Make CUDA the default compute platform

[IAlibay]

TODO:

• Fix tests for limiting the compute platforms
• Add news entry

Checklist

• Added a news entry

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[mikemhenry]

I know we like to use .lower() to make things easier for users, but do we think that breaking roundtrip serialization is worth it? Looks like we need to update a fixture so that our tests work. While its nice for testing and can be done with a fixture, do we want to expose a get_test_settings() method that just runs a little like these tests or do you think it depends too much on what you are trying to do?

[IAlibay]

but do we think that breaking roundtrip serialization is worth it

I might be missing something, we're storing the string as-is, unless you mean something else?

[mikemhenry]

I see what you are saying, we use .lower() on the check but don't enforce any regularization on serialization, so if a user sets the default platform to CuDA that is what will be written in the transformation + result json.

[IAlibay]

I see what you are saying, we use .lower() on the check but don't enforce any regularization on serialization, so if a user sets the default platform to CuDA that is what will be written in the transformation + result json.

That's the behaviour we've always had - if you want to change this, I would suggest we do this in a separate PR. I'm only scoping this as "changing the default from None to cuda".

[mikemhenry]

Just adding a link here so if we ever decide we need HIP support, I can find this easily

#951

[mikemhenry]

LGTM! Really just wondering if it makes sense to set s.protocol_repeats = 1 in the testing fixtures instead of in most of the tests that use the fixture

[mikemhenry]

I am not sure if any tests here actually need more than one repeat

[IAlibay]

Really just wondering if it makes sense to set s.protocol_repeats = 1 in the testing fixtures instead of in most of the tests that use the fixture

Thanks, I will manually check and update - apologies in advance, for my own sanity I might not merge your suggestions from the github interface (so I can keep track of what has and hasn't been updated).

[codecov]

Codecov Report

❌ Patch coverage is 90.56604% with 15 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.42%. Comparing base (ec229cc) to head (063efe8).

Files with missing lines	Patch %	Lines
...s/protocols/openmm_rfe/test_hybrid_top_protocol.py	75.00%	14 Missing ⚠️
...ests/protocols/openmm_md/test_plain_md_protocol.py	92.85%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1576      +/-   ##
==========================================
- Coverage   95.45%   93.42%   -2.03%     
==========================================
  Files         174      174              
  Lines       14552    14534      -18     
==========================================
- Hits        13891    13579     -312     
- Misses        661      955     +294     

Flag	Coverage Δ
fast-tests	93.42% <90.56%> (?)
slow-tests	?

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[mikemhenry]

Really just wondering if it makes sense to set s.protocol_repeats = 1 in the testing fixtures instead of in most of the tests that use the fixture

Thanks, I will manually check and update - apologies in advance, for my own sanity I might not merge your suggestions from the github interface (so I can keep track of what has and hasn't been updated).

That is fine! I haven't been able to get the "add suggestion to batch" to work with the new PR UI anyway so it would have been a separate commit for each one. I mostly did it so I could keep track of how many there were set to one versus how many were set to the default.

[IAlibay]

Ok that's all of the protocol repeats dealt with @mikemhenry !

[mikemhenry]

I'm happy with it!

[github-actions]

No API break detected ✅

[IAlibay]

Failure is unrelated to this PR - merging so we can fix other things elsewhere.