Add NMODL Language (#6776)

* Add NMODL Language

This is the NEURON extension to MODL, a model description language used
within the neuroscientific community.  See also:

https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/mechanisms/nmodl2.html

* Add some heuristics

* Try to add some tests

lib/linguist/heuristics.yml

@@ -469,6 +469,8 @@ disambiguations:
   rules:
   - language: XML
     pattern: '<!ENTITY '
+  - language: NMODL
+    pattern: '\b(NEURON|INITIAL|UNITS)\b'
   - language: Modula-2
     pattern: '^\s*(?i:MODULE|END) [\w\.]+;'
   - language: [Linux Kernel Module, AMPL]

lib/linguist/languages.yml

@@ -4487,6 +4487,14 @@ NL:
   tm_scope: none
   ace_mode: text
   language_id: 241
+NMODL:
+  type: programming
+  color: "#00356B"
+  extensions:
+  - ".mod"
+  tm_scope: none
+  ace_mode: text
+  language_id: 136456478
 NPM Config:
   type: data
   color: "#cb3837"

samples/NMODL/fornetcon.mod

@@ -0,0 +1,40 @@
+: Each NetCon maintains a count of external events.
+: And time of last external event
+: On each internal event all connecting NetCon get the internal event count.
+: And time of last external event
+
+NEURON {
+  POINT_PROCESS ForNetConTest
+  RANGE tbegin
+}
+
+UNITS {
+}
+
+PARAMETER {
+  tbegin = 0 (ms)
+}
+
+INITIAL {
+  net_send(tbegin, 1)
+}
+
+NET_RECEIVE(w, npre, tpre (ms), npost, tpost (ms)) {
+  INITIAL {
+    npre=0  tpre=-1  npost=0  tpost=-1
+  }
+
+  if (flag == 0) { : external (pre) event
+    npre = npre + 1
+    tpre = t
+  }
+
+  if (flag == 1) { : internal (post) event
+    FOR_NETCONS(w, fnpre, ftpre (ms), fnpost, ftpost (ms)) {
+      fnpost = fnpost + 1
+      ftpost = t
+    }
+    net_send(3, 1) : in 3 ms another 1 event
+    net_event(t)
+  }
+}

samples/NMODL/k3st.mod

@@ -0,0 +1,62 @@
+: Three state kinetic scheme for HH-like potassium channel
+: Steady-state v-dependent state transitions have been fit
+: Needs v-dependent time constants from tables created under hoc
+NEURON {
+    SUFFIX k3st
+    USEION k READ ek WRITE ik
+    RANGE g, gbar
+    RANGE tau1_rec, tau2_rec
+}
+UNITS { (mV) = (millivolt) }
+PARAMETER {
+    gbar = 33 (millimho/cm2)
+    d1 = -38 (mV)
+    k1 = 0.151 (/mV)
+    d2 = -25 (mV)
+    k2 = 0.044 (/mV)
+}
+
+ASSIGNED {
+    v     (mV)
+    ek    (mV)
+    g     (millimho/cm2)
+    ik    (milliamp/cm2)
+    kf1 (/ms)
+    kb1 (/ms)
+    kf2 (/ms)
+    kb2 (/ms)
+    tau1_rec
+    tau2_rec
+}
+
+STATE { c1 c2 o }
+
+BREAKPOINT {
+    SOLVE kin METHOD sparse
+    g = gbar*o
+    ik = g*(v - ek)*(1e-3)
+}
+
+INITIAL { SOLVE kin STEADYSTATE sparse }
+
+KINETIC kin {
+    rates(v)
+    ~ c1 <-> c2 (kf1, kb1)
+    ~ c2 <-> o (kf2, kb2)
+    CONSERVE c1 + c2 + o = 1
+}
+
+FUNCTION_TABLE tau1(v(mV)) (ms)
+FUNCTION_TABLE tau2(v(mV)) (ms)
+
+PROCEDURE rates(v(millivolt)) {
+    LOCAL K1, K2
+    K1 = exp(k2*(d2 - v) - k1*(d1 - v))
+    kf1 = K1/(tau1(v)*(1+K1))
+    kb1 = 1/(tau1(v)*(1+K1))
+    K2 = exp(-k2*(d2 - v))
+    kf2 = K2/(tau2(v)*(1+K2))
+    kb2 = 1/(tau2(v)*(1+K2))
+    tau1_rec = tau1(v)
+    tau2_rec = tau2(v)
+}

test/test_heuristics.rb

@@ -689,6 +689,7 @@ def test_ml_by_heuristics
   def test_mod_by_heuristics
     assert_heuristics({
       "Modula-2" => all_fixtures("Modula-2", "*.mod"),
+      "NMODL" => all_fixtures("NMODL", "*.mod"),
       "XML" => all_fixtures("XML", "*.mod"),
       ["Linux Kernel Module", "AMPL"] => all_fixtures("Linux Kernel Module", "*.mod"),
       ["Linux Kernel Module", "AMPL"] => all_fixtures("AMPL", "*.mod"),