

It is just missing a small test to make sure that the warning popup.

Furthermore, I need to test it quickly. Thank you !

[gabknight]

@skoudoro, Thanks I added the test.

Do you know why those build failed?

[skoudoro]

Not yet, needs to look into it.

• it seems that something change in Nibabel and their Numpy minimum version is different from ours.
• Or maybe, they just dropped python3.5

Anyway, I need to look.

[skoudoro]

You can rebase this PR @gabknight, error on Travis has been fixed.

As I said below, There is one more deprecation to do and this PR will be ready to go. Thank you

[skoudoro]

BaseDirectionGetter needs a deprecation cycle as you did for EuDXDirectionGetter.

Can you add this deprecation and a small test for it?

Thank you

[skoudoro]

Sorry for the delay but thank you @gabknight! Everything looks good and you can continue with #2036. merging