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Parameter table subset files. #407

Merged
merged 15 commits into from
Mar 31, 2020
Merged

Parameter table subset files. #407

merged 15 commits into from
Mar 31, 2020

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dilpath
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@dilpath dilpath commented Mar 24, 2020

Addresses issue #307 (allows a parameter table .tsv file to be split into multiple subset .tsv files).

At the moment, the same parameterId can have definitions in different (or the same) subset files. However, if these definitions for the same parameterId have any differences, then a ValueError will be raised.

Are parameter duplicates handled already?

@dilpath dilpath self-assigned this Mar 25, 2020
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Would be neat to have a test-case for this, not sure whether this should go here or added to the testsuite (ping @yannikschaelte)

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Would be neat to have a test-case for this, not sure whether this should go here or added to the testsuite (ping @yannikschaelte)

I would prefer a test case here. The test suite for petab version 1 does not yet cover such tests (e.g. on yaml support, integration of files etc.). But would make sense to add a test at some point. PEtab-dev/petab_test_suite#26

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can you change base branch to develop?

@MerktSimon MerktSimon self-requested a review March 26, 2020 08:47
@dilpath dilpath changed the base branch from master to develop March 26, 2020 10:59
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can you change base branch to develop?

thanks for noting. yes, base branch should always be develop, and then once from develop to master at some point. see here https://pyabc.readthedocs.io/en/latest/contribute.html#contribute-code for a similarly set up project

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looks great, even better if a test passes ;)

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yannikschaelte commented Mar 26, 2020

it could be that the unit tests (via github actions) do not run at all, in that case maybe to the PR from inside petab-dev/petab, not a fork (not sure if there's a possibility to enable those tests automatically for forks).

@MerktSimon MerktSimon removed their request for review March 26, 2020 13:36
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codecov bot commented Mar 26, 2020

Codecov Report

Merging #407 into develop will increase coverage by 0.01%.
The diff coverage is 73.91%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #407      +/-   ##
===========================================
+ Coverage    77.93%   77.95%   +0.01%     
===========================================
  Files           22       22              
  Lines         2126     2141      +15     
  Branches       498      506       +8     
===========================================
+ Hits          1657     1669      +12     
- Misses         343      345       +2     
- Partials       126      127       +1     
Impacted Files Coverage Δ
petab/problem.py 71.86% <33.33%> (-0.51%) ⬇️
petab/parameters.py 82.43% <71.42%> (+0.41%) ⬆️
petab/core.py 82.35% <100.00%> (+0.11%) ⬆️
petab/yaml.py 90.16% <100.00%> (+0.33%) ⬆️

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@dilpath dilpath merged commit c0a50f2 into PEtab-dev:develop Mar 31, 2020
@dilpath dilpath deleted the issue_307 branch March 31, 2020 10:26
@yannikschaelte yannikschaelte mentioned this pull request Mar 31, 2020
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4 participants