Speedup conservation law computation #1754

FFroehlich · 2022-04-03T02:35:49Z

So it turns out, using sum for symbolic variables is a really bad idea (see sympy/sympy#13945).

Tested on a model with ~8k species.
Previous:

2022-04-02 20:52:20.502 - amici.pysb_import - INFO - Finished computing PySB conservation laws    + (3.17E+03s)

Now:

2022-04-03 09:30:18.220 - amici.pysb_import - INFO - Finished computing PySB conservation laws    + (1.90E+02s)

codecov · 2022-04-03T02:47:44Z

Codecov Report

Merging #1754 (836391f) into develop (da56a08) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff            @@
##           develop    #1754   +/-   ##
========================================
  Coverage    77.76%   77.77%           
========================================
  Files           74       74           
  Lines        12012    12012           
========================================
+ Hits          9341     9342    +1     
+ Misses        2671     2670    -1

Flag	Coverage Δ
cpp	`74.87% <ø> (+0.01%)`	⬆️
petab	`59.26% <0.00%> (ø)`
python	`68.20% <100.00%> (ø)`

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

Impacted Files	Coverage Δ
python/amici/pysb_import.py	`93.90% <100.00%> (ø)`
src/sundials_matrix_wrapper.cpp	`80.08% <0.00%> (-0.45%)`	⬇️
src/solver_cvodes.cpp	`70.43% <0.00%> (+0.16%)`	⬆️
src/exception.cpp	`81.08% <0.00%> (+5.40%)`	⬆️