From a0824916fdbef17c00f240e40d09d86baecdf6b5 Mon Sep 17 00:00:00 2001 From: edoapra Date: Mon, 29 Jun 2026 15:24:48 -0700 Subject: [PATCH] fix bandit text warnings --- contrib/python/nwchem_tddft_spectrum.py | 8 ++-- src/nwxc/maxima/bin/call_subroutine.py | 56 ++++++++++++------------- src/nwxc/maxima/bin/rewrap.py | 24 +++++------ src/tce/oce.py | 8 ++-- 4 files changed, 48 insertions(+), 48 deletions(-) diff --git a/contrib/python/nwchem_tddft_spectrum.py b/contrib/python/nwchem_tddft_spectrum.py index 08c49d2076..dec036cb84 100755 --- a/contrib/python/nwchem_tddft_spectrum.py +++ b/contrib/python/nwchem_tddft_spectrum.py @@ -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]) diff --git a/src/nwxc/maxima/bin/call_subroutine.py b/src/nwxc/maxima/bin/call_subroutine.py index d9989b290d..beab8144c5 100755 --- a/src/nwxc/maxima/bin/call_subroutine.py +++ b/src/nwxc/maxima/bin/call_subroutine.py @@ -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:]+" " diff --git a/src/nwxc/maxima/bin/rewrap.py b/src/nwxc/maxima/bin/rewrap.py index d21f3109db..bedde95030 100755 --- a/src/nwxc/maxima/bin/rewrap.py +++ b/src/nwxc/maxima/bin/rewrap.py @@ -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) diff --git a/src/tce/oce.py b/src/tce/oce.py index 34ff710fc0..c74f6ceb23 100644 --- a/src/tce/oce.py +++ b/src/tce/oce.py @@ -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