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Bugfix Release 1.2.1 #98

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merged 7 commits into from
May 10, 2024
Merged

Bugfix Release 1.2.1 #98

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810d7e1
Fix matching of symbols in assignment rules for 'data_sim_string'
jmrohwer May 7, 2024
47d5251
Remove 'Error 766' error message
jmrohwer May 7, 2024
bcc6a66
use f-strings for data_sim_string bug fix
jmrohwer May 9, 2024
8919299
update version to 1.2.1
jmrohwer May 9, 2024
f9b56f5
Update changelog.
jmrohwer May 9, 2024
0fb3afc
update docs submodule
jmrohwer May 10, 2024
999deba
update install instructions for 1.2.1
jmrohwer May 10, 2024
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16 changes: 12 additions & 4 deletions pysces/PyscesModel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@

'''
import os, copy, time
import re
import pickle
import warnings
try:
Expand Down Expand Up @@ -4814,14 +4815,21 @@ def _update_assignment_rule_code(self, rule):
or s in self.__rules__
or s in self.__species__
):
# catch any _init so it doesn't get replaced
replacements.append((s + '_init', '_zzzz_'))
# deal with substrings in symbols
partialmatches = []
for sym in rule['symbols']:
if not re.fullmatch(s, sym) and re.search(s, sym):
partialmatches.append(sym)
# catch any partial matches so they don't get replaced
for e in enumerate(partialmatches):
replacements.append((e[1], '_zzzz_' + str(e[0]) + '_z'))
# replace symbol to get sim data
replacements.append(
('self.' + s, 'self.data_sim.getSimData("' + s + '")[p:q,1]')
)
# revert the _init
replacements.append(('_zzzz_', s + '_init'))
# revert the partial match symbol
for e in enumerate(partialmatches):
replacements.append(('_zzzz_' + str(e[0]) + '_z', e[1]))

for old, new in replacements:
rule['data_sim_string'] = rule['data_sim_string'].replace(old, new)
Expand Down
7 changes: 0 additions & 7 deletions pysces/PyscesStoich.py
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Original file line number Diff line number Diff line change
Expand Up @@ -753,19 +753,12 @@ def PLUfactorize(self, a_in):
## except Exception, e:
## print "CLAPACK error", e

if a.shape[0] >= 500 or a.shape[1] >= 500:
print('\nMatrix {} using SciPy version: {} on {}'.format(a.shape, scipy.__version__, os.sys.platform))
print('Error 766 error detector: only report this if your Python crashes now ...')

if Using_FLAPACK == 1:
## results = getrf(numpy.transpose(a)) # brett 20041226
results = getrf(a) # brett 201106

results = list(results)

if a.shape[0] >= 500 or a.shape[1] >= 500:
print('766 error did not occur please continue as normal {} ...'.format(a.shape))

if results[2] < 0:
print('Argument ', results['info'], ' had an illegal value')
raise LinAlgError
Expand Down