comp-chem/NWChem
1
0
Fork 0
mirror of https://github.com/nwchemgit/nwchem.git synced 2026-07-21 06:25:21 -04:00
Code Issues Projects Releases Packages Wiki Activity Actions 7

fix bandit text warnings

Browse source
This commit is contained in:
edoapra 2026-06-29 15:24:48 -07:00
parent f862f56f04
commit a0824916fd
No known key found for this signature in database
GPG key ID: 9E6A0B70826967BA
4 changed files with 48 additions and 48 deletions
Download patch file Download diff file Expand all files Collapse all files

8
contrib/python/nwchem_tddft_spectrum.py
View file

@ -34,9 +34,9 @@ from pylab import *
def parse_nwchem_output(fname):
import re
from pprint import pprint
singlet_pat = re.compile('\s+Root\s+\d+\s+singlet')
triplet_pat = re.compile('\s+Root\s+\d+\s+triplet')
unrestricted_pat = re.compile('\s+Root\s+\d')
singlet_pat = re.compile(r'\s+Root\s+\d+\s+singlet')
triplet_pat = re.compile(r'\s+Root\s+\d+\s+triplet')
unrestricted_pat = re.compile(r'\s+Root\s+\d')
singlets = []
triplets = []
unrestricted = []
@ -59,7 +59,7 @@ def parse_nwchem_output(fname):
def parse_element(line,f):
import re
oscillator_pat = re.compile('\s+Oscillator')
oscillator_pat = re.compile(r'\s+Oscillator')
words = line.split()
try:
energy = float(words[4])

56
src/nwxc/maxima/bin/call_subroutine.py
View file

@ -189,7 +189,7 @@ def find_code_skeleton_type(lines,subr_lines):
autoxc-Ds generated subroutine.
"""
(lineno_start,lineno_end) = subr_lines
pattern = re.compile("if \(taua\.gt\.tol_rho\) then")
pattern = re.compile(r"if \(taua\.gt\.tol_rho\) then")
subr_type = type_autoxc
line = lineno_start
while line <= lineno_end:
@ -210,14 +210,14 @@ def find_autoxc_code_skeleton(lines,subr_lines):
ifstart = -1
ifend = -1
#
pattern = re.compile("if \(rhoa\.gt\.tol_rho\) then")
pattern = re.compile(r"if \(rhoa\.gt\.tol_rho\) then")
while line <= lineno_end:
if pattern.search(lines[line]):
ifstart = line+1
break
line += 1
#
pattern = re.compile("endif ! rhoa\.gt\.tol_rho")
pattern = re.compile(r"endif ! rhoa\.gt\.tol_rho")
while line <= lineno_end:
if pattern.search(lines[line]):
ifend = line-1
@ -232,14 +232,14 @@ def find_autoxc_code_skeleton(lines,subr_lines):
ifendb = -1
ifstartc = -1
ifendc = -1
pattern = re.compile("if \(rhoa\.gt\.tol_rho\.and\.rhob\.gt\.tol_rho\) then")
pattern = re.compile(r"if \(rhoa\.gt\.tol_rho\.and\.rhob\.gt\.tol_rho\) then")
while line <= lineno_end:
if pattern.search(lines[line]):
ifstarta = line+1
break
line += 1
#
pattern = re.compile("elseif \(rhoa\.gt\.tol_rho\.and\.rhob\.le\.tol_rho\) then")
pattern = re.compile(r"elseif \(rhoa\.gt\.tol_rho\.and\.rhob\.le\.tol_rho\) then")
while line <= lineno_end:
if pattern.search(lines[line]):
ifenda = line-1
@ -247,7 +247,7 @@ def find_autoxc_code_skeleton(lines,subr_lines):
break
line += 1
#
pattern = re.compile("elseif \(rhoa\.le\.tol_rho\.and\.rhob\.gt\.tol_rho\) then")
pattern = re.compile(r"elseif \(rhoa\.le\.tol_rho\.and\.rhob\.gt\.tol_rho\) then")
while line <= lineno_end:
if pattern.search(lines[line]):
ifendb = line-1
@ -255,7 +255,7 @@ def find_autoxc_code_skeleton(lines,subr_lines):
break
line += 1
#
pattern = re.compile("endif ! rhoa\.gt\.tol_rho\.and\.rhob\.gt\.tol_rho")
pattern = re.compile(r"endif ! rhoa\.gt\.tol_rho\.and\.rhob\.gt\.tol_rho")
while line <= lineno_end:
if pattern.search(lines[line]):
ifendc = line-1
@ -281,14 +281,14 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
ifstartb = -1
ifendb = -1
#
pattern = re.compile("if \(taua\.gt\.tol_rho\) then")
pattern = re.compile(r"if \(taua\.gt\.tol_rho\) then")
while line <= lineno_end:
if pattern.search(lines[line]):
ifstarta = line+1
break
line += 1
#
pattern = re.compile("else")
pattern = re.compile(r"else")
while line <= lineno_end:
if pattern.search(lines[line]):
ifenda = line-1
@ -296,7 +296,7 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
break
line += 1
#
pattern = re.compile("endif")
pattern = re.compile(r"endif")
while line <= lineno_end:
if pattern.search(lines[line]):
ifendb = line-1
@ -315,14 +315,14 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
ifendc = -1
ifstartd = -1
ifendd = -1
pattern = re.compile("if \(taua\.gt\.tol_rho\.and\.taub\.gt\.tol_rho\) then")
pattern = re.compile(r"if \(taua\.gt\.tol_rho\.and\.taub\.gt\.tol_rho\) then")
while line <= lineno_end:
if pattern.search(lines[line]):
ifstarta = line+1
break
line += 1
#
pattern = re.compile("elseif \(taua\.gt\.tol_rho\.and\.taub\.le\.tol_rho\) then")
pattern = re.compile(r"elseif \(taua\.gt\.tol_rho\.and\.taub\.le\.tol_rho\) then")
while line <= lineno_end:
if pattern.search(lines[line]):
ifenda = line-1
@ -330,7 +330,7 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
break
line += 1
#
pattern = re.compile("elseif \(taua\.le\.tol_rho\.and\.taub\.gt\.tol_rho\) then")
pattern = re.compile(r"elseif \(taua\.le\.tol_rho\.and\.taub\.gt\.tol_rho\) then")
while line <= lineno_end:
if pattern.search(lines[line]):
ifendb = line-1
@ -340,7 +340,7 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
#
# needed because "else" is a substring of "elseif ..."
line = ifstartc
pattern = re.compile("else")
pattern = re.compile(r"else")
while line <= lineno_end:
if pattern.search(lines[line]):
ifendc = line-1
@ -348,7 +348,7 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
break
line += 1
#
pattern = re.compile("endif")
pattern = re.compile(r"endif")
while line <= lineno_end:
if pattern.search(lines[line]):
ifendd = line-1
@ -368,7 +368,7 @@ def find_type_declaration_insertion_point(lines,subr_lines):
subroutine calls can be inserted.
"""
(lineno_start,lineno_end) = subr_lines
pattern = re.compile("#include \"nwxc_param.fh\"")
pattern = re.compile(r"#include \"nwxc_param.fh\"")
line_insert = -1
line = lineno_start
while line <= lineno_end:
@ -412,7 +412,7 @@ def collect_subroutine_calls(lines,ifbranch_lines):
"""
(lineno_start,lineno_end) = ifbranch_lines
dict = {}
pattern = re.compile("nwxc")
pattern = re.compile(r"nwxc")
line = lineno_start
while line <= lineno_end:
if pattern.search(lines[line]):
@ -640,8 +640,8 @@ def find_max_order_diff(lines,subr_lines):
(lineno_start,lineno_end) = subr_lines
aline = lines[lineno_start]
orderdiff = 0
pattern_d2 = re.compile("_d2\(")
pattern_d3 = re.compile("_d3\(")
pattern_d2 = re.compile(r"_d2\(")
pattern_d3 = re.compile(r"_d3\(")
if pattern_d2.search(aline):
orderdiff = 2
elif pattern_d3.search(aline):
@ -740,9 +740,9 @@ def find_varname(dict,diffstr):
#DEBUG
lengthl = len(list)
if num == lengthl:
sys.stdout.write("entity %s not found\n"%callref)
sys.stdout.write(r"entity %s not found\n"%callref)
for jj in range(0,length):
sys.stdout.write("list %d: %s\n"%(jj,list[jj]))
sys.stdout.write(r"list %d: %s\n"%(jj,list[jj]))
sys.exit(10)
# num is now the variable set number
lengthd = len(data)
@ -764,8 +764,8 @@ def find_varname(dict,diffstr):
#print "find_varname: orderdiff:",orderdiff
#DEBUG
# orderdiff is now the order of differentiation
patternc = re.compile("gamma")
patternt = re.compile("tau")
patternc = re.compile(r"gamma")
patternt = re.compile(r"tau")
var_func = func_lda
if lengthd >= 3:
if patternc.match(data[1]):
@ -909,7 +909,7 @@ def find_indent(line):
Given a line of source code work the indentation out and return a string
containing as many spaces as the indentation.
"""
pattern = re.compile("\s*")
pattern = re.compile(r"\s*")
obj = pattern.match(line)
indent = obj.group()
return indent
@ -919,13 +919,13 @@ def find_var_in_line(line,var_name):
Find all locations where the variable given by "var_name" is used.
The locations are stored in a list which is returned.
"""
patterne = re.compile(" = ")
patterne = re.compile(r" = ")
# If var_name = t2 we need to make sure we do not replace
# cmat2 as well. Patternw is needed to achieve that. So we look for
# t2 as well at2, if the end-points are equal the string found does
# not match the variable t2.
patternv = re.compile(var_name+"[^0-9]")
patternw = re.compile("a"+var_name+"[^0-9]")
patternw = re.compile(r"a"+var_name+"[^0-9]")
aline = line+" "
found = patterne.search(aline)
list = []
@ -952,7 +952,7 @@ def expand_var_in_line(line,list):
Here we expand the tuples in the list to cover these strings in full.
The list with updated tuples is returned.
"""
pattern = re.compile("\)")
pattern = re.compile(r"\)")
item = 0
length = len(list)
while item < length:
@ -1006,7 +1006,7 @@ def rewrap_line(longline):
conform the Fortran77 standard. The chunks are written to standard output.
In addition we do not want to break the line in the middle of numbers.
"""
pattern = re.compile("\S")
pattern = re.compile(r"\S")
i = (pattern.search(longline)).start()
indent = longline[:i]
indent = indent[:5]+"+"+indent[7:]+" "

24
src/nwxc/maxima/bin/rewrap.py
View file

@ -39,18 +39,18 @@ def rewrap_line(longline):
while len(longline)-1 > 72:
i = -1
# wrap before * / ( ) + or -
i = max(i,rfind(longline,"+",0,71))
i = max(i,rfind(longline,"-",0,71))
i = max(i,rfind(longline,"/",0,71))
i = max(i,rfind(longline,"\,",0,70))
i = max(i,rfind(longline,", ",0,70))
i = max(i,rfind(longline,"\it",0,69))
i = max(i,rfind(longline,"\rho",0,68))
i = max(i,rfind(longline,"\sigma",0,66))
i = max(i,rfind(longline,"\tau",0,68))
i = max(i,rfind(longline,"\left",0,67))
i = max(i,rfind(longline,"\over",0,67))
i = max(i,rfind(longline,"\right",0,66))
i = max(i,rfind(longline,r"+",0,71))
i = max(i,rfind(longline,r"-",0,71))
i = max(i,rfind(longline,r"/",0,71))
i = max(i,rfind(longline,r"\,",0,70))
i = max(i,rfind(longline,r", ",0,70))
i = max(i,rfind(longline,r"\it",0,69))
i = max(i,rfind(longline,r"\rho",0,68))
i = max(i,rfind(longline,r"\sigma",0,66))
i = max(i,rfind(longline,r"\tau",0,68))
i = max(i,rfind(longline,r"\left",0,67))
i = max(i,rfind(longline,r"\over",0,67))
i = max(i,rfind(longline,r"\right",0,66))
if i == -1:
sys.stderr.write("No sensible break point found in:\n")
sys.stderr.write(longline)

8
src/tce/oce.py
View file

@ -286,7 +286,7 @@ class Operator:
"""Returns a LaTex form of output"""
show = string.join([self.type[0],"_{",repr(self.index),"}"], "")
if (self.dagger == "creation"):
show = string.join([show, "^{\dagger}"], "")
show = string.join([show, r"^{\dagger}"], "")
return show
def duplicate(self):
@ -507,7 +507,7 @@ class Amplitude:
show = string.join([show, index.texwithoutdagger()])
show = string.join([show,"}"])
if (self.conjugate):
show = string.join(["\\left(",show,"\\right)^{\\dagger}"],"")
show = string.join([r"\\left(",show,"\\right)^{\\dagger}"],"")
return show
def duplicate(self):
@ -845,10 +845,10 @@ class OperatorSequence:
if (self.sequence):
show = string.join([show, "\\langle 0 |"])
for sequence in self.sequence:
show = string.join([show, "\{"])
show = string.join([show, r"\{"])
for operator in sequence:
show = string.join([show, operator.tex()])
show = string.join([show, "\}"])
show = string.join([show, r"\}"])
show = string.join([show, "|0\\rangle"])
return show