mech_api.h: expose more declarations to translated MOD files

[alexsavulescu]

Include more headers in mech_api.h. This means that when updating MOD files to be compatible with C++ / #1597 then we can assume that NEURON-internal methods do not need to be declared for versions >=8.2.

As a brief reminder of the plan:

• 8.2 comes from master after this PR is merged
• 9.0 comes from master after Compile NEURON mechanisms as C++ #1597 is merged

In this PR:

• mcell_ran4_init, mcell_ran4, ... are declared
  • Note that MOD files that include incorrect declarations of mcell_ran4_init exist in ModelDB (example: https://github.com/ModelDBRepository/106891/blob/7f825c80ef3a76fb181607a346de730b8f740005/stats.mod#L56), and exposing the correct declaration breaks compilation.
• ivoc_list_item is declared
• hoc_get_symbol is declared
  • As above, this breaks some MOD files (example: https://github.com/ModelDBRepository/116862/blob/02f5832973fbf15b5fad210e5e6afd8d0e5eb651/misc.h#L75) that included incorrect declarations of this method.
• cvode_fadvance, clear_event_queue, ... are declared

(description by @olupton, don't blame @alexsavulescu for it)

[alexsavulescu]

also need

extern void mcell_ran4_init(uint32_t idum);
extern double mcell_ran4(unsigned int* idum,double* ran_vec,unsigned int n,double range);

[nrnhines]

mcell_ran4(unsigned int* idum, ...
This does not look right to me. I would expect it to be uint32_t idum

[olupton]

Also need

extern uint32_t nrnRan4int(uint32_t* idx1, uint32_t idx2);

[iomaganaris]

Also

extern Symbol *hoc_get_symbol(char *);

is needed

[olupton]

I think we want

nrn/src/oc/hocdec.h

Lines 234 to 238 in 571ab16

	#if defined(__cplusplus)
	cTemplate* ctemplate;
	#else
	cTemplate* template;
	#endif

to change in this PR too, so that this member is called ctemplate in 8.2.0. Then we can use #ifndef NRN_VERSION_GTEQ_8_2_0 instead of #ifdef __cplusplus.

[olupton]

With the current state of this PR there is a problem with ivoc_list_item: if oc_ansi.h is included in a C mechanism then it is expected to have C linkage, but the definition in src/ivoc/oclist.cpp includes oc_ansi.h as C++ and therefore exports a C++ linkage version of the function.

To fix this, we should move ivoc_list_item into the extern "C" block in the header so that for NEURON 8.2 this function always has C linkage.

[olupton]

mcell_ran4(unsigned int* idum, ... This does not look right to me. I would expect it to be uint32_t idum

I think the problem is not the type but the (unhelpful) parameter name. In the definition it's called high:
https://github.com/neuronsimulator/nrn/blob/d0fb3b38f7c717c1283c94fb02770ff6fee3a4c0/src/oc/mcran4.cpp#L57

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 47.05%. Comparing base (7b2a888) to head (695c99e).
Report is 1770 commits behind head on master.

Files with missing lines	Patch %	Lines
src/ivoc/oclist.cpp	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1825   +/-   ##
=======================================
  Coverage   47.05%   47.05%           
=======================================
  Files         543      543           
  Lines      112949   112949           
=======================================
  Hits        53143    53143           
  Misses      59806    59806           

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[olupton]

Other possible additions:

• cvode_fadvance
• clear_event_queue

[pramodk]

LGTM!

@nrnhines: we are ready to merge this and get 8.2a tagged today. Before we do this, do you have anything that you would like to have in 8.2a?

[nrnhines]

anything that you would like to have in 8.2a?

As formatting is a nice feature, it would be nice to merge #1820