fix MUSIC setup.py and add coverage

.github/workflows/coverage.yml

@@ -49,6 +49,22 @@ jobs:
           cmake ..
           make && sudo make install
 
+      - name: Setup MUSIC
+        run: |
+          python3 -m venv music-venv
+          source music-venv/bin/activate
+          python3 -m pip install mpi4py cython numpy
+          # Stable build: https://github.com/INCF/MUSIC/archive/refs/heads/switch-to-MPI-C-interface.zip  @ f33b66ea9348888eed1761738ab48c23ffc8a0d0
+          curl -L -o MUSIC.zip https://codeload.github.com/INCF/MUSIC/zip/f33b66ea9348888eed1761738ab48c23ffc8a0d0 &&
+              unzip MUSIC.zip &&
+              mv MUSIC-* MUSIC &&
+              cd MUSIC &&
+              ./autogen.sh &&
+              ./configure --with-python-sys-prefix --disable-anysource &&
+              sudo make -j install
+          deactivate
+        working-directory: ${{runner.temp}} 
+
       - name: Setup Xvfb
         run: |
           sudo apt-get install xvfb
@@ -97,7 +113,7 @@ jobs:
 
           # CMake options & flags
           export COVERAGE_FLAGS="--coverage -O0 -fno-inline -g";
-          export CMAKE_OPTION="-DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=ON -DNRN_ENABLE_PYTHON=ON -DNRN_ENABLE_PYTHON_DYNAMIC=ON -DNRN_PYTHON_DYNAMIC=${PYTHON_MIN};${PYTHON_MAX} -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_PROFILING=ON -DNRN_ENABLE_BACKTRACE=ON";
+          export CMAKE_OPTION="-DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=ON -DNRN_ENABLE_PYTHON=ON -DNRN_ENABLE_PYTHON_DYNAMIC=ON -DNRN_PYTHON_DYNAMIC=${PYTHON_MIN};${PYTHON_MAX} -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_PROFILING=ON -DNRN_ENABLE_BACKTRACE=ON -DNRN_ENABLE_MUSIC=ON";
           cmake $CMAKE_OPTION -DCMAKE_C_COMPILER=$CC -DCMAKE_CXX_COMPILER=$CXX -DNRN_ENABLE_TESTS=ON -DCMAKE_C_FLAGS="${COVERAGE_FLAGS}" -DCMAKE_CXX_FLAGS="${COVERAGE_FLAGS}" -DCORENRN_ENABLE_UNIT_TESTS=ON ..;
 
           # Coverage

cmake/NeuronFileLists.cmake

@@ -526,6 +526,8 @@ set(IVOS_FILES_LIST listimpl.cpp string.cpp observe.cpp regexp.cpp resource.cpp)
 
 set(MPI_DYNAMIC_INCLUDE nrnmpi_dynam.h nrnmpi_dynam_cinc nrnmpi_dynam_wrappers.inc)
 
+set(NRN_MUSIC_FILES_LIST nrnmusic.cpp)
+
 # =============================================================================
 # Top level directories under src
 # =============================================================================
@@ -538,6 +540,7 @@ set(NRN_NRNIV_SRC_DIR ${PROJECT_SOURCE_DIR}/src/nrniv)
 set(NRN_MODLUNIT_SRC_DIR ${PROJECT_SOURCE_DIR}/src/modlunit)
 set(NRN_NMODL_SRC_DIR ${PROJECT_SOURCE_DIR}/src/nmodl)
 set(NRN_IVOS_SRC_DIR ${PROJECT_SOURCE_DIR}/src/ivos)
+set(NRN_MUSIC_SRC_DIR ${PROJECT_SOURCE_DIR}/src/neuronmusic)
 
 # =============================================================================
 # Create source file lists by gathering from various directories
@@ -569,6 +572,7 @@ nrn_create_file_list(NRN_MODLUNIT_SRC_FILES ${NRN_MODLUNIT_SRC_DIR} ${MODLUNIT_F
 nrn_create_file_list(NRN_NMODL_SRC_FILES ${NRN_NMODL_SRC_DIR} ${NMODL_FILES_LIST})
 nrn_create_file_list(NRNMPI_DYNAMIC_INCLUDE_FILE ${PROJECT_SOURCE_DIR}/src/nrnmpi
                      ${MPI_DYNAMIC_INCLUDE})
+nrn_create_file_list(NRN_MUSIC_SRC_FILES ${NRN_MUSIC_SRC_DIR} ${NRN_MUSIC_FILES_LIST})                     
 nrn_create_file_list(NRN_IVOS_SRC_FILES ${NRN_IVOS_SRC_DIR} ${IVOS_FILES_LIST})
 list(APPEND NRN_OC_SRC_FILES ${PROJECT_BINARY_DIR}/src/oc/hocusr.h)
 

src/nrniv/nrnmusic.cpp → src/neuronmusic/nrnmusic.cpp

@@ -1,5 +1,15 @@
+#include <../../nrnconf.h>
 #define NO_PYTHON_H 1
-#include <../neuronmusic/nrnmusic.h>
+#define IN_NRNMUSIC_CPP
+#include "nrnmusicapi.h"
+#include "hocdec.h"
+#include "nrn_ansi.h"
+#include "netcon.h"
+#include "cvodeobj.h"
+#include "netcvode.h"
+#include "multicore.h"
+#include "nrnmusic.h"
+#include "netpar.h"
 #include <unordered_map>
 
 extern int nrnmusic;
@@ -15,6 +25,7 @@ void nrnmusic_spikehandle(void* vport, double tt, int gindex);
 extern Object* nrnpy_po2ho(PyObject*);
 extern PyObject* nrnpy_ho2po(Object*);
 extern Object* hoc_new_object(Symbol*, void*);
+extern NetCvode* net_cvode_instance;
 
 MUSIC::Setup* nrnmusic_setup;
 MUSIC::Runtime* nrnmusic_runtime;
@@ -73,7 +84,7 @@ static PortTable* music_output_ports;
 NetParMusicEvent::NetParMusicEvent() {}
 NetParMusicEvent::~NetParMusicEvent() {}
 void NetParMusicEvent::send(double t, NetCvode* nc, NrnThread* nt) {
-    nc->event(t + usable_mindelay_, this, nt);
+    nc->event(t + nrn_usable_mindelay(), this, nt);
 }
 void NetParMusicEvent::deliver(double t, NetCvode* nc, NrnThread* nt) {
     nrnmusic_runtime->tick();
@@ -127,8 +138,8 @@ void NRNMUSIC::EventOutputPort::gid2index(int gid, int gi) {
     // except pc.cell(gid, nc) has already been called and this
     // will add this to the PreSyn.music_out_ list.
     alloc_music_space();
-    auto iter = gid2out_.find(gid);
-    if (iter == gid2out_.end()) {
+    auto iter = nrn_gid2out().find(gid);
+    if (iter == nrn_gid2out().end()) {
         return;
     }
     PreSyn* ps = iter->second;
@@ -179,7 +190,7 @@ PyObject* NRNMUSIC::EventInputPort::index2target(int gi, PyObject* ptarget) {
         ps = (*gi_table)[gi];
     }
     NetCon* nc = new NetCon(ps, target);
-    Object* o = hoc_new_object(netcon_sym_, nc);
+    Object* o = hoc_new_object(nrn_netcon_sym(), nc);
     nc->obj_ = o;
     PyObject* po = nrnpy_ho2po(o);
     // printf("index2target %d %s\n", gi, hoc_object_name(target));
@@ -198,6 +209,7 @@ void nrnmusic_init(int* pargc, char*** pargv) {
             nrnmusic = 1;
         }
     }
+
     if (getenv("_MUSIC_CONFIG_"))
         nrnmusic = 1;  // temporary kludge
     if (nrnmusic) {
@@ -216,7 +228,7 @@ void nrnmusic_terminate() {
 
 // Called from nrn_spike_exchange_init so usable_mindelay is ready to use
 // For now, can only be called once.
-static void nrnmusic_runtime_phase() {
+void nrnmusic_runtime_phase() {
     static int called = 0;
     assert(!called);
     called = 1;
@@ -237,7 +249,7 @@ static void nrnmusic_runtime_phase() {
         }
         eh->filltable(eip, cnt);
         MUSIC::PermutationIndex indices(&gindices.front(), gindices.size());
-        eip->map(&indices, eh, usable_mindelay_ / 1000.0);
+        eip->map(&indices, eh, nrn_usable_mindelay() / 1000.0);
         delete eip->gi_table;
     }
     delete music_input_ports;
@@ -260,8 +272,8 @@ static void nrnmusic_runtime_phase() {
     delete music_output_ports;
 
     // switch to the runtime phase
-    // printf("usable_mindelay = %g\n", usable_mindelay_);
-    nrnmusic_runtime = new MUSIC::Runtime(nrnmusic_setup, usable_mindelay_ / 1000.0);
+    // printf("usable_mindelay = %g\n", nrn_usable_mindelay());
+    nrnmusic_runtime = new MUSIC::Runtime(nrnmusic_setup, nrn_usable_mindelay() / 1000.0);
     npme = new NetParMusicEvent();
     npme->send(0, net_cvode_instance, nrn_threads);
-}
+}

src/neuronmusic/nrnmusicapi.h

@@ -0,0 +1,14 @@
+#pragma once
+
+extern int nrnmusic;
+
+extern "C" {
+
+// Note: MPI_Comm nrnmusic_comm; in nrnmpi.cpp and nrnmusic.cpp
+
+extern void nrnmusic_runtime_phase();
+extern void nrnmusic_injectlist(void*, double);
+extern void nrnmusic_init(int* parg, char*** pargv);
+extern void nrnmusic_terminate();
+
+}  // end of extern "C"

src/neuronmusic/setup.py.in

@@ -12,7 +12,7 @@ import os
 os.environ["CC"]=mpicc_bin
 os.environ["CXX"]=mpicxx_bin
 
-include_dirs = ['@MUSIC_INCDIR@', '@MPI_INCLUDE_PATH@', nrn_srcdir+'/src/neuronmusic', nrn_srcdir + '/src/nrnpython', '.']
+include_dirs = ['@MUSIC_INCDIR@', nrn_srcdir+'/src/neuronmusic', nrn_srcdir + '/src/nrnpython', '.'] + '@MPI_INCLUDE_PATH@'.split(';')
 libdirs = ['@MUSIC_LIBDIR@', @NRN_LIBDIR@]
 
 

src/nrncvode/netcvode.cpp

@@ -118,7 +118,7 @@ extern "C" void nrnthread_trajectory_return(int tid,
                                             double t);
 bool nrn_trajectory_request_per_time_step_ = false;
 #if NRN_MUSIC
-extern void nrnmusic_injectlist(void*, double);
+#include "nrnmusicapi.h"
 #endif
 
 extern int hoc_return_type_code;

src/nrniv/CMakeLists.txt

@@ -167,6 +167,10 @@ if(NOT NRN_ENABLE_INTERVIEWS)
   list(APPEND NRN_NRNIV_LIB_SRC_FILES ${NRN_IVOS_SRC_FILES})
 endif()
 
+if(NRN_ENABLE_MUSIC)
+    list(APPEND NRN_NRNIV_LIB_SRC_FILES ${NRN_MUSIC_SRC_FILES})
+endif()
+
 # =============================================================================
 # Include directories for #include <../../nrnconf.h>
 # =============================================================================
@@ -199,6 +203,9 @@ set(NRN_INCLUDE_DIRS
     ${PROJECT_SOURCE_DIR}/src/sundials/cvodes
     ${PROJECT_SOURCE_DIR}/src/sundials/ida
     ${PROJECT_SOURCE_DIR}/src/sundials/shared)
+if(NRN_ENABLE_MUSIC)
+  list(APPEND NRN_INCLUDE_DIRS ${NRN_MUSIC_SRC_DIR})
+endif()
 set(NRN_INCLUDE_DIRS
     ${NRN_INCLUDE_DIRS}
     PARENT_SCOPE)
@@ -335,7 +342,7 @@ if(NRN_ENABLE_MPI_DYNAMIC)
 endif()
 
 if(NRN_ENABLE_MUSIC)
-  set_source_files_properties(${PROJECT_SOURCE_DIR}/src/nrniv/netpar.cpp
+  set_source_files_properties(${PROJECT_SOURCE_DIR}/src/neuronmusic/nrnmusic.cpp
                               PROPERTIES INCLUDE_DIRECTORIES ${MUSIC_INCDIR})
 endif()
 

src/nrniv/netpar.cpp

@@ -202,9 +202,20 @@ static NrnThread* last_nt_;
 #endif
 
 #if NRN_MUSIC
-#include "nrnmusic.cpp"
+#include "nrnmusicapi.h"
+int nrnmusic;
 #endif
 
+double nrn_usable_mindelay() {
+    return usable_mindelay_;
+}
+Symbol* nrn_netcon_sym() {
+    return netcon_sym_;
+}
+Gid2PreSyn& nrn_gid2out() {
+    return gid2out_;
+}
+
 NetParEvent::NetParEvent() {
     wx_ = ws_ = 0.;
     ithread_ = -1;

src/nrniv/netpar.h

@@ -0,0 +1,13 @@
+#pragma once
+
+// Some things in netpar.cpp that were static but needed by nrnmusic.cpp
+
+#include "netcon.h"
+#include <unordered_map>
+struct Symbol;
+
+using Gid2PreSyn = std::unordered_map<int, PreSyn*>;
+
+double nrn_usable_mindelay();
+Symbol* nrn_netcon_sym();
+Gid2PreSyn& nrn_gid2out();

src/nrnmpi/nrnmpi.cpp

@@ -30,11 +30,10 @@ extern double nrn_timeus();
 #include <libhpm.h>
 #endif
 
-int nrnmusic;
 #if NRN_MUSIC
 MPI_Comm nrnmusic_comm;
-extern void nrnmusic_init(int* parg, char*** pargv);
-extern void nrnmusic_terminate();
+#include "nrnmusicapi.h"
+extern int nrnmusic;
 #endif
 
 MPI_Comm nrnmpi_world_comm;
@@ -98,9 +97,11 @@ for (i=0; i < *pargc; ++i) {
             b = 1;
             nrnmpi_under_nrncontrol_ = 1;
         }
+#if NRN_MUSIC
         if (nrnmusic) {
             b = 1;
         }
+#endif
         if (!b) {
             nrnmpi_under_nrncontrol_ = 0;
             return;
@@ -121,7 +122,9 @@ for (i=0; i < *pargc; ++i) {
             asrt(MPI_Init(pargc, pargv));
 #endif
             nrnmpi_under_nrncontrol_ = 1;
+#if NRN_MUSIC
         } else if (!nrnmusic) {
+#endif
             nrnmpi_under_nrncontrol_ = 0;
         }