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fix simulate #479

Merged
merged 8 commits into from
Jan 11, 2021
Merged

fix simulate #479

merged 8 commits into from
Jan 11, 2021

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dilpath
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@dilpath dilpath commented Oct 22, 2020

TODOs

  • default noise distribution wasn't handled in some cases
  • ensure synthetic data file rows are ordered as in the measurements file
    • should be done by the specific simulator (e.g. AMICI)
  • add option to ensure synthetic data is non-negative (can become negative after noise is added)

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codecov bot commented Oct 22, 2020

Codecov Report

Merging #479 (9f4d0e6) into master (d948970) will decrease coverage by 0.03%.
The diff coverage is 71.42%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #479      +/-   ##
==========================================
- Coverage   78.03%   78.00%   -0.04%     
==========================================
  Files          23       23              
  Lines        2295     2300       +5     
  Branches      544      546       +2     
==========================================
+ Hits         1791     1794       +3     
- Misses        369      370       +1     
- Partials      135      136       +1     
Impacted Files Coverage Δ
petab/simulate.py 78.84% <71.42%> (-2.01%) ⬇️

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@dilpath dilpath changed the title fix default noise distribution fix simulate Oct 23, 2020
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sonarcloud bot commented Nov 6, 2020

Kudos, SonarCloud Quality Gate passed!

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities (and Security Hotspot 0 Security Hotspots to review)
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@dilpath dilpath requested a review from dweindl November 6, 2020 01:09
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@dilpath dilpath requested a review from dweindl January 10, 2021 21:00
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petab/simulate.py Outdated Show resolved Hide resolved
Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
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sonarcloud bot commented Jan 11, 2021

Kudos, SonarCloud Quality Gate passed!

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@dweindl dweindl merged commit 91612f0 into master Jan 11, 2021
@dweindl dweindl deleted the fix_simulate branch January 11, 2021 22:20
dweindl added a commit that referenced this pull request Jan 11, 2021
Default noise distribution wasn't handled in some cases

Add option to ensure synthetic data is non-negative (can become negative after noise is added)

* fix default noise distribution

* switch to pandas isna

* Return negative values by default.

* change non-negative argument to zero-bounded

* docs, set random seed

Co-authored-by: dilpath <59329744+dilpath@users.noreply.github.com>
Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
jvanhoefer added a commit that referenced this pull request Jan 12, 2021
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2 participants