Upgrade cvode

[spco]

No description provided.

[spco]

Should this be a breaking change, or perhaps use preprocessor directives? It might be useful to change the wiki to tell users to install cvode into a cvode2/3 directory.

[codecov]

Codecov Report

Merging #286 into master will increase coverage by 0.02%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #286      +/-   ##
==========================================
+ Coverage   89.89%   89.91%   +0.02%     
==========================================
  Files          14       14              
  Lines        2009     2013       +4     
==========================================
+ Hits         1806     1810       +4     
  Misses        203      203

Flag	Coverage Δ
#build	65.01% <37.5%> (-0.1%)	⬇️
#tests	89.36% <100%> (+0.02%)	⬆️
#unittests	30.5% <25%> (-0.02%)	⬇️

Impacted Files	Coverage Δ
src/atchem2.f90	91.63% <100%> (+0.13%)	⬆️
src/outputFunctions.f90	88.15% <100%> (ø)	⬆️

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[rs028]

Are we dealing with different versions of CVODE or we just ignore that and let the user deal with it if they need to rerun older models? Probably the latter would be the less messy solution.

[spco]

The latter is certainly the less messy and easiest from a development point of view. I'd suggest we go with that, but it might sway us into having to make this a 2.0 release, perhaps? It's quite a big compatibility change.

[rs028]

You mean this PR was not meant to be merged with #303? I am not exceedingly worried about the versioning, tbh.

I think it is okay to overwrite CVODE with the new version. We just have to document the behaviour. Users who want to use a previous version of either Atchem or CVODE are probably also skilled enough to install them by themselves.

[spco]

Upon reflection, I think this should probably go into v1.1 actually, so it can go before #303. I agree with your rationale for not caring about backwards compatibility at this stage.

[spco]

So unfortunately this seems to break the carefully-balanced behaviour tests in quite a few places. Essentially, the solver change means we get differences in 8 linux tests (and 1 of the MacOS for good measure too). I'm not sure that I want to go through the whole rigmarole of tweaking the tests to pass - that seems rather a backwards way to do things. Perhaps it's better that I do some more unit testing and then focus on getting some of the exact-solution tests out of the door?

[rs028]

Yes, I think that would make more sense. I don't mind postponing the upgrade to CVODE. I'd rather have solid results.