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YAML file for grouping PEtab files #183

Merged
merged 15 commits into from
Dec 16, 2019
Merged

YAML file for grouping PEtab files #183

merged 15 commits into from
Dec 16, 2019

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dweindl
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@dweindl dweindl commented Dec 15, 2019 •
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Closes #49

  • Validation of contents (e.g. files exist)
  • petab.Problem from yaml
  • Adapt schema to multiple measurement files
  • Use in petablint
  • Implement petab.CompositeProblem
  • Multiple measurement files for petab.Problem (only in from_files, merge during loading)

To be done, but out of scope here:

  • Add more human-readable format description
  • Visualization files?
  • Implement mapping functions for CompositeProblem
  • Implement validation functions for CompositeProblem
  • Option to specify training and validation data in YAML?

dweindl added a commit to LeonardSchmiester/Benchmark-Models that referenced this pull request Dec 15, 2019
@dweindl
Generate PEtab yaml files for PEtab-dev/PEtab#183
09fdb82
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codecov-io commented Dec 15, 2019 •
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Codecov Report

Merging #183 into develop will decrease coverage by 2.14%.
The diff coverage is 41.66%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #183      +/-   ##
===========================================
- Coverage     71.2%   69.05%   -2.15%     
===========================================
  Files           16       18       +2     
  Lines         1153     1241      +88     
  Branches       262      280      +18     
===========================================
+ Hits           821      857      +36     
- Misses         285      335      +50     
- Partials        47       49       +2
Impacted Files Coverage Δ
petab/visualize/helper_functions.py 95.8% <ø> (ø) ⬆️
petab/core.py 90.9% <ø> (ø) ⬆️
petab/petablint.py 0% <0%> (ø) ⬆️
petab/sampling.py 85% <100%> (ø) ⬆️
petab/measurements.py 81.44% <100%> (+1.44%) ⬆️
petab/problem.py 63.3% <26.66%> (-6.49%) ⬇️
petab/composite_problem.py 43.47% <43.47%> (ø)
petab/yaml.py 52.63% <52.63%> (ø)
petab/lint.py 50.71% <75%> (-0.7%) ⬇️
... and 1 more

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@dweindl
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dweindl commented Dec 15, 2019

@yannikschaelte : How do we want to handle problems with multiple models with petab.Problem? Either we change the structure there, which will require a load of downstream changes, or we introduce something like petab.CompositeProblem, that manages a bunch of petab.Problems. Not completely sure, but I think I prefer the latter, as the default still seems to be having only one model.

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@yannikschaelte : How do we want to handle problems with multiple models with petab.Problem? Either we change the structure there, which will require a load of downstream changes, or we introduce something like petab.CompositeProblem, that manages a bunch of petab.Problems. Not completely sure, but I think I prefer the latter, as the default still seems to be having only one model.

I would agree to keep the single-anything petab.Problem, since that will remain the default, and have a petab.CompositeProblem in addition. However, it won't just hold a list of petab.Problems, but need to overwrite/aggregate the single functions that the Problem offers in different ways, if we have e.g. just one parameters file.
Whether to generate a Problem or CompositeProblem could easily be automatized when reading in the yaml.

dweindl and others added 2 commits December 16, 2019 10:15
@dweindl
Merge branch 'develop' into feature_49_yaml
8830909
@dweindl
Add petab.CompositeProblem
1d7192c 
* petab.CompositeProblem
* Add from_yaml() to petab.CompositeProblem and petab.Problem
* extend petab.Problem for use with multiple measurement files
* Cleanup
* Adapt petablint for use with yaml file
yannikschaelte
yannikschaelte reviewed Dec 16, 2019
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some comments on the yaml.

doc/documentation_data_format.md Show resolved Hide resolved
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petab/composite_problem.py Outdated Show resolved Hide resolved
petab/petab_schema.yaml Show resolved Hide resolved
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dweindl commented Dec 16, 2019

Thanks for comments. All done.

dweindl added a commit to LeonardSchmiester/Benchmark-Models that referenced this pull request Dec 16, 2019
@dweindl
Generate PEtab yaml files for PEtab-dev/PEtab#183 (#84)
60dc94b
yannikschaelte
yannikschaelte approved these changes Dec 16, 2019
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minor stuff

doc/documentation_data_format.md Outdated Show resolved Hide resolved
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doc/documentation_data_format.md Outdated Show resolved Hide resolved
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dweindl and others added 3 commits December 16, 2019 18:46
@dweindl
Fix documentation; exclude most imports
89ff163
@dweindl @yannikschaelte
Apply suggestions from code review
2239028 
Co-Authored-By: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
@dweindl
Apply suggestions from code review
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@dweindl dweindl changed the title [WIP] YAML file for grouping PEtab files YAML file for grouping PEtab files Dec 16, 2019
@dweindl dweindl merged commit 54c526a into develop Dec 16, 2019
@dweindl dweindl deleted the feature_49_yaml branch December 16, 2019 18:12
dweindl added a commit that referenced this pull request Dec 17, 2019
@dweindl
Merge pull request #200 from ICB-DCM/release_0.0.1
ea121dc 
Release 0.0.1

Data format:
* Update format and documentation with respect to data and parameter scales
  (#169)
* Define YAML schema for grouping PEtab files, also allowing for more complex
  combinations of files (#183)

Library:
* Refactor library. Reorganize `petab.core` functions.
* Fix visualization w/o condition names #142
* Extend validator
* Removed deprecated functions petab.Problem.get_constant_parameters
  and petab.sbml.constant_species_to_parameters
* Minor fixes and extensions
@dweindl dweindl mentioned this pull request Dec 17, 2019
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@dweindl @codecov-io @yannikschaelte