Fix numpy DeprecationWarnings

[dweindl]

Closes #1074

[codecov-commenter]

Codecov Report

Merging #1076 (aa37b02) into develop (160c2a8) will decrease coverage by 4.61%.
The diff coverage is 87.68%.

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@@             Coverage Diff             @@
##           develop    #1076      +/-   ##
===========================================
- Coverage    88.16%   83.56%   -4.61%     
===========================================
  Files           79      147      +68     
  Lines         5257    11392    +6135     
===========================================
+ Hits          4635     9520    +4885     
- Misses         622     1872    +1250     

Impacted Files	Coverage Δ
pypesto/engine/mpi_pool.py	0.00% <0.00%> (ø)
pypesto/objective/amici/__init__.py	100.00% <ø> (ø)
pypesto/objective/amici/amici.py	84.71% <ø> (ø)
pypesto/objective/amici/amici_calculator.py	83.33% <ø> (ø)
pypesto/objective/amici/amici_util.py	71.65% <ø> (ø)
pypesto/objective/base.py	87.62% <ø> (-0.10%)	⬇️
pypesto/objective/finite_difference.py	94.16% <ø> (ø)
pypesto/objective/function.py	94.91% <ø> (+19.91%)	⬆️
pypesto/objective/jax/__init__.py	100.00% <ø> (ø)
pypesto/objective/jax/base.py	91.56% <ø> (ø)
... and 137 more