Add support for inserting nmodl flags in nrnivmodl-core calls (#398)

* Add support for inserting nmodl flags in nrnivmodl-core calls
    For example, this enables the call:
        nrnivmodl-core -a "sympy --analytic" mod/
* Runtime nmodl flags replace build nmodl flags

Author: cattabiani

extra/nrnivmodl-core.in

@@ -20,17 +20,20 @@ params_MODS_PATH="."
 params_BUILD_TYPE="@COMPILE_LIBRARY_TYPE@"
 
 # prefix for common options : make sure to rename these if options are changed.
-MAKE_OPTIONS="MECHLIB_SUFFIX NMODL_BINARY DEST_DIR INCFLAGS LINKFLAGS MODS_PATH VERBOSE BUILD_TYPE"
+MAKE_OPTIONS="MECHLIB_SUFFIX NMODL_BINARY NMODL_RUNTIME_FLAGS DEST_DIR INCFLAGS LINKFLAGS MODS_PATH VERBOSE BUILD_TYPE"
 
 # parse CLI args
-while getopts "n:m:v:d:i:l:p:b:hV" OPT; do
+while getopts "n:m:a:d:i:l:V:p:b:h" OPT; do
     case "$OPT" in
     n)
         # suffix for mechanism library
         params_MECHLIB_SUFFIX="$OPTARG";;
     m)
         # nmodl or mod2c binary to use
         params_NMODL_BINARY="$OPTARG";;
+    a)
+        # additional nmodl flags to be used
+        params_NMODL_RUNTIME_FLAGS="$OPTARG";;
     d)
         # destination install directory
         params_DEST_DIR="$OPTARG";;
@@ -52,14 +55,15 @@ while getopts "n:m:v:d:i:l:p:b:hV" OPT; do
     h)
         echo "$APP_NAME [options, ...] [mods_path]"
         echo "Options:"
-        echo "  -n <name>          The model name, used as a suffix in the shared library"
-        echo "  -m <mod2c_bin>     NMODL code generation compiler path"
-        echo "  -i <incl_flags>    Definitions passed to the compiler, typically '-I dir..'"
-        echo "  -l <link_flags>    Definitions passed to the linker, typically '-Lx -lylib..'"
-        echo "  -d <dest_dir>      Install to dest_dir. Default: Off."
-        echo "  -V                 Verbose: show commands executed by make"
-        echo "  -p <n_procs>       Number of parallel builds (Default: $PARALLEL_BUILDS)"
-        echo "  -b <STATIC|SHARED> libcorenrnmech library type"
+        echo "  -n <name>                 The model name, used as a suffix in the shared library"
+        echo "  -m <nmodl_bin>            NMODL/mod2c code generation compiler path"
+        echo "  -a <nmodl_runtime_flags>  Runtime flags for NMODL/mod2c"
+        echo "  -i <incl_flags>           Definitions passed to the compiler, typically '-I dir..'"
+        echo "  -l <link_flags>           Definitions passed to the linker, typically '-Lx -lylib..'"
+        echo "  -d <dest_dir>             Install to dest_dir. Default: Off."
+        echo "  -V                        Verbose: show commands executed by make"
+        echo "  -p <n_procs>              Number of parallel builds (Default: $PARALLEL_BUILDS)"
+        echo "  -b <STATIC|SHARED>        libcorenrnmech library type"
         exit 0;;
     ?)
         exit 1;;

extra/nrnivmodl_core_makefile.in

@@ -141,6 +141,13 @@ ALL_OBJS = $(MOD_FUNC_OBJ) $(DIMPLIC_OBJ) $(mod_cpp_objs) $(mod_ispc_objs)
 C_RESET := \033[0m
 C_GREEN := \033[32m
 
+# Default nmodl flags. Override if NMODL_RUNTIME_FLAGS is not empty
+NMODL_FLAGS_ISPC = $(if $(NMODL_RUNTIME_FLAGS),$(NMODL_RUNTIME_FLAGS),@nmodl_arguments_ispc@)
+NMODL_FLAGS_C = $(if $(NMODL_RUNTIME_FLAGS),$(NMODL_RUNTIME_FLAGS),@nmodl_arguments_c@)
+$(info Default nmodl flags: $(if (@CORENRN_ENABLE_ISPC@ == ON), @nmodl_arguments_ispc@, @nmodl_arguments_c@))
+ifneq ($(NMODL_RUNTIME_FLAGS),)
+    $(warning Runtime nmodl flags (they replace the default ones): $(NMODL_RUNTIME_FLAGS))
+endif
 
 # ======== MAIN BUILD RULES ============
 
@@ -186,11 +193,11 @@ $(MOD_OBJS_DIR)/%.obj: $(MOD_TO_CPP_DIR)/%.ispc | $(MOD_OBJS_DIR)
 
 # translate MOD files to ISPC using NMODL
 $(mod_ispc_files): $(MOD_TO_CPP_DIR)/%.ispc: $(MODS_PATH)/%.mod | $(MOD_TO_CPP_DIR)
-	$(NMODL_ENV_VAR) $(NMODL_BINARY_PATH) $< -o $(MOD_TO_CPP_DIR)/ @nmodl_arguments_ispc@
+	$(NMODL_ENV_VAR) $(NMODL_BINARY_PATH) $< -o $(MOD_TO_CPP_DIR)/ $(NMODL_FLAGS_ISPC)
 
 # translate MOD files to CPP using mod2c/NMODL
 $(mod_cpp_files): $(MOD_TO_CPP_DIR)/%.cpp: $(MODS_PATH)/%.mod | $(MOD_TO_CPP_DIR)
-	$(NMODL_ENV_VAR) $(NMODL_BINARY_PATH) $< -o $(MOD_TO_CPP_DIR)/ @nmodl_arguments_c@
+	$(NMODL_ENV_VAR) $(NMODL_BINARY_PATH) $< -o $(MOD_TO_CPP_DIR)/ $(NMODL_FLAGS_C)
 
 # static pattern to set up the dependencies for the previous recipe
 $(mod_ispc_cpp_files): $(MOD_TO_CPP_DIR)/%.cpp: $(MOD_TO_CPP_DIR)/%.ispc