Merge pull request #344 from DiODeProject/def_sympy_funcs

Unpin sympy version (WIP) - close #170

.travis.yml

@@ -4,7 +4,7 @@ python:
   - "3.6"
   - "3.7"
 before_install:
-  - sudo apt-get install -y texlive graphviz dvipng
+  - sudo apt-get install -y texlive texlive-latex-extra graphviz dvipng
 install:
   - pip install tox-travis codecov
 script: 

mumot/models.py

@@ -22,6 +22,7 @@
     solve,
     Symbol,
     symbols,
+    Function
 )
 
 from . import (
@@ -438,7 +439,8 @@ def getMasterEquation(self):
             Dictionary of substitutions used, this defaults to `None` if no substitutions were made
 
         """
-        P, t = symbols('P t')
+        t = symbols('t')
+        P = Function('P')
         stoich = self._stoichiometry
         nvec = []
         for key1 in stoich:
@@ -468,7 +470,8 @@ def showMasterEquation(self):
 
         """
 
-        P, t = symbols('P t')
+        t = symbols('t')
+        P = Function('P')
         out_rhs = ""
         stoich = self._stoichiometry
         nvec = []
@@ -2208,7 +2211,8 @@ def _get_orderedLists_vKE(stoich):
 
 def _getFokkerPlanckEquation(_get_orderedLists_vKE, stoich):
     """Return the Fokker-Planck equation."""
-    P, t = symbols('P t')
+    t = symbols('t')
+    P = Function('P')
     V = Symbol(r'\overline{V}', real=True, constant=True)
     Vlist_lhs, Vlist_rhs, substring = _get_orderedLists_vKE(stoich)
     rhsFPE = 0
@@ -2261,7 +2265,10 @@ def _getNoiseEOM(_getFokkerPlanckEquation, _get_orderedLists_vKE, stoich):
     Returns equations of motion for noise.
 
     """
-    P, M_1, M_2, t = symbols('P M_1 M_2 t')
+    t = symbols('t')
+    P = Function('P')
+    M_1 = Function('M_1')
+    M_2 = Function('M_2')
 
     # A,B, alpha, beta, gamma = symbols('A B alpha beta gamma')
     # custom_stoich= {'reaction1': {'rate': alpha, A: [0,1]}, 'reaction2': {'rate': gamma, A: [2,0], B: [0,1]},
@@ -2440,7 +2447,10 @@ def _getNoiseStationarySol(_getNoiseEOM, _getFokkerPlanckEquation, _get_orderedL
     Returns analytical solution for stationary noise.
 
     """
-    P, M_1, M_2, t = symbols('P M_1 M_2 t')
+    t = symbols('t')
+    P = Function('P')
+    M_1 = Function('M_1')
+    M_2 = Function('M_2')
 
     EQsys1stOrdMom, EOM_1stOrderMom, NoiseSubs1stOrder, EQsys2ndOrdMom, EOM_2ndOrderMom, NoiseSubs2ndOrder = _getNoiseEOM(_getFokkerPlanckEquation, _get_orderedLists_vKE, stoich)
 
@@ -2562,7 +2572,8 @@ def _getNoiseStationarySol(_getNoiseEOM, _getFokkerPlanckEquation, _get_orderedL
 
 def _getODEs_vKE(_get_orderedLists_vKE, stoich):
     """Return the ODE system derived from Master equation."""
-    P, t = symbols('P t')
+    t = symbols('t')
+    P = Function('P')
     V = Symbol(r'\overline{V}', real=True, constant=True)
     Vlist_lhs, Vlist_rhs, substring = _get_orderedLists_vKE(stoich)
     rhsODE = 0

mumot/views.py

@@ -24,6 +24,7 @@
     default_sort_key,
     Derivative,
     factorial,
+    Function,
     lambdify,
     latex,
     simplify,
@@ -1188,7 +1189,8 @@ def _plot_NumSolODE(self, _=None):
             for key in EOM_1stOrdMomDict:
                 noiseCorrEOMdict[sym * key] = sympy.expand(sym * EOM_1stOrdMomDict[key])
 
-        M_1, M_2 = sympy.symbols('M_1 M_2')
+        M_1 = Function('M_1')
+        M_2 = Function('M_2')
         eta_SV1 = sympy.Symbol(f"eta_{self._stateVariable1}")
         cVar1 = sympy.symbols('cVar1')
         if self._stateVariable2:
@@ -1332,7 +1334,8 @@ def _numericSol2ndOrdMoment(self, EOM_2ndOrdMomDict, steadyStateDict, argDict):
         # if len(self._stateVarList) == 3:
         #     eta_SV3 = sympy.Symbol('eta_' + str(self._stateVarList[2]))
 
-        M_1, M_2 = sympy.symbols('M_1 M_2')
+        M_1 = Function('M_1')
+        M_2 = Function('M_2')
         eta_SV1 = sympy.Symbol('eta_' + str(self._stateVariable1))
         if self._stateVariable2:
             eta_SV2 = sympy.Symbol('eta_' + str(self._stateVariable2))
@@ -1680,7 +1683,7 @@ def _plot_field(self) -> None:
                 Phi_stateVar2 = sympy.Symbol('Phi_' + str(self._stateVariable2))
                 eta_stateVar1 = sympy.Symbol('eta_' + str(self._stateVariable1))
                 eta_stateVar2 = sympy.Symbol('eta_' + str(self._stateVariable2))
-                M_2 = sympy.Symbol('M_2')
+                M_2 = sympy.Function('M_2')
 
                 systemSize = sympy.Symbol('systemSize')
                 argDict = self._get_argDict()
@@ -5643,8 +5646,13 @@ def _deriveMasterEquation(stoichiometry):
     Returns dictionary used in :method:`MuMoTmodel.showMasterEquation`.
     """
     substring = None
-    P, E_op, x, y, v, w, t, m = symbols('P E_op x y v w t m')
+
+    x, y, v, w, t, m = symbols('x y v w t m')
+    E_op = Function('E_op')
+    z = Function('z')
+    P = Function('P')
     V = Symbol(r'\overline{V}', real=True, constant=True)
+
     stoich = stoichiometry
     nvec = []
     for key1 in stoich:
@@ -5665,7 +5673,7 @@ def _deriveMasterEquation(stoichiometry):
 
     rhs = 0
     sol_dict_rhs = {}
-    f = lambdify((x(y, v - w)), x(y, v - w), modules='sympy')
+    f = lambdify(z(y, v - w), z(y, v - w), modules='sympy')
     g = lambdify((x, y, v), (factorial(x) / factorial(x - y)) / v**y, modules='sympy')
     for key1 in stoich:
         prod1 = 1
@@ -5692,7 +5700,9 @@ def _deriveMasterEquation(stoichiometry):
 
 def _doVanKampenExpansion(rhs, stoich):
     """Return the left-hand side and right-hand side of van Kampen expansion."""
-    P, E_op, x, y, v, w, t, m = symbols('P E_op x y v w t m')
+    x, y, v, w, t, m = symbols('x y v w t m')
+    E_op = Function('E_op')
+    P = Function('P')
     V = Symbol(r'\overline{V}', real=True, constant=True)
     nvec = []
     nconstvec = []

setup.py

@@ -39,7 +39,7 @@
         'pydstool>=0.90.3',  # min version that allows scipy >= 1.0.0 to be used
         'pyzmq<17',  # needed if using tornado < 5
         'scipy',
-        'sympy >= 1.1.1, < 1.3',  # see https://github.com/DiODeProject/MuMoT/issues/170
+        'sympy>=1.4',
         'tornado<5'  # needed to avoid errors with older ipykernel
     ],
     extras_require={