Update deprecated functions in tests

[yannikschaelte]

I'd argue that when marking arguments as deprecated, tests should proceed to use the new arguments (and optionally keep some tests using the old ones, but only as extras)?

number of test warnings reduced from ~42 to 5

[dweindl]

I'd argue that when marking arguments as deprecated, tests should proceed to use the new arguments (and optionally keep some tests using the old ones, but only as extras)?
Generally, I'd say it makes sense to check that the deprecated functionality still works until it is removed. But fine for me to remove in this specific case.

I now added test routines with deprecation warning checks for most of the changed calls

[codecov-commenter]

Codecov Report

Merging #181 (125e099) into develop (7455e03) will decrease coverage by 0.34%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           develop     #181      +/-   ##
===========================================
- Coverage    78.06%   77.72%   -0.35%     
===========================================
  Files           29       29              
  Lines         2644     2644              
  Branches       591      591              
===========================================
- Hits          2064     2055       -9     
- Misses         421      431      +10     
+ Partials       159      158       -1     

Impacted Files	Coverage Δ
petab/problem.py	64.75% <ø> (-1.92%)	⬇️
petab/parameter_mapping.py	65.96% <0.00%> (-2.10%)	⬇️

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