Enable prepared deprecations

[lgoettgens]

This should be adapted once #1729 adds more prepared deprecations.

[lgoettgens]

This is now ready from my POV. We just need to iterate until CI reports no more calls to deprecated methods.

[codecov]

Codecov Report

❌ Patch coverage is 50.00000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 88.29%. Comparing base (90b8c7c) to head (3639f7e).
⚠️ Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
src/Deprecations.jl	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2261      +/-   ##
==========================================
- Coverage   88.31%   88.29%   -0.02%     
==========================================
  Files         126      126              
  Lines       31790    31786       -4     
==========================================
- Hits        28074    28067       -7     
- Misses       3716     3719       +3     

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