Use full f.p. precision with BNG and Kappa (#490)

Fixes: #443
pysb · Jan 31, 2020 · dccf662 · dccf662
1 parent 681428b
commit dccf662
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Showing 4 changed files with 4 additions and 7 deletions.
diff --git a/pysb/export/potterswheel.py b/pysb/export/potterswheel.py
@@ -104,11 +104,11 @@ def export(self):
             ic_values[self.model.get_species_index(ic.pattern)] = ic.value.value
 
         # list of "dynamic variables"
-        pw_x = ["m = pwAddX(m, 's%d', %e);" % (i, ic_values[i])
+        pw_x = ["m = pwAddX(m, 's%d', %.17g);" % (i, ic_values[i])
                 for i in range(len(self.model.odes))]
 
         # parameters
-        pw_k = ["m = pwAddK(m, '%s', %e);" % (p.name, p.value)
+        pw_k = ["m = pwAddK(m, '%s', %.17g);" % (p.name, p.value)
                 for p in self.model.parameters]
 
         # equations (one for each dynamic variable)

diff --git a/pysb/generator/bng.py b/pysb/generator/bng.py
@@ -46,7 +46,7 @@ def generate_parameters(self):
         max_length = max(len(p.name) for p in
                          self.model.parameters | self.model.expressions)
         for p in self.model.parameters:
-            self.__content += (("  %-" + str(max_length) + "s   %e\n") %
+            self.__content += (("  %-" + str(max_length) + "s   %.17g\n") %
                                (p.name, p.value))
         for e in exprs:
             self.__content += (("  %-" + str(max_length) + "s   %s\n") %

diff --git a/pysb/generator/kappa.py b/pysb/generator/kappa.py
@@ -56,7 +56,7 @@ def generate_content(self):
 
     def generate_parameters(self):
         for p in self.model.parameters:
-            self.__content += "%%var: '%s' %e\n" % (p.name, p.value)
+            self.__content += "%%var: '%s' %.17g\n" % (p.name, p.value)
         for e in self.model.expressions:
             str_expr = str(expression_to_muparser(e))
             self.__content += "%%var: '%s' %s\n" % (e.name, str_expr)

diff --git a/pysb/tests/test_importers.py b/pysb/tests/test_importers.py
@@ -17,9 +17,6 @@
     'CaOscillate_Func': 1e-4,
     'michment': 1e-8,
     'motor': 1e-8,
-    'fceri_ji': 1e-4,
-    'test_paramname': 1e-4,
-    'tlmr': 1e-4,
     'Repressilator': 1e-11,
 }