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

bnet.mod

@@ -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
 }
@@ -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
@@ -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);
     }
@@ -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;
@@ -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);
@@ -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",
@@ -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);

misc.h

@@ -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>
 
@@ -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);
@@ -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;
@@ -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);
-
-
-
-
-

misc.mod

@@ -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()
@@ -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);
 
@@ -85,7 +86,6 @@ FUNCTION sassign() {
 VERBATIM
     FILE *pipein;
     char string[BUFSIZ], **strname, *syscall;
-    char** hoc_pgargstr();
 
     strname = hoc_pgargstr(1);
     syscall = gargstr(2);
@@ -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': "); 
@@ -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

readme.html

@@ -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>