NF/ADD CED spike2 file IO

[htwangtw]

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Addresses #405.

The current implementation uses the official API, sonpy, from CED. sonpy is closed sourced. In order to support sonpy, the minimal python version should be 3.7. Hence I will mark this as part of the major release.

The scanner volume trigger in the test file was stored as a "marker" channel. The sonpy API returns time points of markers, rather than a timeseries. The module I wrote has been tested locally. I cannot run the full test due to bandwidth and data limit. Will check if this breaks other tests.

Proposed Changes

• Add phys2bids.io.load_smr

Change Type

• [ ] bugfix (+0.0.1)
• [x] minor (+0.1.0)
• [x] 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.
• [ ] 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!

[htwangtw]

~Looks like conda doesn't support the latest version of sonpy - I am not familiar with Cirrus CI, if anyone can look into how to get pip to install certain libraries, that would be grand.~

Found the reason. How sonpy uses release version number is unorthodox. It is an easy fix.

[codecov[bot]]

Codecov Report

Merging #410 (a54e85c) into master (d3a7443) will increase coverage by 0.76%. The diff coverage is 100.00%.

:exclamation: Current head a54e85c differs from pull request most recent head fea0e0d. Consider uploading reports for the commit fea0e0d to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #410      +/-   ##
==========================================
+ Coverage   94.25%   95.01%   +0.76%     
==========================================
  Files           8        8              
  Lines         974      903      -71     
==========================================
- Hits          918      858      -60     
+ Misses         56       45      -11     

Impacted Files	Coverage Δ
phys2bids/io.py	99.50% <100.00%> (+2.86%)	:arrow_up:

... and 5 files with indirect coverage changes

[htwangtw]

hmmm all python 3.6 checks failed. Looks like a sonpy problem - they use the versioning numbers in a very special way (1.6.x -> python 3.6 support; 1.7.x -> python 3.7 etc)

[smoia]

More than that, I believe that sonpy only supports python 3.7 and above (If I understood their page ) Python 3.6 reaches its EOL in a month, so I see two options here:

• we add an exception to not run this test when running python 3.6, or
• we can speed up things and end support for python 3.6 earlier on, removing its tests alltogether.

WDYT?

[htwangtw]

Ah good to know! I would prefer

1. explicitly exclude 3.6 for sonpy related functions
2. end support for 3.6 in future iteration.

Dealing with deprecation and adding a new function in one PR might be too much

[smoia]

Agreed! Let's exclude 3.6 testing for sonpy. Do you need help with it?

[htwangtw]

I will have a look and likely working on this next week

[smoia]

@htwangtw I tried to update this PR to merge it in. At the moment, I still cannot figure out how to fix the installation of sonpy - mainly due to the fact that python 3.10 cannot install it.

As a temporary solution, I marked as xfail the sonpy test. I don't love this, but I don't know how to solve it at the moment.

If you agree with the changes, we merge!

[smoia]

:rocket: PR was released in 2.9.0 :rocket: