Add smoothness metric

[hugofluhr]

Closes #71

PR that add smoothness computation for signals that are defined on nodes of the graph. It's my first contribution to such a project so I'm happy to get feedback :)

Proposed Changes

• add a smoothness fct in operations.metrics.
• add corresponding test fct.
• add corresponding class method in objects.

Change Type

• [ ] bugfix (+0.0.1)
• [x] minor (+0.1.0)
• [ ] major (+1.0.0)
• [ ] refactoring (no version update)
• [ ] test (no version update)
• [ ] infrastructure (no version update)
• [ ] documentation (no version update)
• [ ] other

Checklist before review

• [x] I added everything I wanted to add to this PR.
• [x] [Code or tests only] I wrote/updated the necessary docstrings.
• [x] [Code or tests only] I ran and passed tests locally.
• [ ] [Documentation only] I built the docs locally.
• [x] My contribution is harmonious with the rest of the code: I'm not introducing repetitions.
• [x] My code respects the adopted style, especially linting conventions.
• [x] The title of this PR is explanatory on its own, enough to be understood as part of a changelog.
• [x] I added or indicated the right labels.
• [ ] I added information regarding the timeline of completion for this PR.
• [ ] Please, comment on my PR while it's a draft and give me feedback on the development!

[codecov[bot]]

Codecov Report

Merging #72 (854c047) into master (4ffa7cb) will increase coverage by 0.13%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master      #72      +/-   ##
==========================================
+ Coverage   90.93%   91.06%   +0.13%     
==========================================
  Files          14       14              
  Lines        1235     1254      +19     
==========================================
+ Hits         1123     1142      +19     
  Misses        112      112              

Files Changed	Coverage Δ
nigsp/cli/run.py	97.14% <100.00%> (+0.08%)	:arrow_up:
nigsp/objects.py	100.00% <100.00%> (ø)
nigsp/operations/metrics.py	100.00% <100.00%> (ø)
nigsp/references.py	100.00% <100.00%> (ø)

[venkateshness]

Looks good to me !

Some nice-to-have things: a) Worth embedding a ref paper e.g: https://www.nature.com/articles/srep42013.pdf in the docstring b) Compare the size of nodes in laplacian and signal and raise an error message if there's a mismatch; before the np.dot()

[hugofluhr]

Thanks for the inputs!

Progress tracker :

• [x] add ref
• [x] check input sizes
• [x] add smoothness to CLI
• [x] add smoothness to list of supported metrics
• [x] try transposing signal if dimension mismatch
• [x] add corresponding tests
• [ ] allow for 3rd dimension of signal, e.g. subjects
• [ ] change structure to match functional_connectivity, hidden sub-function

[hugofluhr]

@smoia the coverage is decreasing partly due to LGR.warning not being covered in tests, any guidance on how to cover those?

[venkateshness]

Unless I am missing (had a quick look on my mobile), LGF.warning is triggered by if statements in 2 cases. You can push to kick these if statements in the break tests ?

[smoia]

If the coverage decreases a little, that's ok. If you do want to test particular cases, I would add a couple of asserts in the main test of the function that do specific checks on those cases!

Break tests are only for raising errors!

[smoia]

@hugofluhr can we merge this in?