updated pyparsing to be 3.10 safe

Author: bgoli

cbmpy/CBWrite.py

@@ -159,7 +159,7 @@ def writeSBML3FBCV2(
     add_cbmpy_annot=True,
     add_cobra_annot=False,
     validate=False,
-    compress_bounds=True,
+    compress_bounds=False,
     zip_model=False,
     return_model_string=False,
 ):

cbmpy/CBXML.py

@@ -1856,20 +1856,21 @@ def addModelHistory(self):
             self.model.setModelHistory(sbmh)
         del sbmh
 
-    def addBoundsV2(self, compress_bounds=False):
+    def addBoundsV2(self, compress_bounds=False, sig_dig=20):
         """
         Add FBC V2 style fluxbounds to model
 
          - *compress_bounds* [default=False] enable parameter compression
+         - *sig_dig* [default=20] round off to significant digits
 
         """
         if compress_bounds:
             print('INFO: V2 bounds compression enabled')
             bounds = {}
             shared_values = {}
             for r_ in self.fba.reactions:
-                lb = round(r_.getLowerBound(), 12)
-                ub = round(r_.getUpperBound(), 12)
+                lb = round(r_.getLowerBound(), sig_dig)
+                ub = round(r_.getUpperBound(), sig_dig)
                 rid = r_.getId()
                 bounds[rid] = (lb, ub)
 

cbmpy/pyparsing.py

@@ -685,7 +685,10 @@ def __setstate__(self,state):
     def __dir__(self):
         return dir(super(ParseResults,self)) + list(self)  # Python 3 compatible bgoli 20140728
 
-collections.MutableMapping.register(ParseResults)
+if PY_3:
+    collections.abc.MutableMapping
+else:
+    collections.MutableMapping.register(ParseResults)
 
 def col (loc,strg):
     """Returns current column within a string, counting newlines as line separators.
@@ -2228,7 +2231,7 @@ def __init__( self, exprs, savelist = False ):
 
         if isinstance( exprs, basestring ):
             self.exprs = [ Literal( exprs ) ]
-        elif isinstance( exprs, collections.Sequence ):
+        elif isinstance( exprs, collections.abc.Sequence ):
             # if sequence of strings provided, wrap with Literal
             if all(isinstance(expr, basestring) for expr in exprs):
                 exprs = map(Literal, exprs)
@@ -3233,7 +3236,7 @@ def oneOf( strs, caseless=False, useRegex=True ):
 
     if isinstance(strs,basestring):
         symbols = strs.split()
-    elif isinstance(strs, collections.Sequence):
+    elif isinstance(strs, collections.abc.Sequence):
         symbols = list(strs[:])
     elif isinstance(strs, _generatorType):
         symbols = list(strs)