Skip to content

Commit

Permalink
refactor two dunder class variables to single underscores to avoid ma…
Browse files Browse the repository at this point in the history 
…ngling
  • Loading branch information
@jmrohwer
jmrohwer committed Aug 25, 2020
1 parent 976b6fd commit bc166cb
Showing 1 changed file with 21 additions and 21 deletions.
42 changes: 21 additions & 21 deletions pysces/PyscesModel.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2696,7 +2696,7 @@ def InitialiseModel(self):
"""
# TODO killkillkill
self.__inspec__ = numpy.zeros((len(self.__species__)), 'd')
self.__D_s_Order, DvarUpString = self.__initvar__() # Initialise s[] array
self._D_s_Order, DvarUpString = self.__initvar__() # Initialise s[] array

self.__CDvarUpString__ = compile(DvarUpString, 'DvarUpString', 'exec')

Expand All @@ -2709,7 +2709,7 @@ def InitialiseModel(self):
self.__tvec_a__ = None
self.__tvec_c__ = None

self.__CVODE_Vtemp = numpy.zeros((self.__Nshape__[1]), 'd')
self._CVODE_Vtemp = numpy.zeros((self.__Nshape__[1]), 'd')

# #debug
# self.display_debugcount = 0
Expand Down Expand Up @@ -3819,9 +3819,9 @@ def ffull(t, y, ydot, f_data):
output[0, :] = out0

if not self.mode_integrate_all_odes:
self._EvalODE(out0.copy(), self.__CVODE_Vtemp)
self._EvalODE(out0.copy(), self._CVODE_Vtemp)
else:
self._EvalODE_CVODE(out0.copy(), self.__CVODE_Vtemp)
self._EvalODE_CVODE(out0.copy(), self._CVODE_Vtemp)
rates[0] = self.__vvec__

if CVODE_XOUT:
Expand Down Expand Up @@ -3995,9 +3995,9 @@ def ffull(t, y, ydot, f_data):
# this gets everything into the current tout state
tmp = None
if not self.mode_integrate_all_odes:
tmp = self._EvalODE(ya.copy(), self.__CVODE_Vtemp)
tmp = self._EvalODE(ya.copy(), self._CVODE_Vtemp)
else:
tmp = self._EvalODE_CVODE(ya.copy(), self.__CVODE_Vtemp)
tmp = self._EvalODE_CVODE(ya.copy(), self._CVODE_Vtemp)
del tmp

# here we regenerate Sd's and fix concentrations
Expand Down Expand Up @@ -4048,9 +4048,9 @@ def ffull(t, y, ydot, f_data):
# this gets everything into the current tout state
tmp = None
if not self.mode_integrate_all_odes:
tmp = self._EvalODE(ya.copy(), self.__CVODE_Vtemp)
tmp = self._EvalODE(ya.copy(), self._CVODE_Vtemp)
else:
tmp = self._EvalODE_CVODE(ya.copy(), self.__CVODE_Vtemp)
tmp = self._EvalODE_CVODE(ya.copy(), self._CVODE_Vtemp)
del tmp
# here we regenerate Sd's and fix concentrations
rrules = None
Expand Down Expand Up @@ -4165,9 +4165,9 @@ def CVODE_EVENTS(self, t, svec, eout, f_data):
rrules = []
tmp = None
if not self.mode_integrate_all_odes:
tmp = self._EvalODE(svec.copy(), self.__CVODE_Vtemp)
tmp = self._EvalODE(svec.copy(), self._CVODE_Vtemp)
else:
tmp = self._EvalODE_CVODE(svec.copy(), self.__CVODE_Vtemp)
tmp = self._EvalODE_CVODE(svec.copy(), self._CVODE_Vtemp)
del tmp
eventFired = False
for ev in range(len(self.__events__)):
Expand Down Expand Up @@ -4262,7 +4262,7 @@ def function_sim(s, t):

tmp = None
for r in range(sim_res.shape[0]):
tmp = self._EvalODE(sim_res[r].copy(), self.__CVODE_Vtemp)
tmp = self._EvalODE(sim_res[r].copy(), self._CVODE_Vtemp)
# set with self._EvalODE above
rates[r] = self.__vvec__
del tmp
Expand Down Expand Up @@ -5321,14 +5321,14 @@ def showConserved(self, File=None, screenwrite=1, fmt='%2.3f'):
if self.conservation_matrix[Tlist[x], y] > 0.0:
# coeff = self.__settings__['mode_number_format'] % (s_init[y]*abs(conservation_matrix[Tlist[x],y]))
coeff = fmt % abs(self.conservation_matrix[Tlist[x], y])
met = self.__D_s_Order[self.conservation_matrix_col[y]]
met = self._D_s_Order[self.conservation_matrix_col[y]]
ConSumPstr += (
' + {' + coeff + '}' + met.replace('self.', '')
)
elif self.conservation_matrix[Tlist[x], y] < 0.0:
# coeff = self.__settings__['mode_number_format'] % (s_init[y]*abs(conservation_matrix[Tlist[x],y]))
coeff = fmt % abs(self.conservation_matrix[Tlist[x], y])
met = self.__D_s_Order[self.conservation_matrix_col[y]]
met = self._D_s_Order[self.conservation_matrix_col[y]]
ConSumPstr += (
' - {' + coeff + '}' + met.replace('self.', '')
)
Expand Down Expand Up @@ -5581,8 +5581,8 @@ def EvalEvar(self, input=None, input2=None):

# create tuples of the rows and columns for the Ev matrix
self.elas_var_row = tuple(copy.copy(self.__reactions__))
col = copy.copy(self.__D_s_Order)
for x in range(len(self.__D_s_Order)):
col = copy.copy(self._D_s_Order)
for x in range(len(self._D_s_Order)):
col[x] = col[x].replace('self.', '')
self.elas_var_col = tuple(col)
del col
Expand Down Expand Up @@ -5689,7 +5689,7 @@ def EvalEvar(self, input=None, input2=None):
for x in range(0, r):
react = self.__reactions__[x]
for y in range(0, c):
met = self.__D_s_Order[y]
met = self._D_s_Order[y]
if self.__settings__['mode_mca_scaled']:
setattr(
self,
Expand Down Expand Up @@ -5723,7 +5723,7 @@ def EvalEvar(self, input=None, input2=None):

if self.__settings__['display_debug'] == 1:
print('\ne_vmatrix')
print(repr(self.__D_s_Order).replace('self.', ''))
print(repr(self._D_s_Order).replace('self.', ''))
print(self.__reactions__)
print(self.__evmatrix__)

Expand Down Expand Up @@ -5962,7 +5962,7 @@ def showEvar(self, File=None):
self.__settings__['mode_number_format']
% self.__evmatrix__[x, y]
)
met = self.__D_s_Order[y]
met = self._D_s_Order[y]
if self.__evmatrix__[x, y] != 0.0:
if self.__settings__['mode_mca_scaled']:
elas = '\\ec{' + react + '}{' + met + '} = ' + rtemp
Expand Down Expand Up @@ -6264,7 +6264,7 @@ def EvalCC(self):
Cirow.append(self.__reactions__[self.kmatrix_col[x]])

for x in range(0, len(self.lmatrix_col)):
Cirow.append(self.__D_s_Order[self.lmatrix_col[x]].replace('self.', ''))
Cirow.append(self._D_s_Order[self.lmatrix_col[x]].replace('self.', ''))

self.mca_ci_row = Cirow
self.mca_ci_col = Cicol
Expand Down Expand Up @@ -6344,14 +6344,14 @@ def EvalCC(self):
xFactor = self.__lmatrix__.shape[0] - self.__lzeromatrix__.shape[0]
for x in range(self.__lzeromatrix__.shape[0] - 1, -1, -1):
Lo_row.append(
self.__D_s_Order[self.lzeromatrix_row[x]].replace('self.', '')
self._D_s_Order[self.lzeromatrix_row[x]].replace('self.', '')
)
for y in range(
self.__lzeromatrix__.shape[1] - 1, -1, -1
): # this can be replaced by a row slice operation
sLo[x, y] = self.lmatrix_scaled[x + xFactor, y]
if x == 0:
Lo_col.append(self.__D_s_Order[self.lzeromatrix_col[y]])
Lo_col.append(self._D_s_Order[self.lzeromatrix_col[y]])

Lo_row.reverse()
Lo_col.reverse()
Expand Down

0 comments on commit bc166cb

Please sign in to comment.