Combine code for sparse model functions and their index files

[dweindl]

Combine code for sparse model functions and their index files, i.e. generate only a single file instead of 3 individual files for content, rowvals, and colptrs, respectively.

Advantage: Faster import of smaller models and fewer files. For a toy model, this reduced the build steps from 44 to 28, and reduced build time by >20% on my computer.

Disadvantage: None found, so I don't think it worth adding an option for (not) combining those files. For larger models, there shouldn't be any impact. The extra time for compiling the index arrays should be negligible compared to computing the contents.

Related to #2119

[codecov]

Codecov Report

Merging #2159 (59143c7) into develop (16aad6f) will decrease coverage by 22.52%.
The diff coverage is 100.00%.

Additional details and impacted files

@@             Coverage Diff              @@
##           develop    #2159       +/-   ##
============================================
- Coverage    76.74%   54.23%   -22.52%     
============================================
  Files           82       34       -48     
  Lines        14943     5585     -9358     
============================================
- Hits         11468     3029     -8439     
+ Misses        3475     2556      -919     

Flag	Coverage Δ
cpp	?
petab	54.23% <100.00%> (-0.03%)	⬇️
python	?
sbmlsuite	∅ <ø> (∅)

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

Files Changed	Coverage Δ
python/sdist/amici/de_export.py	78.68% <100.00%> (-13.08%)	⬇️

... and 65 files with indirect coverage changes

[FFroehlich]

I think, historically, this slowed down compilation of larger models

[dweindl]

I think, historically, this slowed down compilation of larger models

Will double-check

[dweindl]

Here a test for a large model (N=1):

File	Size	Compilation time (s)
dwdx	22.4MiB	3413.64
dwdx_colptrs	2.0KiB	2.79
dwdx_rowvals	65.6KiB	2.66
combined		3416.79

I'd consider this time increase negligible.