Description: Use 2to3 to port from Python2 to Python3 Bug-Debian: https://bugs.debian.org/937262 Author: Andreas Tille Last-Update: Thu, 12 Dec 2019 15:41:47 +0100 --- a/SConscript-error.py +++ b/SConscript-error.py @@ -67,11 +67,11 @@ status, failures_message = build_status() if status == 'failed': - print - print "FAILED!!!!" # could display alert, ring bell, etc. + print() + print("FAILED!!!!") # could display alert, ring bell, etc. elif status == 'ok': - print - print "Build succeeded." - print failures_message + print() + print("Build succeeded.") + print(failures_message) atexit.register(display_build_status) \ No newline at end of file --- a/SConscript-install.py +++ b/SConscript-install.py @@ -102,7 +102,7 @@ Alias('install', env.Command(env['PREFIX']+'tmp', None, [Mkdir('$TARGET'), - Chmod('$TARGET', 0777)])) + Chmod('$TARGET', 0o777)])) #Testing stuff to test installed pdb2pqr for dir_name in ('tests/', --- a/SConscript-main.py +++ b/SConscript-main.py @@ -166,13 +166,13 @@ #Set up regex to alternately clear tags or wipe sections if env['OPAL'] == '': #Not using opal for pdb2pqr. - print "not using opal", env['OPAL'] + print("not using opal", env['OPAL']) withOpalRegex = r'@WITHOPAL@.*?@WITHOPAL@' withoutOpalRegex = '@WITHOUTOPAL@' else: #Using opal for pdb2pqr. - print "using opal", env['OPAL'] + print("using opal", env['OPAL']) withOpalRegex = '@WITHOPAL@' withoutOpalRegex = r'@WITHOUTOPAL@.*?@WITHOUTOPAL@' @@ -184,7 +184,7 @@ withOpalRegex:'', withoutOpalRegex:''} -chmodAction = Chmod('$TARGET', 0755) +chmodAction = Chmod('$TARGET', 0o755) serverHtmlCopySub = CopySub('$TARGET', '$SOURCE', serverHtmlDict, useRegex=True) normalCopySub = CopySub('$TARGET', '$SOURCE', replacementDict, useRegex=False) @@ -217,7 +217,7 @@ try: import numpy except ImportError: - print 'WARNING: PDB2PKA build skipped, numpy not installed. Ligand support will not be available.' + print('WARNING: PDB2PKA build skipped, numpy not installed. Ligand support will not be available.') numpy_error = True if not numpy_error: @@ -234,9 +234,9 @@ compile_targets.append(algorithms_pyc) if os.name == 'nt': - alg_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && '+pythonBin+' scons/scons.py algorithms DEBUG=True', - MSVSCLEANCOM='cd .. && '+pythonBin+' scons/scons.py -c algorithms', - MSVSREBUILDCOM='cd .. && '+pythonBin+' scons/scons.py -c algorithms && '+pythonBin+' scons/scons.py algorithms DEBUG=True') + alg_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && scons algorithms DEBUG=True', + MSVSCLEANCOM='cd .. && scons -c algorithms', + MSVSREBUILDCOM='cd .. && scons -c algorithms && scons algorithms DEBUG=True') algorithms_project = alg_msvs_env.MSVSProject(target = 'msvs/Algorithms' + env['MSVSPROJECTSUFFIX'], auto_build_solution=0, @@ -259,9 +259,9 @@ compile_targets.append(pmc_pyc) if os.name == 'nt': - pmc_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && '+pythonBin+' scons/scons.py pmc_mult DEBUG=True'+build_swig, - MSVSCLEANCOM='cd .. && '+pythonBin+' scons/scons.py -c pmc_mult', - MSVSREBUILDCOM='cd .. && '+pythonBin+' scons/scons.py -c pmc_mult && '+pythonBin+' scons/scons.py pmc_mult DEBUG=True'+build_swig) + pmc_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && scons pmc_mult DEBUG=True'+build_swig, + MSVSCLEANCOM='cd .. && scons -c pmc_mult', + MSVSREBUILDCOM='cd .. && scons -c pmc_mult && scons pmc_mult DEBUG=True'+build_swig) pmc_mult_project = pmc_msvs_env.MSVSProject(target = 'msvs/pMC_mult' + env['MSVSPROJECTSUFFIX'], auto_build_solution=0, @@ -285,65 +285,65 @@ SConscript('SConscript-error.py') def print_default_message(target_list): - target_list = map(str, target_list) + target_list = list(map(str, target_list)) if any('test' in x for x in target_list): return if GetOption("clean"): return if not GetOption("help"): - print - print 'TARGETS:', target_list - print - print '========================' - print 'Configuration Parameters' - print '========================' - print - print 'Version:', productVersion - print 'Install directory:', env['PREFIX'] + print() + print('TARGETS:', target_list) + print() + print('========================') + print('Configuration Parameters') + print('========================') + print() + print('Version:', productVersion) + print('Install directory:', env['PREFIX']) if numpy_error: - print - print 'WARNING: PDB2PKA build skipped, numpy not installed. Ligand support will not be available.' - print + print() + print('WARNING: PDB2PKA build skipped, numpy not installed. Ligand support will not be available.') + print() else: - print 'pdb2pka and ligand support:', env['BUILD_PDB2PKA'] - print 'Path to the website directory:', url + print('pdb2pka and ligand support:', env['BUILD_PDB2PKA']) + print('Path to the website directory:', url) if env['OPAL'] == '': - print 'PDB2PQR jobs run via the web interface will be forked on the server.' + print('PDB2PQR jobs run via the web interface will be forked on the server.') else: - print 'PDB2PQR jobs run via the web interface will be run via opal at', env['OPAL'] + print('PDB2PQR jobs run via the web interface will be run via opal at', env['OPAL']) else: - print - print 'Run "python scons/scons.py" to build pdb2pqr.' + print() + print('Run "scons" to build pdb2pqr.') - print - print 'The preferred way to configure the build is by editing the file', config_file - print - print 'Run scons with the python that you intend to use with pdb2pqr.' - print 'For example: "/opt/bin/python scons/scons.py" will setup pdb2pqr to be run with /opt/bin/python' + print() + print('The preferred way to configure the build is by editing the file', config_file) + print() + print('Run scons with the python3 that you intend to use with pdb2pqr.') + print('For example: "scons" will setup pdb2pqr to be run with Debian default Python3 interpreter') if 'install' not in target_list: - print - print 'Run "python scons/scons.py install" to install pdb2pqr in', env['PREFIX'] + print() + print('Run "scons install" to install pdb2pqr in', env['PREFIX']) - print - print 'Run "python scons/scons.py basic-test" for a basic functionality test' - print 'Run "python scons/scons.py advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.' - print 'Run "python scons/scons.py complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.' - print 'Run "python scons/scons.py pdb2pka-test" for a test of PDB2PKA functionality.' - print ' Requires numpy, PDB2PKA support compiled AND the APBS python libraries compiled and installed in the pdb2pka directory.' - - print - print 'To setup a web service create a symbolic link to', env['PREFIX'], 'that enables you to view', env['URL'],'after running "scons/scons.py install"' - print - print 'Run "python scons/scons.py msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.' - print 'VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.' - print 'The resulting projects will need to modified to use VS natively to compile the code or debug.' + print() + print('Run "scons basic-test" for a basic functionality test') + print('Run "scons advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.') + print('Run "scons complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.') + print('Run "scons pdb2pka-test" for a test of PDB2PKA functionality.') + print(' Requires numpy, PDB2PKA support compiled AND the APBS python3 libraries compiled and installed in the pdb2pka directory.') + + print() + print('To setup a web service create a symbolic link to', env['PREFIX'], 'that enables you to view', env['URL'],'after running "scons install"') + print() + print('Run "scons msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.') + print('VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.') + print('The resulting projects will need to modified to use VS natively to compile the code or debug.') if 'install' in target_list: - print - print 'pdb2pqr installed in', env['PREFIX'] + print() + print('pdb2pqr installed in', env['PREFIX']) atexit.register(print_default_message, BUILD_TARGETS) --- a/fabfile.py +++ b/fabfile.py @@ -51,7 +51,7 @@ arcname = os.path.join(self.prefix, name) self.tar.add(name, arcname) - print('Packing file: ' + name if arcname is None else arcname) + print(('Packing file: ' + name if arcname is None else arcname)) def close(self): self.tar.close() @@ -97,7 +97,7 @@ local("move pdb2pqr-src-"+pv+'.tar.gz dist_files\\') def deploy(): - python = 'python2.7' + python = 'python3' put('pdb2pqr.tgz', '~/') with settings(warn_only=True): @@ -106,15 +106,15 @@ with cd('~/tmp/'): run('tar -zxvf ~/pdb2pqr.tgz') - run(python+' scons/scons.py') + run('scons') if run_tests: - run(python+' scons/scons.py -j 4 pdb2pka-test') - run(python+' scons/scons.py -j 4 complete-test') + run('scons -j 4 pdb2pka-test') + run('scons -j 4 complete-test') def install_on_deployed(): - python = 'python2.7' + python = 'python3' with settings(warn_only=True): with cd('~/www/pdb2pqr'): @@ -147,8 +147,8 @@ # configopts += ' PREFIX=/Users/d3k084/www/pdb2pqr/' # configopts += ' URL=http://PT24098/d3k084/pdb2pqr' - run(python+' scons/scons.py ' + configopts) - run(python+' scons/scons.py install ' + configopts) + run('scons ' + configopts) + run('scons install ' + configopts) def build_binary_from_deploy(): create_dist_folder() @@ -190,11 +190,11 @@ @runs_once def build_windows(): local(r'copy apbs_libs\windows\* pdb2pka\\') - local(r'python scons\scons.py -c') - local(r'python scons\scons.py') + local(r'python3 scons\scons.py -c') + local(r'python3 scons\scons.py') if run_tests: - local(r'python scons\scons.py -j 4 pdb2pka-test') - local(r'python scons\scons.py -j 7 complete-test') + local(r'python3 scons\scons.py -j 4 pdb2pka-test') + local(r'python3 scons\scons.py -j 7 complete-test') build_windows_binary() if run_tests: @@ -219,12 +219,12 @@ zip_file = zipfile.ZipFile(name + '.zip', 'w', zipfile.ZIP_DEFLATED) for root, _, files in os.walk(r'dist\\'+name): new_root = root.split('/', 1)[-1] - print root + print(root) for f in files: zip_file_path = os.path.join(new_root,f) real_file_path = os.path.join(root,f) zip_file.write(real_file_path, zip_file_path) - print 'Zipping ' + zip_file_path + print('Zipping ' + zip_file_path) zip_file.close() create_dist_folder() local('move /Y ' + name + '.zip' + r' dist_files\\' + name + '.zip') --- a/scons/scons-time.py +++ b/scons/scons-time.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 # # scons-time - run SCons timings and collect statistics # @@ -29,8 +29,8 @@ # LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION # OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION # WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -from __future__ import division -from __future__ import nested_scopes + + __revision__ = "src/script/scons-time.py 2014/08/24 12:12:31 garyo" @@ -109,8 +109,8 @@ internal functions. ''' if not args: exec(cmd) - elif len(args) == 1: exec cmd in args[0] - else: exec cmd in args[0], args[1] + elif len(args) == 1: exec(cmd, args[0]) + else: exec(cmd, args[0], args[1]) class Plotter(object): def increment_size(self, largest): @@ -146,7 +146,7 @@ def print_label(self, inx, x, y): if self.label: - print 'set label %s "%s" at %s,%s right' % (inx, self.label, x, y) + print('set label %s "%s" at %s,%s right' % (inx, self.label, x, y)) def plot_string(self): if self.title: @@ -159,15 +159,15 @@ if fmt is None: fmt = self.fmt if self.comment: - print '# %s' % self.comment + print('# %s' % self.comment) for x, y in self.points: # If y is None, it usually represents some kind of break # in the line's index number. We might want to represent # this some way rather than just drawing the line straight # between the two points on either side. if not y is None: - print fmt % (x, y) - print 'e' + print(fmt % (x, y)) + print('e') def get_x_values(self): return [ p[0] for p in self.points ] @@ -253,8 +253,8 @@ return if self.title: - print 'set title "%s"' % self.title - print 'set key %s' % self.key_location + print('set title "%s"' % self.title) + print('set key %s' % self.key_location) min_y = self.get_min_y() max_y = self.max_graph_value(self.get_max_y()) @@ -269,7 +269,7 @@ inx += 1 plot_strings = [ self.plot_string(l) for l in self.lines ] - print 'plot ' + ', \\\n '.join(plot_strings) + print('plot ' + ', \\\n '.join(plot_strings)) for line in self.lines: line.print_points() @@ -540,7 +540,7 @@ header_fmt = ' '.join(['%12s'] * len(columns)) line_fmt = header_fmt + ' %s' - print header_fmt % columns + print(header_fmt % columns) for file in files: t = line_function(file, *args, **kw) @@ -550,7 +550,7 @@ if diff > 0: t += [''] * diff t.append(file_function(file)) - print line_fmt % tuple(t) + print(line_fmt % tuple(t)) def collect_results(self, files, function, *args, **kw): results = {} @@ -690,13 +690,13 @@ """ try: import pstats - except ImportError, e: + except ImportError as e: sys.stderr.write('%s: func: %s\n' % (self.name, e)) sys.stderr.write('%s This version of Python is missing the profiler.\n' % self.name_spaces) sys.stderr.write('%s Cannot use the "func" subcommand.\n' % self.name_spaces) sys.exit(1) statistics = pstats.Stats(file).stats - matches = [ e for e in statistics.items() if e[0][2] == function ] + matches = [ e for e in list(statistics.items()) if e[0][2] == function ] r = matches[0] return r[0][0], r[0][1], r[0][2], r[1][3] @@ -751,7 +751,7 @@ return self.default(argv) try: return func(argv) - except TypeError, e: + except TypeError as e: sys.stderr.write("%s %s: %s\n" % (self.name, cmdName, e)) import traceback traceback.print_exc(file=sys.stderr) @@ -856,7 +856,7 @@ self.title = a if self.config_file: - exec open(self.config_file, 'rU').read() in self.__dict__ + exec(open(self.config_file, 'rU').read(), self.__dict__) if self.chdir: os.chdir(self.chdir) @@ -889,13 +889,13 @@ try: f, line, func, time = \ self.get_function_profile(file, function_name) - except ValueError, e: + except ValueError as e: sys.stderr.write("%s: func: %s: %s\n" % (self.name, file, e)) else: if f.startswith(cwd_): f = f[len(cwd_):] - print "%.3f %s:%d(%s)" % (time, f, line, func) + print("%.3f %s:%d(%s)" % (time, f, line, func)) elif format == 'gnuplot': @@ -1233,7 +1233,7 @@ sys.exit(1) if self.config_file: - exec open(self.config_file, 'rU').read() in self.__dict__ + exec(open(self.config_file, 'rU').read(), self.__dict__) if args: self.archive_list = args @@ -1466,7 +1466,7 @@ elif o in ('--title',): self.title = a elif o in ('--which',): - if not a in self.time_strings.keys(): + if not a in list(self.time_strings.keys()): sys.stderr.write('%s: time: Unrecognized timer "%s".\n' % (self.name, a)) sys.stderr.write('%s Type "%s help time" for help.\n' % (self.name_spaces, self.name)) sys.exit(1) --- a/scons/scons.py +++ b/scons/scons.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#!/usr/bin/python3 # # SCons - a Software Constructor # @@ -191,7 +191,7 @@ except: print("Import failed. Unable to find SCons files in:") for path in libs: - print " %s" % path + print(" %s" % path) raise # this does all the work, and calls sys.exit --- a/scons/sconsign.py +++ b/scons/sconsign.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#!/usr/bin/python3 # # SCons - a Software Constructor # @@ -171,7 +171,7 @@ import SCons.compat # so pickle will import cPickle instead -import whichdb +import dbm import time import pickle import imp @@ -189,8 +189,8 @@ pass return _orig_whichdb(filename) -_orig_whichdb = whichdb.whichdb -whichdb.whichdb = my_whichdb +_orig_whichdb = dbm.whichdb +dbm.whichdb = my_whichdb def my_import(mname): if '.' in mname: @@ -310,14 +310,14 @@ outlist = field("implicit", entry, 0) if outlist: if Verbose: - print " implicit:" - print " " + outlist + print(" implicit:") + print(" " + outlist) outact = field("action", entry, 0) if outact: if Verbose: - print " action: " + outact + print(" action: " + outact) else: - print " " + outact + print(" " + outact) def printentries(entries, location): if Print_Entries: @@ -330,9 +330,9 @@ try: ninfo = entry.ninfo except AttributeError: - print name + ":" + print(name + ":") else: - print nodeinfo_string(name, entry.ninfo) + print(nodeinfo_string(name, entry.ninfo)) printfield(name, entry.binfo) else: for name in sorted(entries.keys()): @@ -340,9 +340,9 @@ try: ninfo = entry.ninfo except AttributeError: - print name + ":" + print(name + ":") else: - print nodeinfo_string(name, entry.ninfo) + print(nodeinfo_string(name, entry.ninfo)) printfield(name, entry.binfo) class Do_SConsignDB(object): @@ -361,7 +361,7 @@ # .sconsign => .sconsign.dblite # .sconsign.dblite => .sconsign.dblite.dblite db = self.dbm.open(fname, "r") - except (IOError, OSError), e: + except (IOError, OSError) as e: print_e = e try: # That didn't work, so try opening the base name, @@ -375,7 +375,7 @@ # suffix-mangling). try: open(fname, "r") - except (IOError, OSError), e: + except (IOError, OSError) as e: # Nope, that file doesn't even exist, so report that # fact back. print_e = e @@ -386,7 +386,7 @@ except pickle.UnpicklingError: sys.stderr.write("sconsign: ignoring invalid `%s' file `%s'\n" % (self.dbm_name, fname)) return - except Exception, e: + except Exception as e: sys.stderr.write("sconsign: ignoring invalid `%s' file `%s': %s\n" % (self.dbm_name, fname, e)) return @@ -403,13 +403,13 @@ self.printentries(dir, db[dir]) def printentries(self, dir, val): - print '=== ' + dir + ':' + print('=== ' + dir + ':') printentries(pickle.loads(val), dir) def Do_SConsignDir(name): try: fp = open(name, 'rb') - except (IOError, OSError), e: + except (IOError, OSError) as e: sys.stderr.write("sconsign: %s\n" % (e)) return try: @@ -419,7 +419,7 @@ except pickle.UnpicklingError: sys.stderr.write("sconsign: ignoring invalid .sconsign file `%s'\n" % (name)) return - except Exception, e: + except Exception as e: sys.stderr.write("sconsign: ignoring invalid .sconsign file `%s': %s\n" % (name, e)) return printentries(sconsign.entries, args[0]) @@ -471,13 +471,13 @@ dbm = my_import(dbm_name) except: sys.stderr.write("sconsign: illegal file format `%s'\n" % a) - print helpstr + print(helpstr) sys.exit(2) Do_Call = Do_SConsignDB(a, dbm) else: Do_Call = Do_SConsignDir elif o in ('-h', '--help'): - print helpstr + print(helpstr) sys.exit(0) elif o in ('-i', '--implicit'): Print_Flags['implicit'] = 1 @@ -497,7 +497,7 @@ Do_Call(a) else: for a in args: - dbm_name = whichdb.whichdb(a) + dbm_name = dbm.whichdb(a) if dbm_name: Map_Module = {'SCons.dblite' : 'dblite'} dbm = my_import(dbm_name) --- a/site_scons/site_init.py +++ b/site_scons/site_init.py @@ -48,35 +48,35 @@ contents = f.read() f.close() except: - raise SCons.Errors.UserError, "Can't read source file %s"%sourcefile + raise SCons.Errors.UserError("Can't read source file %s"%sourcefile) if useRegex: - for (k,v) in dict.items(): + for (k,v) in list(dict.items()): #In 2.6 re.sub has no "flags" argument. mo = re.compile(k, flags=re.DOTALL) contents = mo.sub(v, contents) else: - for (k,v) in dict.items(): + for (k,v) in list(dict.items()): contents = contents.replace(k, v) try: f = open(targetfile, 'wb') f.write(contents) f.close() except: - raise SCons.Errors.UserError, "Can't write target file %s"%targetfile + raise SCons.Errors.UserError("Can't write target file %s"%targetfile) return 0 # success def subst_in_file(target, source, env): useRegex = env['SUBST_USE_REGEX'] if 'SUBST_USE_REGEX' in env else False if 'SUBST_DICT' not in env: - raise SCons.Errors.UserError, "SubstInFile requires SUBST_DICT to be set." + raise SCons.Errors.UserError("SubstInFile requires SUBST_DICT to be set.") d = dict(env['SUBST_DICT']) # copy it - for (k,v) in d.items(): + for (k,v) in list(d.items()): if callable(v): d[k] = env.subst(v()) elif SCons.Util.is_String(v): d[k]=env.subst(v) else: - raise SCons.Errors.UserError, "SubstInFile: key %s: %s must be a string or callable"%(k, repr(v)) + raise SCons.Errors.UserError("SubstInFile: key %s: %s must be a string or callable"%(k, repr(v))) for (t,s) in zip(target, source): return do_subst_in_file(str(t), str(s), d, useRegex) @@ -90,7 +90,7 @@ Returns original target, source tuple unchanged. """ d = env['SUBST_DICT'].copy() # copy it - for (k,v) in d.items(): + for (k,v) in list(d.items()): if callable(v): d[k] = env.subst(v()) elif SCons.Util.is_String(v): @@ -108,25 +108,25 @@ 1.2345 etc. """ try: - f = open(sourcefile, 'rb') + f = open(sourcefile, 'r') contents = f.read() f.close() except: - raise SCons.Errors.UserError, "Can't read source file %s"%sourcefile + raise SCons.Errors.UserError("Can't read source file %s"%sourcefile) if useRegex: - for (k,v) in dict.items(): + for (k,v) in list(dict.items()): #In 2.6 re.sub has no "flags" argument. mo = re.compile(k, flags=re.DOTALL) contents = mo.sub(v, contents) else: - for (k,v) in dict.items(): + for (k,v) in list(dict.items()): contents = contents.replace(k, v) try: - f = open(targetfile, 'wb') + f = open(targetfile, 'w') f.write(contents) f.close() except: - raise SCons.Errors.UserError, "Can't write target file %s"%targetfile + raise SCons.Errors.UserError("Can't write target file %s"%targetfile) return 0 # success def CopySubActionStringFunc(targetfile, sourcefile, dict, useRegex): @@ -138,12 +138,12 @@ try: import py_compile except ImportError: - raise SCons.Errors.InternalError, "Couldn't import py_compile module" + raise SCons.Errors.InternalError("Couldn't import py_compile module") try: py_compile.compile(sourcefile, targetfile, doraise=True) except py_compile.PyCompileError: - raise SCons.Errors.InternalError, "Couldn't compile {0}".format(sourcefile) + raise SCons.Errors.InternalError("Couldn't compile {0}".format(sourcefile)) --- a/site_scons/test_tools.py +++ b/site_scons/test_tools.py @@ -1,4 +1,4 @@ -from itertools import ifilter, izip_longest, izip +from itertools import zip_longest from glob import glob from os import path import csv @@ -31,19 +31,19 @@ return strings,ints,floats def compareParsedAtoms(atom1, atom2): - return atom1[0:1] == atom2[0:1] and all(abs(x-y)<0.1 for x,y in izip(atom1[2],atom2[2])) + return atom1[0:1] == atom2[0:1] and all(abs(x-y)<0.1 for x,y in zip(atom1[2],atom2[2])) def ComparePQRAction(outputFileName, testFileName, correctFileName, has_chain=False): failure = False results = [] with open(testFileName) as testFile: with open(correctFileName) as correctFile: - testAtoms = ifilter(isAtomLine, testFile) - correctAtoms = ifilter(isAtomLine, correctFile) + testAtoms = filter(isAtomLine, testFile) + correctAtoms = filter(isAtomLine, correctFile) check_error = False correct_total = 0.0 test_total = 0.0 - for testAtom, correctAtom in izip_longest(testAtoms, correctAtoms, fillvalue=None): + for testAtom, correctAtom in zip_longest(testAtoms, correctAtoms, fillvalue=None): if testAtom is None or correctAtom is None: results.append('TEST ERROR: Result file is the wrong length!\n') failure = True @@ -99,7 +99,7 @@ else: combined[ph][1] = value - keys = combined.keys() + keys = list(combined.keys()) keys.sort() combined_list = [(combined[ph][0], combined[ph][1]) for ph in keys] @@ -166,12 +166,12 @@ def getSummaryLines(sourceFile): - while 'SUMMARY' not in sourceFile.next(): + while 'SUMMARY' not in next(sourceFile): pass #Skip header - sourceFile.next() - line = sourceFile.next() + next(sourceFile) + line = next(sourceFile) results = [] @@ -184,7 +184,7 @@ results.append((strings,floats)) - line = sourceFile.next() + line = next(sourceFile) return results @@ -197,7 +197,7 @@ correctPKAs = getSummaryLines(correctFile) correct_total = 0.0 test_total = 0.0 - for testPKA, correctPKA in izip_longest(testPKAs, correctPKAs, fillvalue=None): + for testPKA, correctPKA in zip_longest(testPKAs, correctPKAs, fillvalue=None): if testPKA is None or correctPKA is None: results.append('TEST ERROR: Result file is the wrong length!') failure = True --- a/tests/complete-test/SConscript +++ b/tests/complete-test/SConscript @@ -108,7 +108,7 @@ '--ff=AMBER --ligand=${SOURCES[1]} --whitespace') #Test ph and ligand -for ph in xrange(1,14): +for ph in range(1,14): out_file_name = 'test-output-1HPX-ligand-ph{0}.pqr'.format(ph) correct_file_name = 'test-output-1HPX-ligand-ph{0}-correct.pqr'.format(ph) @@ -169,4 +169,4 @@ 'test-misc-options', '--ff=AMBER --apbs-input --whitespace --typemap --include-header') -Alias('complete-test', testList) \ No newline at end of file +Alias('complete-test', testList)