Merge branch 'master' into python-package-name

Author: mgeplf

.github/workflows/formatting.yml

@@ -18,7 +18,7 @@ on:
 jobs:
   all:
     name: C/C++, CMake and Python
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     timeout-minutes: 5
     steps:
       - uses: actions/checkout@v4

CMakeLists.txt

@@ -949,21 +949,43 @@ add_custom_target(
   COMMAND ${PROJECT_SOURCE_DIR}/external/coding-conventions/bin/format
   WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
 
-# Prepare a shell script to format only files modified with respect to master branch
+# Prepare a shell script to format only files modified with respect to master/main branch that still
+# exist on disk (filters out deleted files).
 file(
   WRITE ${CMAKE_CURRENT_BINARY_DIR}/format-pr.sh
-  "\
-#!bash\n\
-set -e\n\
-cmd='cd ${PROJECT_SOURCE_DIR} && external/coding-conventions/bin/format `git diff --name-only master`'\n\
-echo $cmd\n\
-cd ${PROJECT_SOURCE_DIR} && external/coding-conventions/bin/format `git diff --name-only master`\n\
+  "#!/bin/bash
+set -euo pipefail
+
+# Try 'main' first, then fall back to 'master'
+for base in main master; do
+    if git rev-parse --verify \"\$base\" >/dev/null 2>&1; then
+        BASE_BRANCH=\"\$base\"
+        break
+    fi
+done
+
+if [ -z \"\${BASE_BRANCH:-}\" ]; then
+    echo \"Error: Neither 'main' nor 'master' branch found.\" >&2
+    exit 1
+fi
+
+echo \"Formatting changes vs '\$BASE_BRANCH' (existing files only)...\" >&2
+
+# Get changed files (null-delimited so names with spaces work), only pass
+# files that still exist.
+git diff -z --name-only \"\$BASE_BRANCH\" | \\
+while IFS= read -r -d '' file; do
+    if [ -e \"\$file\" ]; then
+        printf '%s\\0' \"\$file\"
+    fi
+done | \\
+xargs -0 --no-run-if-empty external/coding-conventions/bin/format \"\$@\"
 ")
 
 add_custom_target(
   format-pr
   COMMAND bash ${CMAKE_CURRENT_BINARY_DIR}/format-pr.sh
-  COMMENT "Format only files modified with respect to master branch."
+  COMMENT "Format only files modified with respect to main/master (existing files only)"
   WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
 
 # =============================================================================

external/coding-conventions

@@ -1094,10 +1094,18 @@ int ECS_Grid_node::add_multicompartment_reaction(int nstates, int* indices, int
 void ECS_Grid_node::clear_multicompartment_reaction() {
     free(all_reaction_states);
     free(react_offsets);
-    if (multicompartment_inititalized)
+    if (multicompartment_inititalized) {
         free(all_reaction_indices);
-    else
+#if NRNMPI
+        if (nrnmpi_use)
+            free(reaction_indices);
+#endif
+    } else {
         free(reaction_indices);
+    }
+    free(induced_currents);
+    induced_currents = NULL;
+    local_induced_currents = NULL;
     all_reaction_indices = NULL;
     all_reaction_states = NULL;
     reaction_indices = NULL;
@@ -1126,12 +1134,11 @@ void ECS_Grid_node::initialize_multicompartment_reaction() {
                 break;
 
         if (i != nrnmpi_numprocs) {
+            total_reaction_states = 0;
             // number of offsets (Reaction) stored in each process
-            proc_num_reactions = (int*) calloc(nrnmpi_numprocs, sizeof(int));
             proc_num_reactions[nrnmpi_myid] = react_offset_count;
 
             // number of states/indices stored in each process
-            proc_num_reaction_states = (int*) calloc(nrnmpi_numprocs, sizeof(int));
             proc_num_reaction_states[nrnmpi_myid] = react_offsets[react_offset_count - 1];
             nrnmpi_int_allgather_inplace(proc_num_reactions, 1);
             nrnmpi_int_allgather_inplace(proc_num_reaction_states, 1);
@@ -1142,35 +1149,31 @@ void ECS_Grid_node::initialize_multicompartment_reaction() {
                 proc_num_reactions[i] = total_reaction_states;
                 total_reaction_states += proc_num_reaction_states[i];
             }
-
-            // Move the offsets for each reaction so they reference the
-            // corresponding indices in the all_reaction_indices array
-            for (j = 0; j < react_offset_count; j++)
-                react_offsets[j] += start_state;
+            free(all_reaction_indices);
+            free(all_reaction_states);
 
             all_reaction_indices = (int*) malloc(total_reaction_states * sizeof(int));
             all_reaction_states = (double*) calloc(total_reaction_states, sizeof(double));
-
             memcpy(&all_reaction_indices[start_state],
                    reaction_indices,
                    proc_num_reaction_states[nrnmpi_myid] * sizeof(int));
             nrnmpi_int_allgatherv_inplace(all_reaction_indices,
                                           proc_num_reaction_states,
                                           proc_num_reactions);
-            free(reaction_indices);
-            reaction_indices = NULL;
+
             multicompartment_inititalized = TRUE;
 
             // Handle currents induced by multicompartment reactions.
+            int local_induced_current_count = induced_current_count;
             proc_induced_current_count[nrnmpi_myid] = induced_current_count;
             nrnmpi_int_allgather_inplace(proc_induced_current_count, 1);
+
             proc_induced_current_offset[0] = 0;
             for (i = 1; i < nrnmpi_numprocs; i++)
                 proc_induced_current_offset[i] = proc_induced_current_offset[i - 1] +
                                                  proc_induced_current_count[i - 1];
             induced_current_count = proc_induced_current_offset[nrnmpi_numprocs - 1] +
                                     proc_induced_current_count[nrnmpi_numprocs - 1];
-
             all_scales = (double*) malloc(induced_current_count * sizeof(double));
             all_indices = (int*) malloc(induced_current_count * sizeof(int));
             memcpy(&all_scales[proc_induced_current_offset[nrnmpi_myid]],
@@ -1193,16 +1196,18 @@ void ECS_Grid_node::initialize_multicompartment_reaction() {
             free(induced_currents);
             induced_currents_scale = all_scales;
             induced_currents_index = all_indices;
-            induced_currents = (double*) malloc(induced_current_count * sizeof(double));
+            induced_currents = (double*) calloc(induced_current_count, sizeof(double));
             local_induced_currents = &induced_currents[proc_induced_current_offset[nrnmpi_myid]];
+            // set to local count to avoid accumulation with repeated calls
+            induced_current_count = local_induced_current_count;
         }
     } else {
         if (!multicompartment_inititalized) {
             total_reaction_states = react_offsets[react_offset_count - 1];
             all_reaction_indices = reaction_indices;
             all_reaction_states = (double*) calloc(total_reaction_states, sizeof(double));
             multicompartment_inititalized = TRUE;
-            induced_currents = (double*) malloc(induced_current_count * sizeof(double));
+            induced_currents = (double*) calloc(induced_current_count, sizeof(double));
             local_induced_currents = induced_currents;
         }
     }
@@ -1212,7 +1217,7 @@ void ECS_Grid_node::initialize_multicompartment_reaction() {
         all_reaction_indices = reaction_indices;
         all_reaction_states = (double*) calloc(total_reaction_states, sizeof(double));
         multicompartment_inititalized = TRUE;
-        induced_currents = (double*) malloc(induced_current_count * sizeof(double));
+        induced_currents = (double*) calloc(induced_current_count, sizeof(double));
         local_induced_currents = induced_currents;
     }
 #endif
@@ -1237,7 +1242,7 @@ void ECS_Grid_node::do_multicompartment_reactions(double* result) {
         for (i = 0; i < total_reaction_states; i++)
             result[all_reaction_indices[i]] += all_reaction_states[i];
     }
-    memset(all_reaction_states, 0, total_reaction_states * sizeof(int));
+    memset(all_reaction_states, 0, total_reaction_states * sizeof(double));
 }
 
 // TODO: Implement this
@@ -1261,12 +1266,18 @@ ECS_Grid_node::~ECS_Grid_node() {
         free(proc_num_fluxes);
         free(proc_num_reaction_states);
         free(proc_num_reactions);
+        free(reaction_indices);
     }
 #endif
+    free(all_reaction_indices);
+    reaction_indices = nullptr;
+    free(react_offsets);
     free(all_currents);
     free(ecs_adi_dir_x);
     free(ecs_adi_dir_y);
     free(ecs_adi_dir_z);
+    if (get_alpha == get_alpha_scalar)
+        free(alpha);
     if (node_flux_count > 0) {
         free(node_flux_idx);
         free(node_flux_scale);

src/nrnpython/grids.cpp

@@ -614,8 +614,10 @@ static void free_currents() {
     for (i = 0; i < _memb_count; i++) {
         for (j = 0; j < _memb_species_count[i]; j++) {
             free(_memb_cur_mapped[i][j]);
+            free(_memb_cur_mapped_ecs[i][j]);
         }
         free(_memb_cur_mapped[i]);
+        free(_memb_cur_mapped_ecs[i]);
     }
     _memb_cur_ptrs.clear();
     free(_memb_cur_mapped);
@@ -973,6 +975,8 @@ extern "C" NRN_EXPORT void register_rate(int nspecies,
         react->flux = (double**) malloc(react->icsN * sizeof(double*));
         for (i = 0; i < react->icsN; i++)
             react->flux[i] = (double*) malloc(react->num_regions * sizeof(double));
+    } else {
+        react->flux = nullptr;
     }
     react->states_for_reaction = (double**) malloc(react->num_species * sizeof(double*));
     react->states_for_reaction_dx = (double**) malloc(react->num_species * sizeof(double*));
@@ -991,8 +995,6 @@ extern "C" NRN_EXPORT void register_rate(int nspecies,
     react->params_for_reaction = (double**) malloc(react->num_params * sizeof(double*));
     for (i = 0; i < react->num_params; i++)
         react->params_for_reaction[i] = (double*) malloc(react->num_regions * sizeof(double));
-    if (react->num_mult > 0)
-        react->mc_mult = (double*) malloc(react->num_mult * sizeof(double));
 
     if (_reactions == NULL) {
         _reactions = react;
@@ -1017,28 +1019,34 @@ extern "C" NRN_EXPORT void clear_rates() {
         if (react->vptrs != NULL)
             free(react->vptrs);
         for (i = 0; i < react->num_segments; i++) {
-            for (j = 0; j < react->num_species; j++) {
+            for (j = 0; j < react->num_species + react->num_params; j++) {
                 free(react->state_idx[i][j]);
             }
             free(react->state_idx[i]);
 
             if (react->num_ecs_species + react->num_ecs_params > 0) {
                 free(react->ecs_state[i]);
+                free(react->ecs_index[i]);
             }
         }
+        free(react->state_idx);
+        if (react->num_ecs_species + react->num_ecs_params > 0) {
+            free(react->ecs_index);
+            free(react->ecs_state);
+            free(react->ecs_offset_index);
+            free(react->ecs_grid);
+        }
         if (react->num_mult > 0) {
             for (i = 0; i < react->num_mult; i++)
                 free(react->mc_multiplier[i]);
             free(react->mc_multiplier);
         }
 
-        free(react->state_idx);
-        free(react->ecs_state);
         prev = react;
 
         if (react->num_mult > 0)
             free(react->mc_mult);
-        if (_membrane_flux) {
+        if (react->flux != NULL) {
             for (i = 0; i < react->icsN; i++)
                 free(react->flux[i]);
             free(react->flux);
@@ -1052,10 +1060,15 @@ extern "C" NRN_EXPORT void clear_rates() {
         }
         for (i = 0; i < react->num_species; i++) {
             free(react->states_for_reaction[i]);
+            free(react->states_for_reaction_dx[i]);
             free(react->result_array[i]);
+            free(react->result_array_dx[i]);
         }
         free(react->states_for_reaction);
+        free(react->states_for_reaction_dx);
+
         free(react->result_array);
+        free(react->result_array_dx);
         for (i = 0; i < react->num_params; i++) {
             free(react->params_for_reaction[i]);
         }