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Function to create basic/default yaml file #398

Merged
merged 10 commits into from
Mar 23, 2020
Merged

Function to create basic/default yaml file #398

merged 10 commits into from
Mar 23, 2020

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MerktSimon
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codecov bot commented Mar 20, 2020

Codecov Report

Merging #398 into develop will increase coverage by 0.09%.
The diff coverage is 90%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #398      +/-   ##
===========================================
+ Coverage    77.78%   77.88%   +0.09%     
===========================================
  Files           22       22              
  Lines         2098     2116      +18     
  Branches       486      493       +7     
===========================================
+ Hits          1632     1648      +16     
- Misses         343      344       +1     
- Partials       123      124       +1
Impacted Files Coverage Δ
petab/problem.py 72.36% <0%> (-0.65%) ⬇️
petab/yaml.py 89.83% <100%> (+3.78%) ⬆️

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@dweindl dweindl left a comment

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Not so much in favor of adding that, as all those get_default_*_file_name functions are marked for removal.

@yannikschaelte
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I agree that this function won't be too useful, since the employed default names are marked for removal already (they originated from back when there was no yaml yet but just standardized file names).

What would however make a lot of sense, not sure if it exists yet @dweindl , is the ability for a given petab problem (or rather a collection of file names) to write a yaml file linking all files.

@JanHasenauer
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I agree and vote for not include this

@dweindl
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dweindl commented Mar 22, 2020

What would however make a lot of sense, not sure if it exists yet @dweindl , is the ability for a given petab problem (or rather a collection of file names) to write a yaml file linking all files.

Yeah, may make sense to extend petab.Problem.to_files by an optional yaml_file argument instead.

@MerktSimon
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I got rid of all the get_default_name...functions. Now you have to enter file paths by hand.
It is also now included as optional in problem.to_file(). But I left it as a stand alone function so that users who have old petab folders can just use it to create yaml without detour over `petab.problem

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@PEtab-dev PEtab-dev deleted a comment from MerktSimon Mar 23, 2020
@dweindl dweindl merged commit e713f8b into develop Mar 23, 2020
@MerktSimon MerktSimon deleted the create_yaml branch March 23, 2020 16:15
@yannikschaelte yannikschaelte mentioned this pull request Mar 31, 2020
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4 participants