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Merge branch 'master' of github.com:PySCeS/pysces
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@jmrohwer
jmrohwer committed Aug 25, 2020
2 parents bc166cb + c13b1d1 commit c2c8754
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28 changes: 28 additions & 0 deletions conda-environment.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
name: psc
channels:
- defaults
- sbmlteam
- conda-forge
dependencies:
- jupyter
- ipython
- pandas
- python-libsbml
- python=3.6
- scipy
- sympy
- conda-build
- wheel
- flask
- pyqt
- biopython
- pip
- assimulo
- pytest
- sundials
- numpy
- nose
- black
- matplotlib
prefix: c:\Anaconda3\envs\psc

22 changes: 22 additions & 0 deletions conda-requirements.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: win-64
assimulo>=3.2
biopython
black
conda-build
ipython
jupyter
matplotlib
nose
numpy>=1.19.1
pandas
pip
pyparsing
pyqt
python=3.6
python-libsbml>=5.18.0
scipy>=1.5.2
setuptools
sympy
wheel
127 changes: 62 additions & 65 deletions pysces/PyscesModel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -126,7 +126,6 @@

# We now welcome a prototype StomPy interface to PySCeS which will provide expanding stochastic simulation support.


# for future fun
_HAVE_VPYTHON = False
_VPYTHON_LOAD_ERROR = ''
Expand Down Expand Up @@ -2597,15 +2596,14 @@ def InitialiseCompartments(self):
self.__sDict__[sp]['compartment'] == None
and len(list(self.__compartments__.keys())) > 1
):
assert self.__sDict__[sp]['compartment'] != None, (
'\nCOMPARTMENT ERROR: this model has multiple compartments defined %s but \"%s\" is not in one!'
% (
[
self.__compartments__[c]['name']
for c in list(self.__compartments__.keys())
],
sp,
)
assert (
self.__sDict__[sp]['compartment'] != None
), '\nCOMPARTMENT ERROR: this model has multiple compartments defined {} but \"{}\" is not in one!'.format(
[
self.__compartments__[c]['name']
for c in list(self.__compartments__.keys())
],
sp,
)
# brett 2008 fudge this!
if not self.__KeyWords__['Species_In_Conc'] and I_AM_FUDGING:
Expand All @@ -2614,10 +2612,11 @@ def InitialiseCompartments(self):
/ self.__settings__['compartment_fudge_factor']
)
setattr(self, sp, self.__sDict__[sp]['initial'])
setattr(self, '%s_init' % sp, self.__sDict__[sp]['initial'])
setattr(self, '{}_init'.format(sp), self.__sDict__[sp]['initial'])
print(
'INFO: Rescaling species (%s) to size %s.'
% (sp, self.__sDict__[sp]['initial'])
'INFO: Rescaling species ({}) to size {}.'.format(
sp, self.__sDict__[sp]['initial']
)
)

self.__CsizeAllIdx__ = []
Expand Down Expand Up @@ -8341,7 +8340,7 @@ def ResetNumberFormat(self):
self.__settings__['mode_number_format'] = '%2.4e'

def Write_array(
self, input, File=None, Row=None, Col=None, close_file=0, separator=' '
self, inputd, File=None, Row=None, Col=None, close_file=0, separator=' '
):
"""
Write_array(input,File=None,Row=None,Col=None,close_file=0,separator=' ')
Expand Down Expand Up @@ -8371,16 +8370,16 @@ def Write_array(
)

# seeing as row indexes are now tuples and not arrays - brett 20050713
if type(input) == tuple or type(input) == list:
input = numpy.array(input)
if type(inputd) == tuple or type(inputd) == list:
inputd = numpy.array(inputd)

if Row != None:
assert (
len(Row) == input.shape[0]
len(Row) == inputd.shape[0]
), 'len(Row) must be equal to len(input_row)'
if Col != None:
assert (
len(Col) == input.shape[1]
len(Col) == inputd.shape[1]
), 'len(Col) must be equal to len(input_col)'

if File != None:
Expand All @@ -8394,18 +8393,18 @@ def Write_array(
File.write('#')
try:
input_width = (
len(self.__settings__['mode_number_format'] % input[0, 0])
len(self.__settings__['mode_number_format'] % inputd[0, 0])
+ 1
+ len(str(separator))
)
except:
input_width = (
len(self.__settings__['mode_number_format'] % input[0])
len(self.__settings__['mode_number_format'] % inputd[0])
+ 1
+ len(str(separator))
)
for x in Col:
if len(str(x)) <= len(str(input[0, 0])):
if len(str(x)) <= len(str(inputd[0, 0])):
spacer = (input_width - len(str(x))) * ' '
File.write(str(x) + spacer)
else:
Expand All @@ -8419,19 +8418,19 @@ def Write_array(
if self.__settings__['write_arr_lflush'] < 2:
print('INFO: LineFlush must be >= 2')
self.__settings__['write_arr_lflush'] = 2
for x in range(input.shape[0]):
for x in range(inputd.shape[0]):
flush_count += 1
for y in range(input.shape[1]):
if input[x, y] < 0.0:
for y in range(inputd.shape[1]):
if inputd[x, y] < 0.0:
File.write(
self.__settings__['mode_number_format'] % input[x, y]
self.__settings__['mode_number_format'] % inputd[x, y]
)
else:
File.write(
' '
+ self.__settings__['mode_number_format'] % input[x, y]
+ self.__settings__['mode_number_format'] % inputd[x, y]
)
if y < input.shape[1] - 1:
if y < inputd.shape[1] - 1:
File.write(separator)
File.write('\n')
if flush_count == self.__settings__['write_arr_lflush']:
Expand All @@ -8441,9 +8440,9 @@ def Write_array(
# File.write('\n')
except IndexError as e:
print('\nWriting vector (normal) to file')
for x in range(len(input)):
File.write(self.__settings__['mode_number_format'] % input[x])
if x < len(input) - 1:
for x in range(len(inputd)):
File.write(self.__settings__['mode_number_format'] % inputd[x])
if x < len(inputd) - 1:
File.write(separator)
File.write('\n')
if Row != None:
Expand All @@ -8459,7 +8458,7 @@ def Write_array(
'INFO: You need to supply an open writable file as the 2nd argument to this function'
)

def Write_array_latex(self, input, File=None, Row=None, Col=None, close_file=0):
def Write_array_latex(self, inputa, File=None, Row=None, Col=None, close_file=0):
"""
Write_array_latex(input,File=None,Row=None,Col=None,close_file=0)
Expand All @@ -8475,22 +8474,22 @@ def Write_array_latex(self, input, File=None, Row=None, Col=None, close_file=0):
"""
# seeing as row indexes are now tuples and not arrays - brett 20050713
if type(input) == tuple or type(input) == list:
input = numpy.array(input)
if type(inputa) == tuple or type(inputa) == list:
inputa = numpy.array(inputa)

try:
a = input.shape[1]
a = inputa.shape[1]
except:
input.shape = (1, input.shape[0])
inputa.shape = (1, inputa.shape[0])

if Row != None:
assert (
len(Row) == input.shape[0]
len(Row) == inputa.shape[0]
), 'len(Row) must be equal to len(input_row)'
print('Writing row')
if Col != None:
assert (
len(Col) == input.shape[1]
len(Col) == inputa.shape[1]
), 'len(Col) must be equal to len(input_col)'
print('Writing column')

Expand All @@ -8508,18 +8507,18 @@ def Write_array_latex(self, input, File=None, Row=None, Col=None, close_file=0):
# assert File != file, 'WriteArray(input,File=None,Row=None,Col=None,close_file=0)'
File.write('\n%% ' + fname + '\n')
try:
a = input.shape
a = inputa.shape
print('\nWriting array (LaTeX) to file')
File.write('\\[\n')
File.write('\\begin{array}{')
if Row != None:
File.write('r|')
for x in range(input.shape[1]):
for x in range(inputa.shape[1]):
File.write('r')

File.write('}\n ')
flush_count = 0
for x in range(input.shape[0]):
for x in range(inputa.shape[0]):
if Col != None and x == 0:
for el in range(len(Col)):
elx = str(Col[el]).replace('_', '\_')
Expand All @@ -8537,14 +8536,14 @@ def Write_array_latex(self, input, File=None, Row=None, Col=None, close_file=0):
el2 = str(Row[x]).replace('_', '\\_')
File.write('$\\small{' + el2 + '}$ &')

for y in range(input.shape[1]):
if input[x, y] < 0.0:
val = '%2.4f' % input[x, y]
for y in range(inputa.shape[1]):
if inputa[x, y] < 0.0:
val = '%2.4f' % inputa[x, y]
else:
val = ' ' + '%2.4f' % input[x, y]
val = ' ' + '%2.4f' % inputa[x, y]

File.write(val)
if y < input.shape[1] - 1:
if y < inputa.shape[1] - 1:
File.write(' &')
File.write(' \\\\\n ')
if flush_count == self.__settings__['write_arr_lflush']:
Expand All @@ -8566,7 +8565,7 @@ def Write_array_latex(self, input, File=None, Row=None, Col=None, close_file=0):
)

def Write_array_html(
self, input, File=None, Row=None, Col=None, name=None, close_file=0
self, inputa, File=None, Row=None, Col=None, name=None, close_file=0
):
"""
Write_array_html(input,File=None,Row=None,Col=None,name=None,close_file=0)
Expand All @@ -8588,22 +8587,21 @@ def Write_array_html(
"""
# seeing as row indexes are now tuples and not arrays - brett 20050713
if type(input) == tuple or type(input) == list:
input = numpy.array(input)

if type(inputa) == tuple or type(inputa) == list:
inputa = numpy.array(inputa)
try:
a = input.shape[1]
a = inputa.shape[1]
except:
input.shape = (1, input.shape[0])
inputa.shape = (1, inputa.shape[0])

if Row != None:
assert (
len(Row) == input.shape[0]
len(Row) == inputa.shape[0]
), 'len(Row) must be equal to len(input_row)'
print('Writing row')
if Col != None:
assert (
len(Col) == input.shape[1]
len(Col) == inputa.shape[1]
), 'len(Col) must be equal to len(input_col)'
print('Writing column')
if self.__settings__['write_arr_lflush'] < 2:
Expand Down Expand Up @@ -8664,7 +8662,7 @@ def Write_array_html(
'\n<table border="1" cellpadding="2" cellspacing="2" bgcolor="#FFFFFF">'
)
try:
a = input.shape
a = inputa.shape
print('Writing array (HTML) to file')

double_index = 15
Expand All @@ -8679,7 +8677,7 @@ def Write_array_html(
+ str(col)
+ '</b></div></td>\n'
)
if Row != None and input.shape[1] + 1 >= double_index:
if Row != None and inputa.shape[1] + 1 >= double_index:
File.write(' <td>&nbsp;</td>\n')
File.write('</tr>')

Expand All @@ -8688,11 +8686,11 @@ def Write_array_html(
colour_count_col = 6
rowcntr = 0
html_colour = '#FFFFCC'
for x in range(input.shape[0]):
for x in range(inputa.shape[0]):
rowcntr += 1
if (
rowcntr == colour_count_row
and input.shape[0] > 3 * colour_count_row
and inputa.shape[0] > 3 * colour_count_row
):
File.write('\n<tr bgcolor="' + html_colour + '">\n')
rowcntr = 0
Expand All @@ -8705,30 +8703,30 @@ def Write_array_html(
+ '</b></div></td>\n'
)
colcntr = 0
for y in range(input.shape[1]):
for y in range(inputa.shape[1]):
colcntr += 1
if (
colcntr == colour_count_col
and input.shape[1] > 3 * colour_count_row
and inputa.shape[1] > 3 * colour_count_row
):
File.write(
' <td nowrap bgcolor="'
+ html_colour
+ '">'
+ self.__settings__['write_array_html_format']
% input[x, y]
% inputa[x, y]
+ '</td>\n'
)
colcntr = 0
else:
File.write(
' <td nowrap>'
+ self.__settings__['write_array_html_format']
% input[x, y]
% inputa[x, y]
+ '</td>\n'
)
## File.write(' <td nowrap>' + self.__settings__['write_array_html_format'] % input[x,y] + '</td>\n')
if Row != None and input.shape[1] + 1 >= double_index:
if Row != None and inputa.shape[1] + 1 >= double_index:
File.write(
' <td bgcolor="#CCCCCC"><div align="center"><b>'
+ Row[x]
Expand All @@ -8740,7 +8738,7 @@ def Write_array_html(
File.flush()
flush_count = 0
# print 'flushing'
if Col != None and input.shape[0] + 1 >= double_index:
if Col != None and inputa.shape[0] + 1 >= double_index:
File.write('\n<tr>\n')
if Row != None:
File.write(' <td>&nbsp;</td>\n')
Expand All @@ -8750,7 +8748,7 @@ def Write_array_html(
+ col
+ '</b></div></td>\n'
)
if Row != None and input.shape[1] + 1 >= double_index:
if Row != None and inputa.shape[1] + 1 >= double_index:
File.write(' <td>&nbsp;</td>\n')
File.write('</tr>\n')
except:
Expand Down Expand Up @@ -9307,4 +9305,3 @@ class WasteManagement(object):

if __name__ == '__main__':
print('\nTo use PySCeS import it from a Python Shell: \n\timport pysces\n')
input('Press <enter> to continue')
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