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Update list of papers using AMICI #1509

Merged
merged 3 commits into from
May 28, 2021
Merged

Update list of papers using AMICI #1509

merged 3 commits into from
May 28, 2021

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dweindl
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@dweindl dweindl commented May 28, 2021

Closes #1504

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codecov bot commented May 28, 2021 •
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Codecov Report

Merging #1509 (52758a5) into develop (e805411) will decrease coverage by 2.86%.
The diff coverage is n/a.

❗ Current head 52758a5 differs from pull request most recent head 42f99df. Consider uploading reports for the commit 42f99df to get more accurate results
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@@             Coverage Diff             @@
##           develop    #1509      +/-   ##
===========================================
- Coverage    79.46%   76.60%   -2.87%     
===========================================
  Files           67       23      -44     
  Lines        10399     3420    -6979     
===========================================
- Hits          8264     2620    -5644     
+ Misses        2135      800    -1335
Flag Coverage Δ
cpp ?
petab 67.66% <ø> (ø)
python ?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
python/amici/pandas.py 10.96% <0.00%> (-87.10%) ⬇️
python/amici/pysb_import.py 57.19% <0.00%> (-36.70%) ⬇️
python/amici/import_utils.py 69.76% <0.00%> (-30.24%) ⬇️
python/amici/numpy.py 65.67% <0.00%> (-16.42%) ⬇️
python/amici/setuptools.py 50.00% <0.00%> (-7.70%) ⬇️
python/amici/__init__.py 83.58% <0.00%> (-7.47%) ⬇️
python/amici/parameter_mapping.py 69.91% <0.00%> (-6.20%) ⬇️
python/amici/gradient_check.py 82.60% <0.00%> (-5.44%) ⬇️
python/amici/ode_export.py 88.23% <0.00%> (-4.92%) ⬇️
python/amici/sbml_import.py 93.98% <0.00%> (-2.06%) ⬇️
... and 45 more

@dweindl dweindl requested a review from dilpath May 28, 2021 19:06
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dilpath approved these changes May 28, 2021
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documentation/amici_refs.bib Outdated Show resolved Hide resolved
documentation/references.md
<p>Sten, Sebastian, Henrik Podéus, Nicolas Sundqvist, Fredrik Elinder, Maria Engström, and Gunnar Cedersund. 2021. “A Multi-Data Based Quantitative Model for the Neurovascular Coupling in the Brain.” <em>bioRxiv</em>. <a href="https://doi.org/10.1101/2021.03.25.437053">https://doi.org/10.1101/2021.03.25.437053</a>.</p>
</div>
<div id="ref-VanhoeferMat2021">
<p>Vanhoefer, Jakob, Marta R. a. Matos, Dilan Pathirana, Yannik Schälte, and Jan Hasenauer. 2021. “Yaml2sbml: Human-Readable and -Writable Specification of Ode Models and Their Conversion to Sbml.” <em>Journal of Open Source Software</em> 6 (61): 3215. <a href="https://doi.org/10.21105/joss.03215">https://doi.org/10.21105/joss.03215</a>.</p>
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Suggested change
<p>Vanhoefer, Jakob, Marta R. a. Matos, Dilan Pathirana, Yannik Schälte, and Jan Hasenauer. 2021. “Yaml2sbml: Human-Readable and -Writable Specification of Ode Models and Their Conversion to Sbml.” <em>Journal of Open Source Software</em> 6 (61): 3215. <a href="https://doi.org/10.21105/joss.03215">https://doi.org/10.21105/joss.03215</a>.</p>
<p>Vanhoefer, Jakob, Marta R. A. Matos, Dilan Pathirana, Yannik Schälte, and Jan Hasenauer. 2021. “yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML.” <em>Journal of Open Source Software</em> 6 (61): 3215. <a href="https://doi.org/10.21105/joss.03215">https://doi.org/10.21105/joss.03215</a>.</p>

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Is this generated automatically from the .bib? There, the title is capitalized as in the publication.

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Yes, it's auto-generated. With the current solution, it's unfortunately not easily possible to change the style. Maybe needs to be rewritten at some point.

documentation/references.md
@@ -15,13 +18,22 @@ If you applied AMICI in your work and your publication is missing, please let us
<div id="ref-StaedterSch2021">
<p>Städter, Philipp, Yannik Schälte, Leonard Schmiester, Jan Hasenauer, and Paul L. Stapor. 2021. “Benchmarking of Numerical Integration Methods for Ode Models of Biological Systems.” <em>Scientific Reports</em> 11 (1): 2696. <a href="https://doi.org/10.1038/s41598-021-82196-2">https://doi.org/10.1038/s41598-021-82196-2</a>.</p>
</div>
<div id="ref-StenPod2021">
<p>Sten, Sebastian, Henrik Podéus, Nicolas Sundqvist, Fredrik Elinder, Maria Engström, and Gunnar Cedersund. 2021. “A Multi-Data Based Quantitative Model for the Neurovascular Coupling in the Brain.” <em>bioRxiv</em>. <a href="https://doi.org/10.1101/2021.03.25.437053">https://doi.org/10.1101/2021.03.25.437053</a>.</p>
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Is it intentional that many publications appear to have the first author as [Last Name], [First Name] then subsequent authors as [First Name] [Last Name]?

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Not my favorite, but that's what pandoc-citeproc does :)

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How about also adding https://arxiv.org/abs/2105.12008 and https://www.biorxiv.org/content/10.1101/2021.05.20.445065v1.abstract ?

@dweindl dweindl removed the request for review from paulstapor May 28, 2021 20:06
@dweindl dweindl merged commit 95d40ed into develop May 28, 2021
@dweindl dweindl deleted the update_refs branch May 28, 2021 20:10
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sonarcloud bot commented May 28, 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
No Duplication information No Duplication information

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@dilpath dilpath dilpath approved these changes

@FFroehlich FFroehlich FFroehlich approved these changes

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