Build modlunit/nocmodl with their own CMakeLists.txt

CMakeLists.txt

@@ -572,6 +572,8 @@ endif()
 # =============================================================================
 add_subdirectory(src/sparse13)
 add_subdirectory(src/gnu)
+add_subdirectory(src/modlunit)
+add_subdirectory(src/nmodl)
 add_subdirectory(src/nrniv)
 
 # Collect the environment variables that are needed to execute NEURON from the build directory. This

cmake/MacroHelper.cmake

@@ -142,30 +142,23 @@ macro(nrn_print_matching_variables prefix_regex)
 endmacro()
 
 # =============================================================================
-# Run nocmodl to convert NMODL to C
+# Run nocmodl to convert NMODL to C++
 # =============================================================================
-macro(nocmodl_mod_to_cpp modfile_basename)
+macro(nocmodl_mod_to_cpp modfile_basename source_dir target_dir)
   set(NOCMODL_SED_EXPR "s/_reg()/_reg_()/")
   if(NOT MSVC)
     set(NOCMODL_SED_EXPR "'${NOCMODL_SED_EXPR}'")
   endif()
-  set(REMOVE_CMAKE_COMMAND "rm")
-  if(CMAKE_VERSION VERSION_LESS "3.17")
-    set(REMOVE_CMAKE_COMMAND "remove")
-  endif()
   add_custom_command(
-    OUTPUT ${PROJECT_BINARY_DIR}/${modfile_basename}.cpp
+    OUTPUT "${target_dir}/${modfile_basename}.cpp"
     COMMAND
       ${CMAKE_COMMAND} -E env "MODLUNIT=${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib"
-      ${NRN_NOCMODL_SANITIZER_ENVIRONMENT} $<TARGET_FILE:nocmodl>
-      ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod
-    COMMAND sed ${NOCMODL_SED_EXPR} ${PROJECT_SOURCE_DIR}/${modfile_basename}.cpp >
-            ${PROJECT_BINARY_DIR}/${modfile_basename}.cpp
-    COMMAND ${CMAKE_COMMAND} -E ${REMOVE_CMAKE_COMMAND}
-            ${PROJECT_SOURCE_DIR}/${modfile_basename}.cpp
-    DEPENDS nocmodl ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod
-            ${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib
-    WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/src/nrniv)
+      ${NRN_NOCMODL_SANITIZER_ENVIRONMENT} $<TARGET_FILE:nocmodl> -o "${target_dir}"
+      "${source_dir}/${modfile_basename}.mod"
+    COMMAND sed -i -e ${NOCMODL_SED_EXPR} "${target_dir}/${modfile_basename}.cpp"
+    DEPENDS nocmodl "${source_dir}/${modfile_basename}.mod"
+            "${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib"
+    WORKING_DIRECTORY ${target_dir})
 endmacro()
 
 # =============================================================================

cmake/NeuronFileLists.cmake

@@ -363,59 +363,6 @@ set(NRNPYTHON_FILES_LIST
     rxd_marching_cubes.cpp
     rxd_llgramarea.cpp)
 
-# built-in mod files
-set(MODFILE_BASE_NAMES
-    apcount
-    exp2syn
-    expsyn
-    feature
-    hh
-    intfire1
-    intfire2
-    intfire4
-    netstim
-    oclmp
-    passive
-    pattern
-    ppmark
-    stim
-    svclmp
-    syn
-    vclmp)
-
-set(MODLUNIT_FILES_LIST
-    consist.cpp
-    declare.cpp
-    init.cpp
-    io.cpp
-    kinunit.cpp
-    list.cpp
-    model.cpp
-    nrnunit.cpp
-    passn.cpp
-    symbol.cpp
-    units.cpp
-    units1.cpp
-    version.cpp)
-
-set(NMODL_FILES_LIST
-    consist.cpp
-    deriv.cpp
-    discrete.cpp
-    init.cpp
-    io.cpp
-    kinetic.cpp
-    list.cpp
-    modl.cpp
-    nocpout.cpp
-    noccout.cpp
-    parsact.cpp
-    netrec_discon.cpp
-    simultan.cpp
-    solve.cpp
-    symbol.cpp
-    version.cpp)
-
 set(IVOS_FILES_LIST observe.cpp resource.cpp)
 
 set(MPI_DYNAMIC_INCLUDE nrnmpi_dynam.h nrnmpi_dynam_cinc nrnmpi_dynam_wrappers.inc)
@@ -442,8 +389,6 @@ set(NRN_IVOC_SRC_DIR ${PROJECT_SOURCE_DIR}/src/ivoc)
 set(NRN_NODEORDEROPTIM_SRC_DIR ${PROJECT_SOURCE_DIR}/src/coreneuron/permute)
 set(NRN_NRNCVODE_SRC_DIR ${PROJECT_SOURCE_DIR}/src/nrncvode)
 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)
 set(NRN_PARALLEL_SRC_DIR ${PROJECT_SOURCE_DIR}/src/parallel)
@@ -473,11 +418,8 @@ nrn_create_file_list(NRN_SCOPMATH_SRC_FILES ${PROJECT_SOURCE_DIR}/src/scopmath
 nrn_create_file_list(NRN_NRNMPI_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrnmpi ${NRNMPI_FILES_LIST})
 nrn_create_file_list(NRN_NRNPYTHON_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrnpython
                      ${NRNPYTHON_FILES_LIST})
-nrn_create_file_list(NRN_MODFILE_BASE_NAMES src/nrnoc ${MODFILE_BASE_NAMES})
 nrn_create_file_list(NRN_BIN_SRC_FILES ${PROJECT_SOURCE_DIR}/src/ivoc/ nrnmain.cpp)
 nrn_create_file_list(NRN_BIN_SRC_FILES ${PROJECT_SOURCE_DIR}/src/oc/ ockludge.cpp modlreg.cpp)
-nrn_create_file_list(NRN_MODLUNIT_SRC_FILES ${NRN_MODLUNIT_SRC_DIR} ${MODLUNIT_FILES_LIST})
-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_IVOS_SRC_FILES ${NRN_IVOS_SRC_DIR} ${IVOS_FILES_LIST})

src/modlunit/CMakeLists.txt

@@ -0,0 +1,32 @@
+flex_target(modlunit_lex lex.lpp ${CMAKE_CURRENT_BINARY_DIR}/lex.cpp)
+bison_target(modlunit_parse parse1.ypp ${CMAKE_CURRENT_BINARY_DIR}/parse1.cpp
+             DEFINES_FILE ${CMAKE_CURRENT_BINARY_DIR}/parse1.hpp)
+
+add_executable(
+  modlunit
+  consist.cpp
+  declare.cpp
+  init.cpp
+  io.cpp
+  kinunit.cpp
+  list.cpp
+  model.cpp
+  nrnunit.cpp
+  passn.cpp
+  symbol.cpp
+  units.cpp
+  units1.cpp
+  version.cpp
+  "${CMAKE_CURRENT_BINARY_DIR}/lex.cpp"
+  "${CMAKE_CURRENT_BINARY_DIR}/parse1.cpp")
+target_compile_definitions(modlunit PRIVATE NRNUNIT=1)
+cpp_cc_configure_sanitizers(TARGET modlunit)
+target_include_directories(
+  modlunit PRIVATE "${CMAKE_CURRENT_BINARY_DIR}" "${PROJECT_SOURCE_DIR}/src"
+                   "${CMAKE_CURRENT_SOURCE_DIR}")
+
+if(NRN_NMODL_CXX_FLAGS)
+  target_compile_options(modlunit PRIVATE ${NRN_NMODL_CXX_FLAGS})
+endif()
+
+install(TARGETS modlunit DESTINATION bin)

src/modlunit/model.h

@@ -1,5 +1,5 @@
 /* /local/src/master/nrn/src/modlunit/model.h,v 1.2 1997/11/24 16:19:13 hines Exp */
-#include "wrap_sprintf.h"
+#include "utils/wrap_sprintf.hpp"
 #include <stdio.h>
 #include <assert.h>
 

src/modlunit/units.cpp

@@ -6,7 +6,6 @@
 /* /local/src/master/nrn/src/modlunit/units.c,v 1.5 1997/11/24 16:19:13 hines Exp */
 /* Mostly from Berkeley */
 #include "model.h"
-#include "nrnassrt.h"
 #include <stdio.h>
 #include <stdlib.h>
 #include <signal.h>

src/nmodl/CMakeLists.txt

@@ -0,0 +1,51 @@
+flex_target(nocmodl_lex lex.lpp ${CMAKE_CURRENT_BINARY_DIR}/lex.cpp)
+bison_target(nocmodl_parse parse1.ypp ${CMAKE_CURRENT_BINARY_DIR}/parse1.cpp
+             DEFINES_FILE ${CMAKE_CURRENT_BINARY_DIR}/parse1.hpp)
+bison_target(nocmodl_diffeq diffeq.ypp ${CMAKE_CURRENT_BINARY_DIR}/diffeq.cpp
+             DEFINES_FILE ${CMAKE_CURRENT_BINARY_DIR}/diffeq.hpp)
+
+add_custom_target(
+  nocmodl_generated_files
+  DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/lex.cpp" "${CMAKE_CURRENT_BINARY_DIR}/parse1.hpp"
+          "${CMAKE_CURRENT_BINARY_DIR}/parse1.cpp" "${CMAKE_CURRENT_BINARY_DIR}/diffeq.hpp"
+          "${CMAKE_CURRENT_BINARY_DIR}/diffeq.cpp")
+# add_dependencies(generated_source_files nocmodl_generated_files)
+add_executable(
+  nocmodl
+  consist.cpp
+  deriv.cpp
+  discrete.cpp
+  init.cpp
+  io.cpp
+  kinetic.cpp
+  list.cpp
+  modl.cpp
+  nocpout.cpp
+  noccout.cpp
+  parsact.cpp
+  netrec_discon.cpp
+  simultan.cpp
+  solve.cpp
+  symbol.cpp
+  ../modlunit/units.cpp
+  version.cpp
+  "${CMAKE_CURRENT_BINARY_DIR}/lex.cpp"
+  "${CMAKE_CURRENT_BINARY_DIR}/parse1.cpp"
+  "${CMAKE_CURRENT_BINARY_DIR}/diffeq.cpp")
+cpp_cc_configure_sanitizers(TARGET nocmodl)
+target_compile_definitions(nocmodl PRIVATE COMPILE_DEFINITIONS NMODL=1 CVODE=1)
+
+# Otherwise the generated code in the binary directory does not find headers in the modlunit source
+# directory and the source files in the source directory do not find generated headers in the binary
+# directory. TODO: (see also coreneuron) fix adding a dependency on CLI11::CLI11 when CLI11 is a
+# submodule. Right now this doesn't work because the CLI11 targets are not exported/installed but
+# coreneuron-core is.
+get_target_property(CLI11_HEADER_DIRECTORY CLI11::CLI11 INTERFACE_INCLUDE_DIRECTORIES)
+target_include_directories(
+  nocmodl PRIVATE "${CMAKE_CURRENT_BINARY_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}"
+                  "${CLI11_HEADER_DIRECTORY}" "${PROJECT_SOURCE_DIR}/src")
+if(NRN_NMODL_CXX_FLAGS)
+  target_compile_options(nocmodl PRIVATE ${NRN_NMODL_CXX_FLAGS})
+endif()
+
+install(TARGETS nocmodl DESTINATION bin)

src/nmodl/modl.h

@@ -1,5 +1,5 @@
 #pragma once
-#include "wrap_sprintf.h"
+#include "utils/wrap_sprintf.hpp"
 
 #include <stdio.h>
 #include <string.h>