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Fix numpy DeprecationWarning in burn_in_by_sequential_geweke #1217

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merged 1 commit into from
Nov 28, 2023

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@dweindl dweindl commented Nov 28, 2023

Fixes

test/sample/test_sample.py: 542 warnings
  pyPESTO/pypesto/sample/geweke_test.py:202: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    alpha2[idxs[i]] = alpha2[idxs[i]] / (

Fixes #1207

Fixes
```
test/sample/test_sample.py: 542 warnings
  pyPESTO/pypesto/sample/geweke_test.py:202: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    alpha2[idxs[i]] = alpha2[idxs[i]] / (
```

Fixes ICB-DCM#1207
@dweindl dweindl linked an issue Nov 28, 2023 that may be closed by this pull request
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codecov-commenter commented Nov 28, 2023

Codecov Report

Attention: 417 lines in your changes are missing coverage. Please review.

Comparison is base (160c2a8) 88.16% compared to head (b71a171) 81.52%.
Report is 444 commits behind head on develop.

Files Patch % Lines
pypesto/ensemble/ensemble.py 68.46% 70 Missing ⚠️
pypesto/ensemble/util.py 55.04% 49 Missing ⚠️
...ypesto/hierarchical/spline_approximation/solver.py 83.68% 47 Missing ⚠️
pypesto/history/base.py 84.76% 32 Missing ⚠️
pypesto/hierarchical/optimal_scaling/solver.py 93.53% 26 Missing ⚠️
pypesto/hierarchical/petab.py 84.56% 23 Missing ⚠️
pypesto/engine/mpi_pool.py 0.00% 22 Missing ⚠️
pypesto/hierarchical/inner_calculator_collector.py 89.04% 16 Missing ⚠️
...pesto/hierarchical/spline_approximation/problem.py 89.18% 16 Missing ⚠️
pypesto/hierarchical/optimal_scaling/calculator.py 75.86% 14 Missing ⚠️
... and 19 more

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Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #1217      +/-   ##
===========================================
- Coverage    88.16%   81.52%   -6.65%     
===========================================
  Files           79      148      +69     
  Lines         5257    11826    +6569     
===========================================
+ Hits          4635     9641    +5006     
- Misses         622     2185    +1563     

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@dweindl dweindl merged commit 00514bc into ICB-DCM:develop Nov 28, 2023
18 checks passed
@dweindl dweindl deleted the fix_1207 branch November 28, 2023 19:22
This was referenced Dec 5, 2023
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Fix pypesto/sample/geweke_test.py:202: DeprecationWarning
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