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fix bandit text warnings

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edoapra 2026-06-29 15:24:48 -07:00
parent f862f56f04
commit a0824916fd
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4 changed files with 48 additions and 48 deletions
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8
contrib/python/nwchem_tddft_spectrum.py
View file

@ -34,9 +34,9 @@ from pylab import *
def parse_nwchem_output(fname): def parse_nwchem_output(fname):
import re import re
from pprint import pprint from pprint import pprint
singlet_pat = re.compile('\s+Root\s+\d+\s+singlet') singlet_pat = re.compile(r'\s+Root\s+\d+\s+singlet')
triplet_pat = re.compile('\s+Root\s+\d+\s+triplet') triplet_pat = re.compile(r'\s+Root\s+\d+\s+triplet')
unrestricted_pat = re.compile('\s+Root\s+\d') unrestricted_pat = re.compile(r'\s+Root\s+\d')
singlets = [] singlets = []
triplets = [] triplets = []
unrestricted = [] unrestricted = []
@ -59,7 +59,7 @@ def parse_nwchem_output(fname):
def parse_element(line,f): def parse_element(line,f):
import re import re
oscillator_pat = re.compile('\s+Oscillator') oscillator_pat = re.compile(r'\s+Oscillator')
words = line.split() words = line.split()
try: try:
energy = float(words[4]) 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. autoxc-Ds generated subroutine.
""" """
(lineno_start,lineno_end) = subr_lines (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 subr_type = type_autoxc
line = lineno_start line = lineno_start
while line <= lineno_end: while line <= lineno_end:
@ -210,14 +210,14 @@ def find_autoxc_code_skeleton(lines,subr_lines):
ifstart = -1 ifstart = -1
ifend = -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: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifstart = line+1 ifstart = line+1
break break
line += 1 line += 1
# #
pattern = re.compile("endif ! rhoa\.gt\.tol_rho") pattern = re.compile(r"endif ! rhoa\.gt\.tol_rho")
while line <= lineno_end: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifend = line-1 ifend = line-1
@ -232,14 +232,14 @@ def find_autoxc_code_skeleton(lines,subr_lines):
ifendb = -1 ifendb = -1
ifstartc = -1 ifstartc = -1
ifendc = -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: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifstarta = line+1 ifstarta = line+1
break break
line += 1 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: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifenda = line-1 ifenda = line-1
@ -247,7 +247,7 @@ def find_autoxc_code_skeleton(lines,subr_lines):
break break
line += 1 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: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifendb = line-1 ifendb = line-1
@ -255,7 +255,7 @@ def find_autoxc_code_skeleton(lines,subr_lines):
break break
line += 1 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: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifendc = line-1 ifendc = line-1
@ -281,14 +281,14 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
ifstartb = -1 ifstartb = -1
ifendb = -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: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifstarta = line+1 ifstarta = line+1
break break
line += 1 line += 1
# #
pattern = re.compile("else") pattern = re.compile(r"else")
while line <= lineno_end: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifenda = line-1 ifenda = line-1
@ -296,7 +296,7 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
break break
line += 1 line += 1
# #
pattern = re.compile("endif") pattern = re.compile(r"endif")
while line <= lineno_end: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifendb = line-1 ifendb = line-1
@ -315,14 +315,14 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
ifendc = -1 ifendc = -1
ifstartd = -1 ifstartd = -1
ifendd = -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: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifstarta = line+1 ifstarta = line+1
break break
line += 1 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: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifenda = line-1 ifenda = line-1
@ -330,7 +330,7 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
break break
line += 1 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: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifendb = line-1 ifendb = line-1
@ -340,7 +340,7 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
# #
# needed because "else" is a substring of "elseif ..." # needed because "else" is a substring of "elseif ..."
line = ifstartc line = ifstartc
pattern = re.compile("else") pattern = re.compile(r"else")
while line <= lineno_end: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifendc = line-1 ifendc = line-1
@ -348,7 +348,7 @@ def find_autoxcDs_code_skeleton(lines,subr_lines):
break break
line += 1 line += 1
# #
pattern = re.compile("endif") pattern = re.compile(r"endif")
while line <= lineno_end: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
ifendd = line-1 ifendd = line-1
@ -368,7 +368,7 @@ def find_type_declaration_insertion_point(lines,subr_lines):
subroutine calls can be inserted. subroutine calls can be inserted.
""" """
(lineno_start,lineno_end) = subr_lines (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_insert = -1
line = lineno_start line = lineno_start
while line <= lineno_end: while line <= lineno_end:
@ -412,7 +412,7 @@ def collect_subroutine_calls(lines,ifbranch_lines):
""" """
(lineno_start,lineno_end) = ifbranch_lines (lineno_start,lineno_end) = ifbranch_lines
dict = {} dict = {}
pattern = re.compile("nwxc") pattern = re.compile(r"nwxc")
line = lineno_start line = lineno_start
while line <= lineno_end: while line <= lineno_end:
if pattern.search(lines[line]): if pattern.search(lines[line]):
@ -640,8 +640,8 @@ def find_max_order_diff(lines,subr_lines):
(lineno_start,lineno_end) = subr_lines (lineno_start,lineno_end) = subr_lines
aline = lines[lineno_start] aline = lines[lineno_start]
orderdiff = 0 orderdiff = 0
pattern_d2 = re.compile("_d2\(") pattern_d2 = re.compile(r"_d2\(")
pattern_d3 = re.compile("_d3\(") pattern_d3 = re.compile(r"_d3\(")
if pattern_d2.search(aline): if pattern_d2.search(aline):
orderdiff = 2 orderdiff = 2
elif pattern_d3.search(aline): elif pattern_d3.search(aline):
@ -740,9 +740,9 @@ def find_varname(dict,diffstr):
#DEBUG #DEBUG
lengthl = len(list) lengthl = len(list)
if num == lengthl: 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): 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) sys.exit(10)
# num is now the variable set number # num is now the variable set number
lengthd = len(data) lengthd = len(data)
@ -764,8 +764,8 @@ def find_varname(dict,diffstr):
#print "find_varname: orderdiff:",orderdiff #print "find_varname: orderdiff:",orderdiff
#DEBUG #DEBUG
# orderdiff is now the order of differentiation # orderdiff is now the order of differentiation
patternc = re.compile("gamma") patternc = re.compile(r"gamma")
patternt = re.compile("tau") patternt = re.compile(r"tau")
var_func = func_lda var_func = func_lda
if lengthd >= 3: if lengthd >= 3:
if patternc.match(data[1]): 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 Given a line of source code work the indentation out and return a string
containing as many spaces as the indentation. containing as many spaces as the indentation.
""" """
pattern = re.compile("\s*") pattern = re.compile(r"\s*")
obj = pattern.match(line) obj = pattern.match(line)
indent = obj.group() indent = obj.group()
return indent 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. Find all locations where the variable given by "var_name" is used.
The locations are stored in a list which is returned. 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 # 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 # 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 # t2 as well at2, if the end-points are equal the string found does
# not match the variable t2. # not match the variable t2.
patternv = re.compile(var_name+"[^0-9]") 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+" " aline = line+" "
found = patterne.search(aline) found = patterne.search(aline)
list = [] 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. Here we expand the tuples in the list to cover these strings in full.
The list with updated tuples is returned. The list with updated tuples is returned.
""" """
pattern = re.compile("\)") pattern = re.compile(r"\)")
item = 0 item = 0
length = len(list) length = len(list)
while item < length: while item < length:
@ -1006,7 +1006,7 @@ def rewrap_line(longline):
conform the Fortran77 standard. The chunks are written to standard output. 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. 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() i = (pattern.search(longline)).start()
indent = longline[:i] indent = longline[:i]
indent = indent[:5]+"+"+indent[7:]+" " 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: while len(longline)-1 > 72:
i = -1 i = -1
# wrap before * / ( ) + or - # wrap before * / ( ) + or -
i = max(i,rfind(longline,"+",0,71)) i = max(i,rfind(longline,r"+",0,71))
i = max(i,rfind(longline,"-",0,71)) i = max(i,rfind(longline,r"-",0,71))
i = max(i,rfind(longline,"/",0,71)) i = max(i,rfind(longline,r"/",0,71))
i = max(i,rfind(longline,"\,",0,70)) i = max(i,rfind(longline,r"\,",0,70))
i = max(i,rfind(longline,", ",0,70)) i = max(i,rfind(longline,r", ",0,70))
i = max(i,rfind(longline,"\it",0,69)) i = max(i,rfind(longline,r"\it",0,69))
i = max(i,rfind(longline,"\rho",0,68)) i = max(i,rfind(longline,r"\rho",0,68))
i = max(i,rfind(longline,"\sigma",0,66)) i = max(i,rfind(longline,r"\sigma",0,66))
i = max(i,rfind(longline,"\tau",0,68)) i = max(i,rfind(longline,r"\tau",0,68))
i = max(i,rfind(longline,"\left",0,67)) i = max(i,rfind(longline,r"\left",0,67))
i = max(i,rfind(longline,"\over",0,67)) i = max(i,rfind(longline,r"\over",0,67))
i = max(i,rfind(longline,"\right",0,66)) i = max(i,rfind(longline,r"\right",0,66))
if i == -1: if i == -1:
sys.stderr.write("No sensible break point found in:\n") sys.stderr.write("No sensible break point found in:\n")
sys.stderr.write(longline) sys.stderr.write(longline)

8
src/tce/oce.py
View file

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