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@dweindl dweindl commented Feb 28, 2020

File format:

  • Updated documentation
  • Observables table in YAML file now mandatory in schema (was implicitly
    mandatory before, as observable table was required already)

Library:

dweindl and others added 21 commits February 21, 2020 13:28
* replace relative links in readme

* cont

* write script to generate absolute links in setup
* make libcombine optional

* add combine dep to github actions wf
…ting with ind_meas (Closes #322)



Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
More consistent terminology
* add basic docs on rtd

* fix errors

* fix errors

* ignore tmp files
* change all barplot colors to blue

* adjust angle for barplot ticks
implement scatterplots

* implementing scatter plots (resolves #263)
putting xScale=order in docs

* barplot: fix noise, legend

* make scatterplots square
* gitignore tmp files

* fix docs

* add residual computation function

* fix flake8

* extend test coverage

* address reviewer comments

* fix codacy

* make codacy happier
* gitignore tmp files

* fix docs

* add residual computation function

* fix flake8

* extend test coverage

* address reviewer comments

* fix codacy

* make codacy happier

* allow parametric noise formulas

* address reviewer comments
* allow to compute chi2 values

* add docs

* fix w602 errors

* fix docstring coverage

* fix codacy warnings
* allow to compute chi2 values

* add docs

* init llh

* fix w602 errors

* fix docstring coverage

* fix codacy warnings

* allow calculating likelihoods

* fixup

* add documentation

* fix codacy
* Fix / refactor parameter mapping (breaking change)

Fixes #342

Parameter value and parameter scale mapping now always done together.
Fixed handling of parameter scale for non-estimated scaled parameters.


Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
* check optional measurement cols in mapping

* fix typos

* fix usage of unused measurement cols
* check optional measurement cols in mapping

* fix typos

* fix usage of unused measurement cols

* define output
* Clarify YAML problems specification (Closes #301)

* Update Fujita example to new observable table format

Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
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codecov bot commented Feb 28, 2020

Codecov Report

Merging #357 into master will increase coverage by 0.57%.
The diff coverage is n/a.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #357      +/-   ##
==========================================
+ Coverage   76.63%   77.21%   +0.57%     
==========================================
  Files          22       23       +1     
  Lines        1849     2032     +183     
  Branches      411      452      +41     
==========================================
+ Hits         1417     1569     +152     
- Misses        329      348      +19     
- Partials      103      115      +12     
Impacted Files Coverage Δ
petab/calculate.py 89.14% <0.00%> (ø)
petab/lint.py 76.61% <0.00%> (+2.41%) ⬆️

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docs build script needs to be fixed, otherwise good to go

@dweindl dweindl merged commit 7b9d189 into master Feb 28, 2020
@dweindl dweindl deleted the release_0.1.3 branch February 28, 2020 18:18
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