Merge remote-tracking branch 'origin/jelic/refactor_coverage' into jelic/refactor_coverage

Goran Jelic-Cizmek · Goran Jelic-Cizmek · commit 47fa629b38b6 · 2025-08-04T12:14:41.000+02:00
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -248,7 +248,7 @@ jobs:
               PATH="${PWD}/bin:${PATH}" \
               LD_LIBRARY_PATH="${PWD}/lib:${LD_LIBRARY_PATH}" \
               DYLD_LIBRARY_PATH="${PWD}/lib:${DYLD_LIBRARY_PATH}" \
-              "${python}" -c "from neuron import h; import neuron; neuron.test();neuron.test_rxd();"
+              "${python}" -c "from neuron import h; import neuron; neuron.test();neuron.test_rxd(); from neuron.tests import test_nmodl; test_nmodl.test_nmodl()"
           done
           cmake --build . --target cover_collect
           cmake --build . --target cover_combine
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
@@ -59,15 +59,15 @@ jobs:
             config:
               build_mode: cmake
               cmake_option: -DNRN_ENABLE_CORENEURON=ON
-                -DNRN_ENABLE_INTERVIEWS=OFF -DNMODL_SANITIZERS=undefined
+                -DNRN_ENABLE_INTERVIEWS=OFF
               flag_warnings: ON
               sanitizer: undefined
           - os: ubuntu-22.04
             config:
               build_mode: cmake
               # TODO: CoreNEURON is only LeakSanitizer-clean if we disable MPI
               cmake_option: -DNRN_ENABLE_CORENEURON=ON
-                -DNRN_ENABLE_INTERVIEWS=OFF -DNMODL_SANITIZERS=address
+                -DNRN_ENABLE_INTERVIEWS=OFF
               # TODO: address-leak is the dream, but there are many problems,
               # including external ones from the MPI implementations
               sanitizer: address
@@ -85,14 +85,14 @@ jobs:
               build_mode: cmake
               # TODO: investigate rxd test timeouts in this build and re-enable them
               cmake_option: -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF
-                -DNRN_ENABLE_RX3D=OFF -DNMODL_SANITIZERS=address
+                -DNRN_ENABLE_RX3D=OFF
               sanitizer: address
           - os: macOS-14
             config:
               build_mode: cmake
               # TODO: investigate rxd test timeouts in this build and re-enable them
               cmake_option: -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF
-                -DNRN_ENABLE_RX3D=OFF -DNMODL_SANITIZERS=address
+                -DNRN_ENABLE_RX3D=OFF
               sanitizer: thread
       fail-fast: false
 
diff --git a/docs/cmake_doc/index.rst b/docs/cmake_doc/index.rst
diff --git a/docs/cmake_doc/options.rst b/docs/cmake_doc/options.rst
@@ -1,3 +1,6 @@
+CMake Build Options
+~~~~~~~~~~~~~~~~~~~
+
 Introduction
 ============
 The NEURON build system now uses CMake as of version 7.8 circa Nov 2019.
diff --git a/docs/index.rst b/docs/index.rst
@@ -17,7 +17,7 @@ and more (use the links on the side or search).
    :hidden:
 
    install/install
-   cmake_doc/index
+   cmake_doc/options.rst
    install/developer
 
 .. toctree::
diff --git a/packaging/python/test_wheels.sh b/packaging/python/test_wheels.sh
@@ -105,6 +105,7 @@ run_serial_test () {
 
     # Test 3: run coreneuron binary shipped inside wheel
     if [[ "$has_coreneuron" == "true" ]]; then
+        $python_exe -c "from neuron.tests import test_nmodl; test_nmodl.test_nmodl()"
         HOC_LIBRARY_PATH=${PWD}/test/ringtest nrniv test/ringtest/ring.hoc
         mv out.dat out.nrn.dat
         nrniv-core --datpath .
@@ -190,7 +191,7 @@ run_parallel_test() {
       run_mpi_test "mpirun.mpich" "MPICH" ""
       # choose openmpi
       sudo update-alternatives --set mpi-${ARCH_DIR}-linux-gnu /usr/lib/${ARCH_DIR}-linux-gnu/openmpi/include
-      run_mpi_test "mpirun.openmpi" "OpenMPI" ""
+      run_mpi_test "mpirun.openmpi --oversubscribe" "OpenMPI" ""
 
     # linux desktop or docker container used for wheel
     else
diff --git a/share/lib/python/neuron/CMakeLists.txt b/share/lib/python/neuron/CMakeLists.txt
@@ -46,6 +46,7 @@ set(NRN_PYTHON_FILES_LIST
     tests/test_rxd.json)
 
 set(NRN_PYTHON_NMODL_FILES_LIST
+    tests/test_nmodl.py
     nmodl/dsl.py
     nmodl/symtab.py
     nmodl/ext/example/passive.mod
diff --git a/share/lib/python/neuron/rxd/geometry3d/FullJoinMorph.py b/share/lib/python/neuron/rxd/geometry3d/FullJoinMorph.py
@@ -141,10 +141,7 @@ def minmax(lst, old):
     # soma: modified when ctng properly assigns soma obj to segments
     if soma_objects:
         for item, seg in soma_objects.items():
-            if seg in final_seg_dict:
-                final_seg_dict[seg].append(item)
-            else:
-                final_seg_dict[seg] = [item]
+            final_seg_dict.setdefault(seg, []).append(item)
 
     # assign join objects
     for jg in join_groups:
@@ -154,18 +151,12 @@ def minmax(lst, old):
             if (not (isinstance(item, Cone) or isinstance(item, Cylinder))) or (
                 item in join_objects
             ):
-                if seg in final_seg_dict.keys():
-                    final_seg_dict[seg].append(item)
-                else:
-                    final_seg_dict[seg] = [item]
+                final_seg_dict.setdefault(seg, []).append(item)
 
     # complete final segment dictionary
     for cone in cones:
         seg = segment_dict[(cone._x0, cone._y0, cone._z0, cone._x1, cone._y1, cone._z1)]
-        if seg in final_seg_dict.keys():
-            final_seg_dict[seg].append(cone)
-        else:
-            final_seg_dict[seg] = [cone]
+        final_seg_dict.setdefault(seg, []).append(cone)
 
     # voxelize all the objects and assign voxels
     # output dictionaries of internal and surface voxels
diff --git a/share/lib/python/neuron/rxd/geometry3d/triangularMesh.py b/share/lib/python/neuron/rxd/geometry3d/triangularMesh.py
@@ -11,10 +11,7 @@
 
 def _register_on_neighbor_map(the_map, pt, neighbor):
     # does not assume neighbor relations are bidirectional
-    if pt in the_map:
-        the_map[pt].append(neighbor)
-    else:
-        the_map[pt] = [neighbor]
+    the_map.setdefault(pt, []).append(neighbor)
 
 
 class TriangularMesh:
diff --git a/share/lib/python/neuron/rxd/region.py b/share/lib/python/neuron/rxd/region.py
@@ -77,10 +77,7 @@ def __init__(self, regions):
             self._overlap = h.SectionList(
                 [sec for sec in r._secs1d if sec in self._overlap]
             )
-            if r in _c_region_lookup:
-                _c_region_lookup[rptr].append(self)
-            else:
-                _c_region_lookup[rptr] = [self]
+            _c_region_lookup.setdefault(rptr, []).append(self)
 
     def add_reaction(self, rptr, region):
         # for multicompartment reaction -- check all regions are present
diff --git a/share/lib/python/neuron/rxd/rxd.py b/share/lib/python/neuron/rxd/rxd.py
@@ -1250,10 +1250,7 @@ def _compile_reactions():
             for reg in react_regions:
                 if isinstance(reg, region.Extracellular):
                     continue
-                if reg in regions_inv:
-                    regions_inv[reg].append(rptr)
-                else:
-                    regions_inv[reg] = [rptr]
+                regions_inv.setdefault(reg, []).append(rptr)
                 if reg in species_by_region:
                     species_by_region[reg] = species_by_region[reg].union(
                         species_involved
@@ -1290,10 +1287,7 @@ def _compile_reactions():
                 for reg in react_regions:
                     if not isinstance(reg, region.Extracellular):
                         continue
-                    if reg in ecs_regions_inv:
-                        ecs_regions_inv[reg].append(rptr)
-                    else:
-                        ecs_regions_inv[reg] = [rptr]
+                    ecs_regions_inv.setdefault(reg, []).append(rptr)
                     if reg in ecs_species_by_region:
                         ecs_species_by_region[reg] = ecs_species_by_region[reg].union(
                             ecs_species_involved
diff --git a/share/lib/python/neuron/tests/test_nmodl.py b/share/lib/python/neuron/tests/test_nmodl.py
@@ -0,0 +1,28 @@
+import unittest
+
+from neuron import h
+
+
+class NmodlTestCase(unittest.TestCase):
+    """
+    Tests for NMODL
+    """
+
+    def test_nmodl_ast(self):
+        """
+        Test for https://github.com/neuronsimulator/nrn/issues/3517
+        """
+        assert h.hh.ast
+
+
+def suite():
+    return unittest.defaultTestLoader.loadTestsFromTestCase(NmodlTestCase)
+
+
+def test_nmodl():
+    runner = unittest.TextTestRunner(verbosity=2)
+    runner.run(suite())
+
+
+if __name__ == "__main__":
+    test_nmodl()
diff --git a/src/modlunit/units.cpp b/src/modlunit/units.cpp
@@ -26,6 +26,11 @@
 #include <windows.h>
 #endif
 
+#ifndef _WIN32
+#include <unistd.h>
+#include <fcntl.h>
+#endif
+
 int unitonflag = 1;
 static int UnitsOn = 0;
 extern "C" {
@@ -110,13 +115,47 @@ static constexpr std::string_view embedded_nrnunits =
 // https://github.com/neuronsimulator/nrn/issues/3470
 // the API requires a FILE handle instead of a std::string or similar
 // so we write a temporary file
+// Note: with posix we experience
+// warning: 'tmpnam' is deprecated: This function is provided for
+// compatibility reasons only.  Due to security concerns inherent in the
+// design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead
+// [-Wdeprecated-declarations]
 static FILE* open_embedded_nrnunits_as_file() {
-    auto tmp_path = std::string(std::tmpnam(nullptr));
-    auto out = std::ofstream(tmp_path, std::ios::out);
+#ifdef _WIN32
+    // Windows: Use GetTempPath and CreateFile for a secure temp file
+    char temp_path[MAX_PATH];
+    GetTempPath(MAX_PATH, temp_path);
+    char temp_file[MAX_PATH];
+    GetTempFileName(temp_path, "nrn", 0, temp_file);
+
+    // Write embedded_nrnunits to the temp file
+    std::ofstream out(temp_file, std::ios::out | std::ios::binary);
+    out.write(embedded_nrnunits.data(), embedded_nrnunits.size());
+    out.close();
+
+    // Open the temp file for reading
+    return fopen(temp_file, "r");
+#else
+    // POSIX: Use mkstemp for a secure temp file
+    char temp_file[] = "/tmp/nrnunitsXXXXXX";
+    int fd = mkstemp(temp_file);
+    if (fd == -1) {
+        return nullptr;  // Handle error appropriately
+    }
+
+    // Write embedded_nrnunits to the temp file
+    std::ofstream out(temp_file, std::ios::out | std::ios::binary);
     out.write(embedded_nrnunits.data(), embedded_nrnunits.size());
     out.close();
 
-    return std::fopen(tmp_path.c_str(), "r");
+    // Open the temp file for reading
+    FILE* file = fdopen(fd, "r");
+    if (!file) {
+        close(fd);
+        unlink(temp_file);  // Clean up
+    }
+    return file;
+#endif
 }
 
 static int Getc(FILE* inp) {
diff --git a/src/nmodl/lexer/CMakeLists.txt b/src/nmodl/lexer/CMakeLists.txt
@@ -228,6 +228,14 @@ add_custom_command(
 
 add_library(lexer STATIC ${LEXER_SOURCE_FILES} ${BISON_GENERATED_SOURCE_FILES}
                          ${AST_GENERATED_SOURCES} ${UNIT_SOURCE_FILES})
+if(NRN_MACOS_BUILD)
+  # ~~~
+  # bug with NMODL lexer, see:
+  # https://github.com/neuronsimulator/nrn/issues/3517
+  # should not have an effect on performance
+  # ~~~
+  target_compile_options(lexer BEFORE PRIVATE "-O0")
+endif()
 set_property(TARGET lexer PROPERTY POSITION_INDEPENDENT_CODE ON)
 target_link_libraries(lexer PRIVATE util)
 
diff --git a/src/nrniv/neuronapi.cpp b/src/nrniv/neuronapi.cpp
@@ -373,6 +373,14 @@ bool nrn_prop_exists(const Object* obj) {
     return ob2pntproc_0(const_cast<Object*>(obj))->prop;
 }
 
+double nrn_distance(Section* sec0, double x0, Section* sec1, double x1) {
+    Node* node0 = node_exact(sec0, x0);
+    Node* node1 = node_exact(sec1, x1);
+    Section* dummy_sec = nullptr;
+    Node* dummy_node = nullptr;
+    return topol_distance(sec0, node0, sec1, node1, &dummy_sec, &dummy_node);
+}
+
 /****************************************
  * Plot Shape
  ****************************************/
@@ -616,4 +624,51 @@ void nrn_register_function(void (*proc)(), const char* func_name, int type) {
     sym->u.u_proc->nauto = 0;
     sym->u.u_proc->nobjauto = 0;
 }
+
+void nrn_hoc_ret() {
+    hoc_ret();
+}
+
+/****************************************
+ * Parameter-reading functions
+ ****************************************/
+Object** nrn_objgetarg(int arg) {
+    return hoc_objgetarg(arg);
+}
+
+char* nrn_gargstr(int arg) {
+    return hoc_gargstr(arg);
+}
+
+double* nrn_getarg(int arg) {
+    return hoc_getarg(arg);
+}
+
+std::FILE* nrn_obj_file_arg(int i) {
+    return hoc_obj_file_arg(i);
+}
+
+bool nrn_ifarg(int arg) {
+    return ifarg(arg);
+}
+
+
+bool nrn_is_object_arg(int arg) {
+    return hoc_is_object_arg(arg);
+}
+
+
+bool nrn_is_str_arg(int arg) {
+    return hoc_is_str_arg(arg);
+}
+
+
+bool nrn_is_double_arg(int arg) {
+    return hoc_is_double_arg(arg);
+}
+
+
+bool nrn_is_pdouble_arg(int arg) {
+    return hoc_is_pdouble_arg(arg);
+}
 }
diff --git a/src/nrniv/neuronapi.h b/src/nrniv/neuronapi.h
@@ -3,7 +3,11 @@
 #include <stdbool.h>
 
 #ifdef __cplusplus
+#include <cstdio>
+using std::FILE;
 extern "C" {
+#else
+#include <stdio.h>
 #endif
 
 // forward declarations (c++) and opaque c types
@@ -96,6 +100,7 @@ void nrn_object_ref(Object* obj);
 void nrn_object_unref(Object* obj);
 char const* nrn_class_name(const Object* obj);
 bool nrn_prop_exists(const Object* obj);
+double nrn_distance(Section* sec0, double x0, Section* sec1, double x1);
 
 /****************************************
  * Shape Plot
@@ -132,6 +137,20 @@ Symlist* nrn_global_symbol_table(void);
 Symlist* nrn_top_level_symbol_table(void);
 int nrn_symbol_array_length(const Symbol* sym);
 void nrn_register_function(void (*proc)(), const char* func_name, int type);
+void nrn_hoc_ret(void);
+
+/****************************************
+ * Parameter-reading functions
+ ****************************************/
+Object** nrn_objgetarg(int arg);
+char* nrn_gargstr(int arg);
+double* nrn_getarg(int arg);
+FILE* nrn_obj_file_arg(int i);
+bool nrn_ifarg(int arg);
+bool nrn_is_object_arg(int arg);
+bool nrn_is_str_arg(int arg);
+bool nrn_is_double_arg(int arg);
+bool nrn_is_pdouble_arg(int arg);
 
 #ifdef __cplusplus
 }
diff --git a/src/nrniv/shapeplt.h b/src/nrniv/shapeplt.h
diff --git a/src/nrnpython/grids.cpp b/src/nrnpython/grids.cpp
