Better way of fixing hh.mod issue

CMakeLists.txt

@@ -789,30 +789,6 @@ add_custom_target(
   COMMENT "Format only files modified with respect to master branch."
   WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
 
-# =============================================================================
-# ~~~
-# Update hh.mod for CoreNEURON compatibility
-# - Replace GLOBAL variable by RANGE
-# - Comment out TABLE
-# ~~~
-# =============================================================================
-if(NRN_ENABLE_CORENEURON OR NRN_ENABLE_MOD_COMPATIBILITY)
-  set(GLOBAL_VAR_TOGGLE_COMMAND "'s/ GLOBAL minf/ RANGE minf/'")
-else()
-  set(GLOBAL_VAR_TOGGLE_COMMAND "'s/ RANGE minf/ GLOBAL minf/'")
-endif()
-separate_arguments(GLOBAL_VAR_TOGGLE_COMMAND UNIX_COMMAND "${GLOBAL_VAR_TOGGLE_COMMAND}")
-add_custom_target(
-  hh_update
-  COMMAND sed ${GLOBAL_VAR_TOGGLE_COMMAND} ${CMAKE_SOURCE_DIR}/src/nrnoc/hh.mod >
-          ${CMAKE_BINARY_DIR}/hh.mod.1
-  COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/hh.mod.1
-          ${CMAKE_SOURCE_DIR}/src/nrnoc/hh.mod
-  COMMAND ${CMAKE_COMMAND} -E remove ${CMAKE_BINARY_DIR}/hh.mod.1
-  COMMENT "Update hh.mod for CoreNEURON compatibility"
-  VERBATIM)
-add_dependencies(nrniv_lib hh_update)
-
 # =============================================================================
 # Generate help_data.dat
 # =============================================================================

cmake/MacroHelper.cmake

@@ -144,7 +144,7 @@ endmacro()
 # =============================================================================
 # Run nocmodl to convert NMODL to C
 # =============================================================================
-macro(nocmodl_mod_to_cpp modfile_basename)
+macro(nocmodl_mod_to_cpp modfile_basename modfile_subdir)
   set(NOCMODL_SED_EXPR "s/_reg()/_reg_()/")
   if(NOT MSVC)
     set(NOCMODL_SED_EXPR "'${NOCMODL_SED_EXPR}'")
@@ -153,18 +153,44 @@ macro(nocmodl_mod_to_cpp modfile_basename)
   if(CMAKE_VERSION VERSION_LESS "3.17")
     set(REMOVE_CMAKE_COMMAND "remove")
   endif()
-  get_filename_component(modfile_output_dir ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod DIRECTORY)
+  string(REPLACE "/" ";" path_parts "${modfile_basename}")
+
+  # Create a variable to hold the base path (all but the last part)
+  set(base_path "")
+  list(LENGTH path_parts path_length)
+  math(EXPR last_index "${path_length} - 1")
+
+  # Append all parts except the last one to base_path
+  foreach(i RANGE 0 ${last_index})
+    list(GET path_parts ${i} part)
+    if(${i} LESS ${last_index})
+      if(base_path STREQUAL "")
+        set(base_path "${part}")
+      else()
+        set(base_path "${base_path}/${part}")
+      endif()
+    endif()
+  endforeach()
+
+  # Append the custom part and the last part
+  list(GET path_parts ${last_index} last_part)
+  set(modfile_basename_real "${base_path}/${modfile_subdir}/${last_part}")
+  message(WARNING ${modfile_basename_real})
+
+  get_filename_component(modfile_output_dir ${PROJECT_SOURCE_DIR}/${modfile_basename_real}.mod
+                         DIRECTORY)
   add_custom_command(
     OUTPUT ${PROJECT_BINARY_DIR}/${modfile_basename}.cpp
     COMMAND
       ${CMAKE_COMMAND} -E env "MODLUNIT=${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib"
       ${NRN_NOCMODL_SANITIZER_ENVIRONMENT} $<TARGET_FILE:${NRN_CODEGENERATOR_TARGET}>
-      ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod ${NRN_NMODL_--neuron} -o ${modfile_output_dir}
-    COMMAND sed ${NOCMODL_SED_EXPR} ${PROJECT_SOURCE_DIR}/${modfile_basename}.cpp >
+      ${PROJECT_SOURCE_DIR}/${modfile_basename_real}.mod ${NRN_NMODL_--neuron} -o
+      ${modfile_output_dir}
+    COMMAND sed ${NOCMODL_SED_EXPR} ${PROJECT_SOURCE_DIR}/${modfile_basename_real}.cpp >
             ${PROJECT_BINARY_DIR}/${modfile_basename}.cpp
     COMMAND ${CMAKE_COMMAND} -E ${REMOVE_CMAKE_COMMAND}
-            ${PROJECT_SOURCE_DIR}/${modfile_basename}.cpp
-    DEPENDS ${NRN_CODEGENERATOR_TARGET} ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod
+            ${PROJECT_SOURCE_DIR}/${modfile_basename_real}.cpp
+    DEPENDS ${NRN_CODEGENERATOR_TARGET} ${PROJECT_SOURCE_DIR}/${modfile_basename_real}.mod
             ${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib
     WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/src/nrniv)
 endmacro()

src/nrniv/CMakeLists.txt

@@ -115,7 +115,17 @@ endif()
 # Translate all MOD files to C and mark them generated
 # =============================================================================
 foreach(modfile ${NRN_MODFILE_BASE_NAMES})
-  nocmodl_mod_to_cpp(${modfile})
+  # =============================================================================
+  # ~~~
+  # Set the correct supported keyword for CoreNEURON compatibility
+  # - Replace GLOBAL variable by RANGE
+  # ~~~
+  # =============================================================================
+  if(NRN_ENABLE_CORENEURON OR NRN_ENABLE_MOD_COMPATIBILITY)
+    nocmodl_mod_to_cpp(${modfile} "modfiles/coreneuron")
+  else()
+    nocmodl_mod_to_cpp(${modfile} "modfiles/neuron")
+  endif()
   list(APPEND NRN_MODFILE_CPP ${PROJECT_BINARY_DIR}/${modfile}.cpp)
 endforeach()
 set_property(

src/nrnoc/modfiles/coreneuron/apcount.mod

@@ -0,0 +1 @@
+../neuron/apcount.mod

src/nrnoc/modfiles/coreneuron/exp2syn.mod

@@ -0,0 +1 @@
+../neuron/exp2syn.mod

src/nrnoc/modfiles/coreneuron/expsyn.mod

@@ -0,0 +1 @@
+../neuron/expsyn.mod

src/nrnoc/modfiles/coreneuron/feature.mod

@@ -0,0 +1 @@
+../neuron/feature.mod

src/nrnoc/modfiles/coreneuron/hh.mod

@@ -0,0 +1,128 @@
+TITLE hh.mod   squid sodium, potassium, and leak channels
+
+COMMENT
+ This is the original Hodgkin-Huxley treatment for the set of sodium, 
+  potassium, and leakage channels found in the squid giant axon membrane.
+  ("A quantitative description of membrane current and its application 
+  conduction and excitation in nerve" J.Physiol. (Lond.) 117:500-544 (1952).)
+ Membrane voltage is in absolute mV and has been reversed in polarity
+  from the original HH convention and shifted to reflect a resting potential
+  of -65 mV.
+ Remember to set a squid-appropriate temperature
+ (e.g. in HOC: "celsius=6.3" or in Python: "h.celsius=6.3").
+ See squid.hoc for an example of a simulation using this model.
+ SW Jaslove  6 March, 1992
+ENDCOMMENT
+
+UNITS {
+        (mA) = (milliamp)
+        (mV) = (millivolt)
+	(S) = (siemens)
+}
+
+? interface
+NEURON {
+        SUFFIX hh
+        REPRESENTS NCIT:C17145   : sodium channel
+        REPRESENTS NCIT:C17008   : potassium channel
+        USEION na READ ena WRITE ina REPRESENTS CHEBI:29101
+        USEION k READ ek WRITE ik REPRESENTS CHEBI:29103
+        NONSPECIFIC_CURRENT il
+        RANGE gnabar, gkbar, gl, el, gna, gk
+        RANGE minf, hinf, ninf, mtau, htau, ntau
+	THREADSAFE : assigned GLOBALs will be per thread
+}
+
+PARAMETER {
+        gnabar = .12 (S/cm2)	<0,1e9>
+        gkbar = .036 (S/cm2)	<0,1e9>
+        gl = .0003 (S/cm2)	<0,1e9>
+        el = -54.3 (mV)
+}
+
+STATE {
+        m h n
+}
+
+ASSIGNED {
+        v (mV)
+        celsius (degC)
+        ena (mV)
+        ek (mV)
+
+	gna (S/cm2)
+	gk (S/cm2)
+        ina (mA/cm2)
+        ik (mA/cm2)
+        il (mA/cm2)
+        minf hinf ninf
+	mtau (ms) htau (ms) ntau (ms)
+}
+
+? currents
+BREAKPOINT {
+        SOLVE states METHOD cnexp
+        gna = gnabar*m*m*m*h
+	ina = gna*(v - ena)
+        gk = gkbar*n*n*n*n
+	ik = gk*(v - ek)      
+        il = gl*(v - el)
+}
+
+
+INITIAL {
+	rates(v)
+	m = minf
+	h = hinf
+	n = ninf
+}
+
+? states
+DERIVATIVE states {  
+        rates(v)
+        m' =  (minf-m)/mtau
+        h' = (hinf-h)/htau
+        n' = (ninf-n)/ntau
+}
+
+:LOCAL q10
+
+
+? rates
+PROCEDURE rates(v(mV)) {  :Computes rate and other constants at current v.
+                      :Call once from HOC to initialize inf at resting v.
+        LOCAL  alpha, beta, sum, q10
+        : `TABLE minf` will be replaced with `:TABLE minf` if CoreNEURON enabled)
+        TABLE minf, mtau, hinf, htau, ninf, ntau DEPEND celsius FROM -100 TO 100 WITH 200
+
+UNITSOFF
+        q10 = 3^((celsius - 6.3)/10)
+                :"m" sodium activation system
+        alpha = .1 * vtrap(-(v+40),10)
+        beta =  4 * exp(-(v+65)/18)
+        sum = alpha + beta
+	mtau = 1/(q10*sum)
+        minf = alpha/sum
+                :"h" sodium inactivation system
+        alpha = .07 * exp(-(v+65)/20)
+        beta = 1 / (exp(-(v+35)/10) + 1)
+        sum = alpha + beta
+	htau = 1/(q10*sum)
+        hinf = alpha/sum
+                :"n" potassium activation system
+        alpha = .01*vtrap(-(v+55),10) 
+        beta = .125*exp(-(v+65)/80)
+	sum = alpha + beta
+        ntau = 1/(q10*sum)
+        ninf = alpha/sum
+}
+
+FUNCTION vtrap(x,y) {  :Traps for 0 in denominator of rate eqns.
+        if (fabs(x/y) < 1e-6) {
+                vtrap = y*(1 - x/y/2)
+        }else{
+                vtrap = x/(exp(x/y) - 1)
+        }
+}
+
+UNITSON

src/nrnoc/modfiles/coreneuron/intfire1.mod

@@ -0,0 +1 @@
+../neuron/intfire1.mod

src/nrnoc/modfiles/coreneuron/intfire2.mod

@@ -0,0 +1 @@
+../neuron/intfire2.mod

src/nrnoc/modfiles/coreneuron/intfire4.mod

@@ -0,0 +1 @@
+../neuron/intfire4.mod

src/nrnoc/modfiles/coreneuron/netstim.mod

@@ -0,0 +1 @@
+../neuron/netstim.mod

src/nrnoc/modfiles/coreneuron/oclmp.mod

@@ -0,0 +1 @@
+../neuron/oclmp.mod

src/nrnoc/modfiles/coreneuron/passive.mod

@@ -0,0 +1 @@
+../neuron/passive.mod

src/nrnoc/modfiles/coreneuron/pattern.mod

@@ -0,0 +1 @@
+../neuron/pattern.mod

src/nrnoc/modfiles/coreneuron/ppmark.mod

@@ -0,0 +1 @@
+../neuron/ppmark.mod

src/nrnoc/modfiles/coreneuron/stim.mod

@@ -0,0 +1 @@
+../neuron/stim.mod

src/nrnoc/modfiles/coreneuron/svclmp.mod

@@ -0,0 +1 @@
+../neuron/svclmp.mod

src/nrnoc/modfiles/coreneuron/syn.mod

@@ -0,0 +1 @@
+../neuron/syn.mod

src/nrnoc/modfiles/coreneuron/vclmp.mod

@@ -0,0 +1 @@
+../neuron/vclmp.mod

src/nrnoc/modfiles/coreneuron/xmech.mod

@@ -0,0 +1 @@
+../neuron/xmech.mod

src/nrnoc/hh.mod → src/nrnoc/modfiles/neuron/hh.mod

@@ -29,7 +29,6 @@ NEURON {
         USEION k READ ek WRITE ik REPRESENTS CHEBI:29103
         NONSPECIFIC_CURRENT il
         RANGE gnabar, gkbar, gl, el, gna, gk
-        : `GLOBAL minf` will be replaced with `RANGE minf` if CoreNEURON enabled
         GLOBAL minf, hinf, ninf, mtau, htau, ntau
 	THREADSAFE : assigned GLOBALs will be per thread
 }