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Make DEModel._sparsesyms symbols sympy.Symbols#2894

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dweindl merged 2 commits intoAMICI-dev:mainfrom
dweindl:fix_1061
Jul 22, 2025
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Make DEModel._sparsesyms symbols sympy.Symbols#2894
dweindl merged 2 commits intoAMICI-dev:mainfrom
dweindl:fix_1061

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@dweindl dweindl commented Jul 9, 2025

Previously, sparse matrix symbols in DEModel._sparsesyms were strings, as opposed to other model "syms" which were sympy.Symbol. Make that consistent.

Fixes #1061.

@dweindl dweindl self-assigned this Jul 9, 2025
@dweindl dweindl force-pushed the fix_1061 branch 2 times, most recently from 963a0cc to 94723c9 Compare July 9, 2025 12:17
@dweindl dweindl changed the title Fix #1061 Fix incorrect types in DEModel._syms Jul 9, 2025
@dweindl dweindl changed the title Fix incorrect types in DEModel._syms Fix incorrect types in DEModel._sparsesyms Jul 9, 2025
@dweindl dweindl force-pushed the fix_1061 branch 2 times, most recently from c62cbe6 to c1a2693 Compare July 9, 2025 12:49
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codecov bot commented Jul 9, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.98%. Comparing base (34043c6) to head (218c1a6).
⚠️ Report is 51 commits behind head on main.

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@@            Coverage Diff             @@
##             main    #2894      +/-   ##
==========================================
- Coverage   79.55%   78.98%   -0.57%     
==========================================
  Files         362      362              
  Lines       23106    23104       -2     
  Branches     1587     1587              
==========================================
- Hits        18381    18248     -133     
- Misses       4714     4845     +131     
  Partials       11       11              
Flag Coverage Δ
cpp 74.90% <100.00%> (-0.01%) ⬇️
cpp_python 33.18% <100.00%> (-0.01%) ⬇️
petab 38.89% <100.00%> (-0.01%) ⬇️
python 73.76% <100.00%> (-0.01%) ⬇️
sbmlsuite-jax ?

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

Files with missing lines Coverage Δ
python/sdist/amici/cxxcodeprinter.py 95.57% <100.00%> (ø)
python/sdist/amici/de_export.py 97.23% <100.00%> (-0.02%) ⬇️
python/sdist/amici/de_model.py 92.43% <100.00%> (-0.43%) ⬇️
python/sdist/amici/de_model_components.py 91.27% <ø> (-1.75%) ⬇️

... and 4 files with indirect coverage changes

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@dweindl dweindl changed the title Fix incorrect types in DEModel._sparsesyms Make DEModel._sparsesyms symbols sympy.Symbols Jul 10, 2025
@dweindl dweindl marked this pull request as ready for review July 10, 2025 08:17
@dweindl dweindl requested a review from a team as a code owner July 10, 2025 08:17
@dweindl dweindl enabled auto-merge July 10, 2025 08:17
Previously, sparse matrix symbols in `DEModel._sparsesyms` were strings, as opposed to other model "syms" which were `sympy.Symbol`. Make that consistent.

Fixes AMICI-dev#1061.
@dweindl dweindl added this pull request to the merge queue Jul 22, 2025
Merged via the queue into AMICI-dev:main with commit e366c5b Jul 22, 2025
24 of 25 checks passed
@dweindl dweindl deleted the fix_1061 branch July 22, 2025 10:56
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Use symbolic comparison when writing header files in ode_export

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