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Feature hdf5 profile sample #546

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merged 12 commits into from
Jan 19, 2021
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PaulJonasJost
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Hello,

i created a Reader and Writer for both Profiles and Samples.
I do need to mention that there is still some slight bug, when writing into an already existing file. It then expectes the shape to be the same as before (e.g. a profile of a parameter which ad (20,1) before is now expected to have the same shape). I do have an Idea on how to fix this but this here is already working right now. One only has to create a new file or delete the old before as of now.

@PaulJonasJost PaulJonasJost requested review from dweindl, yannikschaelte and dilpath and removed request for dweindl, yannikschaelte and dilpath January 11, 2021 17:32
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codecov-io commented Jan 11, 2021

Codecov Report

Merging #546 (8bc8846) into develop (e4788e7) will increase coverage by 1.24%.
The diff coverage is 24.74%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #546      +/-   ##
===========================================
+ Coverage    88.22%   89.47%   +1.24%     
===========================================
  Files           71       71              
  Lines         4443     4532      +89     
===========================================
+ Hits          3920     4055     +135     
+ Misses         523      477      -46     
Impacted Files Coverage Δ
pypesto/store/save_to_hdf5.py 61.76% <24.00%> (-31.57%) ⬇️
pypesto/store/read_from_hdf5.py 58.88% <25.53%> (-36.46%) ⬇️
pypesto/store/hdf5.py 82.60% <0.00%> (-4.35%) ⬇️
pypesto/objective/function.py 75.00% <0.00%> (+0.92%) ⬆️
pypesto/objective/amici.py 91.56% <0.00%> (+1.20%) ⬆️
pypesto/objective/amici_util.py 75.89% <0.00%> (+1.78%) ⬆️
pypesto/objective/amici_calculator.py 91.66% <0.00%> (+3.33%) ⬆️
pypesto/optimize/optimizer.py 90.61% <0.00%> (+29.49%) ⬆️

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@dweindl dweindl left a comment

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Good to have HDF5 IO support for profiling/sampling results.

Please also include a test case writing some result, reading it back in and ensuring that it is the same as the original one.

pypesto/store/read_from_hdf5.py Outdated Show resolved Hide resolved
pypesto/store/read_from_hdf5.py Outdated Show resolved Hide resolved
pypesto/store/read_from_hdf5.py Outdated Show resolved Hide resolved
pypesto/store/read_from_hdf5.py Outdated Show resolved Hide resolved
pypesto/store/save_to_hdf5.py Outdated Show resolved Hide resolved
pypesto/store/save_to_hdf5.py Outdated Show resolved Hide resolved
pypesto/store/save_to_hdf5.py Outdated Show resolved Hide resolved
Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
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Good for me now.

@PaulJonasJost PaulJonasJost merged commit 227483c into develop Jan 19, 2021
@PaulJonasJost PaulJonasJost deleted the feature_hdf5_Profile_Sample branch January 19, 2021 12:51
@yannikschaelte yannikschaelte mentioned this pull request Jan 19, 2021
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3 participants