Refactoring and clean-up of legacy code

[alkino]

Here is the list of what to do to clean code.

• Use CLI11 Improved Command Line with CLI11 #179
• remove sdprintf Remove sdprintf #255
• Stop generating files in sources Stop creating test files in source dir #256
• Remove dead code enclose in #if 0 Remove dead code #257
• Put Random123 as submodule Remove Random123 source code but include as submodule #243 Random123 as a submodule #258
• Use bool instead of int 0 / 1 clean code: Use bool instead of int #259
• Remove code related to model duplication factor (-z,--multiple, -x,--extracon command line argument) #291 Remove code related to extra connection and model duplication
• Get rid of warnings from CoreNeuron code
• Use $MPIEXEC for jenkins instead of mpirun
• Use static cast instead of old C style cast
• Remove obvious aliases - Datum, Symbol, Pfri
• remove C style fixed length string/arrays
• assert(!busy_); -> nrn_assert(!busy_);
• replace async(_nt->stream_id) with async(stream_id)
• Clean integration tests mechanism
• Would be nice if we could avoid these ifdefs:

#ifdef _OPENMP
void Phase1::populate(NrnThread& nt, int imult, OMP_Mutex& mut) {
#else
void Phase1::populate(NrnThread& nt, int imult) {
#endif

• Use fstream instead of File*
• Use tie for .first, .second assignment

- [ ] For AoS increment pointer instead of using indexes : we will deprecate AoS separately (soon)
- [ ] Get rid of warnings from generated code : we shouldn't worry about mod2c as it will be replaced by NMODL
- [ ] nrnmpi_pgvts_least remove? : will need it for cvode so we can it for now
- [ ] Use spdlog? #180 CNEUR-22 : there is separate ticket for logging

[alkino]

@pramodk About « nrnmpi_pgvts_least remove? », nobody use it.
Maybe this function is used from outside world?
Are you sure no VERBATIM code use it?

[nrnhines]

nrnmpi_pgvts_least is used by cvode which does not exist (yet) in CoreNEURON.

[alkino]

@pramodk @nrnhines @ohm314 do you agree to use spdlog instead of printf / fprintf?

[ohm314]

I'm definitely in favor of using spdlog and fmt to clean up all logging and string formatting.

[pramodk]

@alkino : I have updated/re-ordered some of the tasks above. With #283 out of the way, this can be now taken up.

[alkino]

I close this, because last items are no more relevant

[nrnhines]

do you agree to use spdlog

First I've heard of it. After a quick look, the benefits seem worth it. It was not clear to me if logging could be turned off.

[alkino]

Yes it can.