Merge branch 'experimental' of github.com:NeuroML/pyNeuroML into experimental

* 'experimental' of github.com:NeuroML/pyNeuroML:
  test(modchananalysis): test to check that nrnivmodl is run when required
  ooops, had forgotten to commit right logic
  handling near zero values
  Checking for compiled mod files. Fixes #165

Author: pgleeson

pyneuroml/neuron/analysis/HHanalyse.py

@@ -8,6 +8,8 @@
 
 import argparse
 import re
+import subprocess
+import sys
 from math import log
 import neuron
 import matplotlib.pyplot as pylab
@@ -198,7 +200,21 @@ def main():
     states = get_states(modFileTxt)
     print("States found in mod file: " + str(states))
     assert chanToTest == get_suffix(modFileTxt), "Channel name could be wrong"
-    sec.insert(str(chanToTest))
+    try:
+        sec.insert(str(chanToTest))
+    except ValueError:
+        print(f"{chanToTest} mechanism has not been compiled yet. Trying to run `nrnivmodl`.")
+        try:
+            subprocess.run("nrnivmodl", check=True, capture_output=True)
+        except subprocess.CalledProcessError as e:
+            print(f"Could not compile {modFileName}. nrivmodl returned {e.returncode}.")
+            #print(e.stderr.decode())
+            print("Try running nrnivmodl manually and checking its output.")
+            print("Exiting...")
+            return 1
+        h.nrn_load_dll("x86_64/.libs/libnrnmech.so")
+        sec.insert(str(chanToTest))
+
 
     for temperature in temperatures:
         h.celsius = temperature
@@ -388,15 +404,16 @@ def main():
                         val = eval("sec(0.5)." + s + "_" + chanToTest)
 
                         if s not in foundInf:
-                            if abs((lastCheckVal[s] - val) / val) > tolerance:
+                            rel_dif = (lastCheckVal[s] - val) / val if val > sys.float_info.epsilon else lastCheckVal[s]
+                            if abs(rel_dif) > tolerance:
                                 if verbose:
                                     print(
                                         "  State %s has failed at %f; lastCheckVal[s] = %f; fract = %f; tolerance = %f"
                                         % (
                                             s,
                                             val,
                                             lastCheckVal[s],
-                                            ((lastCheckVal[s] - val) / val),
+                                            rel_dif,
                                             tolerance,
                                         )
                                     )
@@ -408,7 +425,7 @@ def main():
                                             s,
                                             val,
                                             lastCheckVal[s],
-                                            ((lastCheckVal[s] - val) / val),
+                                            rel_dif,
                                             tolerance,
                                         )
                                     )

test-ghactions.sh

@@ -146,7 +146,7 @@ if [ "$run_neuron_examples" == true ]; then
     echo "################################################"
     echo "##   Test analysis of channel in mod file"
 
-        nrnivmodl
+        # do not run nrnivmodl, modchananalysis should run it if required
         pynml-modchananalysis -stepV 20  NaConductance  -dt 0.01 -nogui