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Add w to root signature#1404

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dilpath merged 3 commits intodevelopfrom
fix_root_headers
Feb 6, 2021
Merged

Add w to root signature#1404
dilpath merged 3 commits intodevelopfrom
fix_root_headers

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@dilpath
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@dilpath dilpath commented Feb 5, 2021

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@FFroehlich
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This will be a bit more tricky since

  • you have to touch the cpp code that calls the generated function
  • the signature is now different from what is used in MATLAB so either that needs to be updated or we need another pythonGenerated switch

Alternatively, a simple subs(zip(self._syms['w'], self._eqs['w'])) applied to the root function may do the trick.

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codecov bot commented Feb 5, 2021

Codecov Report

Merging #1404 (bd4bca4) into develop (bb9706c) will increase coverage by 0.04%.
The diff coverage is n/a.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    #1404      +/-   ##
===========================================
+ Coverage    78.66%   78.71%   +0.04%     
===========================================
  Files           63       63              
  Lines        10008    10008              
===========================================
+ Hits          7873     7878       +5     
+ Misses        2135     2130       -5     
Flag Coverage Δ
cpp 75.24% <ø> (+0.07%) ⬆️
petab 69.48% <ø> (ø)
python 67.72% <ø> (ø)
sbmlsuite 90.88% <ø> (ø)

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

Impacted Files Coverage Δ
python/amici/ode_export.py 92.77% <ø> (ø)
src/sundials_matrix_wrapper.cpp 83.61% <0.00%> (-0.22%) ⬇️
src/spline.cpp 71.57% <0.00%> (+6.31%) ⬆️

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sonarqubecloud bot commented Feb 5, 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

@dilpath
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dilpath commented Feb 6, 2021

Alternatively, a simple subs(zip(self._syms['w'], self._eqs['w'])) applied to the root function may do the trick.

Thanks a lot for the quick fix! Works well in my case.

@dilpath dilpath merged commit 0a85246 into develop Feb 6, 2021
@dilpath dilpath deleted the fix_root_headers branch February 6, 2021 13:00
@dweindl dweindl mentioned this pull request Feb 19, 2021
dweindl added a commit that referenced this pull request Feb 20, 2021
….13)

Breaking changes:
* AMICI requires Python>=3.7
* Updated package installation (PEP517/518): 
  Creating source distributions requires https://github.com/pypa/build (#1384)
  (but now handles all package building dependencies properly)

Features:
* More flexible state reinitialization (#1417)

Updated dependencies:
* Upgrade to sundials 5.7.0 (#1392)

Fixes:
* Python: account for heaviside functions in expressions (#1382)
* Python: allow loading of existing models in import_petab_problem (#1383)
* Python: Don't override user-provided compiler/linker flags (#1389)
* Python: PEtab import reinitialization fixes (#1417)
* Python: Fix PEtab observables for pysb models (#1390)
* Python: Substitute expressions in event condition expressions (#1404)
* Python: Unspecified initial states in PEtab conditions table default to SBML initial value (#1397)
* C++: Fix timepoint out of bounds access (#1402)
* C++: Fix exported CMake config (#1388)
* Fixed Dockerfile: add python3-venv (#1398, #1408)

Other:
* Slim exported swig interface (#1425)
* Updated documentation
    * Getting started tutorial (#1423)
    * List supported SBML test tags (#1428)
    * Add AMICI C++/Python/Matlab feature comparison (#1409)
    * ...
* Various minor CI improvements
* ...
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