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MOD-C-2-CPP: Compatibility fixed for NEURON 9.0, 8.2 and 8.1 #1

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merged 10 commits into from
May 27, 2022
Merged

MOD-C-2-CPP: Compatibility fixed for NEURON 9.0, 8.2 and 8.1 #1

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6cbd79d
MOD-C-2-CPP: Compatibility fixed for NEURON 9.0, 8.2 and 8.1
pramodk May 16, 2022
39ab0e5
Update vecst.mod
alkino May 18, 2022
2f9ff34
fix
alkino May 18, 2022
1348b88
fixup for latest 8.2 wheels, c++17 fwd compat, declare less in 8.2+
olupton May 18, 2022
b8ef422
consistent argument type for vector_newsize
olupton May 19, 2022
92ac8f8
hide more declarations of NEURON methods in 8.2+
olupton May 19, 2022
7c83a1f
Cleanup for merge.
olupton May 23, 2022
2fe1b8f
Object member is called template in C in 8.2
olupton May 23, 2022
01cedc8
mcell_ran4_init: pass a value
olupton May 24, 2022
884803b
mcell_ran4_init: update readme
olupton May 24, 2022
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28 changes: 13 additions & 15 deletions bnet.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -105,21 +105,21 @@ brule* addrule (boonet* pnet, double* psrc, int targid, double weight, double* p
int idx,i;
if(pnet->prules == 0x0) { // take care of memory allocation
pnet->rulebufsz = 16;
pnet->prules = calloc(pnet->rulebufsz, sizeof(brule) );
pnet->prules = (struct BRULE*) calloc(pnet->rulebufsz, sizeof(brule) );
pnet->nrules = 0;
} else if(pnet->nrules >= pnet->rulebufsz) {
pnet->rulebufsz *= 2;
pnet->prules = realloc(pnet->prules, pnet->rulebufsz * sizeof(brule) );
pnet->prules = (struct BRULE*) realloc(pnet->prules, pnet->rulebufsz * sizeof(brule) );
}
idx = pnet->nrules;
pnet->prules[idx].nsrc = nsrc; // set # of sources
pnet->prules[idx].ptarg = &pnet->pnodes[targid]; // set target
pnet->prules[idx].weight = weight; // set weight
// set the sources
pnet->prules[idx].psrc = calloc(nsrc, sizeof(bnode*));
pnet->prules[idx].psrc = (struct BNODE **) calloc(nsrc, sizeof(bnode*));
for(i=0;i<nsrc;i++) pnet->prules[idx].psrc[i] = &pnet->pnodes[(int)psrc[i]];
// set source state for rule to be 'on'
pnet->prules[idx].psrcstate = calloc(nsrc, sizeof(int));
pnet->prules[idx].psrcstate = (int *) calloc(nsrc, sizeof(int));
for(i=0;i<nsrc;i++) pnet->prules[idx].psrcstate[i] = (int) psrcstate[i];
return &pnet->prules[ pnet->nrules++ ]; // return the new rule and inc # rules
}
Expand Down Expand Up @@ -193,7 +193,7 @@ CONSTRUCTOR {
printf("BNET err0: must have a network with positive # of nodes!\n");
hxe();
}
_p_sop = (void*) makeboonet(sz);
_p_sop = (double*) makeboonet(sz);
pnet = BP;
pnet->id = ifarg(2) ? (int) *getarg(2) : 0;
ENDVERBATIM
Expand Down Expand Up @@ -267,7 +267,7 @@ PROCEDURE pr () {
if(prule->psrc[j]->name) {
sprintf(stmp,"%s%s%s ", j>0?"AND ":"", prule->psrcstate[j]?"":"!", prule->psrc[j]->name);
} else {
sprintf(stmp,"%s%s%s ", j>0?"AND ":"", prule->psrcstate[j]?"":"!", prule->psrc[j]->id);
sprintf(stmp,"%s%s%d ", j>0?"AND ":"", prule->psrcstate[j]?"":"!", prule->psrc[j]->id);
}
strcat(srcstr,stmp);
}
Expand All @@ -288,13 +288,12 @@ FUNCTION graphviz () {
int i, j, k, LR, fsz, w, h;
bnode* pnodes = BP->pnodes;
brule* prule;
char *ncolor, *fcolor, *arrowtype, *lstyle, *shape;//node color, font color, arrow type, line style, node shape
char buf[4096], *dotname, *fname, *ext, fontsize[128];
char buf[4096], *dotname, *fname, fontsize[128];
double penw; // penwidth
FILE* fp = 0x0;
dotname = ifarg(1) ? gargstr(1) : 0x0;
fname = ifarg(2) ? gargstr(2) : 0x0;
ext = ifarg(3) ? gargstr(3) : "gif";
const char* ext = ifarg(3) ? gargstr(3) : "gif";
LR = ifarg(4) ? (int) *getarg(4) : 1;
w = ifarg(5) ? (int) *getarg(5) : -1;
h = ifarg(6) ? (int) *getarg(6) : -1;
Expand All @@ -308,9 +307,9 @@ FUNCTION graphviz () {
if(LR){sprintf(buf, "%s", "\trankdir=LR;\n"); if(fp) fprintf(fp,"%s",buf); else fprintf(stdout,"%s",buf); }
if(w>0 && h>0) {sprintf(buf, "size=\"%d,%d\"\n",w,h); if(fp) fprintf(fp,"%s",buf); else fprintf(stdout,"%s",buf);}
for(i=0;i<BP->numnodes;i++) {
ncolor = BP->pnodes[i].knockout ? "white" : BP->pnodes[i].state > 0 ? "black" : "gray";
fcolor = BP->pnodes[i].knockout ? "black" : "white";
shape = pnodes[i].sthresh > 0 ? "invtriangle" : "doublecircle";
const char* ncolor = BP->pnodes[i].knockout ? "white" : BP->pnodes[i].state > 0 ? "black" : "gray";
const char* fcolor = BP->pnodes[i].knockout ? "black" : "white";
const char* shape = pnodes[i].sthresh > 0 ? "invtriangle" : "doublecircle";
if(BP->pnodes[i].name) {
sprintf(buf,"\t%s [fontcolor=%s,%sstyle=filled,shape=%s,fillcolor=%s,color=%s]\n",
BP->pnodes[i].name,fcolor,fontsize,shape,ncolor,ncolor);
Expand All @@ -324,8 +323,8 @@ FUNCTION graphviz () {
prule = &BP->prules[i];
for(j=0;j<prule->nsrc;j++) {
penw = prule->psrcstate[j] == prule->psrc[j]->state ? 6.0 : 1.0;
arrowtype = prule->weight < 0 ? "tee" : "open";
lstyle = prule->psrcstate[j] == 0 ? ",style=dashed" : " ";
const char* arrowtype = prule->weight < 0 ? "tee" : "open";
const char* lstyle = prule->psrcstate[j] == 0 ? ",style=dashed" : " ";
if(prule->psrc[j]->name) {
if(prule->ptarg->name) {
sprintf(buf,"\t%s -> %s [arrowhead=%s,penwidth=%g,color=%s%s]\n",
Expand Down Expand Up @@ -613,7 +612,6 @@ FUNCTION setnname () {
FUNCTION getnname () {
VERBATIM
int i, id, sz; char **pname, string[BUFSIZ];
char** hoc_pgargstr();
id = (int) *getarg(1);
if(id < 0 || id >= BP->numnodes) {
printf("BNET.getnname ERR0: invalid node index %d\n",id);
Expand Down
39 changes: 18 additions & 21 deletions misc.h
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
#include <math.h>
#include <limits.h> /* contains LONG_MAX */
#include <time.h>
#include <sys/time.h>
#include <sys/time.h>
#include <float.h>
#include <pthread.h>

Expand Down Expand Up @@ -54,15 +54,15 @@ typedef unsigned char ui1; /* one byte unsigned integer */
typedef char si1; /* one byte signed integer */
typedef unsigned short ui2; /* two byte unsigned integer */
typedef short si2; /* two byte signed integer */
typedef unsigned int ui4; /* four byte unsigned integer */
typedef int si4; /* four byte signed integer */
typedef float sf4; /* four byte signed floating point number */
typedef double sf8; /* eight byte signed floating point number */
typedef unsigned int ui4; /* four byte unsigned integer */
typedef int si4; /* four byte signed integer */
typedef float sf4; /* four byte signed floating point number */
typedef double sf8; /* eight byte signed floating point number */

extern double ERR,GET,SET,OK,NOP,ALL,NEG,POS,CHK,NOZ,GTH,GTE,LTH,LTE,EQU;
extern double EQV,EQW,EQX,NEQ,SEQ,RXP,IBE,EBI,IBI,EBE;

extern double *vector_newsize();
extern double *vector_newsize(void* v, int n);
extern unsigned int dcrsz;
extern double *dcr;
extern double *dcrset(int);
Expand All @@ -73,50 +73,52 @@ extern unsigned int iscrsz;
extern int *iscr;
extern int *iscrset(int);
extern double BVBASE;
#ifndef NRN_VERSION_GTEQ_8_2_0
extern double* hoc_pgetarg();
extern void hoc_notify_iv();
extern double hoc_call_func(Symbol*, int narg);
extern FILE* hoc_obj_file_arg(int narg);
extern Object** hoc_objgetarg();
char *gargstr();
char** hoc_pgargstr();
extern void vector_resize();
extern int vector_instance_px();
extern void* vector_arg();
extern double* vector_vec();
extern int vector_buffer_size(void*);
extern double hoc_epsilon;
extern int stoprun;
extern void set_seed();
extern void dshuffle(double* x,int nx);
extern void mcell_ran4_init(u_int32_t);
extern double mcell_ran4(u_int32_t *idx1, double *x, unsigned int n, double range);
extern int nrn_mlh_gsort();
extern int ivoc_list_count(Object*);
extern Object* ivoc_list_item(Object*, int);
extern int list_vector_px2();
extern int hoc_is_double_arg(int narg);
extern int hoc_is_str_arg(int narg);
extern int hoc_is_object_arg(int narg);
extern int hoc_is_pdouble_arg(int narg);
extern int hoc_is_tempobj_arg(int narg);
extern Symbol *hoc_get_symbol(char *);
extern Symbol *hoc_lookup(const char*);
extern Point_process* ob2pntproc(Object*);

extern char* hoc_object_name(Object*);
extern int cmpdfn();
#endif
extern void dshuffle(double* x,int nx);
int uniq2(int, double*, double*, double*);
extern int cmpdfn(double, double);
extern int openvec(int, double **);
int list_vector_px();
double *list_vector_resize();
int list_vector_px(Object*, int, double**);
int list_vector_px2(Object *, int, double**, IvocVect**);
int list_vector_px3(Object*, int, double**, IvocVect**);
int list_vector_px4(Object *ob, int i, double** px, unsigned int n);
double *list_vector_resize(Object *ob, int i, int sz);
static void hxe() { hoc_execerror("",0); }
extern void FreeListVec(ListVec** pp);
extern ListVec* AllocListVec(Object* p);
extern ListVec* AllocILV(Object*, int, double *);
void FillListVec(ListVec* p,double dval);
void ListVecResize(ListVec* p,int newsz);
extern short *nrn_artcell_qindex_;
extern double nrn_event_queue_stats(double*);
extern void clear_event_queue();
int IsList(Object*);

static double sc[6];
static FILE* testout;
Expand All @@ -132,8 +134,3 @@ extern double ismono1 (double *x, int n, int flag);
double kcorfast(double* input1, double* input2, double* i1d , double* i2d,int n,double* ps);
double Rktau (double* x, double* y, int n); // R version
double kcorfast (double* input1, double* input2, double* i1d , double* i2d,int n,double* ps);





11 changes: 5 additions & 6 deletions misc.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -41,14 +41,15 @@ NEURON {
}

VERBATIM
#include "misc.h"

#include <unistd.h> /* F_OK */
#include <errno.h> /* errno */
#include <signal.h>
#include <sys/types.h> /* MUST REMEMBER THIS */
#include <time.h>
#include <stdio.h>
#include <limits.h>
extern int hoc_is_tempobj(int narg);
ENDVERBATIM

:* FUNCTION file_exist()
Expand All @@ -58,7 +59,7 @@ VERBATIM
errno else will get a nrnoc error. Seems to be a problem even
if I don't include <errno.h> */

char *gargstr(), *filename;
char *filename;

filename = gargstr(1);

Expand All @@ -85,7 +86,6 @@ FUNCTION sassign() {
VERBATIM
FILE *pipein;
char string[BUFSIZ], **strname, *syscall;
char** hoc_pgargstr();

strname = hoc_pgargstr(1);
syscall = gargstr(2);
Expand Down Expand Up @@ -197,7 +197,7 @@ VERBATIM
size_t x,y;
x=(size_t)_lsz;
pmlc=(char *)malloc(x);
printf("Did %ld: %x\n",x,pmlc);
printf("Did %ld: %p\n",x,pmlc);
y=(unsigned int)_lsz-1;
pmlc[y]=(char)97;
printf("WRITE/READ 'a': ");
Expand All @@ -217,8 +217,7 @@ ENDVERBATIM
FUNCTION hocgetc() {
VERBATIM
{
FILE* f, *hoc_obj_file_arg();
f = hoc_obj_file_arg(1);
FILE* f = hoc_obj_file_arg(1);
_lhocgetc = (double)getc(f);
}
ENDVERBATIM
Expand Down
5 changes: 5 additions & 0 deletions readme.html
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Original file line number Diff line number Diff line change
Expand Up @@ -98,6 +98,11 @@
For questions/comments email: samuel dot neymotin at yale dot edu or
samn at neurosim dot downstate dot edu

<b>Changelog:</b>

20160920 This updated version from the Lytton lab allows this model to
run on the mac.
20220523 Updated MOD files to contain valid C++ and be compatible with
the upcoming versions 8.2 and 9.0 of NEURON. Updated to use post ~2011
signature of mcell_ran4_init function.
</pre></html>
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