Merge branch 'master' into leite/dat_files_use_vec

.github/workflows/coverage.yml

@@ -37,7 +37,8 @@ jobs:
     env:
       DISPLAY: ${{ ':0' }}
       MUSIC_INSTALL_DIR: /opt/MUSIC
-      MUSIC_VERSION: 1.2.0
+      # hash of commit containing mpi4py 4 fix
+      MUSIC_VERSION: '13f312338dcccebfe74d391b1b24f1b6d816ac6c'
 
     steps:
 
@@ -58,10 +59,10 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install 'mpi4py<4' cython numpy setuptools
+          python3 -m pip install mpi4py cython numpy setuptools
           sudo mkdir -p $MUSIC_INSTALL_DIR
           sudo chown -R $USER $MUSIC_INSTALL_DIR
-          curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/${MUSIC_VERSION}.zip
+          curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/${MUSIC_VERSION}.zip
           unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC
           ./autogen.sh
           ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource

.github/workflows/neuron-ci.yml

@@ -41,7 +41,8 @@ jobs:
       PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.9' }}
       PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.12' }}
       MUSIC_INSTALL_DIR: /opt/MUSIC
-      MUSIC_VERSION: 1.2.1
+      # hash of commit containing mpi4py 4 fix
+      MUSIC_VERSION: '13f312338dcccebfe74d391b1b24f1b6d816ac6c'
 
     strategy:
       matrix:
@@ -207,10 +208,10 @@ jobs:
         run: |
           python3 -m venv music-venv
           source music-venv/bin/activate
-          python3 -m pip install 'mpi4py<4' cython numpy setuptools
+          python3 -m pip install mpi4py cython numpy setuptools
           sudo mkdir -p $MUSIC_INSTALL_DIR
           sudo chown -R $USER $MUSIC_INSTALL_DIR
-          curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/${MUSIC_VERSION}.zip
+          curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/${MUSIC_VERSION}.zip
           unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC
           ./autogen.sh
           # on some systems MPI library detection fails, provide exact flags/compilers

ci/win_install_deps.cmd

@@ -64,7 +64,7 @@ mingw-w64-x86_64-ninja ^
 mingw-w64-x86_64-ncurses ^
 mingw-w64-x86_64-readline ^
 mingw-w64-x86_64-python3 ^
-mingw-w64-x86_64-python3-setuptools ^
+mingw-w64-x86_64-python-setuptools ^
 mingw-w64-x86_64-python3-packaging ^
 mingw-w64-x86_64-python3-pip ^
 mingw64/mingw-w64-x86_64-dlfcn ^

cmake/NeuronFileLists.cmake

@@ -35,8 +35,8 @@ set(HEADER_FILES_TO_INSTALL
     nrnoc/options.h
     nrnoc/section_fwd.hpp
     nrnoc/treeset.h
+    oc/classreg.h
     oc/hoc.h
-    oc/hoc_membf.h
     oc/hocassrt.h
     oc/hocdec.h
     oc/hocgetsym.h

nrn_requirements.txt

@@ -4,7 +4,7 @@ setuptools<=70.3.0
 scikit-build
 matplotlib
 ipython
-mpi4py<4 # MUSIC not compatible with MPI 4
+mpi4py
 find_libpython
 -r packaging/python/build_requirements.txt
 -r packaging/python/test_requirements.txt

share/lib/python/neuron/gui.py

@@ -7,12 +7,11 @@
 Note that python threads are not used if nrniv is launched instead of Python
 """
 
-
 from neuron import h
-
 from contextlib import contextmanager
 import threading
 import time
+import atexit
 
 # recursive, especially in case stop/start pairs called from doNotify code.
 _lock = threading.RLock()
@@ -48,9 +47,10 @@ def process_events():
     _lock.acquire()
     try:
         h.doNotify()
-    except:
-        print("Exception in gui thread")
-    _lock.release()
+    except Exception as e:
+        print(f"Exception in gui thread: {e}")
+    finally:
+        _lock.release()
 
 
 class Timer:
@@ -86,30 +86,40 @@ def end(self):
 
 class LoopTimer(threading.Thread):
     """
-    a Timer that calls f every interval
+    A Timer that calls a function at regular intervals.
     """
 
     def __init__(self, interval, fun):
-        """
-        @param interval: time in seconds between call to fun()
-        @param fun: the function to call on timer update
-        """
         self.started = False
         self.interval = interval
         self.fun = fun
+        self._running = threading.Event()
         threading.Thread.__init__(self, daemon=True)
 
     def run(self):
         h.nrniv_bind_thread(threading.current_thread().ident)
         self.started = True
-        while True:
+        self._running.set()
+        while self._running.is_set():
             self.fun()
             time.sleep(self.interval)
 
+    def stop(self):
+        """Stop the timer thread and wait for it to terminate."""
+        self._running.clear()
+        self.join()
 
-if h.nrnversion(9) == "2":  #  launched with python (instead of nrniv)
+
+if h.nrnversion(9) == "2":  # Launched with Python (instead of nrniv)
     timer = LoopTimer(0.1, process_events)
     timer.start()
+
+    def cleanup():
+        if timer.started:
+            timer.stop()
+
+    atexit.register(cleanup)
+
     while not timer.started:
         time.sleep(0.001)
 

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/ivoc/graph.cpp

@@ -1194,7 +1194,7 @@ static Member_func gr_members[] = {{"plot", gr_plot},
                                    {"gif", ivoc_gr_gif},
                                    {"menu_remove", ivoc_gr_menu_remove},
                                    {"line_info", gr_line_info},
-                                   {0, 0}};
+                                   {nullptr, nullptr}};
 
 static void* gr_cons(Object* ho) {
     TRY_GUI_REDIRECT_OBJ("Graph", NULL);

src/ivoc/grglyph.cpp

@@ -184,8 +184,6 @@ static Object** g_gif(void* v) {
 
 static Symbol* sggl_;
 
-Member_func members[] = {{0, 0}};
-
 Member_ret_obj_func objmembers[] = {{"path", g_new_path},
                                     {"m", g_move_to},
                                     {"l", g_line_to},
@@ -197,7 +195,7 @@ Member_ret_obj_func objmembers[] = {{"path", g_new_path},
                                     {"erase", g_erase},
                                     {"gif", g_gif},
                                     {"circle", g_circle},
-                                    {0, 0}};
+                                    {nullptr, nullptr}};
 
 static void* cons(Object* o) {
     TRY_GUI_REDIRECT_OBJ("Glyph", NULL);
@@ -213,7 +211,7 @@ static void destruct(void* v) {
 }
 
 void GrGlyph_reg() {
-    class2oc("Glyph", cons, destruct, members, objmembers, NULL);
+    class2oc("Glyph", cons, destruct, nullptr, objmembers, nullptr);
     sggl_ = hoc_lookup("Glyph");
 }
 

src/ivoc/ivocrand.cpp

@@ -425,7 +425,7 @@ static Member_func r_members[] = {{"MCellRan4", r_MCellRan4},
                                   {nullptr, nullptr}};
 
 void Random_reg() {
-    class2oc("Random", r_cons, r_destruct, r_members, NULL, NULL);
+    class2oc("Random", r_cons, r_destruct, r_members, nullptr, nullptr);
     random_play_list_ = new RandomPlayList;
 }
 

src/ivoc/ivocvect.cpp

@@ -3737,7 +3737,7 @@ static Member_func v_members[] = {
 
     {"scale", v_scale},
 
-    {0, 0}};
+    {nullptr, nullptr}};
 
 static Member_ret_obj_func v_retobj_members[] = {{"c", v_c},
                                                  {"cl", v_cl},
@@ -3813,11 +3813,11 @@ static Member_ret_obj_func v_retobj_members[] = {{"c", v_c},
                                                  {"to_python", v_to_python},
                                                  {"as_numpy", v_as_numpy},
 
-                                                 {0, 0}};
+                                                 {nullptr, nullptr}};
 
 static Member_ret_str_func v_retstr_members[] = {{"label", v_label},
 
-                                                 {0, 0}};
+                                                 {nullptr, nullptr}};
 
 extern int hoc_araypt(Symbol*, int);
 

src/ivoc/matrix.cpp

@@ -657,7 +657,7 @@ static Member_func m_members[] = {
     {"printf", m_printf},
     {"fprint", m_fprint},
     {"scanf", m_scanf},
-    {0, 0}};
+    {nullptr, nullptr}};
 
 static Member_ret_obj_func m_retobj_members[] = {
     // returns Vector
@@ -687,7 +687,7 @@ static Member_ret_obj_func m_retobj_members[] = {
     {"set", m_set},
     {"to_vector", m_to_vector},
     {"from_vector", m_from_vector},
-    {0, 0}};
+    {nullptr, nullptr}};
 
 static void* m_cons(Object* o) {
     int i = 1, j = 1, storage_type = Matrix::MFULL;
@@ -729,7 +729,7 @@ void Matrix_reg();
 #endif
 
 void Matrix_reg() {
-    class2oc("Matrix", m_cons, m_destruct, m_members, m_retobj_members, NULL);
+    class2oc("Matrix", m_cons, m_destruct, m_members, m_retobj_members, nullptr);
     nrn_matrix_sym = hoc_lookup("Matrix");
     // now make the x variable an actual double
     Symbol* sx = hoc_table_lookup("x", nrn_matrix_sym->u.ctemplate->symtable);

src/ivoc/mlinedit.cpp

@@ -101,9 +101,9 @@ static const char** v_text(void* v) {
 }
 
 
-static Member_func members[] = {{"readonly", readonly}, {"map", map}, {0, 0}};
+static Member_func members[] = {{"readonly", readonly}, {"map", map}, {nullptr, nullptr}};
 
-static Member_ret_str_func retstr_members[] = {{"text", v_text}, {0, 0}};
+static Member_ret_str_func retstr_members[] = {{"text", v_text}, {nullptr, nullptr}};
 
 static void* cons(Object*) {
     TRY_GUI_REDIRECT_OBJ("TextEditor", NULL);

src/ivoc/mymath.cpp

@@ -64,7 +64,7 @@ static Member_func members[] = {{"d2line", distance_to_line},
                                 {"d2line_seg", distance_to_line_segment},
                                 {"inside", inside},
                                 {"feround", feround},
-                                {0, 0}};
+                                {nullptr, nullptr}};
 
 static void* cons(Object*) {
     return NULL;
@@ -73,7 +73,7 @@ static void* cons(Object*) {
 static void destruct(void*) {}
 
 void GUIMath_reg() {
-    class2oc("GUIMath", cons, destruct, members, NULL, NULL);
+    class2oc("GUIMath", cons, destruct, members, nullptr, nullptr);
 }
 
 double MyMath::anint(double x) {

src/ivoc/ocbox.cpp

@@ -426,14 +426,14 @@ static Member_func members[] = {{"intercept", intercept},            // #if HAVE
                                 {"dialog", dialog},                  // #if HAVE_IV ok
                                 {"priority", ses_pri},
                                 {"size", b_size},
-                                {0, 0}};
+                                {nullptr, nullptr}};
 
 void HBox_reg() {
-    class2oc("HBox", hcons, destruct, members, NULL, NULL);
+    class2oc("HBox", hcons, destruct, members, nullptr, nullptr);
 }
 
 void VBox_reg() {
-    class2oc("VBox", vcons, destruct, members, NULL, NULL);
+    class2oc("VBox", vcons, destruct, members, nullptr, nullptr);
 }
 #if HAVE_IV
 OcGlyphContainer::OcGlyphContainer()

src/ivoc/ocdeck.cpp

@@ -236,10 +236,10 @@ static Member_func members[] = {{"flip_to", flip_to},
                                 {"remove_last", remove_last},
                                 {"remove", remove},
                                 {"move_last", move_last},
-                                {0, 0}};
+                                {nullptr, nullptr}};
 
 void OcDeck_reg() {
-    class2oc("Deck", cons, destruct, members, NULL, NULL);
+    class2oc("Deck", cons, destruct, members, nullptr, nullptr);
 }
 #if HAVE_IV
 OcDeck::OcDeck()

src/ivoc/ocfile.cpp

@@ -294,12 +294,14 @@ Member_func f_members[] = {{"ropen", f_ropen},
                            {"mktemp", f_mktemp},
                            {"unlink", f_unlink},
                            {"flush", f_flush},
-                           {0, 0}};
+                           {nullptr, nullptr}};
 
-static Member_ret_str_func f_retstr_members[] = {{"getname", f_get_name}, {"dir", f_dir}, {0, 0}};
+static Member_ret_str_func f_retstr_members[] = {{"getname", f_get_name},
+                                                 {"dir", f_dir},
+                                                 {nullptr, nullptr}};
 
 void OcFile_reg() {
-    class2oc("File", f_cons, f_destruct, f_members, NULL, f_retstr_members);
+    class2oc("File", f_cons, f_destruct, f_members, nullptr, f_retstr_members);
     file_class_sym_ = hoc_lookup("File");
 }
 

src/ivoc/oclist.cpp

@@ -454,7 +454,7 @@ OcList::~OcList() {
 
 void OcList_reg() {
     // printf("Oclist_reg\n");
-    class2oc("List", l_cons, l_destruct, l_members, l_retobj_members, NULL);
+    class2oc("List", l_cons, l_destruct, l_members, l_retobj_members, nullptr);
     list_class_sym_ = hoc_lookup("List");
 }
 

src/ivoc/ocpointer.cpp

@@ -68,7 +68,7 @@ static const char** pname(void* v) {
 
 static Member_func members[] = {{"val", 0},          // will be changed below
                                 {"assign", assign},  // will call assign_stmt if it exists
-                                {0, 0}};
+                                {nullptr, nullptr}};
 
 static Member_ret_str_func s_memb[] = {{"s", pname}, {nullptr, nullptr}};
 
@@ -108,7 +108,7 @@ static void steer_val(void* v) {
 }
 
 void OcPointer_reg() {
-    class2oc("Pointer", cons, destruct, members, NULL, s_memb);
+    class2oc("Pointer", cons, destruct, members, nullptr, s_memb);
     // now make the val variable an actual double
     Symbol* sv = hoc_lookup("Pointer");
     Symbol* sx = hoc_table_lookup("val", sv->u.ctemplate->symtable);