If python is launched use nrnpy_pr instead of printf to print to stdout.

This allows h.printf, h.topology, and h.psection to print to
the Jupyter notebook.

share/lib/python/neuron/__init__.py

@@ -422,12 +422,14 @@ def nrn_dll(printpath=False):
     base_path = os.path.join(neuron_home, 'lib' , 'python', 'neuron', 'hoc')
     for extension in ['', '.dll', '.so', '.dylib']:
         dlls = glob.glob(base_path + '*' + extension)
-        try:
-            the_dll = ctypes.cdll[dlls[0]]
-            if printpath : print(dlls[0])
-            success = True
-        except:
-            pass
+        for dll in dlls:
+            try:
+                the_dll = ctypes.cdll[dll]
+                if printpath : print(dll)
+                success = True
+            except:
+                pass
+            if success: break
         if success: break
     else:
         raise Exception('unable to connect to the NEURON library')
@@ -530,3 +532,22 @@ def _has_scipy():
 def _pkl(arg):
   #print 'neuron._pkl arg is ', arg
   return h.Vector(0)
+
+def nrnpy_pr(s):
+  import sys
+  sys.stdout.write(s.decode())
+  return 0
+
+try:
+  # callback in place of hoc printf
+  # ensures consistent with python stdout even with jupyter notebook.
+  nrnpy_pr_proto = ctypes.CFUNCTYPE(ctypes.c_int, ctypes.c_char_p)
+  nrnpy_set_pr = nrn_dll_sym('nrnpy_set_pr')
+  nrnpy_set_pr.argtypes = [nrnpy_pr_proto]
+
+  nrnpy_pr_callback = nrnpy_pr_proto(nrnpy_pr)
+  nrnpy_set_pr(nrnpy_pr_callback)
+except:
+  print("Failed to setup nrnpy_pr")
+  pass
+

src/ivoc/ivocmain.cpp

@@ -250,7 +250,7 @@ extern "C" {
 	extern int nrn_global_argc;
 	extern const char** nrn_global_argv;
 	int always_false;
-	int nrn_is_python_extension;
+	extern int nrn_is_python_extension;
 }
 
 // some things are defined in libraries earlier than they are used so...

src/oc/fileio.c

@@ -3,6 +3,7 @@
 
 #include	<stdio.h>
 #include	<stdlib.h>
+#include	<stdarg.h>
 #include <unistd.h>
 #include	"hoc.h"
 #include "ocmisc.h"
@@ -866,3 +867,52 @@ void hoc_Chdir(void) {
 	ret();
 	pushx((double)i);
 }
+
+int nrn_is_python_extension;
+int (*nrnpy_pr_callback)(char*);
+
+void nrnpy_set_pr(int (*cb)(char*)) {
+    if (nrn_is_python_extension) {
+        nrnpy_pr_callback = cb;
+    }
+}
+
+int nrnpy_pr(const char *fmt, ...) {
+    int size = 0;
+    char *p = NULL;
+    va_list ap;
+
+    if (!nrnpy_pr_callback) {
+        va_start(ap, fmt);
+        size = vprintf(fmt, ap);
+        return size;
+    }
+
+    /* Determine required size */
+
+    va_start(ap, fmt);
+    size = vsnprintf(p, size, fmt, ap);
+    va_end(ap);
+
+    if (size < 0)
+        return 0;
+
+    size++;      /* For '\0' */
+    p = malloc(size);
+    if (p == NULL)
+        return 0;
+
+    va_start(ap, fmt);
+    size = vsnprintf(p, size, fmt, ap);
+    if (size < 0) {
+        free(p);
+        return 0;
+    }
+    va_end(ap);
+
+    (*nrnpy_pr_callback)(p);
+
+    free(p);
+    return size;
+}
+

src/oc/hocdec.h

@@ -323,7 +323,7 @@ int	ilint;
 #define Strcpy          strcpy
 #define Strncpy         strncpy
 #define Sprintf         sprintf
-#define Printf		printf
+#define Printf		nrnpy_pr
 #define Fprintf		fprintf
 #endif
 

src/oc/oc_ansi.h

@@ -211,6 +211,7 @@ extern int hoc_pid(void);
 extern int hoc_ired(const char*, int, int, int);
 extern double hoc_xred(const char*, double, double, double);
 extern int hoc_sred(const char*, char*, char*);
+extern int nrnpy_pr(const char* fmt, ...);
 
 #if defined (__cplusplus)
 extern void hoc_free_allobjects(cTemplate*, Symlist*, Objectdata*);

src/oc/plot.c

@@ -215,7 +215,11 @@ void plprint(const char* s)
 		}else
 #endif
 		{
+#if 0
 			IGNORE(fprintf(stdout, "%s", s));
+#else
+			nrnpy_pr("%s", s);
+#endif
 		}
 	}
 	if (hardplot && hpdev && text && strlen(s)) {