Merge remote-tracking branch 'origin/master' into HEAD

share/lib/python/neuron/rxd/node.py

@@ -35,6 +35,8 @@
 _concentration_node = 0
 _molecule_node = 1
 
+_floor = numpy.floor
+
 
 def _get_data():
     return (_volumes, _surface_area, _diffs)
@@ -650,9 +652,9 @@ def satisfies(self, condition):
             x, y, z = condition
             mesh = self._r._mesh_grid
             return (
-                int((x - mesh["xlo"]) / mesh["dx"]) == self._i
-                and int((y - mesh["ylo"]) / mesh["dy"]) == self._j
-                and int((z - mesh["zlo"]) / mesh["dz"]) == self._k
+                _floor((x - mesh["xlo"]) / mesh["dx"]) == self._i
+                and _floor((y - mesh["ylo"]) / mesh["dy"]) == self._j
+                and _floor((z - mesh["zlo"]) / mesh["dz"]) == self._k
             )
         # check for a position condition so as to provide a more useful error
         checked_for_normalized_position = False
@@ -885,8 +887,8 @@ def satisfies(self, condition):
             x, y, z = condition
             r = self._regionref()
             return (
-                int((x - r._xlo) / r._dx[0]) == self._i
-                and int((y - r._ylo) / r._dx[1]) == self._j
-                and int((z - r._zlo) / r._dx[2]) == self._k
+                _floor((x - r._xlo) / r._dx[0]) == self._i
+                and _floor((y - r._ylo) / r._dx[1]) == self._j
+                and _floor((z - r._zlo) / r._dx[2]) == self._k
             )
         raise RxDException(f"unrecognized node condition: {condition}")

src/nrnoc/seclist.cpp

@@ -1,4 +1,7 @@
 #include <../../nrnconf.h>
+
+#include <functional>
+
 #define HOC_L_LIST 1
 #include "section.h"
 #include "neuron.h"
@@ -8,14 +11,35 @@
 #include "code.h"
 #include "classreg.h"
 
-/* needs trailing '}' */
-#define ITERATE_REMOVE(q1, q2, lst)                \
-    for (q1 = (lst)->next; q1 != (lst); q1 = q2) { \
-        q2 = q1->next;                             \
-        if (q1->element.sec->prop == NULL) {       \
-            hoc_l_delete(q1);                      \
-            continue;                              \
+template <typename F>
+bool seclist_iterate_remove_until(List* sl, F fun, const Section* sec) {
+    Item* q2 = nullptr;
+    for (Item* q1 = sl->next; q1 != sl; q1 = q2) {
+        q2 = q1->next;
+        if (q1->element.sec->prop == nullptr) {
+            hoc_l_delete(q1);
+            continue;
+        }
+        if (q1->element.sec == sec) {
+            fun(q1);
+            return true;
+        }
+    }
+    return false;
+}
+
+template <typename F>
+void seclist_iterate_remove(List* sl, F fun) {
+    Item* q2 = nullptr;
+    for (Item* q1 = sl->next; q1 != sl; q1 = q2) {
+        q2 = q1->next;
+        if (q1->element.sec->prop == nullptr) {
+            hoc_l_delete(q1);
+            continue;
         }
+        fun(q1->element.sec);
+    }
+}
 
 extern int hoc_return_type_code;
 Section* (*nrnpy_o2sec_p_)(Object* o);
@@ -131,102 +155,83 @@ static double allroots(void* v) {
 }
 
 static double seclist_remove(void* v) {
-    Section *sec, *s;
-    Item *q, *q1;
-    List* sl;
-    int i;
-
-    sl = (List*) v;
-    i = 0;
+    List* sl = (List*) v;
+    int i = 0;
 #if USE_PYTHON
     if (!ifarg(1) || (*hoc_objgetarg(1))->ctemplate->sym == nrnpy_pyobj_sym_) {
 #else
     if (!ifarg(1)) {
 #endif
-        sec = nrn_secarg(1);
-        ITERATE_REMOVE(q, q1, sl) /*{*/
-        if (sec == q->element.sec) {
-            hoc_l_delete(q);
-            section_unref(sec);
+        Section* sec = nrn_secarg(1);
+        if (seclist_iterate_remove_until(
+                sl,
+                [](Item* q) {
+                    Section* s = q->element.sec;
+                    hoc_l_delete(q);
+                    section_unref(s);
+                },
+                sec)) {
             return 1.;
         }
+        hoc_warning(secname(sec), "not in this section list");
+    } else {
+        Object* o;
+        o = *hoc_objgetarg(1);
+        check_obj_type(o, "SectionList");
+        seclist_iterate_remove(sl, [](Section* s) { s->volatile_mark = 0; });
+        sl = (List*) o->u.this_pointer;
+        seclist_iterate_remove(sl, [](Section* s) { s->volatile_mark = 1; });
+        sl = (List*) v;
+        Item* q1;
+        for (Item* q = sl->next; q != sl; q = q1) {
+            q1 = q->next;
+            Section* s = hocSEC(q);
+            if (s->volatile_mark) {
+                hoc_l_delete(q);
+                section_unref(s);
+                ++i;
+            }
+        }
     }
-    hoc_warning(secname(sec), "not in this section list");
-}
-else {
-    Object* o;
-    o = *hoc_objgetarg(1);
-    check_obj_type(o, "SectionList");
-    ITERATE_REMOVE(q, q1, sl) /*{*/
-    s = hocSEC(q);
-    s->volatile_mark = 0;
-}
-sl = (List*) o->u.this_pointer;
-ITERATE_REMOVE(q, q1, sl) /*{*/
-s = hocSEC(q);
-s->volatile_mark = 1;
-}
-sl = (List*) v;
-i = 0;
-for (q = sl->next; q != sl; q = q1) {
-    q1 = q->next;
-    s = hocSEC(q);
-    if (s->volatile_mark) {
-        hoc_l_delete(q);
-        section_unref(s);
-        ++i;
-    }
-}
-}
-return (double) i;
+    return (double) i;
 }
 
 static double unique(void* v) {
-    int i; /* number deleted */
-    Section* s;
-    Item *q, *q1;
+    Item* q1;
     List* sl = (List*) v;
     hoc_return_type_code = 1; /* integer */
-    ITERATE_REMOVE(q, q1, sl) /*{*/
-    s = hocSEC(q);
-    s->volatile_mark = 0;
-}
-i = 0;
-for (q = sl->next; q != sl; q = q1) {
-    q1 = q->next;
-    s = hocSEC(q);
-    if (s->volatile_mark++) {
-        hoc_l_delete(q);
-        section_unref(s);
-        ++i;
+    seclist_iterate_remove(sl, [](Section* s) { s->volatile_mark = 0; });
+    int i = 0; /* number deleted */
+    for (Item* q = sl->next; q != sl; q = q1) {
+        q1 = q->next;
+        Section* s = hocSEC(q);
+        if (s->volatile_mark++) {
+            hoc_l_delete(q);
+            section_unref(s);
+            ++i;
+        }
     }
-}
-return (double) i;
+    return (double) i;
 }
 
 static double contains(void* v) {
-    Section* s;
-    Item *q, *q1;
     List* sl = (List*) v;
     hoc_return_type_code = 2; /* boolean */
-    s = nrn_secarg(1);
-    ITERATE_REMOVE(q, q1, sl) /*{*/
-    if (hocSEC(q) == s) {
-        return 1.;
-    }
-}
-return (0.);
+    Section* s = nrn_secarg(1);
+    return seclist_iterate_remove_until(
+               sl, [](Item*) {}, s)
+               ? 1.
+               : 0.;
 }
 
 static double printnames(void* v) {
-    Item *q, *q1;
     List* sl = (List*) v;
-    ITERATE_REMOVE(q, q1, sl) /*{*/
-    if (q->element.sec->prop) {
-        Printf("%s\n", secname(q->element.sec));
-    }
-}
-return 1.;
+    seclist_iterate_remove(sl, [](Section* s) {
+        if (s->prop) {
+            Printf("%s\n", secname(s));
+        }
+    });
+    return 1.;
 }
 
 static Member_func members[] = {{"append", append},
@@ -307,33 +312,31 @@ void forall_sectionlist(void) {
 
 void hoc_ifseclist(void) {
     Inst* savepc = pc;
-    Item *q, *q1;
     Section* sec = chk_access();
-    List* sl;
-    Object* ob;
-    Object** obp;
 
     /* if arg is a string use forall_section */
     if (hoc_stacktype() == STRING) {
         hoc_ifsec();
         return;
     }
-    obp = hoc_objpop();
-    ob = *obp;
+    Object** obp = hoc_objpop();
+    Object* ob = *obp;
     check(ob);
-    sl = (List*) (ob->u.this_pointer);
-    ITERATE_REMOVE(q, q1, sl) /*{*/
-    if (sec == q->element.sec) {
-        hoc_execute(relative(savepc));
-        if (!hoc_returning) {
-            pc = relative(savepc + 1);
-        }
-        hoc_tobj_unref(obp);
+    List* sl = (List*) (ob->u.this_pointer);
+    if (seclist_iterate_remove_until(
+            sl,
+            [&](Item*) {
+                hoc_execute(relative(savepc));
+                if (!hoc_returning) {
+                    pc = relative(savepc + 1);
+                }
+                hoc_tobj_unref(obp);
+            },
+            sec)) {
         return;
     }
-}
-hoc_tobj_unref(obp);
-if (!hoc_returning) {
-    pc = relative(savepc + 1);
-}
+    hoc_tobj_unref(obp);
+    if (!hoc_returning) {
+        pc = relative(savepc + 1);
+    }
 }

src/nrnpython/inithoc.cpp

@@ -222,13 +222,13 @@ static int have_opt(const char* arg) {
 static struct termios original_termios;
 
 static void save_original_terminal_settings() {
-    if (tcgetattr(STDIN_FILENO, &original_termios) == -1) {
+    if (tcgetattr(STDIN_FILENO, &original_termios) == -1 && isatty(STDIN_FILENO)) {
         std::cerr << "Error getting original terminal attributes\n";
     }
 }
 
 static void restore_original_terminal_settings() {
-    if (tcsetattr(STDIN_FILENO, TCSANOW, &original_termios) == -1) {
+    if (tcsetattr(STDIN_FILENO, TCSANOW, &original_termios) == -1 && isatty(STDIN_FILENO)) {
         std::cerr << "Error restoring terminal attributes\n";
     }
 }

test/api/hh_sim.cpp

@@ -73,7 +73,7 @@ int main(void) {
     nrn_function_call(nrn_symbol("finitialize"), 1);
     nrn_double_pop();
 
-    // continuerun(10)
+    // continuerun(10.5)
     nrn_double_push(10.5);
     nrn_function_call(nrn_symbol("continuerun"), 1);
     nrn_double_pop();

test/rxd/3d/test_node_selection.py

@@ -1,3 +1,6 @@
+import weakref
+
+
 def test_node_selection(neuron_instance):
     """Test selection of 3D nodes"""
 
@@ -16,4 +19,8 @@ def test_node_selection(neuron_instance):
     assert nodes((5.2, 0.1, 0.3))[0].x3d == 5.125
     assert nodes((5.2, 0.1, 0.3))[0].y3d == 0.125
     assert nodes((5.2, 0.1, 0.3))[0].z3d == 0.375
+
+    nodes.append(rxd.node.Node3D(0, -1, 0, 0, cyt, 0, dend(0.5), weakref.ref(c)))
+
     assert len(nodes((5, 0, 0))) == 1
+    assert nodes[-1] in nodes((nodes[-1].x3d, nodes[-1].y3d, nodes[-1].z3d))