NEURON 8.2+ compatibility.

misc.h

@@ -1,11 +1,11 @@
 // $Id: misc.h,v 1.33 2010/06/05 15:32:28 billl Exp $
-
+#include <stdint.h> /* uint32_t */
 #include <stdlib.h>
 #include <math.h>
 #include <limits.h> /* contains LONG_MAX */
 #include <time.h>
-#include <sys/time.h> 
-#ifdef __APPLE__&__MACH__
+#include <sys/time.h>
+#if defined(__APPLE__) && defined(__MACH__)
  #include <float.h>
 #else
  #include <values.h>
@@ -57,15 +57,14 @@ 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 unsigned int  dcrsz;
 extern double       *dcr;
 extern double       *dcrset(int);
@@ -76,6 +75,7 @@ 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);
@@ -91,14 +91,12 @@ 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 unsigned int valseed;
-extern void mcell_ran4_init(unsigned int *idum);
-extern double mcell_ran4(unsigned int* idum,double* ran_vec,unsigned int n,double range);
+extern void mcell_ran4_init(uint32_t);
+extern double mcell_ran4(uint32_t* high, 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);
@@ -108,19 +106,29 @@ extern Symbol *hoc_lookup(const char*);
 extern Point_process* ob2pntproc(Object*);
 
 extern char* hoc_object_name(Object*);
-extern int cmpdfn();
-extern int openvec(int, double **);
-int list_vector_px();
-double *list_vector_resize();
-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();
+extern int hoc_is_tempobj(int narg);
+extern int hoc_is_tempobj_arg(int narg);
+#endif
+ListVec* AllocListVec(Object* p);
+ListVec* AllocILV(Object*, int, double *);
+int cmpdfn(double a, double b);
+void dshuffle(double* x, int nx);
+void FreeListVec(ListVec** pp);
+static void hxe() { hoc_execerror("",0); }
+int IsList(Object* p);
+int list_vector_px(Object *ob, int i, double** px);
+int list_vector_px2(Object *ob, int i, double** px, void** vv);
+int list_vector_px3(Object *ob, int i, double** px, void** vv);
+int list_vector_px4(Object *ob, int i, double** px, unsigned int n);
+double* list_vector_resize(Object *ob, int i, int sz);
+int openvec(int, double **);
+int uniq2(int n, double *x, double *y, double *z);
+double *vector_newsize(void* vv, int n);
 
 static double sc[6];
 static FILE*  testout;

misc.mod

@@ -49,7 +49,7 @@ VERBATIM
 #include <time.h>
 #include <stdio.h>
 #include <limits.h>
-extern int hoc_is_tempobj(int narg);
+#include "misc.h"
 ENDVERBATIM
 
 :* FUNCTION file_exist()
@@ -59,10 +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;
-
-    filename = gargstr(1);
-
+    char* filename = gargstr(1);
     if (*filename && !access(filename, F_OK)) {
         _lfile_exist = 1;
 
@@ -86,19 +83,19 @@ PROCEDURE sassign() {
 VERBATIM
     FILE *pipein;
     char string[BUFSIZ], **strname, *syscall;
-    char** hoc_pgargstr();
 
     strname = hoc_pgargstr(1);
     syscall = gargstr(2);
 
     if( !(pipein = popen(syscall, "r"))) {
         fprintf(stderr,"System call failed\n");
-        return; 
+        return 0;
     }
 
     if (fgets(string,BUFSIZ,pipein) == NULL) {
         fprintf(stderr,"System call did not return a string\n");
-        pclose(pipein); return;
+        pclose(pipein);
+        return 0;
     }
 
     /*  assign_hoc_str(strname, string, 0); */
@@ -121,17 +118,20 @@ VERBATIM
 
     if ( !(outfile = fopen("dassign","w"))) {
         fprintf(stderr,"Can't open output file dassign\n");
-        return; 
+        return 0;
     }
 
     if( !(pipein = popen(syscall, "r"))) {
         fprintf(stderr,"System call failed\n");
-        fclose(outfile); return; 
+        fclose(outfile);
+        return 0;
     }
 
     if (fscanf(pipein,"%lf",&num) != 1) {
         fprintf(stderr,"System call did not return a number\n");
-        fclose(outfile); pclose(pipein); return; 
+        fclose(outfile);
+        pclose(pipein);
+        return 0;
     }
 
     fprintf(outfile,"%s=%g\n",strname,num);
@@ -215,8 +215,7 @@ 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.txt

@@ -23,3 +23,8 @@ For questions/comments contact Sam Neymotin:
   or
  samn at neurosim dot downstate dot edu
 
+Changelog
+---------
+2022-05: 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.

stats.mod

@@ -41,6 +41,7 @@ ASSIGNED { seed }
 
 VERBATIM
 #include "misc.h"
+#include <stdint.h> /* uint32_t, uintptr_t */
 #define MIN_MERGESORT_LIST_SIZE    32
 
 union dblint {
@@ -50,7 +51,7 @@ union dblint {
 
 unsigned int valseed;
 static double *x1x, *y1y, *z1z;
-static void vprpr();
+static void vprpr(double x, int base);
 
 static int compare_ul(const void* l1, const void* l2) {
   int retval;
@@ -381,7 +382,7 @@ FUNCTION rpval () {
   // the way to be robust. The scheme used in spearmanr is probably better.
   TINY = 1.0e-20;
   ts = r*sqrt(df/((1.0-r+TINY)*(1.0+r+TINY)));
-  mpval = betai(0.5*df,0.5,df/(df+ts*ts));
+  mpval = betai(_threadargscomma_ 0.5*df,0.5,df/(df+ts*ts));
   return mpval;
   ENDVERBATIM
 }
@@ -424,11 +425,9 @@ static double* getrank (int n, double mdata[])
  * a memory allocation error, it returns NULL.
  */
 { int i;
-  double* rank;
-  int* index;
-  rank = malloc(n*sizeof(double));
+  double* rank = (double*)malloc(n*sizeof(double));
   if (!rank) return NULL;
-  index = malloc(n*sizeof(int));
+  int* index = (int*)malloc(n*sizeof(int));
   if (!index)
   { free(rank);
     return NULL;
@@ -468,11 +467,9 @@ static double spearman(int n, double* data1, double* data2)
   double denom1 = 0.;
   double denom2 = 0.;
   double avgrank;
-  double* tdata1;
-  double* tdata2;
-  tdata1 = malloc(n*sizeof(double));
+  double* tdata1 = (double*)malloc(n*sizeof(double));
   if(!tdata1) return 0.0; /* Memory allocation error */
-  tdata2 = malloc(n*sizeof(double));
+  double* tdata2 = (double*)malloc(n*sizeof(double));
   if(!tdata2) /* Memory allocation error */
   { free(tdata1);
     return 0.0;
@@ -643,7 +640,7 @@ int qsort2 (double *p1in, double* p2in, int n,double* p1out,double* p2out) {
   int i;
   scr=scrset(n);
   for (i=0;i<n;i++) scr[i]=i;
-  nrn_mlh_gsort(p1in, scr, n, cmpdfn);
+  nrn_mlh_gsort(p1in, (int*)scr, n, cmpdfn);
   for (i=0;i<n;i++) {
     p1out[i]=p1in[scr[i]];
     p2out[i]=p2in[scr[i]];
@@ -861,8 +858,8 @@ static double hash (void* vv) {
       } else   {  xx.d=vvo[j][i]; }
       if (xx.i[0]==0) { xx.i[0]=xx.i[1]; xx.i[0]<<=4; } // high order bits may be 0
       if (xx.i[1]==0) { xx.i[1]=xx.i[0]; xx.i[1]<<=4; } // low order bits unlikely 0
-      mcell_ran4_init(&xx.i[1]);
-      mcell_ran4(&xx.i[0], &y, 1, big); // generate a pseudorand number based on these
+      mcell_ran4_init(xx.i[1]);
+      mcell_ran4((uint32_t*)&xx.i[0], &y, 1, big); // generate a pseudorand number based on these
       prod*=y;  // keep multiplying these out
     }
     if (! vfl) x[i]=prod; else return prod; // just return the 1 value
@@ -1043,7 +1040,7 @@ static double setrnd (void* vv) {
       scrset(nex);
       x1x = (double *)realloc(x1x,sizeof(double)*nx*4);
       for (i=0;i<nex;i++) scr[i]=i;
-      nrn_mlh_gsort(ex, scr, nex, cmpdfn);
+      nrn_mlh_gsort(ex, (int*)scr, nex, cmpdfn);
       for (i=0;i<nex;i++) x1x[i]=ex[scr[i]];
       for (i=0;i<nex;i++) ex[i]=x1x[i];
     }
@@ -1446,7 +1443,7 @@ static double rantran (void* vv) {
   int i,j,ix,ixe,ixvn,nvn,rvn,na,xj;
   double *ixv, *nv, *x, y[1], ixn,step,indx;
   rvn=vector_instance_px(vv, &x);
-  for (na=1;ifarg(na);na++); na--; // count args
+  for (na=1;ifarg(na);na++) {} na--; // count args
   for (i=1;i<na;i+=2) {
     if (hoc_is_object_arg(i)) {
       step=-1;
@@ -1664,6 +1661,7 @@ static double vpr2 (void* vv) {
     }
     printf("\n");
   }
+  return 0.0;
 }
 
 static void vprpr (double x, int base) {
@@ -2025,8 +2023,8 @@ unsigned int hashseed2 (int na, double* x) {
     if (xx.i[0]==0) { xx.i[0]=xx.i[1]; xx.i[0]<<=4; } // high order bits may be 0
     if (xx.i[1]==0) { xx.i[1]=xx.i[0]; xx.i[1]<<=4; } // low order bits unlikely 0
     xx.i[0]+=(i+1); xx.i[1]+=(i+1); // so different for different order args
-    mcell_ran4_init(&xx.i[1]);
-    mcell_ran4(&xx.i[0], &y, 1, big); // generate a pseudorand number based on these
+    mcell_ran4_init(xx.i[1]);
+    mcell_ran4((uint32_t*)&xx.i[0], &y, 1, big); // generate a pseudorand number based on these
     while (y>UINT_MAX) y/=1e9; // UINT_MAX is 4.294967e+09
     valseed*=(unsigned int)y;  // keep multiplying these out
   }
@@ -2091,7 +2089,7 @@ FUNCTION mc4seed () {
   for (i=2;ifarg(i);i++) {
     valseed*=(unsigned int)(*getarg(i));
   }
-  mcell_ran4_init(&valseed); // do initialization
+  mcell_ran4_init(valseed); // do initialization
   return valseed;
   ENDVERBATIM
 }
@@ -2119,16 +2117,14 @@ FUNCTION gammln (xx) {
 FUNCTION betai(a,b,x) {
 VERBATIM {
   double bt;
-  double gammln(),betacf();
-
   if (_lx < 0.0 || _lx > 1.0) {printf("Bad x in routine BETAI\n"); hxe();}
   if (_lx == 0.0 || _lx == 1.0) bt=0.0;
   else
-  bt=exp(gammln(_la+_lb)-gammln(_la)-gammln(_lb)+_la*log(_lx)+_lb*log(1.0-_lx));
+  bt=exp(gammln(_threadargscomma_ _la+_lb)-gammln(_threadargscomma_ _la)-gammln(_threadargscomma_ _lb)+_la*log(_lx)+_lb*log(1.0-_lx));
   if (_lx < (_la+1.0)/(_la+_lb+2.0))
-  return bt*betacf(_la,_lb,_lx)/_la;
+  return bt*betacf(_threadargscomma_ _la,_lb,_lx)/_la;
   else
-  return 1.0-bt*betacf(_lb,_la,1.0-_lx)/_lb;
+  return 1.0-bt*betacf(_threadargscomma_ _lb,_la,1.0-_lx)/_lb;
  }
 ENDVERBATIM
 }
@@ -2193,10 +2189,9 @@ FUNCTION tstat() {
 
 FUNCTION tdistrib() {
   VERBATIM
-  double gammln();
   double x = *getarg(1);
   double dof = *getarg(2);
-  double res = (gammln( (dof+1.0) / 2.0 )  / gammln( dof / 2.0 ) );
+  double res = (gammln(_threadargscomma_ (dof+1.0) / 2.0 )  / gammln(_threadargscomma_ dof / 2.0 ) );
   double pi = 3.14159265358979323846;
   res *= (1.0 / sqrt( dof * pi ) );
   res *= pow((1 + x*x/dof),-1.0*((dof+1.0)/2.0));