From 5753ed3f2c9d8a81e73540cd6a3ba4a2fe008abf Mon Sep 17 00:00:00 2001
From: Ioannis Magkanaris <iomagkanaris@gmail.com>
Date: Mon, 16 May 2022 15:19:55 +0200
Subject: [PATCH 01/23] Fix infot.mod

---
 infot.mod | 26 ++++++++++++++++----------
 misc.h    |  2 +-
 2 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/infot.mod b/infot.mod
index 60c86f6..6fd71b4 100644
--- a/infot.mod
+++ b/infot.mod
@@ -29,7 +29,9 @@ VERBATIM
 #include <stdlib.h>
 #include <math.h>
 static const double* ITsortdata = NULL; /* used in the quicksort algorithm */
-static double tetrospks2(), pdfpr(), tetrospks3();
+static double tetrospks2 (double* X1d,double* X2d,double* XO,int szX1,int szXO,int shuf);
+static void pdfpr (double* pdf,int szp,int dim, char* name);
+static double tetrospks3 (double* X1d,double* X2d,double* X3d,double* XO,int szX1,int szXO,int shuf);
 static int dbxi[10];
 
 typedef struct ITNode_ {
@@ -42,9 +44,9 @@ typedef struct ITNode_ {
 
 ITNode* allocITNode(int idims) {
   ITNode* p;
-  p = calloc(1,sizeof(ITNode));
+  p = (ITNode*)calloc(1,sizeof(ITNode));
   if(!p) { printf("allocITNode: out of mem!\n"); hxe(); return 0x0; }
-  p->pvals = calloc(idims,sizeof(int));
+  p->pvals = (int*)calloc(idims,sizeof(int));
   return p;
 }
 
@@ -395,6 +397,8 @@ static double lz76c (void* vv) {
   return lz76complexityd(x,n);
 }
 
+extern void ishuffle(int* x,int nx);
+
 //* tentropd() transfer entropy of y -> x
 //x=time-series 1, y=time-series 2,iLen=# of samples,nbins=# of values to discretize time-series to,
 //xpast=# of past x values to use for prediction,ypast=# of past y values to use for prediction
@@ -508,7 +512,7 @@ double tentropd (double* x,double* y,int iLen,int nbins,int xpast,int ypast,int
       }
       if(verbose>1) {printf("cntjxy=%d\n",cntjxy);
         for(i=0;i<cntjxy;i++) {
-          printf("pjointxy%d: [");
+          printf("pjointxy: [");
           for(j=0;j<jointd;j++) printf("%d ",pjointxy[i][j]);
           printf("] , cnt=%d, p=%g\n",pjointxy[i][jointd],pjointxy[i][jointd]/(double)N);
         }
@@ -723,7 +727,7 @@ static double tentropspks (void* vv) {
   szXO=ifarg(2)?vector_arg_px(2,&XO):0;
   shuf=ifarg(3)?((int)*getarg(3)):0;
   szX3=ifarg(4)?vector_arg_px(4,&X3):0;
-  if(szX3) tetrospks3(X1,X2,X3,XO,szX1,szXO,shuf);
+  if(szX3) return tetrospks3(X1,X2,X3,XO,szX1,szXO,shuf);
   else return tetrospks2(X1,X2,XO,szX1,szXO,shuf);
 }
 
@@ -758,6 +762,8 @@ NTEL2DOFREE:
   return ret;
 }
 
+extern int list_vector_px3 (Object *ob, int i, double** px, void** vv);
+
 //*** Vind0.nte(Vind1,LIST,OUTVEC or OUTLIST) // do normalization with H(X2F|X2P)
 static double nte (void* vv) {
   int i, j, k, ii, jj, oi, nx, ny, omax, sz, ci, bg, flag, nshuf, szX, *x1i, *x2i, x1z, x2z;
@@ -870,7 +876,7 @@ static double entropxfgxp (void* vv) {
   int sz,minv,maxv,cnt,i,j,szp,*X;
   sz = vector_instance_px(vv,&x);
   cnt=0;
-  X=scrset(sz);
+  X=iscrset(sz);
   minv=1e9; maxv=-1e9;
   for (i=0;i<sz;i++) { 
     X[i]=(int)x[i]; 
@@ -1165,7 +1171,7 @@ static double tetrospks2 (double* X1d,double* X2d,double* XO,int szX1,int szXO,i
 }
 
 // for debugging -- print out a pdf
-static double pdfpr (double* pdf,int szp,int dim, char* name) {
+static void pdfpr (double* pdf,int szp,int dim, char* name) {
   double x,ds; int i,j,k,l,m,cnt,*nonzero;
   ds=0.; 
   printf("Contents of PDF %s\n",name);
@@ -1306,9 +1312,9 @@ static double* ITgetrank (int n, double mdata[])
 { int i;
   double* rank;
   int* index;
-  rank = calloc(n,sizeof(double));
+  rank = (double*)calloc(n,sizeof(double));
   if (!rank) return NULL;
-  index = calloc(n,sizeof(int));
+  index = (int*)calloc(n,sizeof(int));
   if (!index)
   { free(rank);
     return NULL;
@@ -1400,7 +1406,7 @@ double entropspksd (double* x,int sz) {
   ret=-1.0; err=0;
   px=NULL; 
   minv=1000000000; maxv=-1000000000;
-  X=scrset(sz*2); // move into integer arrays
+  X=iscrset(sz*2); // move into integer arrays
   cnt=0;
   for (i=0;i<sz;i++) { 
     X[i]=(int)x[i]; 
diff --git a/misc.h b/misc.h
index 40bebca..2e7ed9f 100644
--- a/misc.h
+++ b/misc.h
@@ -107,7 +107,7 @@ extern char* hoc_object_name(Object*);
 extern int cmpdfn();
 extern int openvec(int, double **);
 int list_vector_px();
-double *list_vector_resize();
+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);

From 1df7e71c5d54436a85ff78db2afdb3f20f2e1e71 Mon Sep 17 00:00:00 2001
From: Christos Kotsalos <christos.kotsalos@epfl.ch>
Date: Mon, 16 May 2022 14:50:37 +0200
Subject: [PATCH 02/23] =?UTF-8?q?=E2=80=9Cinitial=E2=80=9D?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 infot.mod | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/infot.mod b/infot.mod
index 6fd71b4..846e3ac 100644
--- a/infot.mod
+++ b/infot.mod
@@ -876,7 +876,7 @@ static double entropxfgxp (void* vv) {
   int sz,minv,maxv,cnt,i,j,szp,*X;
   sz = vector_instance_px(vv,&x);
   cnt=0;
-  X=iscrset(sz);
+  X=scrset(sz);
   minv=1e9; maxv=-1e9;
   for (i=0;i<sz;i++) { 
     X[i]=(int)x[i]; 
@@ -1406,7 +1406,7 @@ double entropspksd (double* x,int sz) {
   ret=-1.0; err=0;
   px=NULL; 
   minv=1000000000; maxv=-1000000000;
-  X=iscrset(sz*2); // move into integer arrays
+  X=scrset(sz*2); // move into integer arrays
   cnt=0;
   for (i=0;i<sz;i++) { 
     X[i]=(int)x[i]; 

From c5d5eb4bedb2f2539070b554e43e3cc33a7ad7f0 Mon Sep 17 00:00:00 2001
From: Christos Kotsalos <christos.kotsalos@epfl.ch>
Date: Mon, 16 May 2022 16:29:51 +0200
Subject: [PATCH 03/23] fixing for neuron 9.0

---
 clampex.mod | 14 ++++++++++----
 field.mod   |  2 +-
 infot.mod   | 24 ++++++++++++------------
 intf_.mod   | 10 +++++-----
 misc.h      |  1 +
 vecst.mod   | 10 +++++-----
 6 files changed, 34 insertions(+), 27 deletions(-)

diff --git a/clampex.mod b/clampex.mod
index c1c958a..71ea7c5 100644
--- a/clampex.mod
+++ b/clampex.mod
@@ -9,7 +9,9 @@ ASSIGNED {
 }
 
 VERBATIM
+#ifndef NRN_VERSION_GTEQ_8_2_0
 extern double chkarg();
+#endif
 
 typedef struct CEXData {
 #if 1
@@ -31,7 +33,7 @@ typedef struct CEXData {
 }CEXData;
 #define CEXD CEXData* cexd = (CEXData*)((unsigned long)pointer);
 	
-static void reverse(b, n ) char* b; int n; {
+static void reverse(char* b, int n) {
 	int i, j, v_;
 	for (i=0, j=n-1; i<j; ++i, --j) {
 		v_ = b[i];
@@ -40,7 +42,7 @@ static void reverse(b, n ) char* b; int n; {
 	}
 }
 
-static void header_endian(h) char* h; {
+static void header_endian(char* h) {
 	char* b;
 	int i;
 	b = h;
@@ -59,7 +61,7 @@ static void header_endian(h) char* h; {
 	}
 }
 
-static double get_parm(i, h) int i; char* h; {
+static double get_parm(int i, char* h) {
 	char* b;
 	float* f;
 	long* n;
@@ -143,8 +145,12 @@ FUNCTION parm() {
 
 PROCEDURE datavec() {
 	VERBATIM
+	#ifndef NRN_VERSION_GTEQ_8_2_0
+	double* hoc_pgetarg();
+	#endif
+
 	int ntrace, trace, i, length;
-	double* pd, *hoc_pgetarg();
+	double* pd;
 	short* tr;
 	CEXD
 	length = (int)get_parm(3, cexd->header);
diff --git a/field.mod b/field.mod
index a73b5c2..5f2818b 100644
--- a/field.mod
+++ b/field.mod
@@ -3,7 +3,7 @@
 VERBATIM
 #include "misc.h"
 #define NSW 5  // store into this many ww field vecs
-static void*   ww[NSW];
+static IvocVect*   ww[NSW];
 static double* wwo[NSW];
 static int ixp1;
 ENDVERBATIM
diff --git a/infot.mod b/infot.mod
index 846e3ac..f922108 100644
--- a/infot.mod
+++ b/infot.mod
@@ -34,6 +34,10 @@ static void pdfpr (double* pdf,int szp,int dim, char* name);
 static double tetrospks3 (double* X1d,double* X2d,double* X3d,double* XO,int szX1,int szXO,int shuf);
 static int dbxi[10];
 
+static double tetrospks2 (double* X1d,double* X2d,double* XO,int szX1,int szXO,int shuf);
+static void pdfpr (double* pdf,int szp,int dim, char* name);
+static double tetrospks3 (double* X1d,double* X2d,double* X3d,double* XO,int szX1,int szXO,int shuf);
+
 typedef struct ITNode_ {
   int idims;
   int icount;
@@ -397,8 +401,6 @@ static double lz76c (void* vv) {
   return lz76complexityd(x,n);
 }
 
-extern void ishuffle(int* x,int nx);
-
 //* tentropd() transfer entropy of y -> x
 //x=time-series 1, y=time-series 2,iLen=# of samples,nbins=# of values to discretize time-series to,
 //xpast=# of past x values to use for prediction,ypast=# of past y values to use for prediction
@@ -721,7 +723,7 @@ static double ntedir (void* vv) {
 // of X1spikecounts,X2spikecounts onto X3spikecounts
 static double tentropspks (void* vv) {
   double *X1,*X2,*XO,*X3; int szX1,szX2,szXO,shuf,szX3;
-  szX1 = vector_instance_px(vv,&X1);
+  szX1 = vector_instance_px((IvocVect*)vv,&X1);
   if((szX2=vector_arg_px(1,&X2))!=szX1) {
     printf("tentropspks ERRA: X1,X2 must have same size (%d,%d)\n",szX1,szX2); return -1.0; }
   szXO=ifarg(2)?vector_arg_px(2,&XO):0;
@@ -762,13 +764,11 @@ NTEL2DOFREE:
   return ret;
 }
 
-extern int list_vector_px3 (Object *ob, int i, double** px, void** vv);
-
 //*** Vind0.nte(Vind1,LIST,OUTVEC or OUTLIST) // do normalization with H(X2F|X2P)
 static double nte (void* vv) {
   int i, j, k, ii, jj, oi, nx, ny, omax, sz, ci, bg, flag, nshuf, szX, *x1i, *x2i, x1z, x2z;
-  ListVec *pLi; Object *obi,*ob;  double *x, *y, *out, o1, o2, cnt, *vvo[3]; void *vvl;
-  nx = vector_instance_px(vv, &x); // index i vector
+  ListVec *pLi; Object *obi,*ob;  double *x, *y, *out, o1, o2, cnt, *vvo[3]; IvocVect *vvl;
+  nx = vector_instance_px((IvocVect*)vv, &x); // index i vector
   ny = vector_arg_px(1, &y);       // index j vectors
   pLi = AllocListVec(obi=*hoc_objgetarg(2)); // input vectors
   ob =   *hoc_objgetarg(3);
@@ -873,10 +873,10 @@ double entropxfgxpd (double* pXP, double* pXFXP,int minv,int maxv,int szp) {
 // Vector has elements of X
 static double entropxfgxp (void* vv) {
   double *x,*pXP,*pXFXP,dret;
-  int sz,minv,maxv,cnt,i,j,szp,*X;
-  sz = vector_instance_px(vv,&x);
+  int sz,minv,maxv,cnt,i,j,szp;
+  sz = vector_instance_px((IvocVect*)vv,&x);
   cnt=0;
-  X=scrset(sz);
+  unsigned int* X=scrset(sz);
   minv=1e9; maxv=-1e9;
   for (i=0;i<sz;i++) { 
     X[i]=(int)x[i]; 
@@ -1400,13 +1400,13 @@ static double mutinfb (void* v) {
 
 double entropspksd (double* x,int sz) {
   double *px,ret,dinf,size;
-  int i,*X,maxv,minv,cnt,err;
+  int i,maxv,minv,cnt,err;
   if(sz<1) {printf("entropspks ERR0: min size must be > 0!\n"); return -1.0;}
   size=(double)sz;
   ret=-1.0; err=0;
   px=NULL; 
   minv=1000000000; maxv=-1000000000;
-  X=scrset(sz*2); // move into integer arrays
+  unsigned int* X=scrset(sz*2); // move into integer arrays
   cnt=0;
   for (i=0;i<sz;i++) { 
     X[i]=(int)x[i]; 
diff --git a/intf_.mod b/intf_.mod
index 80b9b69..38fa8aa 100644
--- a/intf_.mod
+++ b/intf_.mod
@@ -121,7 +121,7 @@ void*    ww[NSW];
 double* wwo[NSW];
 static int AM=0, NM=1, GA=2, GB=3, SU=3, IN=4, DP=2; // from labels.hoc
 static double wts[10],hsh[10];  // for jitcons to use as a junk pointer
-static int spkoutf2();
+static void spkoutf2();
 ENDVERBATIM
 
 :* NEURON, PARAMETER, ASSIGNED blocks
@@ -323,7 +323,7 @@ unsigned int GetDVIDSeedVal(unsigned int id) {
   } else { 
     if (seadsetting==2) printf("Warning: GetDVIDSeedVal called with wt rand turned off\n");
     x[0]=(double)id; x[1]=seaddvioff;
-    sead=hashseed2(2,&x);
+    sead=hashseed2(2,x);
   }
   return sead;
 }
@@ -414,7 +414,7 @@ ENDVERBATIM
           sead=(unsigned int)(floor(_lflag)*ip->id*seedstep); // all integers
         } else { // hash on presynaptic id+FOFFSET,poid,seedstep
           hsh[0]=floor(_lflag); hsh[1]=(double)ip->id; hsh[2]=seedstep;
-          sead=hashseed2(3,&hsh); // hsh[] is just scratch pad
+          sead=hashseed2(3,hsh); // hsh[] is just scratch pad
         }
         mcell_ran4(&sead, &_args[sy], 2, 1.);
         for (ii=sy;ii<sy+2;ii++) { // scale appropriately; 
@@ -834,7 +834,7 @@ ENDVERBATIM
 }
 
 VERBATIM
-static int spkoutf2 () {
+static void spkoutf2 () {
     fprintf(wf1,"//b9 -2 t%0.2f %ld %ld\n",t/1e3,jrj,ftell(wf2));
     fwrite(jrtv,sizeof(double),jrj,wf2); // write times
     fwrite(jrid,sizeof(double),jrj,wf2); // write id
@@ -1095,7 +1095,7 @@ FUNCTION getdvi () {
             sead=(unsigned int)(FOFFSET+ip->id)*qp->id*seedstep; 
           } else { // hashed sead setting
             hsh[0]=(double)(FOFFSET+ip->id); hsh[1]=(double)(qp->id); hsh[2]=seedstep;
-            sead=hashseed2(3,&hsh); 
+            sead=hashseed2(3,hsh); 
           }
           mcell_ran4(&sead, y, 2, 1.);
           for(ii=0;ii<2;ii++) {
diff --git a/misc.h b/misc.h
index 2e7ed9f..1456cb8 100644
--- a/misc.h
+++ b/misc.h
@@ -61,6 +61,7 @@ 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 void ishuffle(int* x,int nx);
 extern double *vector_newsize();
 extern unsigned int  dcrsz;
 extern double       *dcr;
diff --git a/vecst.mod b/vecst.mod
index d191865..2bd5a89 100644
--- a/vecst.mod
+++ b/vecst.mod
@@ -2091,28 +2091,28 @@ int list_vector_px (Object *ob, int i, double** px) {
 
 //* list_vector_px2(LIST,ITEM#,DOUBLE PTR ADDRESS,VEC POINTER ADDRESS) 
 //  returns the vector pointer as well as the double pointer
-int list_vector_px2 (Object *ob, int i, double** px, void** vv) {
+int list_vector_px2 (Object *ob, int i, double** px, IvocVect** vv) {
   Object* obv;
   int sz;
   obv = ivoc_list_item(ob, i);
   if (! ISVEC(obv)) return -1;
   sz = vector_capacity(obv->u.this_pointer);
   *px = vector_vec(obv->u.this_pointer);
-  *vv = (void*) obv->u.this_pointer;
+  *vv = (IvocVect*) obv->u.this_pointer;
   return sz;
 }
 
 //* list_vector_px3(LIST,ITEM#,DOUBLE PTR ADDRESS,VEC POINTER ADDRESS) 
 //  same as px2 but returns max vec size instead of current vecsize
 //  side effect -- increase vector size to maxsize
-int list_vector_px3 (Object *ob, int i, double** px, void** vv) {
+int list_vector_px3 (Object *ob, int i, double** px, IvocVect** vv) {
   Object* obv;
   int sz;
   obv = ivoc_list_item(ob, i);
   if (! ISVEC(obv)) return -1;
   sz = vector_buffer_size(obv->u.this_pointer);
   *px = vector_vec(obv->u.this_pointer);
-  *vv = (void*) obv->u.this_pointer;
+  *vv = (IvocVect*) obv->u.this_pointer;
   vector_resize(*vv,sz);
   return sz;
 }
@@ -2399,7 +2399,7 @@ int openvec (int arg, double **y) {
 }
 
 // vector_newsize() will also increase size of vector
-double *vector_newsize (void* vv, int n) {
+double *vector_newsize (IvocVect* vv, int n) {
   vector_resize(vv,n);
   return vector_vec(vv);
 }

From 11afe8cc1aad23655ddc0f09da0ac7a6605fd7ed Mon Sep 17 00:00:00 2001
From: Christos Kotsalos <christos.kotsalos@epfl.ch>
Date: Mon, 16 May 2022 16:31:20 +0200
Subject: [PATCH 04/23] fixing for neuron 9.0

---
 driver.hoc  | 36 ++++++++++++++++++++++++++++++++++++
 misc.h      | 49 ++++++++++++++++++++++++++-----------------------
 netrand.inc |  2 +-
 3 files changed, 63 insertions(+), 24 deletions(-)
 create mode 100644 driver.hoc

diff --git a/driver.hoc b/driver.hoc
new file mode 100644
index 0000000..5cd147f
--- /dev/null
+++ b/driver.hoc
@@ -0,0 +1,36 @@
+
+strdef verify_dir_ 
+verify_dir_ = "/gpfs/bbp.cscs.ch/data/project/proj16/kotsalos/nrn_HACK/mdb/ncdemo"
+
+if (name_declared("verify_dir_") == 0) {
+	execute("~strdef verify_dir_")
+	execute("verify_dir_ = \".\"")
+}
+strdef verify_tstr_
+objref verify_glist_, verify_xvec_, verify_yvec_, verify_file_
+verify_file_ = new File()
+sprint(verify_tstr_, "%s/gout", verify_dir_)
+verify_file_.wopen(verify_tstr_)
+verify_xvec_ = new Vector()
+verify_yvec_ = new Vector()
+verify_glist_ = new List("Graph")
+
+proc verify_graph_() {local i, j, k
+	verify_file_.printf("Graphs %d\n", verify_glist_.count)
+	for i=0, verify_glist_.count-1 {
+		verify_file_.printf("%s\n", verify_glist_.object(i))
+		k = 0
+		for (j=-1; (j=verify_glist_.object(i).line_info(j, verify_xvec_)) != -1; ){
+			k += 1
+		}
+		verify_file_.printf("lines %d\n", k)
+		for (j=-1; (j=verify_glist_.object(i).getline(j, verify_xvec_, verify_yvec_)) != -1; ){
+			verify_file_.printf("points %d\n", verify_xvec_.size)
+			verify_file_.printf("xvec%d\n", j)
+			verify_xvec_.printf(verify_file_)
+			verify_file_.printf("yvec%d\n", j)
+			verify_yvec_.printf(verify_file_)
+		}
+	}
+}
+verify_graph_()
\ No newline at end of file
diff --git a/misc.h b/misc.h
index 1456cb8..586dff1 100644
--- a/misc.h
+++ b/misc.h
@@ -61,18 +61,8 @@ 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 void ishuffle(int* x,int nx);
-extern double *vector_newsize();
-extern unsigned int  dcrsz;
-extern double       *dcr;
-extern double       *dcrset(int);
-extern unsigned int  scrsz;
-extern unsigned int *scr;
-extern unsigned int *scrset(int);
-extern unsigned int  iscrsz;
-extern int *iscr;
-extern int *iscrset(int);
-extern double BVBASE;
+extern double *vector_newsize (IvocVect* vv, int n);
+#ifndef NRN_VERSION_GTEQ_8_2_0
 extern double* hoc_pgetarg();
 extern void hoc_notify_iv();
 extern double hoc_call_func(Symbol*, int narg);
@@ -85,17 +75,11 @@ 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 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 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);
@@ -103,12 +87,33 @@ extern int hoc_is_pdouble_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 double nrn_event_queue_stats(double*);
+extern void clear_event_queue();
+#endif
+extern unsigned int hashseed2 (int na, double* x);
+extern unsigned int  dcrsz;
+extern double       *dcr;
+extern double       *dcrset(int);
+extern unsigned int  scrsz;
+extern unsigned int *scr;
+extern unsigned int *scrset(int);
+extern unsigned int  iscrsz;
+extern int *iscr;
+extern int *iscrset(int);
+extern double BVBASE;
+extern double hoc_epsilon;
+extern int stoprun;
+extern void set_seed();
+extern void dshuffle(double* x,int nx);
+extern void ishuffle(int* x,int nx);
+extern unsigned int valseed;
+extern int list_vector_px2 (Object *ob, int i, double** px, IvocVect** vv);
+extern int list_vector_px3 (Object *ob, int i, double** px, IvocVect** vv);
 extern int cmpdfn();
 extern int openvec(int, double **);
-int list_vector_px();
-double *list_vector_resize (Object *ob, int i, int sz);
+int list_vector_px(Object *ob, int i, double** px);
+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);
@@ -116,8 +121,6 @@ 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();
 
 static double sc[6];
 static FILE*  testout;
diff --git a/netrand.inc b/netrand.inc
index 5737d41..1a2d7f0 100644
--- a/netrand.inc
+++ b/netrand.inc
@@ -51,7 +51,7 @@ INITIAL {
 CONSTRUCTOR {
 VERBATIM
   cbsv=0x0;
-  _p_sop = (void*)ecalloc(1, sizeof(id0)); // important that calloc sets all flags etc to 0
+  _p_sop = (double*)ecalloc(1, sizeof(id0)); // important that calloc sets all flags etc to 0
   ip = IDP;
 ENDVERBATIM
 }

From b0915063dbfe1fcb6daa5d12c4523a36d7e08acf Mon Sep 17 00:00:00 2001
From: Christos Kotsalos <christos.kotsalos@epfl.ch>
Date: Tue, 17 May 2022 14:12:45 +0200
Subject: [PATCH 05/23] more work

---
 intf_.mod    |  84 +++++++++++++++--------------
 intfsw.mod   |  23 ++++----
 misc.h       |  26 +++++++--
 misc.mod     |  16 +++---
 pregencv.mod |   2 +-
 stats.mod    |  40 +++++++-------
 updown.mod   |  25 +--------
 vecst.mod    | 150 ++++++++++++++++++++++++++-------------------------
 8 files changed, 185 insertions(+), 181 deletions(-)

diff --git a/intf_.mod b/intf_.mod
index 38fa8aa..cf3f9bc 100644
--- a/intf_.mod
+++ b/intf_.mod
@@ -18,6 +18,7 @@ ENDCOMMENT
 :* main VERBATIM block
 VERBATIM
 #include "misc.h"
+#include "unistd.h"
 static int ctt(unsigned int, char**);
 static int setdvi2(double*,double*,int,int);
 
@@ -122,6 +123,7 @@ double* wwo[NSW];
 static int AM=0, NM=1, GA=2, GB=3, SU=3, IN=4, DP=2; // from labels.hoc
 static double wts[10],hsh[10];  // for jitcons to use as a junk pointer
 static void spkoutf2();
+int gsort2 (double *db, Point_process **da,int dvt,double *dbs, Point_process **das);
 ENDVERBATIM
 
 :* NEURON, PARAMETER, ASSIGNED blocks
@@ -231,7 +233,7 @@ CONSTRUCTOR {
     if (ifarg(2)) { lty=(int) *getarg(2); } else { lty= -1; }
     if (ifarg(3)) { lin=(int) *getarg(3); } else { lin= -1; }
     if (ifarg(4)) { lco=(int) *getarg(4); } else { lco= -1; }
-    _p_sop = (void*)ecalloc(1, sizeof(id0)); // important that calloc sets all flags etc to 0
+    _p_sop = (double*)ecalloc(1, sizeof(id0)); // important that calloc sets all flags etc to 0
     ip = IDP;
     ip->id=lid; ip->type=lty; ip->inhib=lin; ip->col=lco; 
     ip->pg=0x0; ip->dvi=0x0; ip->sprob=0x0;
@@ -348,7 +350,7 @@ ENDVERBATIM
   VERBATIM
   if (stopoq && !qsz()) stoprun=1;
   ip=IDP; pg=ip->pg;
-  if (ip->dead) return; // this cell has died
+  if (ip->dead) return;
   _ljcn=ip->jcn; _lid=ip->id;
   tpnt = _pnt; // this pnt
   if (PATHMEASURE) { // do all code for this
@@ -910,7 +912,7 @@ PROCEDURE callback (fl) {
     if (jp->sprob[i]) (*pnt_receive[jp->dvi[i]->_prop->_type])(jp->dvi[i], wts, idty); 
     _p=upnt->_prop->param; _ppvar=upnt->_prop->dparam; // restore pointers
     i++;
-    if (i>=jp->dvt) return; // ran out
+    if (i>=jp->dvt) return 0; // ran out TODO:Ask Michel
     ddel=jp->del[i]-del0;   // delays are relative to event; use difference in delays
   }
   // skip over pruned outputs and dead cells:
@@ -934,7 +936,7 @@ VERBATIM {
   int i,j,k,prty,poty,dv,dvt,dvii; double *x, *db, *dbs; 
   Object *lb;  Point_process *pnnt, **da, **das;
   ip=IDP; pg=ip->pg; // this should be called right after jitcondiv()
-  if (ip->dead) return;
+  if (ip->dead) return 0; // TODO: Ask Michael
   prty=ip->type;
   sead=GetDVIDSeedVal(ip->id);//seed for divergence and delays
   for (i=0,k=0,dvt=0;i<CTYN;i++) { // dvt gives total divergence
@@ -1052,7 +1054,7 @@ FUNCTION getdvi () {
     void* voi, *voi2,*voi3; Point_process **das;
     ip=IDP; pg=ip->pg; // this should be called right after jitcondiv()
     getactive=a2=a3=a4=0;
-    if (ip->dead) return;
+    if (ip->dead) return 0; // TODO: Ask Michael
     dvt=ip->dvt;
     dbs=ip->del;   das=ip->dvi;
     _lgetdvi=(double)dvt; 
@@ -1067,13 +1069,13 @@ FUNCTION getdvi () {
     } else av1=1; // 1st vector arg
     //just get active postsynapses (not dead and non pruned)
     voi=vector_arg(iarg++); 
-    if (flag==2) { x1=vector_newsize(voi,CTYPi); for (i=0;i<CTYPi;i++) x1[i]=0;
-    } else x1=vector_newsize(voi,dvt);
-    if (ifarg(iarg)) { voi=vector_arg(iarg++); x2=vector_newsize(voi,dvt);  a2=1; }
-    if (ifarg(iarg)) { voi=vector_arg(iarg++); x3=vector_newsize(voi,dvt); a3=1;}
+    if (flag==2) { x1=vector_newsize((IvocVect*)voi,CTYPi); for (i=0;i<CTYPi;i++) x1[i]=0;
+    } else x1=vector_newsize((IvocVect*)voi,dvt);
+    if (ifarg(iarg)) { voi=vector_arg(iarg++); x2=vector_newsize((IvocVect*)voi,dvt);  a2=1; }
+    if (ifarg(iarg)) { voi=vector_arg(iarg++); x3=vector_newsize((IvocVect*)voi,dvt); a3=1;}
     if (ifarg(iarg)) { // need 2 weight vecs for AM/NM or GA/GB
-      voi=vector_arg(iarg++); x4=vector_newsize(voi,dvt); a4=1;
-      voi=vector_arg(iarg++); x5=vector_newsize(voi,dvt);
+      voi=vector_arg(iarg++); x4=vector_newsize((IvocVect*)voi,dvt); a4=1;
+      voi=vector_arg(iarg++); x5=vector_newsize((IvocVect*)voi,dvt);
     }
     idty=(double)(FOFFSET+ip->id)+1e-2*(double)ip->type+1e-3*(double)ip->inhib+1e-4;
     prty=ip->type; sy=ip->inhib?GA:AM;
@@ -1129,8 +1131,8 @@ VERBATIM
   }
   if (!ifarg(iarg)) prfl=0; else { prfl=1;
     voi=vector_arg(iarg); 
-    if (flag==2.) { x=vector_newsize(voi,CTYPi); for (i=0;i<CTYPi;i++) x[i]=0;
-    } else x=vector_newsize(voi,sz); 
+    if (flag==2.) { x=vector_newsize((IvocVect*)voi,CTYPi); for (i=0;i<CTYPi;i++) x[i]=0;
+    } else x=vector_newsize((IvocVect*)voi,sz); 
   } 
   for (i=0,k=0; i<cesz; i++) {
     lop(ce,i);
@@ -1140,7 +1142,7 @@ VERBATIM
       if (getactive && qp->sprob[j]==0) continue;
       if (ip==*((id0**) &((das[j]->_prop->dparam)[2]))) {
         if (prfl) {
-          if (flag!=2.0 && k>=sz) x=vector_newsize(voi,sz*=2);
+          if (flag!=2.0 && k>=sz) x=vector_newsize((IvocVect*)voi,sz*=2);
           if (flag==1.0) { x[k]=(double)qp->type; 
           } else if (flag==2.0) { x[qp->type]++; 
           } else x[k]=(double)qp->id;
@@ -1150,7 +1152,7 @@ VERBATIM
       }
     }
   }
-  if (prfl && flag!=2) vector_resize(voi,k);
+  if (prfl && flag!=2) vector_resize((IvocVect*)voi,k);
   _lgetconv=(double)k;
 }
 ENDVERBATIM
@@ -1216,7 +1218,7 @@ FUNCTION rddvi () {
     fread(&qp->dvt,sizeof(unsigned int),1,fp); // read divergence size
     //free up old pointers
     if(qp->del){ free(qp->del); free(qp->dvi); free(qp->sprob);
-      qp->dvt=0; qp->dvi=(Point_process**)0x0; qp->del=(double*)0x0; qp->sprob=(char *)0x0; }
+      qp->dvt=0; qp->dvi=(Point_process**)0x0; qp->del=(double*)0x0; qp->sprob=(unsigned char *)0x0; }
     //if divergence == 0 , continue
     if(!qp->dvt) continue;
     qp->dvi = (Point_process**)malloc(sizeof(Point_process*)*qp->dvt);  
@@ -1319,7 +1321,7 @@ PROCEDURE clrdvi () {
     lop(ce,i);
     if (qp->dvt!=0x0) {
       free(qp->dvi); free(qp->del); free(qp->sprob);
-      qp->dvt=0; qp->dvi=(Point_process**)0x0; qp->del=(double*)0x0; qp->sprob=(char *)0x0;
+      qp->dvt=0; qp->dvi=(Point_process**)0x0; qp->del=(double*)0x0; qp->sprob=(unsigned char *)0x0;
     }
   }
   ENDVERBATIM
@@ -1393,9 +1395,9 @@ ENDVERBATIM
 PROCEDURE setdvi () {
 VERBATIM {
   int i,dvt,flag; double *d, *y;
-  if (! ifarg(1)) {printf("setdvi(v1,v2[,flag]): v1:cell#s; v2:delays\n"); return; }
+  if (! ifarg(1)) {printf("setdvi(v1,v2[,flag]): v1:cell#s; v2:delays\n"); return 0; } // TODO: Ask Michael
   ip=IDP; pg=ip->pg; // this should be called right after jitcondiv()
-  if (ip->dead) return;
+  if (ip->dead) return 0; // TODO: Ask Michael
   dvt=vector_arg_px(1, &y);
   i=vector_arg_px(2, &d);
   if (ifarg(3)) flag=(int)*getarg(3); else flag=0;
@@ -1416,10 +1418,10 @@ static int setdvi2 (double *y,double *d,int dvt,int flag) {
   if (flag==0) { b=0; e=dvt; // begin to end
     if (ip->dvi) { 
       free(ip->dvi); free(ip->del); free(ip->sprob); 
-      ip->dvt=0; ip->dvi=(Point_process**)0x0; ip->del=(double*)0x0; ip->sprob=(char *)0x0;
+      ip->dvt=0; ip->dvi=(Point_process**)0x0; ip->del=(double*)0x0; ip->sprob=(unsigned char *)0x0;
     } // make sure all null pointers for realloc
   } else { 
-    if (ip->dvt==0) {ip->dvi=(Point_process**)0x0; ip->del=(double*)0x0; ip->sprob=(char *)0x0;}
+    if (ip->dvt==0) {ip->dvi=(Point_process**)0x0; ip->del=(double*)0x0; ip->sprob=(unsigned char *)0x0;}
     b=ip->dvt; 
     e=ip->dvt+dvt; // dvt is amount to grow
   }
@@ -1458,7 +1460,7 @@ PROCEDURE prune () {
       printf("INTFpruneB:Div exceeds dscrsz: %d>%d\n",ip->dvt,dscrsz); hxe(); }
     if (p==0.) {
       for (j=0;j<ip->dvt;j++) ip->sprob[j]=1; // unprune completely
-      return; // now that unpruning is done, can return
+      return 0; // now that unpruning is done, can return TODO: Ask Michael
     }
     potype=ifarg(2)?(int)*getarg(2):-1;
     sead=(ifarg(3))?(unsigned int)*getarg(3):GetDVIDSeedVal(ip->id);//seed for divergence and delays
@@ -1529,7 +1531,7 @@ int gsort2 (double *db, Point_process **da,int dvt,double *dbs, Point_process **
   int i;
   scr=scrset(dvt);
   for (i=0;i<dvt;i++) scr[i]=i;
-  nrn_mlh_gsort(db, scr, dvt, cmpdfn);
+  nrn_mlh_gsort(db, (int*)scr, dvt, cmpdfn);
   for (i=0;i<dvt;i++) {
     dbs[i]=db[scr[i]];
     das[i]=da[scr[i]];
@@ -1544,7 +1546,7 @@ PROCEDURE freedvi () {
     jp=IDP;
     if (jp->dvi) {
       free(jp->dvi); free(jp->del); free(jp->sprob);
-      jp->dvt=0; jp->dvi=(Point_process**)0x0; jp->del=(double*)0x0; jp->sprob=(char *)0x0;
+      jp->dvt=0; jp->dvi=(Point_process**)0x0; jp->del=(double*)0x0; jp->sprob=(unsigned char *)0x0;
     }
   }
   ENDVERBATIM
@@ -1637,7 +1639,7 @@ PROCEDURE jitrec () {
   int i;
   if (! ifarg(2)) { // clear with jitrec() or jitrec(0)
     jrmax=0; jridv=0x0; jrtvv=0x0;
-    return;
+    return 0; // TODO: Ask Michael
   }
   i =   vector_arg_px(1, &jrid); // could just set up the pointers once
   jrmax=vector_arg_px(2, &jrtv);
@@ -1780,11 +1782,11 @@ PROCEDURE record () {
   VERBATIM {
   int i,j,k,nz; double ti;
   vp = SOP;
-  if (tg>=t) return;
+  if (tg>=t) return 0; // TODO: Ask Michael
   if (ip->record==1) {
     while ((int)vp->p >= (int)vp->size-(int)((t-tg)/vdt)-10) { 
       vp->size*=2;
-      for (k=0;k<NSV;k++) if (vp->vv[k]!=0x0) vp->vvo[k]=vector_newsize(vp->vv[k], vp->size);
+      for (k=0;k<NSV;k++) if (vp->vv[k]!=0x0) vp->vvo[k]=vector_newsize((IvocVect*)vp->vv[k], vp->size);
       // printf("**** WARNING expanding recording room to %d (type%d id%d at %g)****\n",vp->size,IDP->type,IDP->id,t);
     }
   } else if ((int)vp->p > (int)vp->size-(int)((t-tg)/vdt)) { // shift if record==2
@@ -1818,7 +1820,7 @@ PROCEDURE recspk (x) {
   VERBATIM { int k;
   vp = SOP;
   record();
-  if (vp->p > vp->size || vp->vvo[6]==0) return; 
+  if (vp->p > vp->size || vp->vvo[6]==0) return 0; // TODO: Ask Michael 
   if (vp->vvo[0]!=0x0) vp->vvo[0][vp->p-1]=_lx;
   vp->vvo[6][vp->p-1]=spkht; // the spike
   tg=_lx;
@@ -2040,7 +2042,7 @@ VERBATIM {
   num = ivoc_list_count(ob);
   if (num!=7) { printf("INTF lof ERR %d>7\n",num); hxe(); }
   for (i=0;i<num;i++) { 
-    j = list_vector_px3(ob, i, &vvo[i], &vv[i]);
+    j = list_vector_px3(ob, i, &vvo[i], (IvocVect**)vv[i]);
     if (i==0) nx=j;
     if (j!=nx) { printf("INTF lof ERR %d %d\n",j,nx); hxe(); }
   }
@@ -2142,13 +2144,13 @@ PROCEDURE chk (f) {
     if (SOP!=nil) {
       vp = SOP;
       printf("p %d size %d tg %g\n",vp->p,vp->size,tg);
-      for (i=0;i<NSV;i++) if (vp->vv[i]) printf("%d %x %x;",i,(unsigned int)vp->vv[i],(unsigned int)vp->vvo[i]);
+      for (i=0;i<NSV;i++) if (vp->vv[i]) printf("%d %x %x;",i,vp->vv[i],vp->vvo[i]);
     } else printf("Recording pointers not initialized");
   }
   if (lfg==2) { 
     printf("Global vectors for input and jitter (jttr): \n");
-    if (vsp!=nil) printf("VSP: %x (%d/%d-%d)\n",(unsigned int)vsp,ip->rvi,ip->rvb,ip->rve); else printf("no VSP\n");
-    if (jsp!=nil) printf("JSP: %x (%d/%d)\n",(unsigned int)jsp,jtpt,jtmax); else printf("no JSP\n");
+    if (vsp!=nil) printf("VSP: %x (%d/%d-%d)\n",vsp,ip->rvi,ip->rvb,ip->rve); else printf("no VSP\n");
+    if (jsp!=nil) printf("JSP: %x (%d/%d)\n",jsp,jtpt,jtmax); else printf("no JSP\n");
   }
   if (lfg==3) { 
     if (vsp!=nil) { printf("VSP: (%d/%d-%d)\n",ip->rvi,ip->rvb,ip->rve); 
@@ -2161,7 +2163,7 @@ PROCEDURE chk (f) {
   if (lfg==5) { 
     printf("wwpt %d wwsz %d\n WW vecs: ",wwpt,wwsz);
     printf("wwwid %g wwht %d nsw %g\n WW vecs: ",wwwid,(int)wwht,nsw);
-    for (i=0;i<NSW;i++) printf("%d %x %x;",i,(unsigned int)ww[i],(unsigned int)wwo[i]);
+    for (i=0;i<NSW;i++) printf("%d %x %x;",i,ww[i],wwo[i]);
   }}
   ENDVERBATIM
 }
@@ -2275,7 +2277,7 @@ PROCEDURE initwrec () {
     if (num>NSW) { printf("INTF initwrec() WARN: can only store %d ww vecs\n",NSW); hxe();}
     nsw=(double)num;
     for (k=0;k<num;k++) {
-      cap = list_vector_px2(ob, k, &wwo[k], &ww[k]);
+      cap = list_vector_px2(ob, k, &wwo[k], (IvocVect**)ww[k]);
       if (k==0) wwsz=cap; else if (wwsz!=cap) {
         printf("INTF initwrec ERR w-vecs size err: %d,%d,%d",k,wwsz,cap); hxe(); }
     }
@@ -2314,7 +2316,7 @@ PROCEDURE wrecord (te) {
           wwo[wrp][k+j] += scale*_t_Psk[j+max]; // direct copy from the Psk table
         }
       }
-    } else if (twg>=t) { return;
+    } else if (twg>=t) { return 0; // TODO: Ask Michael
     } else {
       for (ti=twg,k=(int)floor((twg-rebeg)/vdt+0.5);ti<=t && k<wwsz;ti+=vdt,k++) { 
         valps(ti,twg);  // valps() for pop spike calculation
@@ -2485,11 +2487,11 @@ FUNCTION flag () {
   char *sf; static int ix,fi,setfl,nx; static unsigned char val; static double *x, delt;
   if (FLAG==OK) { // callback -- DO NOT SET FROM HOC
     FLAG=0.;
-    if (stoprun) {slowset=0; return;}
+    if (stoprun) {slowset=0; return 0;} // TODO: Ask Michael
     if (IDP->dbx==-1)printf("slowset fi:%d ix:%d ss:%g delt:%g t:%g\n",fi,ix,slowset,delt,t);
     if (t>slowset || ix>=cesz) {  // done
       printf("Slow-setting of flag %d finished at %g: (%d,%g,%g)\n",fi,t,ix,delt,slowset); 
-      slowset=0.; return;
+      slowset=0.; return 0; // TODO: Ask Michael
     }
     if (ix<cesz) {
       lop(ce,ix);
@@ -2501,12 +2503,12 @@ FUNCTION flag () {
       net_send((void**)0x0, wts,tpnt,delt,OK);
       #endif
     }
-    return;
+    return 0; // TODO: Ask Michael
   }  
   if (slowset>0 && ifarg(3)) {
     printf("INTF flag() slowset ERR; attempted set during slowset: fi:%d ix:%d ss:%g delt:%g t:%g",\
            fi,ix,slowset,delt,t); 
-    return;
+    return 0; // TODO: Ask Michael
   }
   ip = IDP; setfl=ifarg(3); 
   if (ifarg(4)) { slowset=*getarg(4); delt=slowset/cesz; slowset+=t; } 
@@ -2554,7 +2556,7 @@ FUNCTION flag () {
 
 FUNCTION allspck () {
   VERBATIM
-  int i; double *x, sum; void *voi;
+  int i; double *x, sum; IvocVect* voi;
   ip = IDP;
   voi=vector_arg(1);  x=vector_newsize(voi,cesz);
   for (i=0,sum=0;i<cesz;i++) { lop(ce,i); 
@@ -2580,7 +2582,7 @@ PROCEDURE resetall () {
 :** floc(x,y[,z]) // find a cell by location
 FUNCTION floc () {
   VERBATIM
-  double x,y,z,r,min,rad, *ix; int ii,i,n,cnt; void* voi;
+  double x,y,z,r,min,rad, *ix; int ii,i,n,cnt; IvocVect* voi;
   cnt=0; n=1000; r=-1;
   ip = IDP;
   x = *getarg(1);
diff --git a/intfsw.mod b/intfsw.mod
index e35cdfe..515e0b5 100644
--- a/intfsw.mod
+++ b/intfsw.mod
@@ -412,7 +412,7 @@ FUNCTION GetCCR () {
   }
 
   double** pLV = pList->pv;
-  int* pLen = pList->plen;
+  unsigned int* pLen = pList->plen;
 
   //init vector of distances to each cell , 0 == no path found
   int* pNeighbors = (int*)calloc(iCells,sizeof(int));
@@ -543,7 +543,7 @@ FUNCTION GetCentrality () {
   }
 
   double** pLV = pList->pv;
-  int* pLen = pList->plen;
+  unsigned int* pLen = pList->plen;
 
   //init vector of avg distances to each cell , 0 == no path found
   double* pCE; 
@@ -655,7 +655,7 @@ FUNCTION GetCC () {
   }
 
   double** pLV = pList->pv;
-  int* pLen = pList->plen;
+  unsigned int* pLen = pList->plen;
 
   //init vector of distances to each cell , 0 == no path found
   int* pNeighbors = (int*)calloc(iCells,sizeof(int));
@@ -753,7 +753,7 @@ FUNCTION CountNeighborsR () {
   }
 
   double** pLV = pList->pv;
-  int* pLen = pList->plen;
+  unsigned int* pLen = pList->plen;
 
   //init vector of avg distances to each cell , 0 == no path found
   double* pVD; 
@@ -1166,7 +1166,7 @@ FUNCTION GetPathR () {
   }
 
   double** pLV = pList->pv;
-  int* pLen = pList->plen;
+  unsigned int* pLen = pList->plen;
 
   //init vector of avg distances to each cell , 0 == no path found
   double* pVD; 
@@ -1313,7 +1313,7 @@ FUNCTION GetCCSubPop () {
   }
 
   double** pLV = pList->pv;
-  int* pLen = pList->plen;
+  unsigned int* pLen = pList->plen;
 
   //init vector of distances to each cell , 0 == no path found
   int* pNeighbors = (int*)calloc(iCells,sizeof(int));
@@ -1422,7 +1422,8 @@ FUNCTION GetCCSubPop () {
 FUNCTION GetRecurCount () {
   VERBATIM
   ListVec* pList;
-  int iCells,*pLen,iFromSz,iThruSz,idx,myID,youID,jdx,iCheckSz,*pVisited,*pCheck;
+  unsigned int* pLen;
+  int iCells,iFromSz,iThruSz,idx,myID,youID,jdx,iCheckSz,*pVisited,*pCheck;
   double **pLV,*pFrom,*pThru,*pR;
 
   pList = AllocListVec(*hoc_objgetarg(1));
@@ -1509,7 +1510,7 @@ FUNCTION GetPairDist () {
   }
 
   double** pLV = pList->pv;
-  int* pLen = pList->plen;
+  unsigned int* pLen = pList->plen;
 
   double* pFrom = 0, *pTo = 0;
   int iFromSz = vector_arg_px(3,&pFrom) , iToSz = vector_arg_px(4,&pTo);
@@ -1632,7 +1633,7 @@ FUNCTION GetPathSubPop () {
   }
 
   double** pLV = pList->pv;
-  int* pLen = pList->plen;
+  unsigned int* pLen = pList->plen;
 
   //init vector of avg distances to each cell , 0 == no path found
   double* pVD; 
@@ -1787,7 +1788,7 @@ FUNCTION GetLoopLength () {
   }
 
   double** pLV = pList->pv;
-  int* pLen = pList->plen;
+  unsigned int* pLen = pList->plen;
 
   //init vector of avg distances to each cell , 0 == no path found
   double* pVD; 
@@ -1928,7 +1929,7 @@ FUNCTION GetPathEV () {
   }
 
   double** pLV = pList->pv;
-  int* pLen = pList->plen;
+  unsigned int* pLen = pList->plen;
 
   //init vector of distances to each cell , 0 == no path found
   double* pVD; 
diff --git a/misc.h b/misc.h
index 586dff1..e02e615 100644
--- a/misc.h
+++ b/misc.h
@@ -7,6 +7,7 @@
 #include <sys/time.h> 
 #include <values.h>
 #include <pthread.h>
+#include <stdint.h>
 
 #if !defined(t)
   #define _pval pval
@@ -75,11 +76,10 @@ extern int vector_instance_px();
 extern void* vector_arg();
 extern double* vector_vec();
 extern int vector_buffer_size(void*);
-extern void mcell_ran4_init(unsigned int *idum);
-extern double mcell_ran4(unsigned int* idum,double* ran_vec,unsigned int n,double range);
-extern int nrn_mlh_gsort();
+extern void mcell_ran4_init(uint32_t idum);
+extern double mcell_ran4(uint32_t* high, double* x, unsigned int n, double range);
+extern int nrn_mlh_gsort(double* vec, int* base_ptr, int total_elems, int (*cmp)(double, double));
 extern int ivoc_list_count(Object*);
-extern Object* ivoc_list_item(Object*, int);
 extern int hoc_is_double_arg(int narg);
 extern int hoc_is_str_arg(int narg);
 extern int hoc_is_object_arg(int narg);
@@ -90,6 +90,18 @@ extern Point_process* ob2pntproc(Object*);
 extern char* hoc_object_name(Object*);
 extern double nrn_event_queue_stats(double*);
 extern void clear_event_queue();
+extern void cvode_fadvance(double);
+extern int hoc_is_tempobj_arg(int narg);
+extern Object* ivoc_list_item(Object*, int);
+#else // TODO: Update nrn master & C++ PR
+#ifdef __cplusplus
+extern "C" {
+#endif
+Object* ivoc_list_item(Object*, int);
+Symbol* hoc_get_symbol(const char* var);
+#ifdef __cplusplus
+}
+#endif
 #endif
 extern unsigned int hashseed2 (int na, double* x);
 extern unsigned int  dcrsz;
@@ -110,7 +122,8 @@ extern void ishuffle(int* x,int nx);
 extern unsigned int valseed;
 extern int list_vector_px2 (Object *ob, int i, double** px, IvocVect** vv);
 extern int list_vector_px3 (Object *ob, int i, double** px, IvocVect** vv);
-extern int cmpdfn();
+extern int list_vector_px4 (Object *ob, int i, double** px, unsigned int n);
+extern int cmpdfn(double a, double b);
 extern int openvec(int, double **);
 int list_vector_px(Object *ob, int i, double** px);
 double *list_vector_resize(Object *ob, int i, int sz);
@@ -121,6 +134,9 @@ extern ListVec* AllocILV(Object*, int, double *);
 void FillListVec(ListVec* p,double dval);
 void ListVecResize(ListVec* p,int newsz);
 extern short *nrn_artcell_qindex_;
+extern int IsList (Object* p);
+extern int uniq2 (int n, double *x, double *y, double *z);
+static void vprpr (double x, int base);
 
 static double sc[6];
 static FILE*  testout;
diff --git a/misc.mod b/misc.mod
index 87b063e..6c5600b 100644
--- a/misc.mod
+++ b/misc.mod
@@ -48,6 +48,7 @@ VERBATIM
 #include <time.h>
 #include <stdio.h>
 #include <limits.h>
+#include <misc.h>
 extern int hoc_is_tempobj(int narg);
 ENDVERBATIM
 
@@ -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);
 
@@ -85,19 +86,18 @@ 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; // TODO: Ask Michael
     }
     
     if (fgets(string,BUFSIZ,pipein) == NULL) {
         fprintf(stderr,"System call did not return a string\n");
-        pclose(pipein); return;
+        pclose(pipein); return 0; // TODO: Ask Michael
     }
 
     /*  assign_hoc_str(strname, string, 0); */
@@ -120,17 +120,17 @@ VERBATIM
 
     if ( !(outfile = fopen("dassign","w"))) {
         fprintf(stderr,"Can't open output file dassign\n");
-        return; 
+        return 0; // TODO: Ask Michael
     }
 
     if( !(pipein = popen(syscall, "r"))) {
         fprintf(stderr,"System call failed\n");
-        fclose(outfile); return; 
+        fclose(outfile); return 0; // TODO: Ask Michael
     }
     
     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; // TODO: Ask Michael
     }
 
     fprintf(outfile,"%s=%g\n",strname,num);
@@ -214,7 +214,7 @@ ENDVERBATIM
 FUNCTION hocgetc() {
 VERBATIM
 {	
-  FILE* f, *hoc_obj_file_arg();
+  FILE* f;
   f = hoc_obj_file_arg(1);
   _lhocgetc = (double)getc(f);
 }
diff --git a/pregencv.mod b/pregencv.mod
index 501f510..3b95dfc 100644
--- a/pregencv.mod
+++ b/pregencv.mod
@@ -87,7 +87,7 @@ PROCEDURE event_time() {
 PROCEDURE generate() {
 	if (at_time(event)) {
           VERBATIM
-          {char func[8] = "pregencv_c";
+          {char func[11] = "pregencv_c";
             Symbol* s = hoc_lookup(func);
             if (s) {
               hoc_pushx(num);
diff --git a/stats.mod b/stats.mod
index 13d4828..fc7b123 100644
--- a/stats.mod
+++ b/stats.mod
@@ -425,9 +425,9 @@ static double* getrank (int n, double mdata[])
 { int i;
   double* rank;
   int* index;
-  rank = malloc(n*sizeof(double));
+  rank = (double*)malloc(n*sizeof(double));
   if (!rank) return NULL;
-  index = malloc(n*sizeof(int));
+  index = (int*)malloc(n*sizeof(int));
   if (!index)
   { free(rank);
     return NULL;
@@ -469,9 +469,9 @@ static double spearman(int n, double* data1, double* data2)
   double avgrank;
   double* tdata1;
   double* tdata2;
-  tdata1 = malloc(n*sizeof(double));
+  tdata1 = (double*)malloc(n*sizeof(double));
   if(!tdata1) return 0.0; /* Memory allocation error */
-  tdata2 = malloc(n*sizeof(double));
+  tdata2 = (double*)malloc(n*sizeof(double));
   if(!tdata2) /* Memory allocation error */
   { free(tdata1);
     return 0.0;
@@ -642,7 +642,7 @@ 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]];
@@ -860,8 +860,8 @@ 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((uint32_t)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
@@ -1042,7 +1042,7 @@ 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];
     }
@@ -1114,9 +1114,9 @@ ENDVERBATIM
 VERBATIM
 static double combi (void* vv) {
   int i,j,k,m,n,prix,prixe,poix,poixe,prn,pon,s,vfl,tot,soc; 
-  double perc, *v1, *v2, *vpr, *vpo, *vec; void *v1v, *v2v;
+  double perc, *v1, *v2, *vpr, *vpo, *vec; IvocVect *v1v, *v2v;
   int nx,cnt,nx1,nvec,nv1,nv2;
-  nx=nvec = vector_instance_px(vv, &vec);
+  nx=nvec = vector_instance_px((IvocVect*)vv, &vec);
   if (ifarg(7)) vfl=0; else vfl=1; 
   nv1 = vector_arg_px((vfl?3:5), &v1); v1v=vector_arg((vfl?3:5)); 
   nv2 = vector_arg_px((vfl?4:6), &v2); v2v=vector_arg((vfl?4:6)); 
@@ -1139,14 +1139,14 @@ static double combi (void* vv) {
   if (perc<1) s=(int)floor(perc*(double)tot+0.5); else s=(int)perc; 
   // soc shortcut -- set self_ok_combi before call when sets are disjoint and s=1
   if (soc && s==1) { // don't need to go through this rigamarole just choose 1 from A,1 from B
-    vec=vector_newsize(vv,1); v1=vector_newsize(v1v,nv1+1); v2=vector_newsize(v2v,nv2+1);
+    vec=vector_newsize((IvocVect*)vv,1); v1=vector_newsize(v1v,nv1+1); v2=vector_newsize(v2v,nv2+1);
     mcell_ran4(&valseed, vec, 1, prn);
     if (vfl) v1[nv1]=vpr[(int)vec[0]]; else v1[nv1]=prix+floor(vec[0]);
     mcell_ran4(&valseed, vec, 1, pon);    
     if (vfl) v2[nv2]=vpo[(int)vec[0]]; else v2[nv2]=poix+floor(vec[0]);    
     return 1.0; // note that vec will not contain the combi#
   }
-  vec=vector_newsize(vv,s); // vec.resize(s)
+  vec=vector_newsize((IvocVect*)vv,s); // vec.resize(s)
   if (tot==s) { for (i=0;i<s;i++) vec[i]=(double)i; // all values
   } else { // vec.setrnd(6,0,tot-1) -- find s unique integers in [0,tot)
     cnt=0; nx1=10*s;
@@ -1484,11 +1484,11 @@ ENDVERBATIM
 VERBATIM
 static double shuffle (void* vv) {
   int i,j,k,n,nx,augfac; double *x, y[1], temp, augstep;
-  nx=vector_instance_px(vv, &x);
+  nx=vector_instance_px((IvocVect*)vv, &x);
   if (ifarg(1)) {
     augfac=(int)*getarg(1);
     if (ifarg(2)) augstep=*getarg(2); else augstep=1.0/augfac;
-    x=vector_newsize(vv,nx*augfac);
+    x=vector_newsize((IvocVect*)vv,nx*augfac);
     for (i=1;i<augfac;i++) for (j=0;j<nx;j++) x[i*nx+j]=x[j]+i*augstep;
     nx*=augfac;
   }
@@ -1692,7 +1692,7 @@ static double bin (void* vv) {
   int i, j, nx, maxsz, lfl;
   double* x, *y, *ix, invl, min, max, maxf, jj;
   Object* ob;
-  void* voi[2];
+  IvocVect* voi[2];
 
   min=0; max=1e9; maxf=-1e9;
   nx = vector_instance_px(vv, &x);
@@ -2024,8 +2024,8 @@ 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((uint32_t)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
   }
@@ -2090,7 +2090,7 @@ FUNCTION mc4seed () {
   for (i=2;ifarg(i);i++) {
     valseed*=(unsigned int)(*getarg(i));
   }
-  mcell_ran4_init(&valseed); // do initialization
+  mcell_ran4_init((uint32_t)valseed); // do initialization
   return valseed;
   ENDVERBATIM
 }
@@ -2118,7 +2118,7 @@ FUNCTION gammln (xx) {
 FUNCTION betai(a,b,x) {
 VERBATIM {
   double bt;
-  double gammln(),betacf();
+  double gammln(double),betacf(double,double,double);
 
   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;
@@ -2192,7 +2192,7 @@ FUNCTION tstat() {
 
 FUNCTION tdistrib() {
   VERBATIM
-  double gammln();
+  double gammln(double);
   double x = *getarg(1);
   double dof = *getarg(2);
   double res = (gammln( (dof+1.0) / 2.0 )  / gammln( dof / 2.0 ) );
diff --git a/updown.mod b/updown.mod
index e9f5c0a..8ecd7dc 100644
--- a/updown.mod
+++ b/updown.mod
@@ -19,28 +19,7 @@ VERBATIM
 #include <math.h>
 #include <limits.h> // contains LONG_MAX 
 #include <sys/time.h> 
-extern double* hoc_pgetarg();
-extern double hoc_call_func(Symbol*, int narg);
-extern FILE* hoc_obj_file_arg(int narg);
-extern Object** hoc_objgetarg();
-extern void vector_resize();
-extern int vector_instance_px();
-extern void* vector_arg();
-extern double* vector_vec();
-extern double hoc_epsilon;
-extern double chkarg();
-extern void set_seed();
-extern int ivoc_list_count(Object*);
-extern Object* ivoc_list_item(Object*, int);
-extern int hoc_is_double_arg(int narg);
-extern char* hoc_object_name(Object*);
-char ** hoc_pgargstr();
-int list_vector_px();
-int list_vector_px2();
-int list_vector_px3();
-double *list_vector_resize();
-int ismono1();
-static void hxe() { hoc_execerror("",0); }
+#include <misc.h>
 static void hxf(void *ptr) { free(ptr); hoc_execerror("",0); }
 ENDVERBATIM
 
@@ -72,7 +51,7 @@ static double updown (void* vv) {
   int i, k, m, n, nqsz, nsrc, jj[UDSL], f[UDSL], lc, dsz[UDSL], nqmax, thsz, lc2, done, dbn;
   double *src, *tvec, *th, *dest[UDSL], *nq[UDNQ], *tmp, *dbx, lt, thdist;
   Object *ob, *ob2;
-  void *vvd[UDSL], *vvth, *vnq[UDNQ];
+  IvocVect *vvd[UDSL], *vvth, *vnq[UDNQ];
   //** read in vectors and verify sizes, etc
   nsrc = vector_instance_px(vv, &src); // trace to analyze
   thsz = vector_arg_px(1, &th);        // vector of thresholds to check
diff --git a/vecst.mod b/vecst.mod
index 2bd5a89..ecb1704 100644
--- a/vecst.mod
+++ b/vecst.mod
@@ -150,7 +150,7 @@ static double ident (void* vv) {
   int nx,bsz; double* x;
   nx = vector_instance_px(vv, &x);
   bsz=vector_buffer_size(vv);
-  printf("Obj*%x Dbl*%x Size: %d Bufsize: %d\n",(unsigned int)vv,(unsigned int)x,nx,bsz);
+  printf("Obj*%x Dbl*%x Size: %d Bufsize: %d\n",vv,x,nx,bsz);
   return (double)nx;
 }
 ENDVERBATIM
@@ -228,7 +228,7 @@ static double circ (void* vv) {
   int i, nx, ny, flag, lnew;
   double *x, *y, x0, y0, x1, y1, rad, theta;
   lnew=0;
-  nx = vector_instance_px(vv, &x);
+  nx = vector_instance_px((IvocVect*)vv, &x);
   ny = vector_arg_px(1, &y);
   if (ny!=nx) { hoc_execerror("v.circ: Vector sizes don't match.", 0); }
   x0=*getarg(2); y0=*getarg(3); rad=*getarg(4); 
@@ -237,7 +237,7 @@ static double circ (void* vv) {
     rad=sqrt((x0-x1)*(x0-x1) + (y0-y1)*(y0-y1));
     lnew=*getarg(6); // resize the vectors
   } else if (ifarg(5)) lnew=*getarg(5); // resize the vectors
-  if (lnew) { nx=lnew; x=vector_newsize(vv,nx); y=vector_newsize(vector_arg(1),ny=nx); }
+  if (lnew) { nx=lnew; x=vector_newsize((IvocVect*)vv,nx); y=vector_newsize(vector_arg(1),ny=nx); }
   for (i=0,theta=0; i<nx; theta+=2*M_PI/(nx-1),i++) {
     x[i]=y0+rad*sin(theta); y[i]=x0+rad*cos(theta); 
   }
@@ -325,10 +325,11 @@ ENDVERBATIM
 : uses ind as index into vecA's to load in vecB's (for select); a nondestructive fewind()
 VERBATIM
 static double findx (void* vv) {
+  IvocVect* vv_tmp = (IvocVect*)vv;
   int i, j, ni, nx, av[VRRY], bv[VRRY], num;
   Object *ob1, *ob2;
   double *ind, *avo[VRRY], *bvo[VRRY];
-  ni = vector_instance_px(vv, &ind);
+  ni = vector_instance_px((IvocVect*)vv, &ind);
   ob1 = *hoc_objgetarg(1);
   ob2 = *hoc_objgetarg(2);
   num = ivoc_list_count(ob1);
@@ -342,12 +343,12 @@ static double findx (void* vv) {
   }
   nx=av[0]; // size of source vecs
   for (i=0;i<num;i++) { 
-    bv[i]=list_vector_px2(ob2, i, &bvo[i], &vv); // dest vectors 
-    if (vector_buffer_size(vv)<ni) { 
+    bv[i]=list_vector_px2(ob2, i, &bvo[i], &vv_tmp); // dest vectors 
+    if (vector_buffer_size((IvocVect*)vv)<ni) { 
       printf("findx ****ERRD**** arg#%d need:%d sz:%d\n",num+i+1,ni,vector_buffer_size(vv));
       hoc_execerror("Destination vector with insufficient size: ", 0); 
     } else {
-      vector_resize(vv, ni);
+      vector_resize((IvocVect*)vv, ni);
     }
   }
   if (ni>scrsz) { 
@@ -369,10 +370,11 @@ ENDVERBATIM
 : ind picks out specific vectors if not doing all of them
 VERBATIM
 static double lma (void* vv) {
+  IvocVect* vv_tmp = (IvocVect*)vv;
   int i, j, k, ia, ib, ni, nj, nx, av[VRRY], bv[VRRY], num, numb, beg, end, *xx;
   Object *ob1, *ob2;
   double *ind, *avo[VRRY], *bvo[VRRY], mul,mmul,add,madd;
-  ni = vector_instance_px(vv, &ind);
+  ni = vector_instance_px((IvocVect*)vv, &ind);
   xx=iscrset(ni);
   ob1 = *hoc_objgetarg(1);    ob2 = *hoc_objgetarg(2);
   beg = (int)*getarg(3);      end= (int)*getarg(4);
@@ -395,8 +397,8 @@ static double lma (void* vv) {
   nx=av[0]; // size of source vecs
   if (beg>=end || beg<0 || end>nx) {printf("lma ERRC1 OOB %d - %d (%d)\n",beg,end,nx); hxe();}
   for (i=0;i<num;i++) { 
-    bv[i]=list_vector_px2(ob2, i, &bvo[i], &vv); // dest vectors 
-    if (bv[i]!=(end-beg)) bvo[i]=vector_newsize(vv, end-beg);
+    bv[i]=list_vector_px2(ob2, i, &bvo[i], &vv_tmp); // dest vectors 
+    if (bv[i]!=(end-beg)) bvo[i]=vector_newsize((IvocVect*)vv, end-beg);
   }
   if (nj>0) {
     for (ia=0,ib=0,mmul=1.,madd=0.;ia<nj;ia++,ib++) {
@@ -708,7 +710,7 @@ VERBATIM
 static double iwr (void* vv) {
   int i, j, nx; size_t r;
   double *x;
-  FILE* f, *hoc_obj_file_arg();
+  FILE* f;
   f = hoc_obj_file_arg(1);
   nx = vector_instance_px(vv, &x);
   scrset(nx);
@@ -724,7 +726,7 @@ VERBATIM
 static double ird (void* vv) {
   int i, j, nx, n; size_t r;
   double *x;
-  FILE* f, *hoc_obj_file_arg();
+  FILE* f;
   f = hoc_obj_file_arg(1);
   nx = vector_instance_px(vv, &x);
   r=fread(&n,sizeof(int),1,f);  // size
@@ -753,7 +755,7 @@ VERBATIM
 static double fread2 (void* vv) {
   int i, j, nx, n, type, maxsz; size_t r;
   double *x;
-  FILE* fp, *hoc_obj_file_arg();
+  FILE* fp;
   BYTEHEADER
 
   fp = hoc_obj_file_arg(1);
@@ -799,20 +801,20 @@ ENDVERBATIM
 VERBATIM
 static double revec (void* vv) {
   int i,j,k, nx, ny; double *x, *y;
-  nx = vector_instance_px(vv, &x);
-  if (nx==0) x=vector_newsize(vv,nx=100);
+  nx = vector_instance_px((IvocVect*)vv, &x);
+  if (nx==0) x=vector_newsize((IvocVect*)vv,nx=100);
   for (i=1,k=0;ifarg(i);i++,k++) {
     if (hoc_is_double_arg(i)) {
-      if (k>=nx) x=vector_newsize(vv,nx*=4);
+      if (k>=nx) x=vector_newsize((IvocVect*)vv,nx*=4);
       x[k]=*getarg(i);
     } else {
       ny=vector_arg_px(i, &y);
-      if (k+ny>=nx) x=vector_newsize(vv,nx=2*(nx+ny));
+      if (k+ny>=nx) x=vector_newsize((IvocVect*)vv,nx=2*(nx+ny));
       for (j=0;j<ny;j++,k++) x[k]=y[j];
       k--; // back up one
     }
   }
-  vector_resize(vv,k);
+  vector_resize((IvocVect*)vv,k);
 }
 ENDVERBATIM
 
@@ -820,8 +822,8 @@ ENDVERBATIM
 VERBATIM
 static double has (void* vv) {
   int i, j, nx, ny;
-  double *x, *y, val; void* vc;
-  nx = vector_instance_px(vv, &x);
+  double *x, *y, val; IvocVect* vc;
+  nx = vector_instance_px((IvocVect*)vv, &x);
   val=*getarg(1);
   ny=0;
   if (ifarg(2)) if (hoc_is_object_arg(2)) {
@@ -851,17 +853,17 @@ VERBATIM
 static double insct (void* vv) {
 	int i, j, k, nx, nv1, nv2, maxsz;
 	double *x, *v1, *v2;
-	nx = vector_instance_px(vv, &x);
+	nx = vector_instance_px((IvocVect*)vv, &x);
         if (maxsz==0) maxsz=1000;
-        maxsz=vector_buffer_size(vv);
-        x=vector_newsize(vv, maxsz);
+        maxsz=vector_buffer_size((IvocVect*)vv);
+        x=vector_newsize((IvocVect*)vv, maxsz);
 	nv1 = vector_arg_px(1, &v1);
 	nv2 = vector_arg_px(2, &v2);
         for (i=0,k=0;i<nv1;i++) for (j=0;j<nv2;j++) if (v1[i]==v2[j]) {
-          if (k==maxsz) x=vector_newsize(vv, maxsz*=2);
+          if (k==maxsz) x=vector_newsize((IvocVect*)vv, maxsz*=2);
           x[k++]=v1[i]; 
         }
-        vector_resize(vv, k);
+        vector_resize((IvocVect*)vv, k);
 	return (double)k;
 }
 ENDVERBATIM
@@ -872,10 +874,10 @@ VERBATIM
 static double linsct (void* vv) {
   int i,j,k,nx,maxsz,min,cnt,lt,rt,p,iv,jv,jj,fl; ListVec* pL;
   double *x, val;
-  nx = vector_instance_px(vv, &x);
-  maxsz=vector_buffer_size(vv);
+  nx = vector_instance_px((IvocVect*)vv, &x);
+  maxsz=vector_buffer_size((IvocVect*)vv);
   if (maxsz==0) maxsz=1000;
-  x=vector_newsize(vv, maxsz);
+  x=vector_newsize((IvocVect*)vv, maxsz);
   pL = AllocListVec(*hoc_objgetarg(1));
   min= (int)*getarg(2);
   for (iv=0;iv<pL->isz;iv++) {
@@ -895,13 +897,13 @@ static double linsct (void* vv) {
       }
       if (fl) cnt++;
       if (cnt>=min) {
-        if (k==maxsz) x=vector_newsize(vv, maxsz*=2);
+        if (k==maxsz) x=vector_newsize((IvocVect*)vv, maxsz*=2);
         x[k++]=val;
         break;
       }
     }
   }
-  vector_resize(vv, k);
+  vector_resize((IvocVect*)vv, k);
   return (double)k;
 }
 ENDVERBATIM
@@ -924,17 +926,17 @@ VERBATIM
 static double cull (void* vv) {
 	int i, j, k, nx, nv1, nv2, flag;
 	double *x, *v1, *v2, val;
-	nx = vector_instance_px(vv, &x);
+	nx = vector_instance_px((IvocVect*)vv, &x);
 	nv1 = vector_arg_px(1, &v1);
         if (hoc_is_double_arg(2)) { val=*getarg(2); nv2=0; } else nv2=vector_arg_px(2, &v2);
-        x=vector_newsize(vv,nx=nv1);
+        x=vector_newsize((IvocVect*)vv,nx=nv1);
         for (i=0,k=0;i<nv1;i++) {
           flag=1;
           if (nv2) { for (j=0;j<nv2;j++) if (v1[i]==v2[j]) flag=0;
           } else                         if (v1[i]==val  ) flag=0;
           if (flag) x[k++]=v1[i];
         }
-        vector_resize(vv, k);
+        vector_resize((IvocVect*)vv, k);
 	return (double)k;
 }
 ENDVERBATIM
@@ -987,16 +989,16 @@ static double mredundout (void* vv) {
   int i, j, k, m, p, q, maxsz, ns, nx, av[VRRY], bv[VRRY], num, numb, indflag, match;
   Object *ob, *ob2;
   double *x, *avo[VRRY], *bvo[VRRY], val[VRRY];
-  void *vva[VRRY],*vvb[VRRY];
-  nx = vector_instance_px(vv, &x);
+  IvocVect *vva[VRRY],*vvb[VRRY];
+  nx = vector_instance_px((IvocVect*)vv, &x);
   ob = *hoc_objgetarg(1);
   if (ifarg(2)) indflag=(int)*getarg(2); else indflag=0; 
   if (ifarg(3)) { 
     ob2 = *hoc_objgetarg(3);
     numb = ivoc_list_count(ob2);
   } else numb=0;
-  maxsz=vector_buffer_size(vv);
-  if (indflag) vector_resize(vv, maxsz); // else vector is not used
+  maxsz=vector_buffer_size((IvocVect*)vv);
+  if (indflag) vector_resize((IvocVect*)vv, maxsz); // else vector is not used
   num = ivoc_list_count(ob);
   if (num>VRRY) hoc_execerror("mredundout ****ERRA****: can only handle VRRY vectors", 0);
   for (i=0;i<num;i++) { 
@@ -1028,7 +1030,7 @@ static double mredundout (void* vv) {
   if (indflag) { // just fill ind with indices of the repeats
     if (k>maxsz){printf("mredundout****ERRE**** vec overflow %d>%d\n",k,maxsz);hxe();}
     for (i=0;i<k;i++) x[i]=(double)scr[i];
-    vector_resize(vv, k);
+    vector_resize((IvocVect*)vv, k);
   } else { // remove all the repeat rows
     if (k == 0) return (double)k;
     for (i=0,p=scr[0]; i<k-1; i++) { // iter thru the inds to remove
@@ -1055,8 +1057,8 @@ static double join (void* vv) {
   int i, j, k, m, p, q, maxsz, npiva, npivb, av[VRRY], bv[VRRY], num, numb, indflag, match;
   Object *ob, *ob2;
   double *piva, *pivb, *avo[VRRY], *bvo[VRRY], val[VRRY];
-  void *vva[VRRY],*vvb[VRRY];
-  npiva = vector_instance_px(vv, &piva);
+  IvocVect *vva[VRRY],*vvb[VRRY];
+  npiva = vector_instance_px((IvocVect*)vv, &piva);
   npivb = vector_arg_px(1, &pivb);
   ob = *hoc_objgetarg(2);
   ob2 = *hoc_objgetarg(3);
@@ -1337,10 +1339,10 @@ static double nearall (void* vv) {
   register int	lo, hi, mid;
   int i, j, k, kk, nx, ny, minind, nv[4];
   Object *ob;
-  void* vvl[4];
-  double *x, *y, *vvo[4], targ, dist, new, max, tmp;
+  IvocVect* vvl[4];
+  double *x, *y, *vvo[4], targ, dist, new_, max_, tmp;
   nx = vector_instance_px(vv, &x);
-  max = *getarg(1);
+  max_ = *getarg(1);
   ny = vector_arg_px(2, &y);
   ob = *hoc_objgetarg(3);
   if ((nv[0]=ivoc_list_count(ob))!=4) {printf("VECST::nearall() ERRA: %d\n",nv[0]); hxe();}
@@ -1356,12 +1358,12 @@ static double nearall (void* vv) {
     }
     dist=fabs(x[mid]-targ); minind=mid;
     for (i=-1;i<=1;i+=2) { kk=mid+i; // check the flanking values
-      if (kk>0 && kk<nx && (new=fabs(x[kk]-targ))<dist) { 
-        dist=new;
+      if (kk>0 && kk<nx && (new_=fabs(x[kk]-targ))<dist) { 
+        dist=new_;
         minind=kk;
       }
     }
-    if (dist<=max) {
+    if (dist<=max_) {
       if (k>=nv[1]) { printf("nearall WARN: oor %d %d\n",k,nv[1]); return -1.; }
       vvo[0][k]=dist; vvo[2][k]=targ; vvo[3][k]=x[minind];
       k++;
@@ -1395,14 +1397,14 @@ ENDVERBATIM
 VERBATIM
 static double nearest (void* vv) {
   int i, nx, minind, flag=0;
-  double *x, targ, dist, new, *to;
+  double *x, targ, dist, new_, *to;
   nx = vector_instance_px(vv, &x);
   targ = *getarg(1);
   if (ifarg(3)) flag = (int)*getarg(3);
   dist = 1e9;
-  for (i=0; i<nx; i++) if ((new=fabs(x[i]-targ))<dist) { 
-    if (flag && new==0) continue; // flag signals to not pick self
-    dist=new;
+  for (i=0; i<nx; i++) if ((new_=fabs(x[i]-targ))<dist) { 
+    if (flag && new_==0) continue; // flag signals to not pick self
+    dist=new_;
     minind=i;
   }
   if (ifarg(2)) *(hoc_pgetarg(2)) = dist;
@@ -1801,11 +1803,11 @@ VERBATIM
 static double l2p (void* vv) {
   int ix, i, j, n, num, cnt;
   double *x, *y;   Object* lob;
-  n = vector_instance_px(vv, &x);
+  n = vector_instance_px((IvocVect*)vv, &x);
   lob = *hoc_objgetarg(1);
   ix=(int)*getarg(2);
   num = ivoc_list_count(lob);
-  x=vector_newsize(vv,num);
+  x=vector_newsize((IvocVect*)vv,num);
   for (i=0;i<num;i++) {     // pick up vectors
     cnt = list_vector_px(lob, i, &y);
     if (ix>=cnt) {printf("vecst:l2p() ERRA: %d %d %d\n",i,ix,cnt); hxe();}
@@ -1835,7 +1837,7 @@ static double fetch (void* vv) {
     ny = vector_arg_px(3, &y);
     if (ny>pL->isz) vector_resize(vector_arg(3),pL->isz); // don't make bigger if only want a few
     for (i=0,j=0,cnt=0;i<pL->isz && j<ny;i++,j++) {
-      if (ix>pL->plen[i]) {printf("vecst:fetch()ERRB: %d %d %x\n",i,ix,(unsigned int)pL->pv[i]); 
+      if (ix>pL->plen[i]) {printf("vecst:fetch()ERRB: %d %d %x\n",i,ix,pL->pv[i]); 
         FreeListVec(&pL); hxe();}
       y[j]=pL->pv[i][ix];
       cnt++;
@@ -1844,7 +1846,7 @@ static double fetch (void* vv) {
   } else {
     for (i=0,j=3,cnt=0;i<pL->isz && ifarg(j);i++,j++) {
       if (hoc_is_double_arg(j)) continue; // skip this one
-      if (ix>pL->plen[i]) {printf("vecst:fetch()ERRB1: %d %d %x\n",i,ix,(unsigned int)pL->pv[i]); 
+      if (ix>pL->plen[i]) {printf("vecst:fetch()ERRB1: %d %d %x\n",i,ix,pL->pv[i]); 
         FreeListVec(&pL); hxe();}
       *hoc_pgetarg(j)=ret=pL->pv[i][ix];
       cnt++;      
@@ -1969,7 +1971,7 @@ static double lcat (void* vv) {
   int i, j, k, n, lc, cap, maxsz;
   Object *ob1;
   double *x, *fr; 
-  void *vw;
+  IvocVect *vw;
   n = vector_instance_px(vv, &x);
   vector_resize(vv,maxsz=vector_buffer_size(vv)); // open it up fully
   ob1 = *hoc_objgetarg(1);
@@ -2232,7 +2234,7 @@ VERBATIM
 static double uniq (void* vv) {
   int i, j, k, n, cnt, ny, nz, flag, lt, rt, mid, res;
   double *x, *y, *z, lastx, num;
-  void* voi[2]; Object* ob; char *ix;
+  IvocVect* voi[2]; Object* ob; char *ix;
   n = vector_instance_px(vv, &x);
   flag=ny=nz=0;
   if (n==0) {printf("vecst:uniq WARNA empty input vector\n"); return 0;}
@@ -2261,7 +2263,7 @@ static double uniq (void* vv) {
   }
   scrset(n);
   for (i=0;i<n;i++) scr[i]=i;
-  nrn_mlh_gsort(x, scr, n, cmpdfn);
+  nrn_mlh_gsort(x, (int*)scr, n, cmpdfn);
   if (ny) y[0]=x[scr[0]]; 
   if (nz>0) z[0]=1.;
   for (i=1, lastx=x[scr[0]], cnt=1; i<n; i++) {
@@ -2304,25 +2306,13 @@ static double uniq (void* vv) {
   return (double)cnt;
 }
 
-// x.unq(y,z) calls uniq2() -- functionality same as uniq(List,1)
-static double unq (void* vv) {
-  int n, cnt; double *x, *y, *z; 
-  n=vector_instance_px(vv, &x);
-  y=vector_newsize(vector_arg(1),n); // all same size
-  z=vector_newsize(vector_arg(2),n);
-  cnt=uniq2(n,x,y,z);
-  y=vector_newsize(vector_arg(1),cnt);
-  z=vector_newsize(vector_arg(2),cnt);
-  return (double)cnt;
-}
-
 //** uniq2() should be called with 3 double arrays and their size
 int uniq2 (int n, double *x, double *y, double *z) {
   int i, j, k, cnt, lt, rt, mid, res;  double lastx, num;
   if (n==0) return 0;
   scrset(n);
   for (i=0;i<n;i++) scr[i]=i;
-  nrn_mlh_gsort(x, scr, n, cmpdfn); // sort x
+  nrn_mlh_gsort(x, (int*)scr, n, cmpdfn); // sort x
   y[0]=x[scr[0]]; // first value
   for (i=1, lastx=x[scr[0]], cnt=1; i<n; i++) {
     if (x[scr[i]]>lastx+hoc_epsilon) {
@@ -2352,6 +2342,18 @@ int uniq2 (int n, double *x, double *y, double *z) {
   return cnt;
 }
 
+// x.unq(y,z) calls uniq2() -- functionality same as uniq(List,1)
+static double unq (void* vv) {
+  int n, cnt; double *x, *y, *z; 
+  n=vector_instance_px(vv, &x);
+  y=vector_newsize(vector_arg(1),n); // all same size
+  z=vector_newsize(vector_arg(2),n);
+  cnt=uniq2(n,x,y,z);
+  y=vector_newsize(vector_arg(1),cnt);
+  z=vector_newsize(vector_arg(2),cnt);
+  return (double)cnt;
+}
+
 // v1.nqsvt() for nqs vt iterator
 static double nqsvt (void* vv) {
   int i, j, n, flag, cols;
@@ -2681,7 +2683,7 @@ ENDVERBATIM
 VERBATIM
 static double rdfile (void* vv) {	
   int i, j, k, ni, vsz, ty, ny, nv, num, cnt, n[2], hd, vflag;
-  void* vnq[10000]; size_t r;
+  IvocVect* vnq[10000]; size_t r;
   size_t sz;
   char* xc; int *xi; float *xf; double *xd; void* xv; unsigned short* xus;
   Object* ob;
@@ -2868,7 +2870,11 @@ FUNCTION isojt () {
   Object *ob1, *ob2;
   ob1 = *hoc_objgetarg(1); ob2 = *hoc_objgetarg(2);
   if (!ob1) if (!ob2) return 1; else return 0;
+#ifndef NRN_VERSION_GTEQ_8_2_0
   if (!ob2 || ob1->template != ob2->template) {
+#else
+  if (!ob2 || ob1->ctemplate != ob2->ctemplate) {
+#endif
     return 0;
   }
   return 1;
@@ -3145,7 +3151,7 @@ void ListVecResize (ListVec* p,int newsz) {
   int i,j; Object* obv;
   for(i=0;i<p->isz;i++){
     obv = ivoc_list_item(p->pL, i);
-    p->pv[i]=vector_newsize(obv->u.this_pointer,newsz);
+    p->pv[i]=vector_newsize((IvocVect*)obv->u.this_pointer,newsz);
     p->plen[i]=newsz;
   }
 }

From ad87672d587ae349d02011ee6ea0673baea66013 Mon Sep 17 00:00:00 2001
From: Christos Kotsalos <christos.kotsalos@epfl.ch>
Date: Tue, 17 May 2022 14:56:00 +0200
Subject: [PATCH 06/23] 9.0.0 works almost without warnings

---
 intf_.mod  |  32 +++++++-------
 intfsw.mod |   6 +--
 stats.mod  |  27 +++++------
 vecst.mod  | 128 ++++++++++++++++++++++++++++-------------------------
 4 files changed, 101 insertions(+), 92 deletions(-)

diff --git a/intf_.mod b/intf_.mod
index cf3f9bc..72f378a 100644
--- a/intf_.mod
+++ b/intf_.mod
@@ -20,7 +20,7 @@ VERBATIM
 #include "misc.h"
 #include "unistd.h"
 static int ctt(unsigned int, char**);
-static int setdvi2(double*,double*,int,int);
+static void setdvi2(double*,double*,int,int);
 
 #define PI 3.141592653589793115997963468544
 #define nil 0
@@ -105,7 +105,7 @@ static int  vspn;
 static double *isp, *vsp, *wsp, *jsp, *invlp;
 static double *lop(Object *ob, unsigned int i); // accessed by all INTF
 static double *jrid, *jrtv;
-static void   *jridv, *jrtvv;
+static IvocVect   *jridv, *jrtvv;
 static unsigned int jtpt,jtmax,jrmax;
 static unsigned long int jri,jrj;
 static unsigned long int spktot, eventtot;
@@ -123,7 +123,7 @@ double* wwo[NSW];
 static int AM=0, NM=1, GA=2, GB=3, SU=3, IN=4, DP=2; // from labels.hoc
 static double wts[10],hsh[10];  // for jitcons to use as a junk pointer
 static void spkoutf2();
-int gsort2 (double *db, Point_process **da,int dvt,double *dbs, Point_process **das);
+void gsort2 (double *db, Point_process **da,int dvt,double *dbs, Point_process **das);
 ENDVERBATIM
 
 :* NEURON, PARAMETER, ASSIGNED blocks
@@ -1356,7 +1356,7 @@ FUNCTION setdviv () {
 
 : finishdvi2 () -- finalize dvi , sort dvi , allocate and set sprob
 VERBATIM
-static int finishdvi2 (struct ID0* p) {
+static void finishdvi2 (struct ID0* p) {
   Point_process **da,**das;
   double *db,*dbs;
   int i, dvt;
@@ -1410,7 +1410,7 @@ ENDVERBATIM
 VERBATIM
 // setdvi2(divid_vec,del_vec,div_cnt,flag)
 // flag 1 means just augment, 0or2: sort by del, 0: clear lists and replace
-static int setdvi2 (double *y,double *d,int dvt,int flag) {
+static void setdvi2 (double *y,double *d,int dvt,int flag) {
   int i,j,ddvi; double *db, *dbs; unsigned char pdead; unsigned int b,e;
   Object *lb; Point_process *pnnt, **da, **das;
   ddvi=(int)DEAD_DIV;
@@ -1527,7 +1527,7 @@ PROCEDURE turnoff () {
 
 VERBATIM 
 // gsort2() sorts 2 parallel vectors -- delays and Point_process pointers
-int gsort2 (double *db, Point_process **da,int dvt,double *dbs, Point_process **das) {
+void gsort2 (double *db, Point_process **da,int dvt,double *dbs, Point_process **das) {
   int i;
   scr=scrset(dvt);
   for (i=0;i<dvt;i++) scr[i]=i;
@@ -1750,7 +1750,7 @@ PROCEDURE vers () {
 
 :** val(t,tstart) fills global vii[] to pass values back to record() (called from record())
 VERBATIM
-double val (double xx, double ta) { 
+void val (double xx, double ta) { 
   vii[1]=VAM*EXP(-(xx - ta)/tauAM);
   vii[2]=VNM*EXP(-(xx - ta)/tauNM);
   vii[3]=VGA*EXP(-(xx - ta)/tauGA);
@@ -1767,7 +1767,7 @@ ENDVERBATIM
 
 :** valps(t,tstart) like val but builds voltages for pop spike
 VERBATIM
-double valps (double xx, double ta) { 
+void valps (double xx, double ta) { 
   vii[1]=VAM*EXP(-(xx - ta)/tauAM);
   vii[2]=VNM*EXP(-(xx - ta)/tauNM);
   vii[3]=VGA*EXP(-(xx - ta)/tauGA);
@@ -2010,7 +2010,7 @@ static double* lop (Object *ob, unsigned int i) {
 }
 
 // use stoppo() as a convenient conditional breakpoint in gdb (gdb watching is too slow)
-int stoppo () {
+void stoppo () {
 }
 
 //** ctt(ITEM#) find cells that exist by name
@@ -2111,7 +2111,7 @@ PROCEDURE recini () {
     vp = SOP;
     vp->p=0;
     // open up the vector maximally before writing into it; will correct size in fini
-    for (k=0;k<NSV;k++) if (vp->vvo[k]!=0) vector_resize(vp->vv[k], vp->size);
+    for (k=0;k<NSV;k++) if (vp->vvo[k]!=0) vector_resize((IvocVect*)vp->vv[k], vp->size);
   }}
   ENDVERBATIM
 }
@@ -2126,7 +2126,7 @@ PROCEDURE fini () {
   if (IDP->record) {
     record(); // finish up
     for (k=0;k<NSV;k++) if (vp->vvo[k]!=0) { // not nil pointer
-      vector_resize(vp->vv[k], vp->p);
+      vector_resize((IvocVect*)vp->vv[k], vp->p);
     }
   }}
   ENDVERBATIM
@@ -2225,9 +2225,9 @@ PROCEDURE initrec () {
   if (i==-1) {printf("INTF record ERR %s not recognized\n",name); hoc_execerror("",0); }
   vp->vv[i]=vector_arg(2);
   vector_arg_px(2, &(vp->vvo[i]));
-  if (vp->size==0) { vp->size=(unsigned int)vector_buffer_size(vp->vv[i]);
-  } else if (vp->size != (unsigned int)vector_buffer_size(vp->vv[i])) {
-    printf("INTF initrec ERR vectors not all same size: %d vs %d",vp->size,vector_buffer_size(vp->vv[i]));
+  if (vp->size==0) { vp->size=(unsigned int)vector_buffer_size((IvocVect*)vp->vv[i]);
+  } else if (vp->size != (unsigned int)vector_buffer_size((IvocVect*)vp->vv[i])) {
+    printf("INTF initrec ERR vectors not all same size: %d vs %d",vp->size,vector_buffer_size((IvocVect*)vp->vv[i]));
     hoc_execerror("", 0); 
   }} 
   ENDVERBATIM
@@ -2427,7 +2427,7 @@ PROCEDURE global_init () {
     printf("Initializing ww to record for %g (%g)\n",vdt*wwsz,vdt);
     wwpt=0;
     for (k=0;k<(int)nsw;k++) {
-      vector_resize(ww[k], wwsz);
+      vector_resize((IvocVect*)ww[k], wwsz);
       for (j=0;j<wwsz;j++) wwo[k][j]=0.;
     }
   }
@@ -2443,7 +2443,7 @@ PROCEDURE global_init () {
 PROCEDURE global_fini () {
   VERBATIM
   int k;
-  for (k=0;k<(int)nsw;k++) vector_resize(ww[k], (int)floor(t/vdt+0.5));
+  for (k=0;k<(int)nsw;k++) vector_resize((IvocVect*)ww[k], (int)floor(t/vdt+0.5));
   if (jridv && jrj<jrmax) {
     vector_resize(jridv, jrj); 
     vector_resize(jrtvv, jrj);
diff --git a/intfsw.mod b/intfsw.mod
index 515e0b5..a79ab1a 100644
--- a/intfsw.mod
+++ b/intfsw.mod
@@ -300,7 +300,7 @@ VERBATIM
 //copynz(valvec,binvec)
 static double copynz (void* vv) {
   double* pV;
-  int n = vector_instance_px(vv,&pV) , iCount = 0 , idx=0;
+  int n = vector_instance_px((IvocVect*)vv,&pV) , iCount = 0 , idx=0;
   int iStartIDx = 0, iEndIDx = n - 1;
   if(ifarg(2)){
     iStartIDx = (int)*getarg(1);
@@ -326,7 +326,7 @@ static double copynz (void* vv) {
     }
   }
 
-  vector_resize(pV,iOutSz);
+  vector_resize((IvocVect*)pV,iOutSz);
 
   return (double)iOutSz;
 }
@@ -965,7 +965,7 @@ FUNCTION GetWPath () {
 
   double* ppre = 0, *ppo = 0, *pwght = 0, *pdel = 0, *pout = 0;
   int iSz,iTmp,i,j,k,l;
-  void* voi;
+  IvocVect* voi;
 
   iSz = vector_arg_px(1,&ppre);
 
diff --git a/stats.mod b/stats.mod
index fc7b123..1e379dc 100644
--- a/stats.mod
+++ b/stats.mod
@@ -43,7 +43,7 @@ VERBATIM
 #define MIN_MERGESORT_LIST_SIZE    32
 
 union dblint {
-  int i[2];
+  uint32_t i[2];
   double d;
 };
 
@@ -860,8 +860,8 @@ 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((uint32_t)xx.i[1]);
-      mcell_ran4((uint32_t*)xx.i[0], &y, 1, big); // generate a pseudorand number based on these
+      mcell_ran4_init(xx.i[1]);
+      mcell_ran4(&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
@@ -1298,7 +1298,7 @@ static double comb (void* vv) {
   }
   memset(x,0,sizeof(double)*kk);
   synccv(nn,kk,cc,x);
-  vector_resize(vv,kk);
+  vector_resize((IvocVect*)vv,kk);
   return 1.0;
 }
 ENDVERBATIM
@@ -1408,18 +1408,18 @@ static double rsampsig(void* vv){
     if(verbose>2){ for(j=0;j<n0;j++) pm[pids[j]]=0; for(;j<na;j++) pm[pids[j]]=1;  printf("pm: ");
       for(j=0;j<40;j++) printf("%d",pm[j]); printf("\n"); }//print out bit-array of element ids
     //compare measures between
-    vector_resize(vhso, n0); memcpy(phso,g0t,sizeof(double)*n0); 
+    vector_resize((IvocVect*)vhso, n0); memcpy(phso,g0t,sizeof(double)*n0); 
     hoc_call_func(pHocVecFunc,0); dm0 = hretval; //get measure on group 0
-    vector_resize(vhso, n1); memcpy(phso,g1t,sizeof(double)*n1); 
+    vector_resize((IvocVect*)vhso, n1); memcpy(phso,g1t,sizeof(double)*n1); 
     hoc_call_func(pHocVecFunc,0); dm1 = hretval; //get measure on group 1
     hoc_pushx(dm0); hoc_pushx(dm1); hoc_call_func(pHocCompFunc,2); //call comparison function
     pthis[i]=onesided?hretval:fabs(hretval); //save value from comparison function
   }
-  vector_resize(vv,nruncombs);//resize calling vec
+  vector_resize((IvocVect*)vv,nruncombs);//resize calling vec
   //get comparison function value for original data groups
-  vector_resize(vhso,n0); memcpy(phso,g0,sizeof(double)*n0); 
+  vector_resize((IvocVect*)vhso,n0); memcpy(phso,g0,sizeof(double)*n0); 
   hoc_call_func(pHocVecFunc,0); dm0 = hretval; //get measure on original group 0
-  vector_resize(vhso,n1); memcpy(phso,g1,sizeof(double)*n1); 
+  vector_resize((IvocVect*)vhso,n1); memcpy(phso,g1,sizeof(double)*n1); 
   hoc_call_func(pHocVecFunc,0); dm1 = hretval; //get measure on original group 1
   hoc_pushx(dm0); hoc_pushx(dm1); hoc_call_func(pHocCompFunc,2); //call comparison function
   dmobs = onesided?hretval:fabs(hretval); // "observed" value of statistic  
@@ -1663,6 +1663,7 @@ static double vpr2 (void* vv) {
     }
     printf("\n");
   }
+  return 0;
 }
 
 static void vprpr (double x, int base) {
@@ -1782,7 +1783,7 @@ static double irate (void* vv) {
   unsigned int i, j, n, nx;
   double *prate,*phist,binsz,t1,t2;
   nx = vector_arg_px(1, &phist);
-  vector_resize(vv,nx);
+  vector_resize((IvocVect*)vv,nx);
   vector_instance_px(vv, &prate);
   binsz = *getarg(2);
   for(i=0;i<nx;i++) {
@@ -2024,8 +2025,8 @@ 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((uint32_t)xx.i[1]);
-    mcell_ran4((uint32_t*)xx.i[0], &y, 1, big); // generate a pseudorand number based on these
+    mcell_ran4_init(xx.i[1]);
+    mcell_ran4(&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
   }
@@ -2090,7 +2091,7 @@ FUNCTION mc4seed () {
   for (i=2;ifarg(i);i++) {
     valseed*=(unsigned int)(*getarg(i));
   }
-  mcell_ran4_init((uint32_t)valseed); // do initialization
+  mcell_ran4_init(valseed); // do initialization
   return valseed;
   ENDVERBATIM
 }
diff --git a/vecst.mod b/vecst.mod
index ecb1704..b158936 100644
--- a/vecst.mod
+++ b/vecst.mod
@@ -149,7 +149,7 @@ VERBATIM
 static double ident (void* vv) {
   int nx,bsz; double* x;
   nx = vector_instance_px(vv, &x);
-  bsz=vector_buffer_size(vv);
+  bsz=vector_buffer_size((IvocVect*)vv);
   printf("Obj*%x Dbl*%x Size: %d Bufsize: %d\n",vv,x,nx,bsz);
   return (double)nx;
 }
@@ -345,7 +345,7 @@ static double findx (void* vv) {
   for (i=0;i<num;i++) { 
     bv[i]=list_vector_px2(ob2, i, &bvo[i], &vv_tmp); // dest vectors 
     if (vector_buffer_size((IvocVect*)vv)<ni) { 
-      printf("findx ****ERRD**** arg#%d need:%d sz:%d\n",num+i+1,ni,vector_buffer_size(vv));
+      printf("findx ****ERRD**** arg#%d need:%d sz:%d\n",num+i+1,ni,vector_buffer_size((IvocVect*)vv));
       hoc_execerror("Destination vector with insufficient size: ", 0); 
     } else {
       vector_resize((IvocVect*)vv, ni);
@@ -585,7 +585,7 @@ static double slct (void* vv) {
       if (flag==1) break;
     } 
   }
-  vector_resize(vv, k);
+  vector_resize((IvocVect*)vv, k);
   return (double)k;
 }
 ENDVERBATIM
@@ -673,7 +673,7 @@ static double slor (void* vv) {
     }
     if (fl) ind[k++]=j; // all equal
   }
-  vector_resize(vv, k);
+  vector_resize((IvocVect*)vv, k);
   return (double)k;
 }
 ENDVERBATIM
@@ -736,9 +736,9 @@ static double ird (void* vv) {
     scr=(unsigned int *)ecalloc(scrsz, sizeof(int));
   }
   if (n!=nx) { 
-    nx=vector_buffer_size(vv);
+    nx=vector_buffer_size((IvocVect*)vv);
     if (n<=nx) {
-      vector_resize(vv, n); nx=n; 
+      vector_resize((IvocVect*)vv, n); nx=n; 
     } else {
       printf("%d > %d :: ",n,nx);
       hoc_execerror("Vector max capacity too small for ird ", 0);
@@ -760,14 +760,14 @@ static double fread2 (void* vv) {
 
   fp = hoc_obj_file_arg(1);
   nx = vector_instance_px(vv, &x);
-  maxsz=vector_buffer_size(vv);
+  maxsz=vector_buffer_size((IvocVect*)vv);
   n = (int)*getarg(2);
   type = (int)*getarg(3);
   if (n>maxsz) {
     printf("%d > %d :: ",n,maxsz);
     hoc_execerror("Vector max capacity too small for fread2 ", 0);
   } else {
-    vector_resize(vv, n);
+    vector_resize((IvocVect*)vv, n);
   }
   if (type==6 || type==16) {         // unsigned ints
     unsigned int *xs;
@@ -794,6 +794,7 @@ static double fread2 (void* vv) {
     }
     free((char *)xf);    
   } else hoc_execerror("Type unsupported in fread2 ", 0);
+  return 0; // TODO: Shoulf we return 0 or 1?
 }
 ENDVERBATIM
 
@@ -815,6 +816,7 @@ static double revec (void* vv) {
     }
   }
   vector_resize((IvocVect*)vv,k);
+  return 0; // TODO: Shoulf we return 0 or 1?
 }
 ENDVERBATIM
 
@@ -842,7 +844,7 @@ static double has (void* vv) {
       }
     } else return 1;
   }
-  if (j>0) vector_resize(vc,j); // only fall through here when doing indvwhere
+  if (j>0) vector_resize((IvocVect*)vc,j); // only fall through here when doing indvwhere
   return (double)j; 
 }
 ENDVERBATIM
@@ -917,6 +919,7 @@ static double vfill (void* vv) {
 	nx = vector_instance_px(vv, &x);
 	nv1 = vector_arg_px(1, &v1);
         for (i=0;i<nx;i++) x[i]=v1[i%nv1];
+  return 0; // TODO: Shoulf we return 0 or 1?
 }
 ENDVERBATIM
 
@@ -952,11 +955,11 @@ static double redundout (void* vv) {
   if (ifarg(2)) indflag=(int)*getarg(2); else indflag=0; 
   if (ifarg(3)) { cntflag=1; 
     ncntr = vector_arg_px(3, &cntr);  vc=vector_arg(3); 
-    ncntr = vector_buffer_size(vc);   vector_resize(vc, ncntr);
+    ncntr = vector_buffer_size((IvocVect*)vc);   vector_resize((IvocVect*)vc, ncntr);
     for (i=0;i<ncntr;i++) cntr[i]=1.; // will be at least 1 of each #
   } else cntflag=0;
   nx = vector_instance_px(vv, &x);
-  maxsz=vector_buffer_size(vv);  vector_resize(vv, maxsz);
+  maxsz=vector_buffer_size((IvocVect*)vv);  vector_resize((IvocVect*)vv, maxsz);
   nv1 = vector_arg_px(1, &v1);
   val=v1[0]; x[0]=(indflag?0:val);
   if (cntflag) {
@@ -968,10 +971,10 @@ static double redundout (void* vv) {
   }
   if (j>=maxsz) { 
     printf("\tredundout WARNING: ran out of room: %d<needed\n",maxsz);
-  } else { vector_resize(vv, j); }
+  } else { vector_resize((IvocVect*)vv, j); }
   if (cntflag) if (j>=ncntr) { 
     printf("\tredundout WARNING: cntr ran out of room: %d<needed\n",ncntr);
-  } else { vector_resize(vc, j); }
+  } else { vector_resize((IvocVect*)vc, j); }
   return (double)j;
 }
 ENDVERBATIM
@@ -1098,6 +1101,7 @@ static double vscl (double *x, double n) {
   r=max-min;  // range
   sf = (b-a)/r; // scaling factor
   for (i=0;i<n;i++) x[i]=(x[i]-min)*sf+a;
+  return 0; // TODO: Shoulf we return 0 or 1?
 }
 ENDVERBATIM
 
@@ -1111,6 +1115,7 @@ static double scl (void* vv) {
   if (nx!=nsrc) { hoc_execerror("scl:Vectors not same size: ", 0); }
   for (i=0;i<nx;i++) x[i]=src[i];
   vscl(x,nx);
+  return 0; // TODO: Shoulf we return 0 or 1?
 }
 ENDVERBATIM
 
@@ -1133,6 +1138,7 @@ static double sccvlv (void* vv) {
     vscl(tmp,j-1);
     for (k=0;k<j;k++) x[i]+=filt[k]*tmp[k];
   }
+  return 0; // TODO: Shoulf we return 0 or 1?
 }
 ENDVERBATIM
 
@@ -1189,6 +1195,7 @@ static double cvlv (void* vv) {
       if (k>0 && k<nsrc-1) x[i]+=filt[j]*src[k];
     }
   }
+  return 0; // TODO: Shoulf we return 0 or 1?
 }
 ENDVERBATIM
 
@@ -1273,7 +1280,7 @@ static double nind (void* vv) {
           }
           for (k=last+1;k<nx;k++,m++) { x[m]=vvo[j][k]; }
           for (i=0;i<c;i++) vvo[j][i]=x[i];   
-          vv=vector_arg(j+2); vector_resize(vv, c);
+          vv=vector_arg(j+2); vector_resize((IvocVect*)vv, c);
         }
 	return c;
 }
@@ -1308,7 +1315,7 @@ static double keyind (void* vv) {
     }
     if (i==nk) ind[k++]=j; // all equal
   }
-  vector_resize(vv, k);
+  vector_resize((IvocVect*)vv, k);
   return (double)k;
 }
 ENDVERBATIM
@@ -1435,10 +1442,10 @@ static double samp (void* vv) {
   nx = vector_instance_px(vv, &x); // dest
   iOrigSz = vector_arg_px(1, &y); // source
   dNewSz = *getarg(2);  // new size
-  maxsz=vector_buffer_size(vv); 
+  maxsz=vector_buffer_size((IvocVect*)vv); 
   iNewSz = (int)dNewSz;
   if (iNewSz>maxsz) {printf("VECST samp ERRA: dest vec too small: %d %d\n",iNewSz,maxsz); hxe();}
-  vector_resize(vv,iNewSz);
+  vector_resize((IvocVect*)vv,iNewSz);
 
   scale = (double) iOrigSz / (double) iNewSz;
   for(i=0;i<iNewSz;i++){
@@ -1508,6 +1515,7 @@ static double bpeval (void* vv) {
   } else {
     for (i=0;i<n;i++) vo[i]=outp[i]*(1.-1.*outp[i])*del[i];
   }
+  return 0; // TODO: Shoulf we return 0 or 1?
 }
 ENDVERBATIM
  
@@ -1577,7 +1585,7 @@ static double slone (void* vv) {
   int i, j, n, ni, nsrc, maxsz;
   double *x, *src, val, max, min;
   n = vector_instance_px(vv, &x);
-  maxsz=vector_buffer_size(vv);  vector_resize(vv, maxsz);
+  maxsz=vector_buffer_size((IvocVect*)vv);  vector_resize((IvocVect*)vv, maxsz);
   nsrc = vector_arg_px(1, &src);
   val = *getarg(2);
   if (ifarg(3)) ni=(int)*getarg(3); else {
@@ -1593,7 +1601,7 @@ static double slone (void* vv) {
   }
   for (j=0;src[i]==val && j<maxsz && i<nsrc;i++,j++) x[j]=i;
   if (j==maxsz) printf("vecst slone WARN: OOR %d %d\n",j,maxsz);
-  vector_resize(vv, j);
+  vector_resize((IvocVect*)vv, j);
   return (double)(i-1);
 }
 ENDVERBATIM
@@ -1616,8 +1624,8 @@ static double xing (void* vv) {
     i++;
     if (ifarg(i) && hoc_is_double_arg(i)) th=*getarg(i++);
   }
-  maxsz=vector_buffer_size(vv);
-  vector_resize(vv, maxsz);
+  maxsz=vector_buffer_size((IvocVect*)vv);
+  vector_resize((IvocVect*)vv, maxsz);
   if (ifarg(i)){dest2=vector_newsize(vector_arg(i),maxsz); d2f=i;} else d2f=0;
   if (tvf && nsrc!=ntvec) hoc_execerror("v.xing: vectors not all same size", 0);
   for (i=0,f=0,j=0; i<nsrc; i++) {
@@ -1655,8 +1663,8 @@ static double xing (void* vv) {
       }
     }
   }
-  vector_resize(vv, j);
-  if (d2f) vector_resize(vector_arg(d2f),j);
+  vector_resize((IvocVect*)vv, j);
+  if (d2f) vector_resize((IvocVect*)vector_arg(d2f),j);
   return (double)j;
 }
 ENDVERBATIM
@@ -1672,13 +1680,13 @@ static double snap (void* vv) {
   nsrc = vector_arg_px(1, &src);
   ntvec = vector_arg_px(2, &tvec);
   mdt = *getarg(3);
-  maxsz=vector_buffer_size(vv);
+  maxsz=vector_buffer_size((IvocVect*)vv);
   tstop = tvec[nsrc-1];
   size=(int)tstop/mdt;
   if (size>maxsz) { 
     printf("%d > %d\n",size,maxsz);
     hoc_execerror("v.snap: insufficient room in dest", 0); }
-  vector_resize(vv, size);
+  vector_resize((IvocVect*)vv, size);
   if (nsrc!=ntvec) hoc_execerror("v.snap: src and tvec not same size", 0);
   for (tt=0,i=0;i<size && tt<=tvec[0];i++,tt+=mdt) dest[i]=src[0];
   for (j=1, i--, tt-=mdt; i<size; i++, val=-1e9, tt+=mdt) {
@@ -1835,7 +1843,7 @@ static double fetch (void* vv) {
   if (ix==n) {if (VERBOSE_VECST) printf("vecst:fetch() WARNING: %g not found\n",val); return ERR;}
   if (hoc_is_object_arg(3)) {
     ny = vector_arg_px(3, &y);
-    if (ny>pL->isz) vector_resize(vector_arg(3),pL->isz); // don't make bigger if only want a few
+    if (ny>pL->isz) vector_resize((IvocVect*)vector_arg(3),pL->isz); // don't make bigger if only want a few
     for (i=0,j=0,cnt=0;i<pL->isz && j<ny;i++,j++) {
       if (ix>pL->plen[i]) {printf("vecst:fetch()ERRB: %d %d %x\n",i,ix,pL->pv[i]); 
         FreeListVec(&pL); hxe();}
@@ -1973,7 +1981,7 @@ static double lcat (void* vv) {
   double *x, *fr; 
   IvocVect *vw;
   n = vector_instance_px(vv, &x);
-  vector_resize(vv,maxsz=vector_buffer_size(vv)); // open it up fully
+  vector_resize((IvocVect*)vv,maxsz=vector_buffer_size((IvocVect*)vv)); // open it up fully
   ob1 = *hoc_objgetarg(1);
   lc = ivoc_list_count(ob1);
   for (i=0,j=0;i<lc && j<maxsz;i++) {
@@ -1981,7 +1989,7 @@ static double lcat (void* vv) {
     for (k=0;k<cap && j<maxsz;k++,j++) x[j]=fr[k];
   }
   if (i<lc || k<cap) printf("vecst lcat WARN: not all vecs copied\n");
-  vector_resize(vv,j);
+  vector_resize((IvocVect*)vv,j);
   return (double)j;
 }
 ENDVERBATIM
@@ -2029,9 +2037,9 @@ static double uncode (void* vv) {
   } else if (!ifarg(2)) { // numarg()==1
     if (hoc_is_double_arg(1)) {
       val = *getarg(1);
-      if (vector_buffer_size(vv)<5) {
+      if (vector_buffer_size((IvocVect*)vv)<5) {
         hoc_execerror("uncode ****ERRA****: vector too small to resize(5)", 0);}
-      vector_resize(vv,5);
+      vector_resize((IvocVect*)vv,5);
       for (i=1;i<=5;i++) UNCODE(val,i,x[i-1])
       return x[0];
     } else {
@@ -2086,8 +2094,8 @@ int list_vector_px (Object *ob, int i, double** px) {
   int sz;
   obv = ivoc_list_item(ob, i);
   if (! ISVEC(obv)) return -1;
-  sz = vector_capacity(obv->u.this_pointer);
-  *px = vector_vec(obv->u.this_pointer);
+  sz = vector_capacity((IvocVect*)obv->u.this_pointer);
+  *px = vector_vec((IvocVect*)obv->u.this_pointer);
   return sz;
 }
 
@@ -2098,8 +2106,8 @@ int list_vector_px2 (Object *ob, int i, double** px, IvocVect** vv) {
   int sz;
   obv = ivoc_list_item(ob, i);
   if (! ISVEC(obv)) return -1;
-  sz = vector_capacity(obv->u.this_pointer);
-  *px = vector_vec(obv->u.this_pointer);
+  sz = vector_capacity((IvocVect*)obv->u.this_pointer);
+  *px = vector_vec((IvocVect*)obv->u.this_pointer);
   *vv = (IvocVect*) obv->u.this_pointer;
   return sz;
 }
@@ -2112,8 +2120,8 @@ int list_vector_px3 (Object *ob, int i, double** px, IvocVect** vv) {
   int sz;
   obv = ivoc_list_item(ob, i);
   if (! ISVEC(obv)) return -1;
-  sz = vector_buffer_size(obv->u.this_pointer);
-  *px = vector_vec(obv->u.this_pointer);
+  sz = vector_buffer_size((IvocVect*)obv->u.this_pointer);
+  *px = vector_vec((IvocVect*)obv->u.this_pointer);
   *vv = (IvocVect*) obv->u.this_pointer;
   vector_resize(*vv,sz);
   return sz;
@@ -2127,14 +2135,14 @@ int list_vector_px4 (Object *ob, int i, double** px, unsigned int n) {
   int sz;
   obv = ivoc_list_item(ob, i);
   if (! ISVEC(obv)) return -1;
-  sz = vector_buffer_size(obv->u.this_pointer);
-  *px = vector_vec(obv->u.this_pointer);
+  sz = vector_buffer_size((IvocVect*)obv->u.this_pointer);
+  *px = vector_vec((IvocVect*)obv->u.this_pointer);
   vv = (void*) obv->u.this_pointer;
   if (n>sz) {
     printf("List vector WARNING: unable to resize to %d requested (%d)\n",n,sz);
-    vector_resize(vv,sz);
+    vector_resize((IvocVect*)vv,sz);
     return 0;
-  } else vector_resize(vv,n);
+  } else vector_resize((IvocVect*)vv,n);
   return 1;
 }
 
@@ -2143,8 +2151,8 @@ double *list_vector_resize (Object *ob, int i, int sz) {
   Object* obv;
   obv = ivoc_list_item(ob, i);
   if (! ISVEC(obv)) return 0x0;
-  vector_resize(obv->u.this_pointer,sz);
-  return vector_vec(obv->u.this_pointer);
+  vector_resize((IvocVect*)obv->u.this_pointer,sz);
+  return vector_vec((IvocVect*)obv->u.this_pointer);
 }
 ENDVERBATIM
 
@@ -2394,16 +2402,16 @@ int openvec (int arg, double **y) {
   if (! ISVEC(ob)) return -1;
   vector_arg_px(arg, y);
   vv=vector_arg(arg);
-  max=vector_buffer_size(vv);
-  vector_resize(vv, max);
+  max=vector_buffer_size((IvocVect*)vv);
+  vector_resize((IvocVect*)vv, max);
   if (max==0) printf("openvec(): 0 size vec\n");
   return max;
 }
 
 // vector_newsize() will also increase size of vector
 double *vector_newsize (IvocVect* vv, int n) {
-  vector_resize(vv,n);
-  return vector_vec(vv);
+  vector_resize((IvocVect*)vv,n);
+  return vector_vec((IvocVect*)vv);
 }
 ENDVERBATIM
 
@@ -2427,7 +2435,7 @@ static double pop (void* vv) {
   double *x;
   n = vector_instance_px(vv, &x);
   if (n==0) {printf("vec.pop ERR: empty vec\n");hxe();}
-  vector_resize(vv,n-1);
+  vector_resize((IvocVect*)vv,n-1);
   return x[n-1];
 }
 ENDVERBATIM
@@ -2480,9 +2488,9 @@ static double smgs (void* vv) {
 
   points = (int)((high-low)/step+hoc_epsilon);
   if (nsum!=points) { 
-    maxsz=vector_buffer_size(vv);
+    maxsz=vector_buffer_size((IvocVect*)vv);
     if (points<=maxsz) {
-      nsum=points;  vector_resize(vv, nsum); 
+      nsum=points;  vector_resize((IvocVect*)vv, nsum); 
     } else {
       printf("%d > %d :: ",points,maxsz);
       hoc_execerror("Vector max capacity too small in smgs ", 0);
@@ -2530,9 +2538,9 @@ static double smsy (void* vv) {
 
   points=(int)(tstop/mdt+hoc_epsilon);
   if (nsum!=points) { 
-    maxsz=vector_buffer_size(vv);
+    maxsz=vector_buffer_size((IvocVect*)vv);
     if (points<=maxsz) {
-      vector_resize(vv, points); points=nsum; 
+      vector_resize((IvocVect*)vv, points); points=nsum; 
     } else {
       printf("%d > %d :: ",points,maxsz);
       hoc_execerror("Dest vector too small in smsy ", 0);
@@ -2555,12 +2563,12 @@ static double vrdh (void* vv) {
   FILE* f;
 
   num = vector_instance_px(vv, &x);
-  maxsz=vector_buffer_size(vv);
+  maxsz=vector_buffer_size((IvocVect*)vv);
   f =     hoc_obj_file_arg(1);
   num = (int)*getarg(2); // number of vectors to look for
 
   if (maxsz<2*num){printf("vrdh ERR0 need %d room in vec\n",2*num);hxe();}
-  vector_resize(vv, 2*num);
+  vector_resize((IvocVect*)vv, 2*num);
 
   for (i=0;i<num;i++) { 
     r=fread(&n,sizeof(int),2,f); // n[1] is type
@@ -2768,7 +2776,7 @@ static double rdfile (void* vv) {
       i+=(vsz*sizeof(short));
     } else printf("rdfile() type %d not implemented\n",ty);
   }
-  if (vflag) vector_resize(vector_arg(2), k);
+  if (vflag) vector_resize((IvocVect*)vector_arg(2), k);
   if (scrsz>1e7) { free(scr); scr=(unsigned int *)NULL; scrsz=0; }
   return (double)num;
 }
@@ -3116,9 +3124,9 @@ ListVec* AllocListVec (Object* p) {
   if(!pList->pv){free(pList->plen); printf("AllocListVec ERRC: Out of memory!\n"); hxe();}
   for(i=0;i<pList->isz;i++) {
     obv = ivoc_list_item(p,i);
-    pList->pv[i]=vector_vec(obv->u.this_pointer);
-    pList->plen[i]=vector_capacity(obv->u.this_pointer);
-    pList->pbuflen[i]=vector_buffer_size(obv->u.this_pointer);;
+    pList->pv[i]=vector_vec((IvocVect*)obv->u.this_pointer);
+    pList->plen[i]=vector_capacity((IvocVect*)obv->u.this_pointer);
+    pList->pbuflen[i]=vector_buffer_size((IvocVect*)obv->u.this_pointer);;
   }
   return pList;
 }
@@ -3140,9 +3148,9 @@ ListVec* AllocILV (Object* p, int nx, double *x) {
   for(i=0;i<iSz;i++){
     if ((j=(int)x[i])>=ilc){printf("AllocILV ERRD: index OOB: %d>=%d\n",j,ilc); hxe();}
     obv = ivoc_list_item(p,j);
-    pList->pv[i]=vector_vec(obv->u.this_pointer);
-    pList->plen[i]=vector_capacity(obv->u.this_pointer);
-    pList->pbuflen[i]=vector_buffer_size(obv->u.this_pointer);;
+    pList->pv[i]=vector_vec((IvocVect*)obv->u.this_pointer);
+    pList->plen[i]=vector_capacity((IvocVect*)obv->u.this_pointer);
+    pList->pbuflen[i]=vector_buffer_size((IvocVect*)obv->u.this_pointer);;
   }
   return pList;
 }

From b99bf52a70a869af07d84c925a9bf92f098fa0b5 Mon Sep 17 00:00:00 2001
From: Christos Kotsalos <christos.kotsalos@epfl.ch>
Date: Tue, 17 May 2022 15:12:11 +0200
Subject: [PATCH 07/23] 8.1.0 & 9.0.0 work, except for 8.2.0 ctemplate issue

---
 intfsw.mod | 12 ++++++------
 misc.h     |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/intfsw.mod b/intfsw.mod
index a79ab1a..4a2d6e6 100644
--- a/intfsw.mod
+++ b/intfsw.mod
@@ -454,7 +454,7 @@ FUNCTION GetCCR () {
     return 0.0;
   }
 
-  unsigned int iSeed = ifarg(7)?(unsigned int)*getarg(7):INT_MAX-109754;
+  uint32_t iSeed = ifarg(7)?(uint32_t)*getarg(7):INT_MAX-109754;
 
   double* pUse = 0; 
   
@@ -562,7 +562,7 @@ FUNCTION GetCentrality () {
     return 0.0;
   }
 
-  unsigned int iSeed = ifarg(4)?(unsigned int)*getarg(4):INT_MAX-109754;
+  uint32_t iSeed = ifarg(4)?(uint32_t)*getarg(4):INT_MAX-109754;
 
   double* pUse = 0; 
   
@@ -780,7 +780,7 @@ FUNCTION CountNeighborsR () {
 
   double dSubsamp = ifarg(6)?*getarg(6):1.0;
 
-  unsigned int iSeed = ifarg(7)?(unsigned int)*getarg(7):INT_MAX-109754;
+  uint32_t iSeed = ifarg(7)?(uint32_t)*getarg(7):INT_MAX-109754;
 
   if(iStartID < 0 || iStartID >= iCells ||
      iEndID < 0 || iEndID >= iCells ||
@@ -1185,7 +1185,7 @@ FUNCTION GetPathR () {
 
   double dSubsamp = ifarg(6)?*getarg(6):1.0;
 
-  unsigned int iSeed = ifarg(7)?(unsigned int)*getarg(7):INT_MAX-109754;
+  uint32_t iSeed = ifarg(7)?(uint32_t)*getarg(7):INT_MAX-109754;
 
   if(iStartID < 0 || iStartID >= iCells ||
      iEndID < 0 || iEndID >= iCells ||
@@ -1657,7 +1657,7 @@ FUNCTION GetPathSubPop () {
 
   int bSelfLoop = ifarg(6)?(int)*getarg(6):0;
 
-  unsigned int iSeed = ifarg(7)?(unsigned int)*getarg(7):INT_MAX-109754;
+  uint32_t iSeed = ifarg(7)?(uint32_t)*getarg(7):INT_MAX-109754;
 
   //init array of cells/neighbors to check
   int* pCheck = (int*)malloc(sizeof(int)*iCells);
@@ -1810,7 +1810,7 @@ FUNCTION GetLoopLength () {
   }
   double dSubsamp = ifarg(5)?*getarg(5):1.0;
 
-  unsigned int iSeed = ifarg(6)?(unsigned int)*getarg(6):INT_MAX-109754;
+  uint32_t iSeed = ifarg(6)?(uint32_t)*getarg(6):INT_MAX-109754;
 
   //init array of cells/neighbors to check
   int* pCheck = (int*)malloc(sizeof(int)*iCells);
diff --git a/misc.h b/misc.h
index e02e615..6c70686 100644
--- a/misc.h
+++ b/misc.h
@@ -77,7 +77,7 @@ extern void* vector_arg();
 extern double* vector_vec();
 extern int vector_buffer_size(void*);
 extern void mcell_ran4_init(uint32_t idum);
-extern double mcell_ran4(uint32_t* high, double* x, unsigned int n, double range);
+extern double mcell_ran4(unsigned int* idum,double* ran_vec,unsigned int n,double range);
 extern int nrn_mlh_gsort(double* vec, int* base_ptr, int total_elems, int (*cmp)(double, double));
 extern int ivoc_list_count(Object*);
 extern int hoc_is_double_arg(int narg);

From 148d1a29c264193fae787fe6349e25903c5ddaa1 Mon Sep 17 00:00:00 2001
From: Christos Kotsalos <christos.kotsalos@epfl.ch>
Date: Tue, 17 May 2022 15:17:27 +0200
Subject: [PATCH 08/23] works with all versions

---
 vecst.mod | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/vecst.mod b/vecst.mod
index b158936..5d978a5 100644
--- a/vecst.mod
+++ b/vecst.mod
@@ -2878,10 +2878,10 @@ FUNCTION isojt () {
   Object *ob1, *ob2;
   ob1 = *hoc_objgetarg(1); ob2 = *hoc_objgetarg(2);
   if (!ob1) if (!ob2) return 1; else return 0;
-#ifndef NRN_VERSION_GTEQ_8_2_0
-  if (!ob2 || ob1->template != ob2->template) {
-#else
+#ifdef __cplusplus
   if (!ob2 || ob1->ctemplate != ob2->ctemplate) {
+#else
+  if (!ob2 || ob1->template != ob2->template) {
 #endif
     return 0;
   }

From fd80ad38a49671b0647aaa9465e747045ce10b49 Mon Sep 17 00:00:00 2001
From: Christos Kotsalos <christos.kotsalos@epfl.ch>
Date: Tue, 17 May 2022 15:25:53 +0200
Subject: [PATCH 09/23] works with all versions

---
 driver.hoc | 36 ------------------------------------
 1 file changed, 36 deletions(-)
 delete mode 100644 driver.hoc

diff --git a/driver.hoc b/driver.hoc
deleted file mode 100644
index 5cd147f..0000000
--- a/driver.hoc
+++ /dev/null
@@ -1,36 +0,0 @@
-
-strdef verify_dir_ 
-verify_dir_ = "/gpfs/bbp.cscs.ch/data/project/proj16/kotsalos/nrn_HACK/mdb/ncdemo"
-
-if (name_declared("verify_dir_") == 0) {
-	execute("~strdef verify_dir_")
-	execute("verify_dir_ = \".\"")
-}
-strdef verify_tstr_
-objref verify_glist_, verify_xvec_, verify_yvec_, verify_file_
-verify_file_ = new File()
-sprint(verify_tstr_, "%s/gout", verify_dir_)
-verify_file_.wopen(verify_tstr_)
-verify_xvec_ = new Vector()
-verify_yvec_ = new Vector()
-verify_glist_ = new List("Graph")
-
-proc verify_graph_() {local i, j, k
-	verify_file_.printf("Graphs %d\n", verify_glist_.count)
-	for i=0, verify_glist_.count-1 {
-		verify_file_.printf("%s\n", verify_glist_.object(i))
-		k = 0
-		for (j=-1; (j=verify_glist_.object(i).line_info(j, verify_xvec_)) != -1; ){
-			k += 1
-		}
-		verify_file_.printf("lines %d\n", k)
-		for (j=-1; (j=verify_glist_.object(i).getline(j, verify_xvec_, verify_yvec_)) != -1; ){
-			verify_file_.printf("points %d\n", verify_xvec_.size)
-			verify_file_.printf("xvec%d\n", j)
-			verify_xvec_.printf(verify_file_)
-			verify_file_.printf("yvec%d\n", j)
-			verify_yvec_.printf(verify_file_)
-		}
-	}
-}
-verify_graph_()
\ No newline at end of file

From 92735a7fec7b90e82179cd9883515ceb82cc8a3a Mon Sep 17 00:00:00 2001
From: Ioannis Magkanaris <iomagkanaris@gmail.com>
Date: Tue, 17 May 2022 18:08:42 +0200
Subject: [PATCH 10/23] Added changelog in readme

---
 readme.txt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/readme.txt b/readme.txt
index 4b19334..c1f0679 100644
--- a/readme.txt
+++ b/readme.txt
@@ -59,3 +59,5 @@ For questions/comments/collaborations please contact
 Samuel Neymotin at samn at neurosim dot downstate dot edu
      or
 Bill Lytton at billl at neurosim dot downstate dot edu
+
+20220517 Edited multiple files to support NEURON versions <8.1.0, 8.2.0 and 9.0.0. -NEURON Developers

From db4d3b76d38f0c73b470c648ec314fdec243b51e Mon Sep 17 00:00:00 2001
From: Christos Kotsalos <christos.kotsalos@epfl.ch>
Date: Wed, 18 May 2022 08:11:07 +0200
Subject: [PATCH 11/23] small fixes based on review

---
 intf_.mod | 38 +++++++++++++++++++-------------------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/intf_.mod b/intf_.mod
index 72f378a..d1b3793 100644
--- a/intf_.mod
+++ b/intf_.mod
@@ -44,7 +44,7 @@ typedef struct VPT {
  unsigned int  id;
  unsigned int  size;
  unsigned int  p;
- void*    vv[NSV];
+ IvocVect*    vv[NSV];
  double* vvo[NSV];
 } vpt;
 
@@ -118,7 +118,7 @@ static int cty[CTYPp], process;
 static int CTYN, CTYPi, STYPi, dscrsz; // from labels.hoc
 static double qlimit, *dscr;
 FILE *wf1, *wf2, *tf;
-void*    ww[NSW];
+IvocVect*    ww[NSW];
 double* wwo[NSW];
 static int AM=0, NM=1, GA=2, GB=3, SU=3, IN=4, DP=2; // from labels.hoc
 static double wts[10],hsh[10];  // for jitcons to use as a junk pointer
@@ -1119,7 +1119,7 @@ FUNCTION getconv () {
 VERBATIM 
 {
   int iarg,i,j,k,dvt,sz,prfl,getactive; double *x,flag;
-  void* voi; Point_process **das; id0 *pp;
+  IvocVect* voi; Point_process **das; id0 *pp;
   ip=IDP; pg=ip->pg; // this should be called right after jitcondiv()
   sz=ip->dvt; //  // assume conv similar to div
   getactive=0;
@@ -1131,8 +1131,8 @@ VERBATIM
   }
   if (!ifarg(iarg)) prfl=0; else { prfl=1;
     voi=vector_arg(iarg); 
-    if (flag==2.) { x=vector_newsize((IvocVect*)voi,CTYPi); for (i=0;i<CTYPi;i++) x[i]=0;
-    } else x=vector_newsize((IvocVect*)voi,sz); 
+    if (flag==2.) { x=vector_newsize(voi,CTYPi); for (i=0;i<CTYPi;i++) x[i]=0;
+    } else x=vector_newsize(voi,sz); 
   } 
   for (i=0,k=0; i<cesz; i++) {
     lop(ce,i);
@@ -1142,7 +1142,7 @@ VERBATIM
       if (getactive && qp->sprob[j]==0) continue;
       if (ip==*((id0**) &((das[j]->_prop->dparam)[2]))) {
         if (prfl) {
-          if (flag!=2.0 && k>=sz) x=vector_newsize((IvocVect*)voi,sz*=2);
+          if (flag!=2.0 && k>=sz) x=vector_newsize(voi,sz*=2);
           if (flag==1.0) { x[k]=(double)qp->type; 
           } else if (flag==2.0) { x[qp->type]++; 
           } else x[k]=(double)qp->id;
@@ -1152,7 +1152,7 @@ VERBATIM
       }
     }
   }
-  if (prfl && flag!=2) vector_resize((IvocVect*)voi,k);
+  if (prfl && flag!=2) vector_resize(voi,k);
   _lgetconv=(double)k;
 }
 ENDVERBATIM
@@ -1786,7 +1786,7 @@ PROCEDURE record () {
   if (ip->record==1) {
     while ((int)vp->p >= (int)vp->size-(int)((t-tg)/vdt)-10) { 
       vp->size*=2;
-      for (k=0;k<NSV;k++) if (vp->vv[k]!=0x0) vp->vvo[k]=vector_newsize((IvocVect*)vp->vv[k], vp->size);
+      for (k=0;k<NSV;k++) if (vp->vv[k]!=0x0) vp->vvo[k]=vector_newsize(vp->vv[k], vp->size);
       // printf("**** WARNING expanding recording room to %d (type%d id%d at %g)****\n",vp->size,IDP->type,IDP->id,t);
     }
   } else if ((int)vp->p > (int)vp->size-(int)((t-tg)/vdt)) { // shift if record==2
@@ -2036,13 +2036,13 @@ PROCEDURE test () {
 : lof can find object information
 PROCEDURE lof () {
 VERBATIM {
-  Object *ob; int num,i,ii,j,k,si,nx;  double *vvo[7], *par; void *vv[7];
+  Object *ob; int num,i,ii,j,k,si,nx;  double *vvo[7], *par; IvocVect *vv[7];
   ob = *(hoc_objgetarg(1));
   si=(int)*getarg(2);
   num = ivoc_list_count(ob);
   if (num!=7) { printf("INTF lof ERR %d>7\n",num); hxe(); }
   for (i=0;i<num;i++) { 
-    j = list_vector_px3(ob, i, &vvo[i], (IvocVect**)vv[i]);
+    j = list_vector_px3(ob, i, &vvo[i], &vv[i]);
     if (i==0) nx=j;
     if (j!=nx) { printf("INTF lof ERR %d %d\n",j,nx); hxe(); }
   }
@@ -2111,7 +2111,7 @@ PROCEDURE recini () {
     vp = SOP;
     vp->p=0;
     // open up the vector maximally before writing into it; will correct size in fini
-    for (k=0;k<NSV;k++) if (vp->vvo[k]!=0) vector_resize((IvocVect*)vp->vv[k], vp->size);
+    for (k=0;k<NSV;k++) if (vp->vvo[k]!=0) vector_resize(vp->vv[k], vp->size);
   }}
   ENDVERBATIM
 }
@@ -2126,7 +2126,7 @@ PROCEDURE fini () {
   if (IDP->record) {
     record(); // finish up
     for (k=0;k<NSV;k++) if (vp->vvo[k]!=0) { // not nil pointer
-      vector_resize((IvocVect*)vp->vv[k], vp->p);
+      vector_resize(vp->vv[k], vp->p);
     }
   }}
   ENDVERBATIM
@@ -2163,7 +2163,7 @@ PROCEDURE chk (f) {
   if (lfg==5) { 
     printf("wwpt %d wwsz %d\n WW vecs: ",wwpt,wwsz);
     printf("wwwid %g wwht %d nsw %g\n WW vecs: ",wwwid,(int)wwht,nsw);
-    for (i=0;i<NSW;i++) printf("%d %x %x;",i,ww[i],wwo[i]);
+    for (i=0;i<NSW;i++) printf("%d %p %p;",i,ww[i],wwo[i]);
   }}
   ENDVERBATIM
 }
@@ -2225,9 +2225,9 @@ PROCEDURE initrec () {
   if (i==-1) {printf("INTF record ERR %s not recognized\n",name); hoc_execerror("",0); }
   vp->vv[i]=vector_arg(2);
   vector_arg_px(2, &(vp->vvo[i]));
-  if (vp->size==0) { vp->size=(unsigned int)vector_buffer_size((IvocVect*)vp->vv[i]);
-  } else if (vp->size != (unsigned int)vector_buffer_size((IvocVect*)vp->vv[i])) {
-    printf("INTF initrec ERR vectors not all same size: %d vs %d",vp->size,vector_buffer_size((IvocVect*)vp->vv[i]));
+  if (vp->size==0) { vp->size=(unsigned int)vector_buffer_size(vp->vv[i]);
+  } else if (vp->size != (unsigned int)vector_buffer_size(vp->vv[i])) {
+    printf("INTF initrec ERR vectors not all same size: %d vs %d",vp->size,vector_buffer_size(vp->vv[i]));
     hoc_execerror("", 0); 
   }} 
   ENDVERBATIM
@@ -2277,7 +2277,7 @@ PROCEDURE initwrec () {
     if (num>NSW) { printf("INTF initwrec() WARN: can only store %d ww vecs\n",NSW); hxe();}
     nsw=(double)num;
     for (k=0;k<num;k++) {
-      cap = list_vector_px2(ob, k, &wwo[k], (IvocVect**)ww[k]);
+      cap = list_vector_px2(ob, k, &wwo[k], &ww[k]);
       if (k==0) wwsz=cap; else if (wwsz!=cap) {
         printf("INTF initwrec ERR w-vecs size err: %d,%d,%d",k,wwsz,cap); hxe(); }
     }
@@ -2427,7 +2427,7 @@ PROCEDURE global_init () {
     printf("Initializing ww to record for %g (%g)\n",vdt*wwsz,vdt);
     wwpt=0;
     for (k=0;k<(int)nsw;k++) {
-      vector_resize((IvocVect*)ww[k], wwsz);
+      vector_resize(ww[k], wwsz);
       for (j=0;j<wwsz;j++) wwo[k][j]=0.;
     }
   }
@@ -2443,7 +2443,7 @@ PROCEDURE global_init () {
 PROCEDURE global_fini () {
   VERBATIM
   int k;
-  for (k=0;k<(int)nsw;k++) vector_resize((IvocVect*)ww[k], (int)floor(t/vdt+0.5));
+  for (k=0;k<(int)nsw;k++) vector_resize(ww[k], (int)floor(t/vdt+0.5));
   if (jridv && jrj<jrmax) {
     vector_resize(jridv, jrj); 
     vector_resize(jrtvv, jrj);

From dcdddbca0f8c91ef2349087779920a925f25f195 Mon Sep 17 00:00:00 2001
From: Olli Lupton <oliver.lupton@epfl.ch>
Date: Thu, 19 May 2022 11:14:46 +0200
Subject: [PATCH 12/23] fixup for new wheels, drop register keyword, drop
 values.h for macOS

---
 misc.h    | 21 ++++++---------------
 vecst.mod |  2 +-
 2 files changed, 7 insertions(+), 16 deletions(-)

diff --git a/misc.h b/misc.h
index 6c70686..6647555 100644
--- a/misc.h
+++ b/misc.h
@@ -2,10 +2,10 @@
 
 #include <stdlib.h>
 #include <math.h>
+#include <float.h> /* contains DBL_MAX */
 #include <limits.h> /* contains LONG_MAX */
 #include <time.h>
-#include <sys/time.h> 
-#include <values.h>
+#include <sys/time.h>
 #include <pthread.h>
 #include <stdint.h>
 
@@ -54,10 +54,10 @@ 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;
@@ -93,15 +93,6 @@ extern void clear_event_queue();
 extern void cvode_fadvance(double);
 extern int hoc_is_tempobj_arg(int narg);
 extern Object* ivoc_list_item(Object*, int);
-#else // TODO: Update nrn master & C++ PR
-#ifdef __cplusplus
-extern "C" {
-#endif
-Object* ivoc_list_item(Object*, int);
-Symbol* hoc_get_symbol(const char* var);
-#ifdef __cplusplus
-}
-#endif
 #endif
 extern unsigned int hashseed2 (int na, double* x);
 extern unsigned int  dcrsz;
diff --git a/vecst.mod b/vecst.mod
index 5d978a5..907b150 100644
--- a/vecst.mod
+++ b/vecst.mod
@@ -1343,7 +1343,7 @@ ENDVERBATIM
 : max is maximum diff to add to the tq db
 VERBATIM
 static double nearall (void* vv) {
-  register int	lo, hi, mid;
+  int lo, hi, mid;
   int i, j, k, kk, nx, ny, minind, nv[4];
   Object *ob;
   IvocVect* vvl[4];

From 0eb8038f92da7752e4b48a9a8294a799e052d4fa Mon Sep 17 00:00:00 2001
From: Olli Lupton <oliver.lupton@epfl.ch>
Date: Thu, 19 May 2022 16:40:07 +0200
Subject: [PATCH 13/23] fixup for new 8.2 wheel

---
 vecst.mod | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vecst.mod b/vecst.mod
index 907b150..6e9a6d9 100644
--- a/vecst.mod
+++ b/vecst.mod
@@ -2878,7 +2878,7 @@ FUNCTION isojt () {
   Object *ob1, *ob2;
   ob1 = *hoc_objgetarg(1); ob2 = *hoc_objgetarg(2);
   if (!ob1) if (!ob2) return 1; else return 0;
-#ifdef __cplusplus
+#ifdef NRN_VERSION_GTEQ_8_2_0
   if (!ob2 || ob1->ctemplate != ob2->ctemplate) {
 #else
   if (!ob2 || ob1->template != ob2->template) {

From 2cce6fab73ba0cc3282ecf04e63996651f93ad38 Mon Sep 17 00:00:00 2001
From: Olli Lupton <oliver.lupton@epfl.ch>
Date: Mon, 23 May 2022 10:27:21 +0200
Subject: [PATCH 14/23] fix warnings

---
 infot.mod   |  2 +-
 intf_.mod   | 12 +++++++-----
 netrand.inc | 10 +++++-----
 readme.txt  |  6 +++++-
 stats.mod   |  2 +-
 vecst.mod   |  2 +-
 6 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/infot.mod b/infot.mod
index f922108..a30b5eb 100644
--- a/infot.mod
+++ b/infot.mod
@@ -865,7 +865,7 @@ double entropxfgxpd (double* pXP, double* pXFXP,int minv,int maxv,int szp) {
       if (usetable && tmp[3]>=MINLOG2 && tmp[3]<=MAXLOG2) {
         tmp[0] -=tmp[2]*_n_LOG2(tmp[3]);
       } else {  tmp[0] -=tmp[2]*  log2d(tmp[3]); if (usetable&&verbose>0.4) { 
-          printf("WARNA:%g outside of [%g,%g] TABLE\n",tmp[4],MINLOG2,MAXLOG2); }}}}
+          printf("WARNA:%g outside of [%g,%g] TABLE\n",tmp[3],MINLOG2,MAXLOG2); }}}}
   return tmp[0];        
 }
 
diff --git a/intf_.mod b/intf_.mod
index d1b3793..ef45989 100644
--- a/intf_.mod
+++ b/intf_.mod
@@ -1950,11 +1950,12 @@ PROCEDURE trvsp ()
 {
   VERBATIM 
   int i, flag; 
-  double ind, t0;
+  double ind, local_t0;
   ip=IDP;
   flag=(int) *getarg(1);
   if (subsvint==0.) {printf("trvsp"); return(0.);}
-  ind=isp[0]; t0=vsp[0];
+  ind=isp[0];
+  local_t0=vsp[0];
   if (flag==1) {
     for (i=0; i<vspn; i++) {
       if (isp[i]!=ind) {
@@ -1966,11 +1967,12 @@ PROCEDURE trvsp ()
   } else if (flag==2) {
     for (i=0; i<vspn; i++) {
       if (isp[i]!=ind) {
-        vsp[i-1]=t0+subsvint;
-        ind=isp[i]; t0=vsp[i];
+        vsp[i-1] = local_t0 + subsvint;
+        ind = isp[i];
+        local_t0 = vsp[i];
       }
     }
-    vsp[vspn-1]=t0+subsvint;
+    vsp[vspn-1] = local_t0 + subsvint;
   } else {printf("trvsp flag %d not recognized\n",flag); hxe();}
   ENDVERBATIM
 }
diff --git a/netrand.inc b/netrand.inc
index 1a2d7f0..59ff392 100644
--- a/netrand.inc
+++ b/netrand.inc
@@ -109,13 +109,13 @@ NET_RECEIVE (weight, on, nspike, r0, t0 (ms)) {
 
 PROCEDURE initrnd () {
   VERBATIM
-  int i,j,max;
-  if (hoc_is_str_arg(i=1)) { 
-    i++;
+  int local_i,j,max;
+  if (hoc_is_str_arg(local_i=1)) {
+    local_i++;
     cbsv=hoc_lookup(gargstr(1));
   }
-  j=vector_arg_px(i++, &ip->tsp);
-  max=vector_arg_px(i++, &ip->wsp);
+  j=vector_arg_px(local_i++, &ip->tsp);
+  max=vector_arg_px(local_i++, &ip->wsp);
   if (max!=j) {printf("initrnd ERR: vecs of different size: %d %d\n",max,j); hxe();}
   if (max==0) {printf("initrnd ERR: vec not initialized\n"); hxe();}
   ENDVERBATIM
diff --git a/readme.txt b/readme.txt
index c1f0679..567957f 100644
--- a/readme.txt
+++ b/readme.txt
@@ -60,4 +60,8 @@ Samuel Neymotin at samn at neurosim dot downstate dot edu
      or
 Bill Lytton at billl at neurosim dot downstate dot edu
 
-20220517 Edited multiple files to support NEURON versions <8.1.0, 8.2.0 and 9.0.0. -NEURON Developers
+--------------------------------------------------------------------------
+                             Changelog
+--------------------------------------------------------------------------
+2022-05: Updated MOD files to contain valid C++ and be compatible with the
+         upcoming versions 8.2 and 9.0 of NEURON.
diff --git a/stats.mod b/stats.mod
index 1e379dc..498a952 100644
--- a/stats.mod
+++ b/stats.mod
@@ -1445,7 +1445,7 @@ 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;
diff --git a/vecst.mod b/vecst.mod
index 6e9a6d9..93a9dda 100644
--- a/vecst.mod
+++ b/vecst.mod
@@ -1293,7 +1293,7 @@ static double keyind (void* vv) {
   int i, j, k, ni, nk, nv[VRRY], num;
   double *ind, *key, *vvo[VRRY];
   ni = vector_instance_px(vv, &ind); // vv is ind
-  for (i=0;ifarg(i);i++); i--; // drop back by one to get numarg()
+  for (i=0;ifarg(i);i++) {} i--; // drop back by one to get numarg()
   if (i>VRRY) hoc_execerror("ERR: keyind can only handle VRRY vectors", 0);
   num = i-1; // number of vectors to be picked apart 
   for (i=0;i<num;i++) { 

From 75466d486f98392d0b38c3f10b2ef8815fdb24b7 Mon Sep 17 00:00:00 2001
From: Olli Lupton <oliver.lupton@epfl.ch>
Date: Mon, 23 May 2022 10:40:14 +0200
Subject: [PATCH 15/23] add comments about C compilation warnings

---
 infot.mod | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/infot.mod b/infot.mod
index a30b5eb..cdfd7e1 100644
--- a/infot.mod
+++ b/infot.mod
@@ -417,6 +417,7 @@ double tentropd (double* x,double* y,int iLen,int nbins,int xpast,int ypast,int
   dsum=0.0;
   *sig=-1e6;//init sig to neg
   *nTE = 0.0;
+  /* 2nd cntpx should be cntpxy? */
   sh=cntjxy=cntjx=cntpx=cntpx=0;   teavg=testd=te=teout=0.0;
 
   px = nbins>0 ? getnormd(x,iLen,nbins) : doublep2intp(x,iLen); //discretize x to nbins, or just copy to ints
@@ -1105,6 +1106,7 @@ static double tetrospks2 (double* X1d,double* X2d,double* XO,int szX1,int szXO,i
     cnt1/=sz; cnt2/=sz; // ignore if not enough of the windows are filled
     if (cnt1<binmin) return -11.; else if (cnt2<binmin) return -12.;
     if (binmax) if (cnt1>binmax) return -11.; else if (cnt2>binmax) return -12.;
+    /* this should perhaps be fabs */
     if (abs(cnt1-cnt2)>cutoff) return -13.;
   }
   if(verbose>2)printf("tentropspks:minv1=%d,maxv1=%d,minv2=%d,maxv2=%d\n",minv1,maxv1,minv2,maxv2);

From 7c83f84130efe5b2754cd8c9c7d2caa7dd6989c6 Mon Sep 17 00:00:00 2001
From: Olli Lupton <oliver.lupton@epfl.ch>
Date: Mon, 23 May 2022 10:47:24 +0200
Subject: [PATCH 16/23] reduce diff and preserve probably-buggy behaviour.

---
 stats.mod | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/stats.mod b/stats.mod
index 498a952..c947b09 100644
--- a/stats.mod
+++ b/stats.mod
@@ -39,6 +39,7 @@ PARAMETER {
 ASSIGNED { seed }
 
 VERBATIM
+#include <stdint.h>
 #include "misc.h"
 #define MIN_MERGESORT_LIST_SIZE    32
 
@@ -860,7 +861,8 @@ 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]);
+      /* casts are trying to preserve (probably buggy) C behaviour in C++ */
+      mcell_ran4_init((uint32_t)(uintptr_t)&xx.i[1]);
       mcell_ran4(&xx.i[0], &y, 1, big); // generate a pseudorand number based on these
       prod*=y;  // keep multiplying these out
     }
@@ -2025,7 +2027,8 @@ 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]);
+    /* casts are trying to preserve (probably buggy) C behaviour in C++ */
+    mcell_ran4_init((uint32_t)(uintptr_t)&xx.i[1]);
     mcell_ran4(&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 +2094,8 @@ FUNCTION mc4seed () {
   for (i=2;ifarg(i);i++) {
     valseed*=(unsigned int)(*getarg(i));
   }
-  mcell_ran4_init(valseed); // do initialization
+  /* casts are trying to preserve (probably buggy) C behaviour in C++ */
+  mcell_ran4_init((uint32_t)(uintptr_t)&valseed); // do initialization
   return valseed;
   ENDVERBATIM
 }

From a1d83b94ebf8d23286b8269d31abdd2c11fe7f5d Mon Sep 17 00:00:00 2001
From: Olli Lupton <oliver.lupton@epfl.ch>
Date: Mon, 23 May 2022 11:01:13 +0200
Subject: [PATCH 17/23] reduce diff and preserve probably-buggy behaviour.

---
 intf_.mod | 39 +++++++++++++++++++++------------------
 misc.mod  | 14 +++++++++-----
 stats.mod |  3 +--
 vecst.mod | 16 ++++++++--------
 4 files changed, 39 insertions(+), 33 deletions(-)

diff --git a/intf_.mod b/intf_.mod
index ef45989..618eb2a 100644
--- a/intf_.mod
+++ b/intf_.mod
@@ -325,7 +325,8 @@ unsigned int GetDVIDSeedVal(unsigned int id) {
   } else { 
     if (seadsetting==2) printf("Warning: GetDVIDSeedVal called with wt rand turned off\n");
     x[0]=(double)id; x[1]=seaddvioff;
-    sead=hashseed2(2,x);
+    /* the cast is trying to preserve (probably buggy) C behaviour in C++ */
+    sead=hashseed2(2, (double*)&x);
   }
   return sead;
 }
@@ -350,7 +351,7 @@ ENDVERBATIM
   VERBATIM
   if (stopoq && !qsz()) stoprun=1;
   ip=IDP; pg=ip->pg;
-  if (ip->dead) return;
+  if (ip->dead) return; // this cell has died
   _ljcn=ip->jcn; _lid=ip->id;
   tpnt = _pnt; // this pnt
   if (PATHMEASURE) { // do all code for this
@@ -416,7 +417,8 @@ ENDVERBATIM
           sead=(unsigned int)(floor(_lflag)*ip->id*seedstep); // all integers
         } else { // hash on presynaptic id+FOFFSET,poid,seedstep
           hsh[0]=floor(_lflag); hsh[1]=(double)ip->id; hsh[2]=seedstep;
-          sead=hashseed2(3,hsh); // hsh[] is just scratch pad
+          /* the cast is trying to preserve (probably buggy) C behaviour in C++ */
+          sead=hashseed2(3,(double*)&hsh); // hsh[] is just scratch pad
         }
         mcell_ran4(&sead, &_args[sy], 2, 1.);
         for (ii=sy;ii<sy+2;ii++) { // scale appropriately; 
@@ -912,7 +914,7 @@ PROCEDURE callback (fl) {
     if (jp->sprob[i]) (*pnt_receive[jp->dvi[i]->_prop->_type])(jp->dvi[i], wts, idty); 
     _p=upnt->_prop->param; _ppvar=upnt->_prop->dparam; // restore pointers
     i++;
-    if (i>=jp->dvt) return 0; // ran out TODO:Ask Michel
+    if (i>=jp->dvt) return 0; // ran out
     ddel=jp->del[i]-del0;   // delays are relative to event; use difference in delays
   }
   // skip over pruned outputs and dead cells:
@@ -936,7 +938,7 @@ VERBATIM {
   int i,j,k,prty,poty,dv,dvt,dvii; double *x, *db, *dbs; 
   Object *lb;  Point_process *pnnt, **da, **das;
   ip=IDP; pg=ip->pg; // this should be called right after jitcondiv()
-  if (ip->dead) return 0; // TODO: Ask Michael
+  if (ip->dead) return 0;
   prty=ip->type;
   sead=GetDVIDSeedVal(ip->id);//seed for divergence and delays
   for (i=0,k=0,dvt=0;i<CTYN;i++) { // dvt gives total divergence
@@ -1054,7 +1056,7 @@ FUNCTION getdvi () {
     void* voi, *voi2,*voi3; Point_process **das;
     ip=IDP; pg=ip->pg; // this should be called right after jitcondiv()
     getactive=a2=a3=a4=0;
-    if (ip->dead) return 0; // TODO: Ask Michael
+    if (ip->dead) return 0;
     dvt=ip->dvt;
     dbs=ip->del;   das=ip->dvi;
     _lgetdvi=(double)dvt; 
@@ -1097,7 +1099,8 @@ FUNCTION getdvi () {
             sead=(unsigned int)(FOFFSET+ip->id)*qp->id*seedstep; 
           } else { // hashed sead setting
             hsh[0]=(double)(FOFFSET+ip->id); hsh[1]=(double)(qp->id); hsh[2]=seedstep;
-            sead=hashseed2(3,hsh); 
+            /* the cast is trying to preserve (probably buggy) C behaviour in C++ */
+            sead=hashseed2(3, (double*)&hsh);
           }
           mcell_ran4(&sead, y, 2, 1.);
           for(ii=0;ii<2;ii++) {
@@ -1395,9 +1398,9 @@ ENDVERBATIM
 PROCEDURE setdvi () {
 VERBATIM {
   int i,dvt,flag; double *d, *y;
-  if (! ifarg(1)) {printf("setdvi(v1,v2[,flag]): v1:cell#s; v2:delays\n"); return 0; } // TODO: Ask Michael
+  if (! ifarg(1)) {printf("setdvi(v1,v2[,flag]): v1:cell#s; v2:delays\n"); return 0; }
   ip=IDP; pg=ip->pg; // this should be called right after jitcondiv()
-  if (ip->dead) return 0; // TODO: Ask Michael
+  if (ip->dead) return 0;
   dvt=vector_arg_px(1, &y);
   i=vector_arg_px(2, &d);
   if (ifarg(3)) flag=(int)*getarg(3); else flag=0;
@@ -1460,7 +1463,7 @@ PROCEDURE prune () {
       printf("INTFpruneB:Div exceeds dscrsz: %d>%d\n",ip->dvt,dscrsz); hxe(); }
     if (p==0.) {
       for (j=0;j<ip->dvt;j++) ip->sprob[j]=1; // unprune completely
-      return 0; // now that unpruning is done, can return TODO: Ask Michael
+      return 0; // now that unpruning is done, can return
     }
     potype=ifarg(2)?(int)*getarg(2):-1;
     sead=(ifarg(3))?(unsigned int)*getarg(3):GetDVIDSeedVal(ip->id);//seed for divergence and delays
@@ -1639,7 +1642,7 @@ PROCEDURE jitrec () {
   int i;
   if (! ifarg(2)) { // clear with jitrec() or jitrec(0)
     jrmax=0; jridv=0x0; jrtvv=0x0;
-    return 0; // TODO: Ask Michael
+    return 0;
   }
   i =   vector_arg_px(1, &jrid); // could just set up the pointers once
   jrmax=vector_arg_px(2, &jrtv);
@@ -1782,7 +1785,7 @@ PROCEDURE record () {
   VERBATIM {
   int i,j,k,nz; double ti;
   vp = SOP;
-  if (tg>=t) return 0; // TODO: Ask Michael
+  if (tg>=t) return 0;
   if (ip->record==1) {
     while ((int)vp->p >= (int)vp->size-(int)((t-tg)/vdt)-10) { 
       vp->size*=2;
@@ -1820,7 +1823,7 @@ PROCEDURE recspk (x) {
   VERBATIM { int k;
   vp = SOP;
   record();
-  if (vp->p > vp->size || vp->vvo[6]==0) return 0; // TODO: Ask Michael 
+  if (vp->p > vp->size || vp->vvo[6]==0) return 0;
   if (vp->vvo[0]!=0x0) vp->vvo[0][vp->p-1]=_lx;
   vp->vvo[6][vp->p-1]=spkht; // the spike
   tg=_lx;
@@ -2318,7 +2321,7 @@ PROCEDURE wrecord (te) {
           wwo[wrp][k+j] += scale*_t_Psk[j+max]; // direct copy from the Psk table
         }
       }
-    } else if (twg>=t) { return 0; // TODO: Ask Michael
+    } else if (twg>=t) { return 0;
     } else {
       for (ti=twg,k=(int)floor((twg-rebeg)/vdt+0.5);ti<=t && k<wwsz;ti+=vdt,k++) { 
         valps(ti,twg);  // valps() for pop spike calculation
@@ -2489,11 +2492,11 @@ FUNCTION flag () {
   char *sf; static int ix,fi,setfl,nx; static unsigned char val; static double *x, delt;
   if (FLAG==OK) { // callback -- DO NOT SET FROM HOC
     FLAG=0.;
-    if (stoprun) {slowset=0; return 0;} // TODO: Ask Michael
+    if (stoprun) {slowset=0; return 0;}
     if (IDP->dbx==-1)printf("slowset fi:%d ix:%d ss:%g delt:%g t:%g\n",fi,ix,slowset,delt,t);
     if (t>slowset || ix>=cesz) {  // done
       printf("Slow-setting of flag %d finished at %g: (%d,%g,%g)\n",fi,t,ix,delt,slowset); 
-      slowset=0.; return 0; // TODO: Ask Michael
+      slowset=0.; return 0;
     }
     if (ix<cesz) {
       lop(ce,ix);
@@ -2505,12 +2508,12 @@ FUNCTION flag () {
       net_send((void**)0x0, wts,tpnt,delt,OK);
       #endif
     }
-    return 0; // TODO: Ask Michael
+    return 0;
   }  
   if (slowset>0 && ifarg(3)) {
     printf("INTF flag() slowset ERR; attempted set during slowset: fi:%d ix:%d ss:%g delt:%g t:%g",\
            fi,ix,slowset,delt,t); 
-    return 0; // TODO: Ask Michael
+    return 0;
   }
   ip = IDP; setfl=ifarg(3); 
   if (ifarg(4)) { slowset=*getarg(4); delt=slowset/cesz; slowset+=t; } 
diff --git a/misc.mod b/misc.mod
index 6c5600b..c5e97c5 100644
--- a/misc.mod
+++ b/misc.mod
@@ -92,12 +92,13 @@ VERBATIM
 
     if( !(pipein = popen(syscall, "r"))) {
         fprintf(stderr,"System call failed\n");
-        return 0; // TODO: Ask Michael
+        return 0;
     }
     
     if (fgets(string,BUFSIZ,pipein) == NULL) {
         fprintf(stderr,"System call did not return a string\n");
-        pclose(pipein); return 0; // TODO: Ask Michael
+        pclose(pipein);
+        return 0;
     }
 
     /*  assign_hoc_str(strname, string, 0); */
@@ -120,17 +121,20 @@ VERBATIM
 
     if ( !(outfile = fopen("dassign","w"))) {
         fprintf(stderr,"Can't open output file dassign\n");
-        return 0; // TODO: Ask Michael
+        return 0;
     }
 
     if( !(pipein = popen(syscall, "r"))) {
         fprintf(stderr,"System call failed\n");
-        fclose(outfile); return 0; // TODO: Ask Michael
+        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 0; // TODO: Ask Michael
+        fclose(outfile);
+        pclose(pipein);
+        return 0;
     }
 
     fprintf(outfile,"%s=%g\n",strname,num);
diff --git a/stats.mod b/stats.mod
index c947b09..d4348b6 100644
--- a/stats.mod
+++ b/stats.mod
@@ -2123,7 +2123,7 @@ FUNCTION gammln (xx) {
 FUNCTION betai(a,b,x) {
 VERBATIM {
   double bt;
-  double gammln(double),betacf(double,double,double);
+  double betacf(double,double,double);
 
   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;
@@ -2197,7 +2197,6 @@ FUNCTION tstat() {
 
 FUNCTION tdistrib() {
   VERBATIM
-  double gammln(double);
   double x = *getarg(1);
   double dof = *getarg(2);
   double res = (gammln( (dof+1.0) / 2.0 )  / gammln( dof / 2.0 ) );
diff --git a/vecst.mod b/vecst.mod
index 93a9dda..b6efa47 100644
--- a/vecst.mod
+++ b/vecst.mod
@@ -794,7 +794,7 @@ static double fread2 (void* vv) {
     }
     free((char *)xf);    
   } else hoc_execerror("Type unsupported in fread2 ", 0);
-  return 0; // TODO: Shoulf we return 0 or 1?
+  return 0;
 }
 ENDVERBATIM
 
@@ -816,7 +816,7 @@ static double revec (void* vv) {
     }
   }
   vector_resize((IvocVect*)vv,k);
-  return 0; // TODO: Shoulf we return 0 or 1?
+  return 0;
 }
 ENDVERBATIM
 
@@ -919,7 +919,7 @@ static double vfill (void* vv) {
 	nx = vector_instance_px(vv, &x);
 	nv1 = vector_arg_px(1, &v1);
         for (i=0;i<nx;i++) x[i]=v1[i%nv1];
-  return 0; // TODO: Shoulf we return 0 or 1?
+  return 0;
 }
 ENDVERBATIM
 
@@ -1101,7 +1101,7 @@ static double vscl (double *x, double n) {
   r=max-min;  // range
   sf = (b-a)/r; // scaling factor
   for (i=0;i<n;i++) x[i]=(x[i]-min)*sf+a;
-  return 0; // TODO: Shoulf we return 0 or 1?
+  return 0;
 }
 ENDVERBATIM
 
@@ -1115,7 +1115,7 @@ static double scl (void* vv) {
   if (nx!=nsrc) { hoc_execerror("scl:Vectors not same size: ", 0); }
   for (i=0;i<nx;i++) x[i]=src[i];
   vscl(x,nx);
-  return 0; // TODO: Shoulf we return 0 or 1?
+  return 0;
 }
 ENDVERBATIM
 
@@ -1138,7 +1138,7 @@ static double sccvlv (void* vv) {
     vscl(tmp,j-1);
     for (k=0;k<j;k++) x[i]+=filt[k]*tmp[k];
   }
-  return 0; // TODO: Shoulf we return 0 or 1?
+  return 0;
 }
 ENDVERBATIM
 
@@ -1195,7 +1195,7 @@ static double cvlv (void* vv) {
       if (k>0 && k<nsrc-1) x[i]+=filt[j]*src[k];
     }
   }
-  return 0; // TODO: Shoulf we return 0 or 1?
+  return 0;
 }
 ENDVERBATIM
 
@@ -1515,7 +1515,7 @@ static double bpeval (void* vv) {
   } else {
     for (i=0;i<n;i++) vo[i]=outp[i]*(1.-1.*outp[i])*del[i];
   }
-  return 0; // TODO: Shoulf we return 0 or 1?
+  return 0;
 }
 ENDVERBATIM
  

From 66dcd359b7d554d177a89bdcf527254c6bf57fbb Mon Sep 17 00:00:00 2001
From: Olli Lupton <oliver.lupton@epfl.ch>
Date: Mon, 23 May 2022 17:03:42 +0200
Subject: [PATCH 18/23] Object member is called template in C in 8.2

---
 vecst.mod | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/vecst.mod b/vecst.mod
index b6efa47..2e7fc83 100644
--- a/vecst.mod
+++ b/vecst.mod
@@ -2878,11 +2878,15 @@ FUNCTION isojt () {
   Object *ob1, *ob2;
   ob1 = *hoc_objgetarg(1); ob2 = *hoc_objgetarg(2);
   if (!ob1) if (!ob2) return 1; else return 0;
+#define ctemplate template
 #ifdef NRN_VERSION_GTEQ_8_2_0
-  if (!ob2 || ob1->ctemplate != ob2->ctemplate) {
-#else
-  if (!ob2 || ob1->template != ob2->template) {
+#if NRN_VERSION_GTEQ(9, 0, 0)
+#undef ctemplate
+#define ctemplate ctemplate
+#endif
 #endif
+  if (!ob2 || ob1->ctemplate != ob2->ctemplate) {
+#undef ctemplate
     return 0;
   }
   return 1;

From b5e40d6b97ef356ca0030976f406e0c74d753965 Mon Sep 17 00:00:00 2001
From: Ioannis Magkanaris <iomagkanaris@gmail.com>
Date: Tue, 24 May 2022 11:00:17 +0200
Subject: [PATCH 19/23] Addressed Pramod's comments

---
 infot.mod  |  4 ----
 misc.mod   |  2 +-
 updown.mod |  2 +-
 vecst.mod  | 10 ++++------
 4 files changed, 6 insertions(+), 12 deletions(-)

diff --git a/infot.mod b/infot.mod
index cdfd7e1..90af70d 100644
--- a/infot.mod
+++ b/infot.mod
@@ -34,10 +34,6 @@ static void pdfpr (double* pdf,int szp,int dim, char* name);
 static double tetrospks3 (double* X1d,double* X2d,double* X3d,double* XO,int szX1,int szXO,int shuf);
 static int dbxi[10];
 
-static double tetrospks2 (double* X1d,double* X2d,double* XO,int szX1,int szXO,int shuf);
-static void pdfpr (double* pdf,int szp,int dim, char* name);
-static double tetrospks3 (double* X1d,double* X2d,double* X3d,double* XO,int szX1,int szXO,int shuf);
-
 typedef struct ITNode_ {
   int idims;
   int icount;
diff --git a/misc.mod b/misc.mod
index c5e97c5..9442107 100644
--- a/misc.mod
+++ b/misc.mod
@@ -48,7 +48,7 @@ VERBATIM
 #include <time.h>
 #include <stdio.h>
 #include <limits.h>
-#include <misc.h>
+#include "misc.h"
 extern int hoc_is_tempobj(int narg);
 ENDVERBATIM
 
diff --git a/updown.mod b/updown.mod
index 8ecd7dc..ec290b7 100644
--- a/updown.mod
+++ b/updown.mod
@@ -19,7 +19,7 @@ VERBATIM
 #include <math.h>
 #include <limits.h> // contains LONG_MAX 
 #include <sys/time.h> 
-#include <misc.h>
+#include "misc.h"
 static void hxf(void *ptr) { free(ptr); hoc_execerror("",0); }
 ENDVERBATIM
 
diff --git a/vecst.mod b/vecst.mod
index 2e7fc83..a6c0170 100644
--- a/vecst.mod
+++ b/vecst.mod
@@ -325,7 +325,6 @@ ENDVERBATIM
 : uses ind as index into vecA's to load in vecB's (for select); a nondestructive fewind()
 VERBATIM
 static double findx (void* vv) {
-  IvocVect* vv_tmp = (IvocVect*)vv;
   int i, j, ni, nx, av[VRRY], bv[VRRY], num;
   Object *ob1, *ob2;
   double *ind, *avo[VRRY], *bvo[VRRY];
@@ -343,7 +342,7 @@ static double findx (void* vv) {
   }
   nx=av[0]; // size of source vecs
   for (i=0;i<num;i++) { 
-    bv[i]=list_vector_px2(ob2, i, &bvo[i], &vv_tmp); // dest vectors 
+    bv[i]=list_vector_px2(ob2, i, &bvo[i], (IvocVect**)&vv); // dest vectors 
     if (vector_buffer_size((IvocVect*)vv)<ni) { 
       printf("findx ****ERRD**** arg#%d need:%d sz:%d\n",num+i+1,ni,vector_buffer_size((IvocVect*)vv));
       hoc_execerror("Destination vector with insufficient size: ", 0); 
@@ -370,7 +369,6 @@ ENDVERBATIM
 : ind picks out specific vectors if not doing all of them
 VERBATIM
 static double lma (void* vv) {
-  IvocVect* vv_tmp = (IvocVect*)vv;
   int i, j, k, ia, ib, ni, nj, nx, av[VRRY], bv[VRRY], num, numb, beg, end, *xx;
   Object *ob1, *ob2;
   double *ind, *avo[VRRY], *bvo[VRRY], mul,mmul,add,madd;
@@ -397,7 +395,7 @@ static double lma (void* vv) {
   nx=av[0]; // size of source vecs
   if (beg>=end || beg<0 || end>nx) {printf("lma ERRC1 OOB %d - %d (%d)\n",beg,end,nx); hxe();}
   for (i=0;i<num;i++) { 
-    bv[i]=list_vector_px2(ob2, i, &bvo[i], &vv_tmp); // dest vectors 
+    bv[i]=list_vector_px2(ob2, i, &bvo[i], (IvocVect**)&vv); // dest vectors 
     if (bv[i]!=(end-beg)) bvo[i]=vector_newsize((IvocVect*)vv, end-beg);
   }
   if (nj>0) {
@@ -2410,8 +2408,8 @@ int openvec (int arg, double **y) {
 
 // vector_newsize() will also increase size of vector
 double *vector_newsize (IvocVect* vv, int n) {
-  vector_resize((IvocVect*)vv,n);
-  return vector_vec((IvocVect*)vv);
+  vector_resize(vv,n);
+  return vector_vec(vv);
 }
 ENDVERBATIM
 

From 927bcdc570ef2f8d386a0d9b71d0da6fa6fc5fb6 Mon Sep 17 00:00:00 2001
From: Olli Lupton <oliver.lupton@epfl.ch>
Date: Tue, 24 May 2022 12:50:35 +0200
Subject: [PATCH 20/23] mcell_ran4_init: pass a value

---
 stats.mod | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/stats.mod b/stats.mod
index d4348b6..6198ce2 100644
--- a/stats.mod
+++ b/stats.mod
@@ -861,8 +861,7 @@ 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
-      /* casts are trying to preserve (probably buggy) C behaviour in C++ */
-      mcell_ran4_init((uint32_t)(uintptr_t)&xx.i[1]);
+      mcell_ran4_init(xx.i[1]);
       mcell_ran4(&xx.i[0], &y, 1, big); // generate a pseudorand number based on these
       prod*=y;  // keep multiplying these out
     }
@@ -2027,8 +2026,7 @@ 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
-    /* casts are trying to preserve (probably buggy) C behaviour in C++ */
-    mcell_ran4_init((uint32_t)(uintptr_t)&xx.i[1]);
+    mcell_ran4_init(xx.i[1]);
     mcell_ran4(&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
@@ -2094,8 +2092,7 @@ FUNCTION mc4seed () {
   for (i=2;ifarg(i);i++) {
     valseed*=(unsigned int)(*getarg(i));
   }
-  /* casts are trying to preserve (probably buggy) C behaviour in C++ */
-  mcell_ran4_init((uint32_t)(uintptr_t)&valseed); // do initialization
+  mcell_ran4_init(valseed); // do initialization
   return valseed;
   ENDVERBATIM
 }

From 8978dccbb34cb7734417111eb0ed4f97e2387f51 Mon Sep 17 00:00:00 2001
From: Olli Lupton <oliver.lupton@epfl.ch>
Date: Tue, 24 May 2022 12:54:06 +0200
Subject: [PATCH 21/23] mcell_ran4_init: update readme

---
 readme.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/readme.txt b/readme.txt
index 567957f..9320e5e 100644
--- a/readme.txt
+++ b/readme.txt
@@ -64,4 +64,5 @@ Bill Lytton at billl 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.
+         upcoming versions 8.2 and 9.0 of NEURON. Updated to use post ~2011
+         signature of mcell_ran4_init function.

From eeca94f9b239fcd1e21da3369155b8258892374e Mon Sep 17 00:00:00 2001
From: Olli Lupton <oliver.lupton@epfl.ch>
Date: Tue, 24 May 2022 14:08:44 +0200
Subject: [PATCH 22/23] hashseed2: probable bugfix

---
 intf_.mod  | 9 +++------
 readme.txt | 2 +-
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/intf_.mod b/intf_.mod
index 618eb2a..7ff463c 100644
--- a/intf_.mod
+++ b/intf_.mod
@@ -325,8 +325,7 @@ unsigned int GetDVIDSeedVal(unsigned int id) {
   } else { 
     if (seadsetting==2) printf("Warning: GetDVIDSeedVal called with wt rand turned off\n");
     x[0]=(double)id; x[1]=seaddvioff;
-    /* the cast is trying to preserve (probably buggy) C behaviour in C++ */
-    sead=hashseed2(2, (double*)&x);
+    sead=hashseed2(2, x);
   }
   return sead;
 }
@@ -417,8 +416,7 @@ ENDVERBATIM
           sead=(unsigned int)(floor(_lflag)*ip->id*seedstep); // all integers
         } else { // hash on presynaptic id+FOFFSET,poid,seedstep
           hsh[0]=floor(_lflag); hsh[1]=(double)ip->id; hsh[2]=seedstep;
-          /* the cast is trying to preserve (probably buggy) C behaviour in C++ */
-          sead=hashseed2(3,(double*)&hsh); // hsh[] is just scratch pad
+          sead=hashseed2(3, hsh); // hsh[] is just scratch pad
         }
         mcell_ran4(&sead, &_args[sy], 2, 1.);
         for (ii=sy;ii<sy+2;ii++) { // scale appropriately; 
@@ -1099,8 +1097,7 @@ FUNCTION getdvi () {
             sead=(unsigned int)(FOFFSET+ip->id)*qp->id*seedstep; 
           } else { // hashed sead setting
             hsh[0]=(double)(FOFFSET+ip->id); hsh[1]=(double)(qp->id); hsh[2]=seedstep;
-            /* the cast is trying to preserve (probably buggy) C behaviour in C++ */
-            sead=hashseed2(3, (double*)&hsh);
+            sead=hashseed2(3, hsh);
           }
           mcell_ran4(&sead, y, 2, 1.);
           for(ii=0;ii<2;ii++) {
diff --git a/readme.txt b/readme.txt
index 9320e5e..d4a6ab8 100644
--- a/readme.txt
+++ b/readme.txt
@@ -65,4 +65,4 @@ Bill Lytton at billl at neurosim dot downstate dot edu
 --------------------------------------------------------------------------
 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.
+         signature of mcell_ran4_init function and fix hashseed2 argument.

From 65313b155a6a8b8fccac045c0e2d7434467ba865 Mon Sep 17 00:00:00 2001
From: Olli Lupton <oliver.lupton@epfl.ch>
Date: Tue, 24 May 2022 14:13:20 +0200
Subject: [PATCH 23/23] cntpx -> cntpxy probable typo (compiler warning fix)

---
 infot.mod | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/infot.mod b/infot.mod
index 90af70d..c09e496 100644
--- a/infot.mod
+++ b/infot.mod
@@ -413,8 +413,7 @@ double tentropd (double* x,double* y,int iLen,int nbins,int xpast,int ypast,int
   dsum=0.0;
   *sig=-1e6;//init sig to neg
   *nTE = 0.0;
-  /* 2nd cntpx should be cntpxy? */
-  sh=cntjxy=cntjx=cntpx=cntpx=0;   teavg=testd=te=teout=0.0;
+  sh=cntjxy=cntjx=cntpx=cntpxy=0;   teavg=testd=te=teout=0.0;
 
   px = nbins>0 ? getnormd(x,iLen,nbins) : doublep2intp(x,iLen); //discretize x to nbins, or just copy to ints
   py = nbins>0 ? getnormd(y,iLen,nbins) : doublep2intp(y,iLen); //discretize y to nbins, or just copy to ints