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Fix for petab 0.2.x #1073

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merged 22 commits into from Jun 6, 2023
Merged

Fix for petab 0.2.x #1073

merged 22 commits into from Jun 6, 2023

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FFroehlich
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@FFroehlich FFroehlich requested review from dweindl and a team as code owners June 2, 2023 15:38
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codecov-commenter commented Jun 2, 2023

Codecov Report

Merging #1073 (eba75fb) into develop (160c2a8) will decrease coverage by 4.61%.
The diff coverage is 87.68%.

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@@             Coverage Diff             @@
##           develop    #1073      +/-   ##
===========================================
- Coverage    88.16%   83.56%   -4.61%     
===========================================
  Files           79      147      +68     
  Lines         5257    11395    +6138     
===========================================
+ Hits          4635     9522    +4887     
- Misses         622     1873    +1251     
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 70.76% <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

@FFroehlich
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looking for volunteers to wrap this up

@dweindl dweindl self-assigned this Jun 5, 2023
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dweindl commented Jun 6, 2023

looking for volunteers to wrap this up

Done

@dweindl dweindl removed their assignment Jun 6, 2023
@@ -73,7 +73,7 @@ jobs:
run: .github/workflows/install_deps.sh amici pysb

- name: Run tests
timeout-minutes: 25
timeout-minutes: 35
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if it takes that long out of a sudden, something should be wrong. was 15 not long ago

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The number of test cases increased:

  • additional test cases
  • running for both SBML and PySB models

@dweindl dweindl merged commit f704cf2 into develop Jun 6, 2023
17 checks passed
@dweindl dweindl deleted the fix_petab branch June 6, 2023 10:35
dweindl added a commit that referenced this pull request Jun 19, 2023
Since #1073, we don't need an extra `PetabImporterPysb`, as anything PySB-specific is handled inside PEtab/AMICI.
dweindl added a commit that referenced this pull request Jun 20, 2023
Since #1073, we don't need an extra `PetabImporterPysb`, as anything PySB-specific is handled inside PEtab/AMICI.
This was referenced Jun 22, 2023
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4 participants