[WIP] fixing cli test for protocol refactor

[atravitz]

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• Added a news entry, or the changes are not user-facing.
• Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

• GPU integration tests
• example notebook testing
• packaging tests: run this for any large feature PRs or PRs that add test data.

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/.

[github-actions]

No API break detected ✅

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
⚠️ Please upload report for BASE (multi-unit-rfe@0b060be). Learn more about missing BASE report.

Additional details and impacted files

@@                Coverage Diff                @@
##             multi-unit-rfe    #1788   +/-   ##
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  Coverage                  ?   93.13%           
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  Files                     ?      194           
  Lines                     ?    17072           
  Branches                  ?        0           
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  Hits                      ?    15900           
  Misses                    ?     1172           
  Partials                  ?        0           

Flag	Coverage Δ
fast-tests	93.13% <100.00%> (?)

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