rem stringlengths 1 226k | add stringlengths 0 227k | context stringlengths 6 326k | meta stringlengths 143 403 | input_ids listlengths 256 256 | attention_mask listlengths 256 256 | labels listlengths 128 128 |
|---|---|---|---|---|---|---|
s.append (prepend_symbols ('--import-impl=', impl_import (obj, prefix))) | if os.path.isdir (obj.impl_dir (prefix)): s.append (prepend_symbols ('--import-impl=', impl_import (obj, prefix))) | def import_options (obj, prefix=''): s = [] if obj.impl_dir () is not None: s.append (prepend_symbols ('--import-impl=', impl_import (obj, prefix))) if obj.sidl_file () is not None: s.append (prepend_symbols ('--import-sidl=', sidl_import (obj, prefix))) return ' '.join (s) | 10e6009abcc5e3aa1bed7c98e16a5ae57263171c /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/5386/10e6009abcc5e3aa1bed7c98e16a5ae57263171c/bocca_command.py | [
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self.__buf = self.__buf + data | self.__buf.write(data) | def pack_fstring(self, n, s): if n < 0: raise ValueError, 'fstring size must be nonnegative' n = ((n+3)/4)*4 data = s[:n] data = data + (n - len(data)) * '\0' self.__buf = self.__buf + data | c47016ee74fdd765bdad0f890c810518501de22a /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/8546/c47016ee74fdd765bdad0f890c810518501de22a/xdrlib.py | [
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print time.time(), "end" | def _expose(self, imageRequest): shutterRequest = imageRequest['shutter'] if shutterRequest == Shutter.OPEN: shutter = SBIGDrv.openShutter elif shutterRequest == Shutter.CLOSE: shutter = SBIGDrv.closeShutter elif shutterRequest == Shutter.LEAVE_AS_IS: shutter = SBIGDrv.leaveShutter else: self.log.warning("Incorrect shutter option (%s)." " Leaving shutter intact" % shutterRequest) shutter = SBIGDrv.leaveShutter # ok, start it self.exposeBegin(imageRequest) self.drv.startExposure(self.ccd, int(imageRequest["exptime"]*100), shutter) # save time exposure started self.lastFrameStartTime = dt.datetime.utcnow() self.lastFrameTemp = self.getTemperature() | cb9501362f8ebb5758f8d4cfb93788cb612fe799 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/3749/cb9501362f8ebb5758f8d4cfb93788cb612fe799/sbig.py | [
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self.assert_(disp in self.msg[headername]) | self.assertNotEqual(self.msg[headername].find(disp), -1) | def test_delNotations(self): # Add each type of notation to each header and check that it # is removed. for headername in ["subject", "to"]: for disp in (self.ham, self.spam, self.unsure): # Add a notation to the header header = self.msg[headername] self.assert_(disp not in header) options["Headers", "notate_%s" % (headername,)] = \ (self.ham, self.unsure, self.spam) prob = {self.ham:self.g_prob, self.spam:self.s_prob, self.unsure:self.u_prob}[disp] self.msg.addSBHeaders(prob, self.clues) self.assert_(disp in self.msg[headername]) # Remove it self.msg.delNotations() self.assertEqual(self.msg[headername], header) | 274fd041277b8777bd1567b84a52d889f51c6bcc /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/6126/274fd041277b8777bd1567b84a52d889f51c6bcc/test_message.py | [
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Update bans in the tracker from channel ban list, | Update bans in the tracker from the channel ban list, | def updatebt(self, irc, msg, args, channel): """[<channel>] Update bans in the tracker from channel ban list, if channel is not given then run in all channels """ | 353e8a3cb6570f78f25b8d8c4070231630fbefe3 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/3106/353e8a3cb6570f78f25b8d8c4070231630fbefe3/plugin.py | [
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if self.GetGeometryType() == ogr.wkbGeometryCollection or \ self.GetGeometryType() == ogr.wkbGeometryCollection25D: | if self.GetGeometryType() == wkbGeometryCollection or \ self.GetGeometryType() == wkbGeometryCollection25D: | def get_coordinates(geometry): gtype = geometry.GetGeometryType() geom_count = geometry.GetGeometryCount() coordinates = [] | fdfdc9d8eb334a016148de8705ca125d94ec7d6c /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/10289/fdfdc9d8eb334a016148de8705ca125d94ec7d6c/ogr.py | [
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assert(self.mcl_state_machine.state == MCAP_STATE_READY) | assert(self.mcl_sm.state == MCAP_STATE_READY) | def check_asserts(self, counter): if (self.counter == 2): assert(self.mcl.count_mdls() == 1) assert(self.mcl_state_machine.state == MCAP_STATE_READY) assert(self.mcl.state == MCAP_MCL_STATE_ACTIVE) elif (self.counter == 3): assert(self.mcl.count_mdls() == 2) assert(self.mcl_state_machine.state == MCAP_STATE_READY) assert(self.mcl.state == MCAP_MCL_STATE_ACTIVE) elif (self.counter == 4): assert(self.mcl.count_mdls() == 3) assert(self.mcl_state_machine.state == MCAP_STATE_READY) assert(self.mcl.state == MCAP_MCL_STATE_ACTIVE) elif (self.counter == 5): assert(self.mcl.count_mdls() == 3) assert(self.mcl.state == MCAP_MCL_STATE_ACTIVE) assert(self.mcl_state_machine.state == MCAP_STATE_READY) elif (self.counter == 6): assert(self.mcl.count_mdls() == 2) assert(self.mcl.state == MCAP_MCL_STATE_ACTIVE) assert(self.mcl_state_machine.state == MCAP_STATE_READY) elif (self.counter == 7): assert(self.mcl.count_mdls() == 0) assert(self.mcl.state == MCAP_MCL_STATE_CONNECTED) assert(self.mcl_state_machine.state == MCAP_STATE_READY) | 58de439d6e74c4b1556bf0b35da03b7a41012af1 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/8028/58de439d6e74c4b1556bf0b35da03b7a41012af1/test1_client.py | [
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if valueType == "password": try: control.SetValue(waitForDeferred( data[field].decryptPassword(window=self))) except password.NoMasterPassword: control.SetValue("") | def __FetchFormData(self, panelType, panel, data): # Pull data out of the "data" dictionary and stick it into the widgets: | b1d959dcb6ea3064db41fef843c06b239e066a69 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/9228/b1d959dcb6ea3064db41fef843c06b239e066a69/AccountPreferences.py | [
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self.smallTitleText.hide() | if self.smallTitleText: self.smallTitleText.hide() | def hideSmallTitleTextTask(self, task): assert(DistributedLevel.notify.debug("hideTitleTextTask()")) self.smallTitleText.hide() return Task.done | cbecb2d3ea0eb29e99a7cc85b3149fa6a807d8ab /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/8543/cbecb2d3ea0eb29e99a7cc85b3149fa6a807d8ab/DistributedLevel.py | [
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if self.logo: GL.glEnable (GL.GL_TEXTURE_2D) x, y = self.x, self.y w,h = self.width, self.height b = 16 GL.glBindTexture (GL.GL_TEXTURE_2D, self.logo_texid) GL.glColor4f (1, 1, 1, .5) GL.glTranslatef (0.0,0.0,0.1) GL.glBegin (GL.GL_QUADS) GL.glTexCoord2f (0.0,0.01), GL.glVertex2f (x+w-128-2*b, b) GL.glTexCoord2f (1.0,0.01), GL.glVertex2f (x+w-2*b, b) GL.glTexCoord2f (1.0,1.0), GL.glVertex2f (x+w-2*b, 128+b) GL.glTexCoord2f (0.0,1.0), GL.glVertex2f (x+w-2*b-128, 128+b) GL.glEnd() | def refresh (self): """ Refresh console texture """ if not self.active: return | fe073540bf8037e9f3becfb981aa7fc05baf437b /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/12213/fe073540bf8037e9f3becfb981aa7fc05baf437b/terminal.py | [
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add_forum_style() | add_forum_style(context) | def view(self, context): namespace = {} | 3b838d86710a06bfa99bd20af2526ac017d5816d /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/12681/3b838d86710a06bfa99bd20af2526ac017d5816d/forum.py | [
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self.hboxlayout38.addWidget(self.light_color_frame) | self.hboxlayout41.addWidget(self.light_color_frame) | def setupUi(self, UserPrefsDialog): UserPrefsDialog.setObjectName("UserPrefsDialog") UserPrefsDialog.resize(QtCore.QSize(QtCore.QRect(0,0,609,642).size()).expandedTo(UserPrefsDialog.minimumSizeHint())) | 30deb2219e016847d91b37e801c50b75fbd1c3cf /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/11221/30deb2219e016847d91b37e801c50b75fbd1c3cf/UserPrefsDialog.py | [
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from sys import getrefcount | def testStringWidth(self): from _rl_accel import stringWidthU from reportlab.pdfbase.pdfmetrics import _py_stringWidth, _py_getFont, registerFont from reportlab.pdfbase.ttfonts import TTFont from sys import getrefcount ttfn = 'Luxi-Serif' t1fn = 'Times-Roman' registerFont(TTFont(ttfn, "luxiserif.ttf")) ttf = _py_getFont(ttfn) t1f = _py_getFont(t1fn) testCp1252 = 'copyright %s trademark %s registered %s ReportLab! Ol%s!' % (chr(169), chr(153),chr(174), chr(0xe9)) enc='cp1252' senc = 'utf8' intern(senc) ts = 'ABCDEF\xce\x91\xce\xb2G' utext = 'ABCDEF\xce\x91\xce\xb2G'.decode('utf8') fontSize = 12. def tfunc(ts,fn,fontSize,enc): w1 = stringWidthU(ts,fn,fontSize,enc) w2 = _py_stringWidth(ts,fn,fontSize,enc) assert abs(w1-w2)<1e-10,"stringWidthU(%r,%r,%s,%r)-->%r != _py_stringWidth(...)-->%r" % (ts,fn,fontSize,enc,w1,w2) tfunc(testCp1252,t1fn,fontSize,enc) tfunc(ts,t1fn,fontSize,senc) tfunc(utext,t1fn,fontSize,senc) tfunc(ts,ttfn,fontSize,senc) tfunc(testCp1252,ttfn,fontSize,enc) tfunc(utext,ttfn,fontSize,senc) | 12e8e9cc55671e5cc6f4a8cba83406f53d6c3513 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/3878/12e8e9cc55671e5cc6f4a8cba83406f53d6c3513/test_rl_accel.py | [
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print " $Revision: 1.2 $" print " $Date: 2005/10/18 10:32:28 $" | print " $Revision: 1.3 $" print " $Date: 2005/10/18 16:01:15 $" | def showVersion(): print print "RCS" print " $Revision: 1.2 $" print " $Date: 2005/10/18 10:32:28 $" print " $Author: noel $" print " $Source: /home/noel/active/otl2tags/RCS/otl2tags.py,v $" print | 521585b86a523d00812deefb15f04d3be3543715 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/6154/521585b86a523d00812deefb15f04d3be3543715/otl2tags.py | [
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env={key: value}) | env=env) | def test_undecodable_env(self): for key, value in (('test', 'abc\uDCFF'), ('test\uDCFF', '42')): value_repr = repr(value).encode("ascii") | edb0535ee695c17a8ed85b95ab57354a27b1653b /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/12029/edb0535ee695c17a8ed85b95ab57354a27b1653b/test_subprocess.py | [
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for filename in FileUtilities.children_in_directory(dirname, False): | for filename in children_in_directory(dirname, False): | def list_files(self): # browser cache if self.options["cache"][1]: dirs = [ os.path.expanduser(self.profile_dir + "cache4/"), \ os.path.expanduser(self.profile_dir + "opcache/") ] for dirname in dirs: for filename in FileUtilities.children_in_directory(dirname, False): yield filename | 905c2a6f962a355b11ab87c2064796c54c6c1af5 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/7853/905c2a6f962a355b11ab87c2064796c54c6c1af5/CleanerBackend.py | [
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""" result = shellCall(0,'runsvctrl %s '+DIRACROOT+'/startup/%s %s' % (mode,system,component) ) | """ template = 'runsvctrl %s '+DIRACROOT+'/startup/%s_%s' result = shellCall(0,template % (mode,system,component) ) | def __startComponent(self,system,component,mode): """ Start the specified component for running with the runsv daemon """ result = shellCall(0,'runsvctrl %s '+DIRACROOT+'/startup/%s %s' % (mode,system,component) ) # Check the runsv status start = time.time() while (time.time()-10) < start: result = self.__getRunitComponentStatus(['%s_%s' % (system,component)]) if not result['OK']: return S_ERROR('Failed to start the component %s_%s' % (system,component) ) if result['Value']['%s_%s' % (system,component)]['RunitStatus'] == "Run": return S_OK("Run") time.sleep(1) # Final check result = self.__getRunitComponentStatus(['%s_%s' % (system,component)]) if not result['OK']: return S_ERROR('Failed to start the component %s_%s' % (system,component) ) return S_OK(result['Value']['%s_%s' % (system,component)]['RunitStatus']) | 0de98dd4dbd644d0526d05f1d541804cf16ccb12 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/12864/0de98dd4dbd644d0526d05f1d541804cf16ccb12/SystemAdministratorHandler.py | [
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date = datetime.date(*time.strptime(test, self.display_format)[:3]) | date = datetime.date(*time.strptime(text, self.display_format)[:3]) | def value_from_text(self, model, text): if not text: return False try: date = datetime.date(*time.strptime(test, self.display_format)[:3]) except: return False return common.datetime_strftime(date, self.server_format) | 4a00f8bf01c1e9d400670dea71a63f8627639440 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/9151/4a00f8bf01c1e9d400670dea71a63f8627639440/parser.py | [
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for line in self.gen_score_map(self.diff_score_map) : self.context.add_line(line) | map(lambda line: self.context.add_line(line), self.gen_score_map(self.diff_score_map)) | def do_some_calc(self): if self.count <= 0: self.add_line("Game Count: %d" % (self.count)) return | ea21cf2f227e6680d6e79971a408072ed68a6347 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/600/ea21cf2f227e6680d6e79971a408072ed68a6347/process.py | [
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self.debug("descend(%s, %s)" % (i1, i2)) | i2_str = str(i2) if isinstance(i2, Comparator): i2_str = i2.render_debug() self.debug("descend(%s, %s)" % (i1, i2_str)) | def descend(self, i1, i2): self.debug("descend(%s, %s)" % (i1, i2)) self.depth += 1 res = super(DebugComparison, self).descend(i1, i2) self.depth -= 1 self.debug(res) return res | c959154be0d99a1cfd8892827f469978251ed3de /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/873/c959154be0d99a1cfd8892827f469978251ed3de/deep.py | [
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from ctypes import byref, sizeof | from ctypes import byref | def test_cw_strings(self): from ctypes import byref, sizeof try: from ctypes import c_wchar, c_wchar_p except ImportError: | 061b14a4a1f64532bfb4d716849ae662c09da62a /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/8546/061b14a4a1f64532bfb4d716849ae662c09da62a/test_parameters.py | [
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return ListOfArithmeticTypes() | return ArithmeticList() | def concat_fields(*fields): if not fields: return ListOfArithmeticTypes() result = fields[0][:] for f in fields[1:]: result.extend(f) return result | 26b00e61b9d12787955b744e839ffed23b4c2c8d /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/12871/26b00e61b9d12787955b744e839ffed23b4c2c8d/arithmetic_container.py | [
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patt = re.compile("^\s+[A-Z\s]+ ATTRIBUTES\s*$") | patt = re.compile("^\s+[A-Z/\s-]+ATTRIBUTES\s*$") m = patt.match(s) if(m): print "Table Name", s return True patt = re.compile("^\s+[A-Za-z\s]+Attributes\s*$") m = patt.match(s) if(m): print "Table Name", s return True patt = re.compile("^\s+[A-Z\s]+MODULE\s*$") | def IsTableName(self,s): patt = re.compile("^\s+[A-Z\s]+ ATTRIBUTES\s*$") #MACRO/MODULE m = patt.match(s) if(m): print "Table Name", s return True return False | 1d98d58968a693abcf40bf18e15775b8ec3b67d8 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/13995/1d98d58968a693abcf40bf18e15775b8ec3b67d8/ParseAttributes.py | [
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content = '<p>%s</p>' % e.text | content = '<p>%s</p>' % cgi.escape(e.text) | def _build_newspages(self,messages): basefile = {u'de allmnna domstolarna': 'allmanna', u'frvaltningsdomstolarna': 'forvaltning', u'Arbetsdomstolen': 'ad', u'Marknadsdomstolen': 'md', u'Migrationsverdomstolen': 'mig', u'Miljverdomstolen': 'mod'} | 5bcaf99fdd88fc1ba95481324c9dad4d2a51f017 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/4027/5bcaf99fdd88fc1ba95481324c9dad4d2a51f017/DV.py | [
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debug(3, "mkdirhier(%s)" % dir) | bb.debug(3, "mkdirhier(%s)" % dir) | def mkdirhier(dir): """Create a directory like 'mkdir -p', but does not complain if directory already exists like os.makedirs """ debug(3, "mkdirhier(%s)" % dir) try: os.makedirs(dir) debug(2, "created " + dir) except OSError, e: if e.errno != 17: raise e | 8f83be3338d7aef4b6fcef5ea89dc69fa587c1f6 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/8123/8f83be3338d7aef4b6fcef5ea89dc69fa587c1f6/utils.py | [
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test.do_test(tbasic_loopback, [vm, send_pt, recv_pt], data) | test.do_test(tbasic_loopback, [vm, send_pt, recv_pt, data], True) | def test_smoke(test, vm, consoles, params): """ Virtio console smoke test. | 4573cdbfbd7c20e3f65127889fc5f1151a85f428 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/10349/4573cdbfbd7c20e3f65127889fc5f1151a85f428/virtio_console.py | [
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elif xopt == 'year': | elif xkey == 'year': | def plot_data(tempo_results, xkey, ykey, postfit=True, prefit=False, \ interactive=True, mark_peri=False, show_legend=True): # figure out what should be plotted # True means to plot postfit # False means to plot prefit if postfit and prefit: to_plot_postfit = [False, True] elif postfit and not prefit: to_plot_postfit = [True] elif not postfit and prefit: to_plot_postfit = [False] else: raise ValueError("At least one of prefit and postfit must be True.") subplot = 1 numsubplots = len(to_plot_postfit) global axes axes = [] handles = [] labels = [] for usepostfit in to_plot_postfit: TOAcount = 0 # All subplots are in a single column if subplot == 1: axes.append(plt.subplot(numsubplots, 1, subplot)) else: axes.append(plt.subplot(numsubplots, 1, subplot, sharex=axes[0])) for lo,hi in tempo_results.freqbands: freq_label = get_freq_label(lo, hi) resids = tempo_results.residuals[freq_label] xlabel, xdata = resids.get_xdata(xkey) ylabel, ydata, yerr = resids.get_ydata(ykey, usepostfit) if len(xdata): # Plot the residuals handle = plt.errorbar(xdata, ydata, yerr=yerr, fmt='.', \ label=freq_label, picker=5) if subplot == 1: handles.append(handle[0]) labels.append(freq_label) TOAcount += xdata.size # Finish off the plot plt.axhline(0, ls='--', label="_nolegend_", c='k', lw=0.5) axes[-1].ticklabel_format(style='plain', axis='x') if mark_peri and hasattr(tempo_results.outpar, 'BINARY'): # Be sure to check if pulsar is in a binary # Cannot mark passage of periastron if not a binary if usepostfit: binpsr = binary_psr.binary_psr(tempo_results.outpar.FILE) else: binpsr = binary_psr.binary_psr(tempo_results.inpar.FILE) xmin, xmax = plt.xlim() mjd_min = tempo_results.min_TOA mjd_max = tempo_results.max_TOA guess_mjds = np.arange(mjd_max + binpsr.par.PB, \ mjd_min - binpsr.par.PB, -binpsr.par.PB) for mjd in guess_mjds: peri_mjd = binpsr.most_recent_peri(float(mjd)) if xopt == 'mjd': plt.axvline(peri_mjd, ls=':', label='_nolegend_', c='k', lw=0.5) elif xopt == 'year': print "plotting peri passage" plt.axvline(mjd_to_year(peri_mjd), ls=':', label='_nolegend_', c='k', lw=0.5) plt.xlim((xmin, xmax)) plt.xlabel(xlabel) plt.ylabel(ylabel) if usepostfit: plt.title("Postfit Redisuals (Number of TOAs: %d)" % TOAcount) else: plt.title("Prefit Redisuals (Number of TOAs: %d)" % TOAcount) subplot += 1 if numsubplots > 1: # Increase spacing between subplots. plt.subplots_adjust(hspace=0.25) # Write name of input files used for timing on figure if interactive: fntext = "TOA file: %s, Parameter file: %s" % \ (tempo_results.intimfn, tempo_results.inparfn) figure_text = plt.figtext(0.01, 0.01, fntext, verticalalignment='bottom', \ horizontalalignment='left') if show_legend: leg = plt.figlegend(handles, labels, 'upper right') leg.legendPatch.set_alpha(0.5) | 965bbd0ee9ee8694f9c3a6acaac793dd676ae9cf /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/3485/965bbd0ee9ee8694f9c3a6acaac793dd676ae9cf/pyplotres.py | [
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graphs.append(tag('img', _class='graph', src="graph/temperature:%s" % length)) | graphs.append('temperature') | def renderInterval(self, length): if not length: return self.renderLatest() graphs = [] | 714af92c4e55d8eaedfe268d172fdad7a6d42f24 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/6757/714af92c4e55d8eaedfe268d172fdad7a6d42f24/web.py | [
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sage: magma(E) Elliptic Curve defined by y^2 = x^3 + 2*x + 5 over GF(41) | def _magma_init_(self): """ Return a Magma command that creates this curve. | 705e8dbdf0cc4cef19f04abae7e44b2fe99c618c /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/9890/705e8dbdf0cc4cef19f04abae7e44b2fe99c618c/ell_finite_field.py | [
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if not self.idExists(): | if not self.ufeed.idExists(): | def feedparser_errback (self, e): if not self.idExists(): return print "Error updating feed: %s: %s" % (self.url, e) self.updating = False self.ufeed.signalChange() self.scheduleUpdateEvents(-1) | f737b0fec25840951c07d52c96224365c027c848 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12354/f737b0fec25840951c07d52c96224365c027c848/feed.py | [
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class hm_upperlimit_job(pipeline.CondorDAGJob): | class far_plot_job(pipeline.CondorDAGJob): | def __init__(self, cp, tag_base='HM_UPPERLIMIT'): """ """ self.__prog__ = 'hm_upperlimit' self.__executable = string.strip(cp.get('condor','hm_upperlimit')) self.__universe = "vanilla" pipeline.CondorDAGJob.__init__(self,self.__universe,self.__executable) self.add_condor_cmd('getenv','True') self.tag_base = tag_base self.add_condor_cmd('environment',"KMP_LIBRARY=serial;MKL_SERIAL=yes") self.set_sub_file(tag_base+'.sub') self.set_stdout_file('logs/'+tag_base+'-$(macroid)-$(process).out') self.set_stderr_file('logs/'+tag_base+'-$(macroid)-$(process).err') | e1cd4fc183f6c74e7477567f8b3addc75175e34e /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/5758/e1cd4fc183f6c74e7477567f8b3addc75175e34e/highmass_post_process.py | [
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g = G(self.gens()[0]) | g = G(self.gens()[0]) | def B(self): G = self.group() | c4436c8abac791e198815503e74478ec5cbb6c54 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/9890/c4436c8abac791e198815503e74478ec5cbb6c54/cubegroup.py | [
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if not html_errors: return [page] return self.add_error(page, html_errors) | if html_errors: page = self.add_error(page, html_errors)[0] headers.remove( ('Content-Length', str(wsgilib.header_value(headers, 'content-length')))) headers.append(('Content-Length', str(len(page)))) return [page] | def writer_start_response(status, headers, exc_info=None): response.extend((status, headers)) start_response(status, headers, exc_info) return output.write | d07f87172851fbb876287cee858e092c639f7749 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/2097/d07f87172851fbb876287cee858e092c639f7749/wdg_validate.py | [
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code = ['if (evtag_unmarshal_string(%s, %s, &%s->%s_data) == -1)' % ( | code = ['if (evtag_unmarshal_string(%s, %s, &%s->%s_data) == -1) {' % ( | def CodeUnmarshal(self, buf, tag_name, var_name): code = ['if (evtag_unmarshal_string(%s, %s, &%s->%s_data) == -1)' % ( buf, tag_name, var_name, self._name), ' return (-1);'] return code | 32acc283c8ae44d9c4e306dbaf6a9fead5e71952 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/13048/32acc283c8ae44d9c4e306dbaf6a9fead5e71952/event_rpcgen.py | [
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c = self.read(1) line = line + c if c=='\n' or c=="": break return line | c = self.read(readsize) i = string.find(c, '\n') if i >= 0 or c == '': bufs.append(c[:i]) self._unread(c[i+1:]) return string.join(bufs, '') bufs.append(c) readsize = readsize * 2 | def readline(self): | f1409e06ab5e40cc3e2a8762690b55a092008400 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/f1409e06ab5e40cc3e2a8762690b55a092008400/gzip.py | [
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self.assertRaises(WindowsError, os.remove, test_support.TESTFN) | self.assertRaises(OSError, os.remove, test_support.TESTFN) | def test_remove(self): self.assertRaises(WindowsError, os.remove, test_support.TESTFN) | 33bd587d158048f44b4958503cb4f2156300e788 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/6934/33bd587d158048f44b4958503cb4f2156300e788/test_os.py | [
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insert_connection = atom.service.AtomService._CreateConnection(self, uri, | insert_connection = self.handler._CreateConnection(self, uri, | def Put(self, data, uri, extra_headers=None, url_params=None, escape_params=True, redirects_remaining=3, media_source=None, converter=None): """Updates an entry at the given URI. Args: data: string, ElementTree._Element, or xml_wrapper.ElementWrapper The XML containing the updated data. uri: string A URI indicating entry to which the update will be applied. Example: '/base/feeds/items/ITEM-ID' extra_headers: dict (optional) HTTP headers which are to be included. The client automatically sets the Content-Type, Authorization, and Content-Length headers. url_params: dict (optional) Additional URL parameters to be included in the URI. These are translated into query arguments in the form '&dict_key=value&...'. Example: {'max-results': '250'} becomes &max-results=250 escape_params: boolean (optional) If false, the calling code has already ensured that the query will form a valid URL (all reserved characters have been escaped). If true, this method will escape the query and any URL parameters provided. converter: func (optional) A function which will be executed on the server's response. Often this is a function like GDataEntryFromString which will parse the body of the server's response and return a GDataEntry. | 2fc3c8b5e04f49e7854d86afdf5c528572665ee2 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/6580/2fc3c8b5e04f49e7854d86afdf5c528572665ee2/service.py | [
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"num_clust_trigs": "int_4s", "ds2_H1H2": "real_4", "ds2_H1L1": "real_4", "ds2_H2L1": "real_4", | "num_clust_trigs": "int_4s", "ds2_H1H2": "real_4", "ds2_H1L1": "real_4", "ds2_H2L1": "real_4", | def get_ifos(self): return instrument_set_from_ifos( self.ifos ) | 259430d1131e692c0fa5c3351cc4e4e71c032412 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/3589/259430d1131e692c0fa5c3351cc4e4e71c032412/lsctables.py | [
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if config.get('msvs_quote_cmd', True): | if quote_cmd: | def _PrepareActionRaw(config, cmd, cygwin_shell, has_input_path): if cygwin_shell: # Find path to cygwin. cygwin_dir = _FixPath(config.get('msvs_cygwin_dirs', ['.'])[0]) # Prepare command. direct_cmd = cmd direct_cmd = [i.replace('$(IntDir)', '`cygpath -m "${INTDIR}"`') for i in direct_cmd] direct_cmd = [i.replace('$(OutDir)', '`cygpath -m "${OUTDIR}"`') for i in direct_cmd] if has_input_path: direct_cmd = [i.replace('$(InputPath)', '`cygpath -m "${INPUTPATH}"`') for i in direct_cmd] direct_cmd = ['"%s"' % i for i in direct_cmd] direct_cmd = [i.replace('"', '\\"') for i in direct_cmd] #direct_cmd = gyp.common.EncodePOSIXShellList(direct_cmd) direct_cmd = ' '.join(direct_cmd) # TODO(quote): regularize quoting path names throughout the module cmd = ( '"$(ProjectDir)%(cygwin_dir)s\\setup_env.bat" && ' 'set CYGWIN=nontsec&& ') if direct_cmd.find('NUMBER_OF_PROCESSORS') >= 0: cmd += 'set /a NUMBER_OF_PROCESSORS_PLUS_1=%%NUMBER_OF_PROCESSORS%%+1&& ' if direct_cmd.find('INTDIR') >= 0: cmd += 'set INTDIR=$(IntDir)&& ' if direct_cmd.find('OUTDIR') >= 0: cmd += 'set OUTDIR=$(OutDir)&& ' if has_input_path and direct_cmd.find('INPUTPATH') >= 0: cmd += 'set INPUTPATH=$(InputPath) && ' cmd += ( 'bash -c "%(cmd)s"') cmd = cmd % {'cygwin_dir': cygwin_dir, 'cmd': direct_cmd} return cmd else: if config.get('msvs_quote_cmd', True): # Support a mode for using cmd directly. # Convert any paths to native form (first element is used directly). # TODO(quote): regularize quoting path names throughout the module direct_cmd = [cmd[0]] + ['"%s"' % _FixPath(i) for i in cmd[1:]] else: direct_cmd = cmd # Collapse into a single command. return ' '.join(direct_cmd) | 4289bfbe7bd08f28a48e04f60f4d65c4b81dbe93 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/6220/4289bfbe7bd08f28a48e04f60f4d65c4b81dbe93/msvs.py | [
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"""Return a string representing the object\'s value in the format: March 1, 1997 1:45 pm""" | """ Return a string representing the object's value in the format: March 1, 1997 1:45 pm Permission -- Always available """ | def fCommon(): """Return a string representing the object\'s value in the format: March 1, 1997 1:45 pm""" | b8c350cc5b36f5ce907db3ed0e2c54460ed7de1c /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/9658/b8c350cc5b36f5ce907db3ed0e2c54460ed7de1c/DateTime.py | [
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cr.execute('select count(*) from res_users where id=%s and password=%s', (int(uid), passwd)) | if passwd: cr.execute('select count(*) from res_users where id=%s and password=%s', (int(uid), passwd)) else: cr.execute('select count(*) from res_users where id=%s and password is null', (int(uid),)) | def check(db, uid, passwd): if _uid_cache.get(db, {}).get(uid) == passwd: return True cr = pooler.get_db(db).cursor() cr.execute('select count(*) from res_users where id=%s and password=%s', (int(uid), passwd)) res = cr.fetchone()[0] cr.close() if not bool(res): raise Exception('AccessDenied') if res: if _uid_cache.has_key(db): ulist = _uid_cache[db] ulist[uid] = passwd else: _uid_cache[db] = {uid:passwd} return bool(res) | 655eada141079901ef8fb16eea5890a92db19608 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/7397/655eada141079901ef8fb16eea5890a92db19608/security.py | [
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continue | ke.uChar.UnicodeChar = u(chr(cnum)) ke.wVirtualKeyCode = ctypes.windll.user32.VkKeyScanA(cnum + 96) ke.dwControlKeyState = LEFT_CTRL_PRESSED | def write_plain (self, text): # {{{ | 1598ce648f476a75fa26c90e9bf3aa46998bb2b2 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/6680/1598ce648f476a75fa26c90e9bf3aa46998bb2b2/conque_sole_subprocess.py | [
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elts[i].style.display = ((cmd=="hide private")?"none":"block"); | elts[i].style.display = ((cmd && cmd.substr(0,4)=="hide")?"none":"block"); | def write_javascript(self, directory): jsfile = open(os.path.join(directory, 'epydoc.js'), 'w') print >> jsfile, self.TOGGLE_PRIVATE_JS print >> jsfile, self.GET_COOKIE_JS print >> jsfile, self.SET_FRAME_JS print >> jsfile, self.HIDE_PRIVATE_JS print >> jsfile, self.TOGGLE_CALLGRAPH_JS print >> jsfile, html_colorize.PYSRC_JAVASCRIPTS print >> jsfile, self.GET_ANCHOR_JS print >> jsfile, self.REDIRECT_URL_JS jsfile.close() | df8fdcdaedad9bb890428949f435cf2d4e45e05d /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/3512/df8fdcdaedad9bb890428949f435cf2d4e45e05d/html.py | [
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if err[0] == errno.EINTR: | err_type = err.message if err_type == errno.EINTR: | def _read(self): buf = '' # put in a loop so that we retry on transient errors while True: try: buf = self._ssl.read(self._bufsize) except socket.sslerror as err: if (err[0] == socket.SSL_ERROR_WANT_READ or err[0] == socket.SSL_ERROR_WANT_WRITE): continue if (err[0] == socket.SSL_ERROR_ZERO_RETURN or err[0] == socket.SSL_ERROR_EOF): break raise except socket.error as err: if err[0] == errno.EINTR: continue if err[0] == errno.EBADF: # XXX socket was closed? break raise else: break return buf | 6f8fe151da16f43fc5d0c5167fc3d9432f993f70 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/8546/6f8fe151da16f43fc5d0c5167fc3d9432f993f70/httplib.py | [
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def __init__(data = None) | def __init__(data = None): | def __init__(data = None) if data == None: quickfix.StringField.__init__(self, 286) else quickfix.StringField.__init__(self, 286, data) | 484890147d4b23aac4b9d0e85e84fceab7e137c3 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/8819/484890147d4b23aac4b9d0e85e84fceab7e137c3/quickfix_fields.py | [
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def alert(self, ctx): if len(ctx.authtype) > 1: ctx.Set("alert.classification.text", "Multiple authentication methods") ctx.Set("alert.correlation_alert.name", "Multiple authentication methods") ctx.Set("alert.assessment.impact.severity", "medium") ctx.Set("alert.assessment.impact.description", "Multiple ways of authenticating a single user have been found over SSH. If passphrase is the only allowed method, make sure you disable passwords.") ctx.alert() | def alert(self, ctx): if len(ctx.authtype) > 1: ctx.Set("alert.classification.text", "Multiple authentication methods") ctx.Set("alert.correlation_alert.name", "Multiple authentication methods") ctx.Set("alert.assessment.impact.severity", "medium") ctx.Set("alert.assessment.impact.description", "Multiple ways of authenticating a single user have been found over SSH. If passphrase is the only allowed method, make sure you disable passwords.") ctx.alert() | 1f4c6bb0cac0876cc9b19dc12d703fc8e53e7151 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/3386/1f4c6bb0cac0876cc9b19dc12d703fc8e53e7151/opensshauth.py | [
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adopt_init_args(self, locals(), hide=0001) | def __init__(self, peak_list, special_position_settings, general_positions_only=00000, min_cross_distance=None, max_clusters=None): adopt_init_args(self, locals(), hide=0001) if (min_cross_distance is None): min_cross_distance = special_position_settings.min_distance_sym_equiv() self._gridding = peak_list.gridding() self._peak_list_indices = flex.size_t() self._peak_list_index = 0 self._sites = flex.vec3_double() self._heights = flex.double() self._fixed_site_indices = flex.size_t() | 4d341582ea0f0849de55988e732bceb2b4337369 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/696/4d341582ea0f0849de55988e732bceb2b4337369/maptbx.py | [
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@version: 1.4 | @version: 1.5 | def createColumns(self): self.InsertSizedColumn(0, "Index") self.InsertSizedColumn(1, "Filename", min=100, max=200) self.InsertSizedColumn(2, "Size", wx.LIST_FORMAT_RIGHT, min=30, greedy=True) self.InsertSizedColumn(3, "Mode", max="MMM") self.InsertSizedColumn(4, "Description", min=100) self.InsertSizedColumn(5, "URL", ok_offscreen=True) self.InsertSizedColumn(6, "Owner", fixed=50) | 055ab42b9c1c7f05265ee06a881bbc1daa13c924 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/11522/055ab42b9c1c7f05265ee06a881bbc1daa13c924/column_autosize.py | [
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self.value = [] valueLen = len(self.value) | valueLen = 0 else: valueLen = len(self.value) | def _keyreleased(self, widget, key_event, *ignore): """ A key has been released: the user might be wanting to insert a row... """ # bugs will come to haunt you at night if you delete this # and don't fix the socking but that is elsewhere # (I whish at least where does he hide, the little frak) if self.value is None: self.value = [] # conditions that assert we're in the fscking last row of data. valueLen = len(self.value) last = self.value is None \ or valueLen == 0 \ or self.index == valueLen-1 # print self.index, `self.value`, last if key_event.keyval == gtk.keysyms.Down and last and \ self.cls is not None and self._tvdatalen == valueLen: # right conditions; insert a new row in the TreeView # without changing the value yet. self._tvdata.append(['' for j in self.columns]) self._tvdatalen += 1 self.index = valueLen # print 'making new', self.index # print self._tv.get_cursor() return False | acde4da04a5f0eca89a2514b9657fd0998d30741 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/2750/acde4da04a5f0eca89a2514b9657fd0998d30741/grid.py | [
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if self._inSack is None: | if not self.pkgSackPackages: pass elif self._inSack is None: | def getNewProvides(self, name, flag=None, version=(None, None, None)): """return dict { packages -> list of matching provides } searches in packages to be installed""" result = { } if self._inSack is None: for pkg, hits in self.pkgSack.getProvides(name, flag, version).iteritems(): if self.getMembersWithState(pkg.pkgtup, TS_INSTALL_STATES): result[pkg] = hits else: for pkg, hits in self._inSack.getProvides(name, flag, version).iteritems(): result[pkg] = hits result.update(self.localSack.getProvides(name, flag, version)) return result | 9d83cabc986283a64d32f4b6983771f3b12ec880 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/5445/9d83cabc986283a64d32f4b6983771f3b12ec880/transactioninfo.py | [
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if not os.path.isdir(subdir) or not subdir.startswith("_"): | if not os.path.isdir(subdir) or not dirname.startswith("_"): | def buildPackages(self): for (pack, (regex_single, regex_split)) in self.packageRegex.items(): for dirname in os.listdir(self.distDir): subdir = os.path.join(self.distDir, dirname) # Ignore non-dir directory members and non-gettor dirs if not os.path.isdir(subdir) or not subdir.startswith("_"): continue for filename in os.listdir(subdir): # Splitfile hacks. XXX: Refactor if re.compile(regex_split).match(filename): if not self.buildSplitFiles(pack, subdir, filename): log.error("Could not build split files packages") return False if re.compile(regex_single).match(filename): file = os.path.join(subdir, filename) ascfile = file + ".asc" zpack = pack + ".z" zipFileName = os.path.join(self.packDir, zpack) # If .asc file is there, build Zip file if os.access(ascfile, os.R_OK): zip = zipfile.ZipFile(zipFileName, "w") zip.write(file, os.path.basename(file)) zip.write(ascfile, os.path.basename(ascfile)) zip.close() self.packageList[pack] = zipFileName break if len(self.packageList) > 0: return True else: log.error("Failed to build packages") return False | 9baa53cdb95816443cdc07209facfae4f8a803b8 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/7360/9baa53cdb95816443cdc07209facfae4f8a803b8/packages.py | [
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""" Install OpenAlea.Deploy with setuptools""" try: from setuptools.command.easy_install import main except ImportError: from easy_install import main main(['-f', ALEA_PI_URL, "openalea.deploy"]) | """ Install OpenAlea.Deploy with setuptools""" from pkg_resources import require require('setuptools') from setuptools.command.easy_install import main try: main(['-f', ALEA_PI_URL, "openalea.deploy"]) except: print "Ex" | def install_deploy(): """ Install OpenAlea.Deploy with setuptools""" try: from setuptools.command.easy_install import main except ImportError: from easy_install import main main(['-f', ALEA_PI_URL, "openalea.deploy"]) | cf1e5e0e4ac09f9ca2a07feeed945694c5e24050 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/4914/cf1e5e0e4ac09f9ca2a07feeed945694c5e24050/ez_alea_setup.py | [
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if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) | def buildChildren(self, child_, nodeName_, from_subclass=False): if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) pass | 9c12e50d449fa27d6f8f3415ece228ae97bb0266 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/14016/9c12e50d449fa27d6f8f3415ece228ae97bb0266/_nexml.py | [
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print startNeighbor, endNeighbor, edge | def copyMapContents(sourceMap, destMap, edgeTransform = None): """copyMapContents(sourceMap, destMap, edgeTransform = None) Adds all nodes and edges of sourceMap to the destMap. The sigma order is preserved. Thus, it is an error to copy the contents of a graph - not sourceMap.edgesSorted() - into a map with destMap.edgesSorted(). You can pass an optional edgeTransform to map edges to other Polygons: edgeTransform may be a callable that is called with Edge instances and must return an object suitable as the geometry parameter of GeoMap.addEdge. Returns a tuple (destMap, nodes, edges), where nodes and edges are lists that map source nodes/edges onto their new counterparts in destMap. If destMap is None, a new GeoMap of the same size is created and returned.""" if destMap == None: destMap = sourceMap.__class__(sourceMap.imageSize()) if sourceMap.edgesSorted(): destMap.sortEdgesDirectly() assert sourceMap.edgesSorted() or not destMap.edgesSorted(), \ "refraining from inserting unsorted edges into sorted map!" nodes = [None] * sourceMap.maxNodeLabel() # for better edgeTransform support, nodes are added on-the-fly now edges = [None] * sourceMap.maxEdgeLabel() for edge in sourceMap.edgeIter(): geometry = edge if edgeTransform: geometry = edgeTransform(geometry) startNeighbor = nodes[edge.startNodeLabel()] if startNeighbor == None: startNeighbor = destMap.addNode(geometry[0]) nodes[edge.startNodeLabel()] = startNeighbor elif not startNeighbor.isIsolated(): if edgeTransform: assert geometry[0] == startNeighbor.position(), "copyMapContents: edgeTransform leads to inconsistent node positions!" neighbor = edge.dart() while neighbor.nextSigma().edgeLabel() > edge.label() \ or neighbor.label() == -edge.label(): pass assert neighbor.edgeLabel() < edge.label(), \ "since !startNeighbor.isIsolated(), there should be an (already handled) edge with a smaller label in this orbit!" startNeighbor = edges[neighbor.edgeLabel()].dart() if neighbor.label() < 0: startNeighbor.nextAlpha() endNeighbor = nodes[edge.endNodeLabel()] if endNeighbor == None: endNeighbor = destMap.addNode(geometry[-1]) nodes[edge.endNodeLabel()] = endNeighbor elif not endNeighbor.isIsolated(): if edgeTransform: assert geometry[-1] == endNeighbor.position(), "copyMapContents: edgeTransform leads to inconsistent node positions!" neighbor = edge.dart().nextAlpha() while neighbor.nextSigma().edgeLabel() > edge.label() \ or neighbor.label() == edge.label(): pass assert neighbor.edgeLabel() < edge.label(), \ "since !endNeighbor.isIsolated(), there should be an (already handled) edge with a smaller label in this orbit!" endNeighbor = edges[neighbor.edgeLabel()].dart() if neighbor.label() < 0: endNeighbor.nextAlpha() print startNeighbor, endNeighbor, edge edges[edge.label()] = destMap.addEdge( startNeighbor, endNeighbor, geometry) print # now add isolated nodes: for node in sourceMap.nodeIter(): if not nodes[node.label()]: nodes[node.label()] = destMap.addNode(node.position()) return destMap, nodes, edges | 897f5acda25a0eeae052b9c2a7a615550585942e /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/10394/897f5acda25a0eeae052b9c2a7a615550585942e/maputils.py | [
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if y is None: self.n_skipped += 1 else: self.n_skipped = 0 factor = 2.0**self.n_skipped**2.0 this_R = factor*self.R | def step2__calculate_a_posteri(self,xhatminus,Pminus,y=None): """ y represents the observation for this time-step """ dot = numpy.dot # shorthand inv = numpy.linalg.inv ############################################ # incorporate observation | e357db73f8375a2ce3cd9f4a905ad06bb221a823 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/14900/e357db73f8375a2ce3cd9f4a905ad06bb221a823/adskalman.py | [
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global __config, configDefaults | global _config, configDefaults | def load(file): """ Returns a dictionary containing the current configuration information, read from the specified .INI file. """ global __config, configDefaults try: if not os.path.exists(file): __WriteINI(file) __config = __ReadINI(file, configDefaults) except: print "ERROR: could not load config file %s" % file sys.exit(-1) return __config | 57a4a624e1c74ec183a41def83450e16af01aebd /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/13130/57a4a624e1c74ec183a41def83450e16af01aebd/configFile.py | [
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def __init__(self, poly, prec, halt, print_mode, names): EisensteinExtensionGeneric.__init__(self, poly, prec, print_mode, names, EisensteinExtensionCappedRelativeElement) | def __init__(self, prepoly, poly, prec, halt, print_mode, shift_seed, names): unram_prec = (prec + poly.degree() - 1) // poly.degree() ntl_poly = ntl_ZZ_pX([a.lift() for a in poly.list()], poly.base_ring().prime()**unram_prec) shift_poly = ntl_ZZ_pX([a.lift() for a in shift_seed.list()], shift_seed.base_ring().prime()**unram_prec) if unram_prec <= 30: self.prime_pow = PowComputer_ext_maker(poly.base_ring().prime(), unram_prec, unram_prec, prec, True, ntl_poly, "small", "e", shift_poly) else: self.prime_pow = PowComputer_ext_maker(poly.base_ring().prime(), 30, unram_prec, prec, True, ntl_poly, "big", "e", shift_poly) self._shift_seed = shift_seed self._pre_poly = prepoly EisensteinExtensionGeneric.__init__(self, poly, prec, print_mode, names, pAdicZZpXCRElement) | def __init__(self, poly, prec, halt, print_mode, names): EisensteinExtensionGeneric.__init__(self, poly, prec, print_mode, names, EisensteinExtensionCappedRelativeElement) | 3f749fc2d07ac2b736b4a6e08cfee62c70e3d53b /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/9890/3f749fc2d07ac2b736b4a6e08cfee62c70e3d53b/padic_extension_leaves.py | [
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dnaStrand = selobj.molecule.parent_node_of_class(self.win.assy.DnaStrand) if dnaStrand: chunkList = [dnaStrand] | dnaStrandOrSegment = selobj.molecule.parent_node_of_class( self.win.assy.DnaStrandOrSegment) if dnaStrandOrSegment: chunkList = [dnaStrandOrSegment] | def _get_objects_to_highlight(self, selobj, hiColor1, hiColor2): """ Returns a python dictionary with objects to be drawn highlighted as its keys and highlight color as their corresponding values. The object to be highlighted is determined based the current graphics mode using the glpane.selobj. The subclasses can override this method to return objects to be highlighted in that particular graphics mode. @param selobj: GLPane.selobj (object under cursoe which can be registered as a GLPane.selobj @param hiColor1 : highlight color 1 @paramhiColor2: alternative highlight color. Example: If there are two chunks that need to be highlighted, one chunk gets hiColor1 and other gets hiColor2. @TODO: - may be hiColors should be in a list to make it more general @return: dictionary of objects to be highlighted. @rtype: dict @see: self._is_dnaGroup_highlighting_enabled() @see: self.drawHighlightedChunk() @see : self.drawHighlightedObjectUnderMouse() | 9b62a45032a66e2bb994ed6192351ad80ddd1d98 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/11221/9b62a45032a66e2bb994ed6192351ad80ddd1d98/SelectChunks_GraphicsMode.py | [
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kernel_fetch_cmd = "wget -q %s/isolinux/%s" % (self.url, self.kernel) initrd_fetch_cmd = "wget -q %s/isolinux/%s" % (self.url, self.initrd) | kernel_fetch_cmd = "wget -q %s/%s/%s" % (self.url, self.boot_path, os.path.basename(self.kernel)) initrd_fetch_cmd = "wget -q %s/%s/%s" % (self.url, self.boot_path, os.path.basename(self.initrd)) | def setup_url(self): """ Download the vmlinuz and initrd.img from URL. """ print "Downloading the vmlinuz and initrd.img" os.chdir(self.image_path) | 295f8a35ea41100c5c7582c4a6b666d666dbf25a /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/12268/295f8a35ea41100c5c7582c4a6b666d666dbf25a/unattended.py | [
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self._parseheaders(root, fp) | firstbodyline = self._parseheaders(root, fp) | def parse(self, fp, headersonly=False): """Create a message structure from the data in a file. | fd75ad1c4ab511c4bd028c66a273ed9117440b57 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/12029/fd75ad1c4ab511c4bd028c66a273ed9117440b57/Parser.py | [
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sel.select_path(path[0]) | sel.select_path(path[1]) | def on_treeview_row_clicked(self, tv, evt): """ Called when the user clicked on a treeview element. """ try: if evt.button == 3: path = tv.get_path_at_pos(int(evt.x), int(evt.y)) sel = tv.get_selection() (rows, _) = sel.get_selected_rows() if path[0] not in rows[1]: sel.unselect_all() sel.select_path(path[0]) tv.grab_focus() self.popup.popup(None, None, None, evt.button, evt.time) return True coords = evt.get_coords() path, c, x, y = tv.get_path_at_pos(int(coords[0]), int(coords[1])) if (len(path) == 1): if tv.row_expanded(path): tv.collapse_row(path) else: tv.expand_row(path, False) self.album_button.set_sensitive(True) except: pass | 9edfcdeed3cd5d937c15049ed60c8c2a5154e55b /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/11070/9edfcdeed3cd5d937c15049ed60c8c2a5154e55b/jamendo.py | [
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low = Status.lowest_severity() | low = Status.default() | def create_events(): for service in Service.all(): low = Status.lowest_severity() day = datetime.today() - timedelta(days=2) e = Event(service=service, status=low, message="This service is operating fine", start=day) e.put() | 243e8e56879d06046872e972c028b3896c81f19a /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/10465/243e8e56879d06046872e972c028b3896c81f19a/install_data.py | [
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j = string.find(sys.version, ")", i) | j = sys.version.find(")", i) | def get_platform (): """Return a string that identifies the current platform. This is used mainly to distinguish platform-specific build directories and platform-specific built distributions. Typically includes the OS name and version and the architecture (as supplied by 'os.uname()'), although the exact information included depends on the OS; eg. for IRIX the architecture isn't particularly important (IRIX only runs on SGI hardware), but for Linux the kernel version isn't particularly important. Examples of returned values: linux-i586 linux-alpha (?) solaris-2.6-sun4u irix-5.3 irix64-6.2 Windows will return one of: win-x86_64 (64bit Windows on x86_64 (AMD64)) win-ia64 (64bit Windows on Itanium) win32 (all others - specifically, sys.platform is returned) For other non-POSIX platforms, currently just returns 'sys.platform'. """ if os.name == 'nt': # sniff sys.version for architecture. prefix = " bit (" i = string.find(sys.version, prefix) if i == -1: return sys.platform j = string.find(sys.version, ")", i) look = sys.version[i+len(prefix):j].lower() if look=='amd64': return 'win-x86_64' if look=='itanium': return 'win-ia64' return sys.platform if os.name != "posix" or not hasattr(os, 'uname'): # XXX what about the architecture? NT is Intel or Alpha, # Mac OS is M68k or PPC, etc. return sys.platform # Try to distinguish various flavours of Unix (osname, host, release, version, machine) = os.uname() # Convert the OS name to lowercase, remove '/' characters # (to accommodate BSD/OS), and translate spaces (for "Power Macintosh") osname = osname.lower().replace('/', '') machine = machine.replace(' ', '_') machine = machine.replace('/', '-') if osname[:5] == "linux": # At least on Linux/Intel, 'machine' is the processor -- # i386, etc. # XXX what about Alpha, SPARC, etc? return "%s-%s" % (osname, machine) elif osname[:5] == "sunos": if release[0] >= "5": # SunOS 5 == Solaris 2 osname = "solaris" release = "%d.%s" % (int(release[0]) - 3, release[2:]) # fall through to standard osname-release-machine representation elif osname[:4] == "irix": # could be "irix64"! return "%s-%s" % (osname, release) elif osname[:3] == "aix": return "%s-%s.%s" % (osname, version, release) elif osname[:6] == "cygwin": osname = "cygwin" rel_re = re.compile (r'[\d.]+') m = rel_re.match(release) if m: release = m.group() elif osname[:6] == "darwin": # # For our purposes, we'll assume that the system version from # distutils' perspective is what MACOSX_DEPLOYMENT_TARGET is set # to. This makes the compatibility story a bit more sane because the # machine is going to compile and link as if it were # MACOSX_DEPLOYMENT_TARGET. from distutils.sysconfig import get_config_vars cfgvars = get_config_vars() macver = os.environ.get('MACOSX_DEPLOYMENT_TARGET') if not macver: macver = cfgvars.get('MACOSX_DEPLOYMENT_TARGET') if not macver: # Get the system version. Reading this plist is a documented # way to get the system version (see the documentation for # the Gestalt Manager) try: f = open('/System/Library/CoreServices/SystemVersion.plist') except IOError: # We're on a plain darwin box, fall back to the default # behaviour. pass else: m = re.search( r'<key>ProductUserVisibleVersion</key>\s*' + r'<string>(.*?)</string>', f.read()) f.close() if m is not None: macver = '.'.join(m.group(1).split('.')[:2]) # else: fall back to the default behaviour if macver: from distutils.sysconfig import get_config_vars release = macver osname = "macosx" if (release + '.') < '10.4.' and \ get_config_vars().get('UNIVERSALSDK', '').strip(): # The universal build will build fat binaries, but not on # systems before 10.4 machine = 'fat' elif machine in ('PowerPC', 'Power_Macintosh'): # Pick a sane name for the PPC architecture. machine = 'ppc' return "%s-%s-%s" % (osname, release, machine) | c49a8d0dc091a213d4117981931f3d1357ba1d02 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/3187/c49a8d0dc091a213d4117981931f3d1357ba1d02/util.py | [
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value = [twc.safe_validate(self.item_validator, v) for v in (value or [])] value = [v for v in value if v is not twc.Invalid] | if self.item_validator: value = [twc.safe_validate(self.item_validator, v) for v in (value or [])] value = [v for v in value if v is not twc.Invalid] elif self.validator: value = twc.safe_validate(self.validator, value) | def _validate(self, value): """ To redisplay correctly on error, selection fields must have the :attr:`item_validator` applies to their value. This function does this in a way that will never raise an exception, before calling the main validator. """ if self.multiple: if isinstance(value, basestring): value = [value,] value = [twc.safe_validate(self.item_validator, v) for v in (value or [])] value = [v for v in value if v is not twc.Invalid] else: value = twc.safe_validate(self.item_validator, value) self.value = value if value is twc.Invalid: value = None return super(SelectionField, self)._validate(value) | 075e50c979c9fbb01316d3b99e609e26458141c4 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/11476/075e50c979c9fbb01316d3b99e609e26458141c4/widgets.py | [
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if c == r"'": | elif c == r"'": | def split_command_line(command_line): '''This splits a command line into a list of arguments. It splits arguments on spaces, but handles embedded quotes, doublequotes, and escaped characters. I couldn't do this with a regular expression, so I wrote a little state machine to parse the command line. ''' arg_list = [] arg = '' state_quote = 0 state_doublequote = 0 state_esc = 0 for c in command_line: if c == '\\': # Escape the next character state_esc = 1 if c == r"'": # Handle single quote if state_esc: state_esc = 0 elif not state_quote: state_quote = 1 else: state_quote = 0 if c == r'"': # Handle double quote if state_esc: state_esc = 0 elif not state_doublequote: state_doublequote = 1 else: state_doublequote = 0 # Add arg to arg_list unless in some other state. if c == ' 'and not state_quote and not state_doublequote and not state_esc: arg_list.append(arg) arg = '' else: arg = arg + c if c != '\\'and state_esc: # escape mode lasts for one character. state_esc = 0 # Handle last argument. if arg != '': arg_list.append(arg) return arg_list | a6436229531e4cc3cceb58c0322f4ecc258e53d4 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/9386/a6436229531e4cc3cceb58c0322f4ecc258e53d4/pexpect.py | [
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direntry.connect('selection-changed', self.prefs_direntry_changed, profiles) | direntry.connect('selection-changed', self._direntry_changed, profiles) | def mpd_tab(self): """Construct and layout the MPD tab""" mpdlabel = ui.label(markup='<b>' + _('MPD Connection') + '</b>', y=1) mpd_frame = gtk.Frame() mpd_frame.set_label_widget(mpdlabel) mpd_frame.set_shadow_type(gtk.SHADOW_NONE) controlbox = gtk.HBox() profiles = ui.combo() add_profile = ui.button(img=ui.image(stock=gtk.STOCK_ADD)) remove_profile = ui.button(img=ui.image(stock=gtk.STOCK_REMOVE)) self.prefs_populate_profile_combo(profiles, self.config.profile_num, remove_profile) controlbox.pack_start(profiles, False, False, 2) controlbox.pack_start(remove_profile, False, False, 2) controlbox.pack_start(add_profile, False, False, 2) namelabel = ui.label(textmn=_("_Name") + ":") nameentry = ui.entry() namelabel.set_mnemonic_widget(nameentry) hostlabel = ui.label(textmn=_("_Host") + ":") hostentry = ui.entry() hostlabel.set_mnemonic_widget(hostentry) portlabel = ui.label(textmn=_("_Port") + ":") portentry = gtk.SpinButton(gtk.Adjustment(0 ,0 ,65535, 1),1) portentry.set_numeric(True) portlabel.set_mnemonic_widget(portentry) dirlabel = ui.label(textmn=_("_Music dir") + ":") direntry = gtk.FileChooserButton(_('Select a Music Directory')) direntry.set_action(gtk.FILE_CHOOSER_ACTION_SELECT_FOLDER) direntry.connect('selection-changed', self.prefs_direntry_changed, profiles) dirlabel.set_mnemonic_widget(direntry) passwordlabel = ui.label(textmn=_("Pa_ssword") + ":") passwordentry = ui.entry(password=True) passwordlabel.set_mnemonic_widget(passwordentry) passwordentry.set_tooltip_text(_("Leave blank if no password is required.")) autoconnect = gtk.CheckButton(_("_Autoconnect on start")) autoconnect.set_active(self.config.autoconnect) autoconnect.connect('toggled', self.prefs_config_widget_active, 'autoconnect') # Fill in entries with current profile: self.prefs_profile_chosen(profiles, nameentry, hostentry, portentry, passwordentry, direntry) # Update display if $MPD_HOST or $MPD_PORT is set: host, port, password = misc.mpd_env_vars() if host or port: using_mpd_env_vars = True if not host: host = "" if not port: port = 0 if not password: password = "" hostentry.set_text(str(host)) portentry.set_value(port) passwordentry.set_text(str(password)) nameentry.set_text(_("Using MPD_HOST/PORT")) for widget in [hostentry, portentry, passwordentry, nameentry, profiles, add_profile, remove_profile]: widget.set_sensitive(False) else: using_mpd_env_vars = False nameentry.connect('changed', self.prefs_nameentry_changed, profiles, remove_profile) hostentry.connect('changed', self.prefs_hostentry_changed, profiles) portentry.connect('value-changed', self.prefs_portentry_changed, profiles) passwordentry.connect('changed', self.prefs_passwordentry_changed, profiles) profiles.connect('changed', self.prefs_profile_chosen, nameentry, hostentry, portentry, passwordentry, direntry) add_profile.connect('clicked', self.prefs_add_profile, nameentry, profiles, remove_profile) remove_profile.connect('clicked', self.prefs_remove_profile, profiles, remove_profile) | 7d41f2105c0d58643150b6472b6b9676150f38e3 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/2312/7d41f2105c0d58643150b6472b6b9676150f38e3/preferences.py | [
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""" A base class for comparators that transform their inout and then perform a simple comparison against a value. """ | """A base class for comparators that transform their inout and then perform a simple comparison against a value.""" | def __repr__(self): return "%s(%s)" % (self.__class__.__name__, `self.value`) | 2e7b15abd167a17bf8f880c7e0bd7891362e04de /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/873/2e7b15abd167a17bf8f880c7e0bd7891362e04de/__init__.py | [
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sage: mathematica.eval('Cos[x] + Sin[y] + x^2 + y^2 + t /. x^2 + y^2 -> t') | sage: mathematica.eval('Cos[x] + Sin[y] + x^2 + y^2 + t /. x^2 + y^2 -> t') | def subs_expr(self, *equations): """ Given a dictionary of key:value pairs, substitute all occurences of key for value in self. | dad535f9b6332d16218fbc94ac430cdc58063cb4 /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/9417/dad535f9b6332d16218fbc94ac430cdc58063cb4/calculus.py | [
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learners = RelationshipProperty(URILearning, URISection, URILearner) | learners = RelationshipProperty(URILearning, URISection, URILearner) | def _getTitle(self): return _('Section of ') + " ".join([c.title for c in self.courses]) | 94e5db2b80df02892213d276a47f6e2de7d534e0 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/7127/94e5db2b80df02892213d276a47f6e2de7d534e0/app.py | [
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if not self._precheck(irc, msg, timeout=(to,factoid.name)): return cur.execute("UPDATE FACTS SET popularity = %d WHERE name = %s", factoid.popularity+1, factoid.name) db.commit() if factoid.value.startswith('<reply>'): irc.queueMsg(ircmsgs.privmsg(to, '%s%s' % (retmsg, factoid.value[7:].strip()))) else: irc.queueMsg(ircmsgs.privmsg(to, '%s%s is %s' % (retmsg, factoid.name, factoid.value.strip()))) | if noalias: if not self._precheck(irc, msg, timeout=(to,factoid.name,1)): return cur.execute("SELECT name FROM facts WHERE value = %s", '<alias> ' + factoid.name) data = cur.fetchall() if(len(data)): aliases = "%s aliases: %s" % (factoid.name, ', '.join([x[0].strip() for x in data])) else: if factoid.value.strip().startswith('<alias>'): aliases = "%s is %s" % (factoid.name, factoid.value.strip()) else: aliases = "%s has no aliases" % factoid.name authorinfo = "Added by %s on %s" % (factoid.author[:factoid.author.find('!')], factoid.added[:factoid.added.find('.')]) irc.queueMsg(ircmsgs.privmsg(to,"%s - %s" % (aliases, authorinfo))) else: factoid = resolve_alias(db,factoid,channel) if not self._precheck(irc, msg, timeout=(to,factoid.name)): return cur.execute("UPDATE FACTS SET popularity = %d WHERE name = %s", factoid.popularity+1, factoid.name) db.commit() irc.queueMsg(ircmsgs.privmsg(to, '%s%s' % (retmsg, factoid.value.strip()))) | def showfactoid(self, irc, msg, match): r"^(!|!?ubotu\S?\s)?(?P<noalias>-)?\s*(tell\s+(?P<nick>\S+)\s+about\s+)?(?P<factoid>\S.+?)(>\s*(?P<nick2>\S+))?$" withnick = bool(match.group(1)) and msg.args[1].startswith('ubotu') db = self._precheck(irc, msg, withnick=True, timeout=(msg.args[0], match.group('nick'), match.group('factoid'), match.group('nick2'))) if not db: return to = channel = msg.args[0] if channel[0] != '#': to = msg.nick cur = db.cursor() retmsg = '' noalias = match.group('noalias') factoid = match.group('factoid').lower().strip() if ' is ' in match.group(0) or \ '=~' in match.group(0) or \ '<sed>' in match.group(0) or \ factoid.startswith('forget ') or \ factoid.startswith('info ') or \ factoid.startswith('find ') or \ factoid.startswith('search ') or \ factoid.startswith('seen'): return | 01f443b02020754b77ae2d59e7040a244cbd5b7c /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/3105/01f443b02020754b77ae2d59e7040a244cbd5b7c/plugin.py | [
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b = ScrollBehaviour((0, start), (0, stop), '_scroll') self._col_animation = self.animate(secs) self._col_animation.behave(b) | self.__col_animation = self.animate(secs) self.__col_animation.behave(ScrollBehaviour((0, y), '_scroll')) | def scroll_to(self, (row, col), secs): """ Scroll to row / cell position | b47bb145b9afab8cd03f9ba37d4dcd175be8f666 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/11702/b47bb145b9afab8cd03f9ba37d4dcd175be8f666/grid.py | [
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environ['TZ'] = 'US/Eastern' | environ['TZ'] = eastern | def test_tzset(self): if not hasattr(time, "tzset"): return # Can't test this; don't want the test suite to fail | 0bb27d52a755bc77f9610e468f23f3c7f5f27863 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/3187/0bb27d52a755bc77f9610e468f23f3c7f5f27863/test_time.py | [
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def get_api_tuple(str): m = re.match("^([a-z]+)_([a-z][a-z0-9_]+)$", str) return 'p_' + m.group(1), m.group(2) | def get_api_tuple(source): match = re.match("^([a-z]+)_([a-z][a-z0-9_]+)$", source) return 'p_' + match.group(1), match.group(2) | def get_api_tuple(str): m = re.match("^([a-z]+)_([a-z][a-z0-9_]+)$", str) return 'p_' + m.group(1), m.group(2) | 48ca569fea7e1a22f2994b3f5a7396ba7cf30959 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/12113/48ca569fea7e1a22f2994b3f5a7396ba7cf30959/genapi.py | [
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template = template.blocks()[blockname] | template = template.blocks().get(blockname) | def template(self, name): if isinstance(name, document.Document) or callable(name): return name shortname = name prefix = None providers = None if isinstance(name, str): template = self.BLOCKS.get(name) if template: return template for blocks in self.BLKSTACK: if blocks: template = blocks.get(name) if template: return template regex = "\w{%d,}:" % (int(os.name == "nt") + 1) match = re.match(regex, name) if match: prefix = match.group(1) if prefix is not None: providers = self.PREFIX_MAP.get(prefix) if not providers: self.throw(constants.ERROR_FILE, "no providers for template prefix '%s'" % prefix) if not providers: providers = self.PREFIX_MAP.get("default") or self.LOAD_TEMPLATES | ee91d8fafaaeb0531affcff79e64c250f94fe3ad /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/1390/ee91d8fafaaeb0531affcff79e64c250f94fe3ad/context.py | [
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maxpage=maxpage, roundsize=roundsize) | maxpage=maxpage, roundsize=roundsize, nonames=nonames ) | def main(): checkext = CHECKEXT verbose = VERBOSE maxpage = MAXPAGE roundsize = ROUNDSIZE dumpfile = DUMPFILE restart = 0 norun = 0 try: # Begin SLB 2/24/99: Added -t option here. opts, args = getopt.getopt(sys.argv[1:], 'Rd:m:nqr:t:vx') # End SLB 2/24/99 except getopt.error, msg: sys.stdout = sys.stderr print msg print __doc__%globals() sys.exit(2) # Begin SLB 2/24/99: Added extra_roots variable to # collect extra roots. extra_roots = [] # End SLB 2/24/99 for o, a in opts: if o == '-R': restart = 1 if o == '-d': dumpfile = a if o == '-m': maxpage = string.atoi(a) if o == '-n': norun = 1 if o == '-q': verbose = 0 if o == '-r': roundsize = string.atoi(a) # Begin SLB 2/24/99: Added processing for # -t option. if o == '-t': extra_roots.append(a) # End SLB 2/24/99 if o == '-v': verbose = verbose + 1 if o == '-x': checkext = not checkext if verbose > 0: print AGENTNAME, "version", __version__ if restart: c = load_pickle(dumpfile=dumpfile, verbose=verbose) else: c = Checker() c.setflags(checkext=checkext, verbose=verbose, maxpage=maxpage, roundsize=roundsize) if not restart and not args: args.append(DEFROOT) for arg in args: c.addroot(arg) # Begin SLB 2/24/99. The -t flag is only needed if external # links are not to be checked. So -t values are ignored unless # -x was specified. if not checkext: for root in extra_roots: # Make sure it's terminated by a slash, # so that addroot doesn't discard the last # directory component. if root[-1] != "/": root = root + "/" c.addroot(root) # End SLB 2/24/99 try: if not norun: try: c.run() except KeyboardInterrupt: if verbose > 0: print "[run interrupted]" try: c.report() except KeyboardInterrupt: if verbose > 0: print "[report interrupted]" finally: if c.save_pickle(dumpfile): if dumpfile == DUMPFILE: print "Use ``%s -R'' to restart." % sys.argv[0] else: print "Use ``%s -R -d %s'' to restart." % (sys.argv[0], dumpfile) | f97eecccb714a71cf5a1ca9399cd9c579014a5b9 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/8546/f97eecccb714a71cf5a1ca9399cd9c579014a5b9/wcnew.py | [
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def is_ref(node): return isinstance(node, Ref) | def is_ir_set(node): return _is_yaml_mapping(node, IrSet) | def is_ref(node): return isinstance(node, Ref) | 8e841208f4c2d35a14c2f7368d9b82801f784d4b /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/12853/8e841208f4c2d35a14c2f7368d9b82801f784d4b/yaml_test.py | [
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'name': fields.char('Name', size=60), | 'name': fields.char('Name', size=60, required=True), | def action_done(self, cr, uid, ids,group=True,type='out_refund', context=None): # need to make perfect checking # remaining to check sale condition # need Improvement invoice_obj = self.pool.get('account.invoice') invoice_line_obj = self.pool.get('account.invoice.line') tax_obj=self.pool.get('account.invoice.tax') partner_obj = self.pool.get('res.partner') res = {} for campaign in self.browse(cr, uid, ids): invoices_group = {} invoices_line_group={} res[campaign.id]=[] cr.execute(""" SELECT invoice.id from account_invoice invoice left join res_partner partner on invoice.partner_id=partner.id where partner.discount_campaign=%d and (invoice.date_invoice BETWEEN %s AND %s) AND invoice.type = 'out_invoice' AND state = 'open' """ , (campaign.id,campaign.date_start,campaign.date_stop,)) invoice_ids = map(lambda x:x[0],cr.fetchall()) | 49ba78affef4aa09d339c2c0860b36f6171a6f1f /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/7339/49ba78affef4aa09d339c2c0860b36f6171a6f1f/discount_campaign.py | [
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R1 = N.zeros([4,4], dtype=N.float64); R2 = N.zeros([4,4], dtype=N.float64); R3 = N.zeros([4,4], dtype=N.float64); T = N.eye(4, dtype=N.float64); | R1 = NP.zeros([4,4], dtype=NP.float64); R2 = NP.zeros([4,4], dtype=NP.float64); R3 = NP.zeros([4,4], dtype=NP.float64); T = NP.eye(4, dtype=NP.float64); | def build_rotate_matrix(img_data_parms): """ rot_matrix = reg.build_rotate_matrix(img_data_parms) takes the 6 element vector (3 angles, 3 translations) and build the 4x4 mapping matrix Parameters ....... img_data_parms : {nd_array} this is the current (6-dim) array with 3 angles and 3 translations. Returns ....... rot_matrix: {nd_array} the 4x4 mapping matrix Examples ........ >>> import numpy as N >>> import _registration as reg >>> imdata = reg.build_structs() >>> x = N.zeros(6, dtype=N.float64) >>> M = reg.build_rotate_matrix(x) >>> M array([[ 1., 0., 0., 0.], [ 0., 1., 0., 0.], [ 0., 0., 1., 0.], [ 0., 0., 0., 1.]]) """ R1 = N.zeros([4,4], dtype=N.float64); R2 = N.zeros([4,4], dtype=N.float64); R3 = N.zeros([4,4], dtype=N.float64); T = N.eye(4, dtype=N.float64); alpha = math.radians(img_data_parms[0]) beta = math.radians(img_data_parms[1]) gamma = math.radians(img_data_parms[2]) R1[0][0] = 1.0 R1[1][1] = math.cos(alpha) R1[1][2] = math.sin(alpha) R1[2][1] = -math.sin(alpha) R1[2][2] = math.cos(alpha) R1[3][3] = 1.0 R2[0][0] = math.cos(beta) R2[0][2] = math.sin(beta) R2[1][1] = 1.0 R2[2][0] = -math.sin(beta) R2[2][2] = math.cos(beta) R2[3][3] = 1.0 R3[0][0] = math.cos(gamma) R3[0][1] = math.sin(gamma) R3[1][0] = -math.sin(gamma) R3[1][1] = math.cos(gamma) R3[2][2] = 1.0 R3[3][3] = 1.0 T[0][0] = 1.0 T[1][1] = 1.0 T[2][2] = 1.0 T[3][3] = 1.0 T[0][3] = img_data_parms[3] T[1][3] = img_data_parms[4] T[2][3] = img_data_parms[5] rot_matrix = N.dot(T, R1); rot_matrix = N.dot(rot_matrix, R2); rot_matrix = N.dot(rot_matrix, R3); return rot_matrix | de681f926e982b0212f2f58bf637917926737f89 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/12971/de681f926e982b0212f2f58bf637917926737f89/_registration.py | [
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before = [l.rstrip('\n') for l in lines[lbound:lineno]] line = lines[lineno].rstrip('\n') after = [l.rstrip('\n') for l in lines[lineno + 1:ubound]] | charset = None rep = re.compile('coding[=:]\s*([-\w.]+)') for linestr in lines[0], lines[1]: match = rep.search(linestr) if match: charset = match.group(1) break before = [to_unicode(l.rstrip('\n'), charset) for l in lines[lbound:lineno]] line = to_unicode(lines[lineno].rstrip('\n'), charset) after = [to_unicode(l.rstrip('\n'), charset) \ for l in lines[lineno + 1:ubound]] | def get_lines_from_file(filename, lineno, context=0): """Return `content` number of lines before and after the specified `lineno` from the file identified by `filename`. Returns a `(lines_before, line, lines_after)` tuple. """ if os.path.isfile(filename): fileobj = open(filename, 'U') try: lines = fileobj.readlines() lbound = max(0, lineno - context) ubound = lineno + 1 + context before = [l.rstrip('\n') for l in lines[lbound:lineno]] line = lines[lineno].rstrip('\n') after = [l.rstrip('\n') for l in lines[lineno + 1:ubound]] return before, line, after finally: fileobj.close() return (), None, () | a947bc01a37d86d695b1d79fc146414e8c7177cb /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/2831/a947bc01a37d86d695b1d79fc146414e8c7177cb/__init__.py | [
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space this function simply returns self. | space this function simply returns self, unless the base field is different. | def vector_space(self): """ Return the vector space associated to self. Since self is a vector space this function simply returns self. EXAMPLES: sage: V = span(Rationals(), [[1,2,3]]); V Vector space of degree 3 and dimension 1 over Rational Field Basis matrix: [1 2 3] sage: V.vector_space() Vector space of degree 3 and dimension 1 over Rational Field Basis matrix: [1 2 3] """ return self | 27c1d953b6798afbc4f6f486098714caebeb979d /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/9890/27c1d953b6798afbc4f6f486098714caebeb979d/free_module.py | [
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print (' NumFrames: %d PlayRate: %0.2f' % (animControl.getNumFrames(), animControl.getPlayRate())) | if animControl == None: print ' (not loaded)' else: print (' NumFrames: %d PlayRate: %0.2f' % (animControl.getNumFrames(), animControl.getPlayRate())) | def pprint(self): """pprint(self) Pretty print actor's details """ for lodName, lodInfo in self.getActorInfo(): print 'LOD:', lodName for partName, bundle, animInfo in lodInfo: print ' Part:', partName print ' Bundle:', `bundle` for animName, file, animControl in animInfo: print ' Anim:', animName print ' File:', file print (' NumFrames: %d PlayRate: %0.2f' % (animControl.getNumFrames(), animControl.getPlayRate())) | f3ecd1b3be1dfb26d71ee04e5cafdbea5f5b53a9 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/8543/f3ecd1b3be1dfb26d71ee04e5cafdbea5f5b53a9/Actor.py | [
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game = libgambit.NewTable([ len(self.contribs) for i in xrange(self.N) ]) | game = libgambit.NewTable([ len(self.choices) for i in xrange(self.N) ]) | def nfg(self): game = libgambit.NewTable([ len(self.contribs) for i in xrange(self.N) ]) | 5b71669e95cb1e59558f3b550ecd43f33998cb0b /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/12755/5b71669e95cb1e59558f3b550ecd43f33998cb0b/msgame.py | [
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n_alpha = self.alpha_selection(limit="and name N").count(True) n_beta = self.beta_selection(limit="and name N").count(True) | alpha_sele = self.alpha_selection(limit="and name N", main_conf_only=True) n_alpha = alpha_sele.count(True) beta_sele = self.beta_selection(limit="and name N", main_conf_only=True) n_beta = beta_sele.count(True) | def calculate_structure_content (self) : isel = self.selection_cache.iselection calpha = isel("name N and (altloc ' ' or altloc 'A')") n_alpha = self.alpha_selection(limit="and name N").count(True) n_beta = self.beta_selection(limit="and name N").count(True) if calpha.size() == 0 : return (0.0, 0.0) return (n_alpha / calpha.size(), n_beta / calpha.size()) | 0010b9e17ff7db6e6d7268f81202d7209b8e2567 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/696/0010b9e17ff7db6e6d7268f81202d7209b8e2567/secondary_structure.py | [
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cmd = self.f90_compiler + ' -dryrun dummy.f' | cmd = self.f90_compiler + ' -dryrun __dummy.f' | def find_lib_dir(self): library_dirs = ["/opt/SUNWspro/prod/lib"] lib_match = r'### f90: Note: LD_RUN_PATH\s*= '\ '(?P<lib_paths>[^\s.]*).*' cmd = self.f90_compiler + ' -dryrun dummy.f' self.announce(yellow_text(cmd)) exit_status, output = run_command(cmd) if not exit_status: libs = re.findall(lib_match,output) if libs and libs[0] == "(null)": del libs[0] if libs: library_dirs = string.split(libs[0],':') self.get_version() # force version calculation compiler_home = os.path.dirname(library_dirs[0]) library_dirs.append(os.path.join(compiler_home, self.version,'lib')) return library_dirs | 18f6cc54d9a0fe3dd53474858e6dc2fcefb0e657 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/14925/18f6cc54d9a0fe3dd53474858e6dc2fcefb0e657/build_flib.py | [
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path, targetfile = util.create_unique_file(os.path.join(self.path, filename)) | def insert(self, filename, fileobj, size, t=None, db=None): if not db: db = self.env.get_db_cnx() handle_ta = True else: handle_ta = False | 18a7e517868a6fd8a4adee5383eeee9ba09e1b82 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/2831/18a7e517868a6fd8a4adee5383eeee9ba09e1b82/attachment.py | [
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str += self._class_summary(classes, 'Classes') str += self._class_summary(excepts, 'Exceptions') str += self._func_summary(doc.functions()) str += self._var_summary(doc.variables()) | str += self._class_summary(classes, doc.sort_order(), 'Classes') str += self._class_summary(excepts, doc.sort_order(), 'Exceptions') str += self._func_summary(doc.functions(), doc.sort_order()) str += self._var_summary(doc.variables(), doc.sort_order()) | def _module_to_html(self, uid): 'Return an HTML page for a Module' doc = self._docmap[uid] descr = doc.descr() if uid.is_package(): moduletype = 'package' else: moduletype = 'module' str = self._header(`uid`) str += self._navbar(moduletype, uid) if self._show_both: str += self._public_private_link(uid) | 29127a15ecd548178da747376d81226f0a835ef6 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/11420/29127a15ecd548178da747376d81226f0a835ef6/html.py | [
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return DictionaryOfArithmeticTypes() | return ArithmeticDictionary() | def _get_empty_self(self): return DictionaryOfArithmeticTypes() | 26b00e61b9d12787955b744e839ffed23b4c2c8d /local1/tlutelli/issta_data/temp/all_python//python/2007_temp/2007/12871/26b00e61b9d12787955b744e839ffed23b4c2c8d/arithmetic_container.py | [
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if vlen: dlen=dlen+16+vlen | if vlen: dlen=dlen+(16+vlen) | def undo(self, transaction_id): self._lock_acquire() try: self._clear_index() transaction_id=base64.decodestring(transaction_id+'==\n') tid, tpos = transaction_id[:8], u64(transaction_id[8:]) packt=self._packt if packt is None or packt > tid: raise POSException.UndoError, ( 'Undo is currently disabled for database maintenance.<p>') | e9aa3bd398cba329c8a421eb6d47f4dba6e400a9 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/10048/e9aa3bd398cba329c8a421eb6d47f4dba6e400a9/FileStorage.py | [
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def __init__(data = None) | def __init__(data = None): | def __init__(data = None) if data == None: quickfix.DoubleField.__init__(self, 135) else quickfix.DoubleField.__init__(self, 135, data) | 484890147d4b23aac4b9d0e85e84fceab7e137c3 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/8819/484890147d4b23aac4b9d0e85e84fceab7e137c3/quickfix_fields.py | [
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" %prog -l\n", | " %prog -l", | def mvbranch(argv, progname=None): progname = progname or os.path.basename(argv[0]) parser = optparse.OptionParser( "usage: %prog [-n] [-m MSG] oldbranch newbranch\n" " %prog -l\n", prog=progname, description="Rename a Subversion branch.") parser.add_option('-l', '--list', help='list existing branches', action='store_true', dest='list_branches', default=False) parser.add_option('-m', help='commit message', action='store', dest='message', default=None) parser.add_option('-n', '--dry-run', help='do not rename the branch, just print the command', action='store_true', dest='dry_run', default=False) try: opts, args = parser.parse_args(argv[1:]) if len(args) > 2: parser.error("too many arguments, try %s --help" % progname) except optparse.OptParseError, e: sys.exit(e) path = '.' if opts.list_branches: # TODO: allow a different wc-path print '\n'.join(listbranches(path)) return if len(args) < 2: parser.error("too few arguments, try %s --help" % progname) oldbranch = determinebranch(args[0], path) newbranch = determinebranch(args[1], path) cmd = "svn mv %s %s" % (oldbranch, newbranch) if opts.message: cmd += " -m '%s'" % opts.message print cmd if not opts.dry_run: os.system(cmd) | 0243003a6f9d9339ec1f01f32f9c410c2307e8c7 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/11524/0243003a6f9d9339ec1f01f32f9c410c2307e8c7/eazysvn.py | [
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relation = self._columns[node.getAttribute('name')]._obj | column = self._columns[node.getAttribute('name')] | def __view_look_dom(self, cr, user, node, view_id, context=None): if not context: context = {} result = False fields = {} childs = True | 45f34ac9eb7f3d2d5bb3e09f3d53f64a9f5e642e /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/12853/45f34ac9eb7f3d2d5bb3e09f3d53f64a9f5e642e/orm.py | [
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self.builder.get_object('button_play_cut').props.visible = cut_ok | self.builder.get_object('button_play_cut').props.visible = cut_ok self.builder.get_object('box_archive').props.visible = cut_ok | def show_conclusion(self, new_iter): self.conclusion_iter = new_iter self.file_conclusion = self.__file_conclusions[self.conclusion_iter] self.builder.get_object('label_count').set_text("Zeige Datei %s/%s" % (str(new_iter + 1), len(self.__file_conclusions))) | 270edd8c959fe53e05f88f1d050c4a41c66345e2 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/11048/270edd8c959fe53e05f88f1d050c4a41c66345e2/ConclusionDialog.py | [
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while Q != []: | while True: EdgeRemoved = True while Q == [] and EdgeRemoved: EdgeRemoved = False for Item in LibraryList: if Item not in Constructor: continue for Node in ConsumedByList[Item]: if Node in Constructor: continue ConsumedByList[Item].remove(Node) EdgeRemoved = True if ConsumedByList[Item] == []: Q.insert(0, Item) break if Q != []: break if Q == []: break | def _MergeModuleInfo(self, Module, ModuleId): ModuleType = Module.ModuleType # merge library class/instance information for LibraryClass in Module.LibraryClasses: if self.LibraryClasses[LibraryClass, ModuleType] == None: continue Module.LibraryClasses[LibraryClass] = self.LibraryClasses[LibraryClass, ModuleType] RecordList = self._Table.Query(MODEL_EFI_LIBRARY_CLASS, Scope1=self.Arch, BelongsToItem=ModuleId) for Record in RecordList: LibraryClass = Record[0] LibraryPath = NormPath(Record[1], self._Macros) LineNo = Record[-1] if not ValidFile(LibraryPath): EdkLogger.error('build', FILE_NOT_FOUND, ExtraData=LibraryPath, File=self.DescFilePath, Line=LineNo) if LibraryClass == '' or LibraryClass == 'NULL': LibraryClass = 'NULL%d' % (self._NullLibraryNumber + 1) LibraryInstance = self._Db.BuildObject[LibraryPath, MODEL_FILE_INF, self._Arch] LibraryInstance.LibraryClass.append(LibraryClassObject(LibraryClass, [ModuleType])) Module.LibraryClasses[LibraryClass] = LibraryPath | ed4f99270fb13f95de3f3566ac92242b62495cd9 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/914/ed4f99270fb13f95de3f3566ac92242b62495cd9/WorkspaceDatabase.py | [
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self.STDIN_FILENO = sys.stdin.fileno() self.STDOUT_FILENO = sys.stdout.fileno() self.STDERR_FILENO = sys.stderr.fileno() | self.STDIN_FILENO = pty.STDIN_FILENO self.STDOUT_FILENO = pty.STDOUT_FILENO self.STDERR_FILENO = pty.STDERR_FILENO | def __init__(self, command, args=[], timeout=30): """This is the constructor. The command parameter may be a string that includes a command and any arguments to the command. For example: p = pexpect.spawn ('/usr/bin/ftp') p = pexpect.spawn ('/usr/bin/ssh user@example.com') p = pexpect.spawn ('ls -latr /tmp') You may also construct it with a list of arguments like so: p = pexpect.spawn ('/usr/bin/ftp', []) p = pexpect.spawn ('/usr/bin/ssh', ['user@example.com']) p = pexpect.spawn ('ls', ['-latr', '/tmp']) After this the child application will be created and will be ready to talk to. For normal use, see expect() and send() and sendline(). | 8c4ecf17710883ea8cc68bcd989ba58de0d2e671 /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/9386/8c4ecf17710883ea8cc68bcd989ba58de0d2e671/pexpect.py | [
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step_type = pooler.get_pool(cr.dbname).get('dm.offer.step.type') | def graph_get(cr, uid, graph, offer_id): offer_obj = pooler.get_pool(cr.dbname).get('dm.offer') offer = offer_obj.browse(cr, uid, offer_id)[0] nodes = {} step_type = pooler.get_pool(cr.dbname).get('dm.offer.step.type') type_ids = step_type.search(cr, uid, []) for step in offer.step_ids: if not step.graph_hide: args = {} """ Get user language """ usr_obj = pooler.get_pool(cr.dbname).get('res.users') user = usr_obj.browse(cr, uid, [uid])[0] user_lang = user.context_lang """ Get Code Translation """ trans_obj = pooler.get_pool(cr.dbname).get('ir.translation') type_trans = trans_obj._get_ids(cr, uid, 'dm.offer.step,code', 'model', user_lang or 'en_US', [step.id]) type_code = type_trans[step.id] or step.code args['label'] = translate_accent( type_code +'\\n' + step.media_id.code) graph.add_node(pydot.Node(step.id, **args)) for step in offer.step_ids: for transition in step.outgoing_transition_ids: if not transition.graph_hide: trargs = { 'label': translate_accent(transition.condition_id.name + '\\n' + str(transition.delay) + ' ' + transition.delay_type), 'arrowtail': 'inv', } graph.add_edge(pydot.Edge( str(transition.step_from_id.id), str(transition.step_to_id.id), fontsize="10", **trargs)) return True | e3d8adc104c00ea9e765f59675644bb6bbd479f6 /local1/tlutelli/issta_data/temp/all_python//python/2010_temp/2010/7339/e3d8adc104c00ea9e765f59675644bb6bbd479f6/dm_print_offer_graph.py | [
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('share/icons/hicolor/16x16/apps', glob.glob('data/icons/16x16/apps/*.svg')), ('share/icons/hicolor/22x22/apps', glob.glob('data/icons/22x22/apps/*.svg')), ('share/icons/hicolor/24x24/apps', glob.glob('data/icons/24x24/apps/*.svg')), | ('share/icons/hicolor/16x16/apps', glob.glob('data/icons/16x16/apps/*.png')), ('share/icons/hicolor/22x22/apps', glob.glob('data/icons/22x22/apps/*.png')), ('share/icons/hicolor/24x24/apps', glob.glob('data/icons/24x24/apps/*.png')), | def _compile_po_files (self): data_files = [] | 3e67611d6f7da6bae7f532e0850c6bb69ebb6913 /local1/tlutelli/issta_data/temp/all_python//python/2008_temp/2008/1032/3e67611d6f7da6bae7f532e0850c6bb69ebb6913/setup.py | [
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def compile_path(skip_curdir=1, maxlevels=0, force=0): | def compile_path(skip_curdir=1, maxlevels=0, force=0, quiet=0): | def compile_path(skip_curdir=1, maxlevels=0, force=0): """Byte-compile all module on sys.path. Arguments (all optional): skip_curdir: if true, skip current directory (default true) maxlevels: max recursion level (default 0) force: as for compile_dir() (default 0) """ success = 1 for dir in sys.path: if (not dir or dir == os.curdir) and skip_curdir: print 'Skipping current directory' else: success = success and compile_dir(dir, maxlevels, None, force) return success | 6fb3494c60cbdbefb2193ec4f676a8916063457f /local1/tlutelli/issta_data/temp/all_python//python/2006_temp/2006/3187/6fb3494c60cbdbefb2193ec4f676a8916063457f/compileall.py | [
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def __unicode__(self): return "<ResultSet: query=%s prefetch=%s>" % (self.query_str, self._prefetch) | def __unicode__(self): return u"<ResultSet: query=%s>" % smart_unicode(self._query_str) | def __unicode__(self): return "<ResultSet: query=%s prefetch=%s>" % (self.query_str, self._prefetch) | d27788323bfd2214ac4f2fe8e518e9392deae687 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/4645/d27788323bfd2214ac4f2fe8e518e9392deae687/resultset.py | [
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In this next example, a Solexa FASTQ file is converted into a standard Sanger style FASTQ file using PHRED qualities: | In this next example, an old style Solexa/Illumina FASTQ file (using Solexa quality scores) is converted into a standard Sanger style FASTQ file using PHRED qualities: | def QualPhredIterator(handle, alphabet = single_letter_alphabet, title2ids = None) : """For QUAL files which include PHRED quality scores, but no sequence. For example, consider this short QUAL file:: >EAS54_6_R1_2_1_413_324 26 26 18 26 26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26 26 26 26 23 23 >EAS54_6_R1_2_1_540_792 26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26 26 12 26 26 26 18 26 23 18 >EAS54_6_R1_2_1_443_348 26 26 26 26 26 26 26 26 26 26 26 24 26 22 26 26 13 22 26 18 24 18 18 18 18 Using this module directly you might run: >>> handle = open("Quality/example.qual", "rU") >>> for record in QualPhredIterator(handle) : ... print record.id, record.seq EAS54_6_R1_2_1_413_324 ????????????????????????? EAS54_6_R1_2_1_540_792 ????????????????????????? EAS54_6_R1_2_1_443_348 ????????????????????????? >>> handle.close() Typically however, you would call this via Bio.SeqIO instead with "qual" as the format: >>> from Bio import SeqIO >>> handle = open("Quality/example.qual", "rU") >>> for record in SeqIO.parse(handle, "qual") : ... print record.id, record.seq EAS54_6_R1_2_1_413_324 ????????????????????????? EAS54_6_R1_2_1_540_792 ????????????????????????? EAS54_6_R1_2_1_443_348 ????????????????????????? >>> handle.close() Becase QUAL files don't contain the sequence string itself, the seq property is set to an UnknownSeq object. As no alphabet was given, this has defaulted to a generic single letter alphabet and the character "?" used. By specifying a nucleotide alphabet, "N" is used instead: >>> from Bio import SeqIO >>> from Bio.Alphabet import generic_dna >>> handle = open("Quality/example.qual", "rU") >>> for record in SeqIO.parse(handle, "qual", alphabet=generic_dna) : ... print record.id, record.seq EAS54_6_R1_2_1_413_324 NNNNNNNNNNNNNNNNNNNNNNNNN EAS54_6_R1_2_1_540_792 NNNNNNNNNNNNNNNNNNNNNNNNN EAS54_6_R1_2_1_443_348 NNNNNNNNNNNNNNNNNNNNNNNNN >>> handle.close() However, the quality scores themselves are available as a list of integers in each record's per-letter-annotation: >>> print record.letter_annotations["phred_quality"] [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 26, 22, 26, 26, 13, 22, 26, 18, 24, 18, 18, 18, 18] You can still slice one of these SeqRecord objects with an UnknownSeq: >>> sub_record = record[5:10] >>> print sub_record.id, sub_record.letter_annotations["phred_quality"] EAS54_6_R1_2_1_443_348 [26, 26, 26, 26, 26] """ #Skip any text before the first record (e.g. blank lines, comments) while True : line = handle.readline() if line == "" : return #Premature end of file, or just empty? if line[0] == ">" : break while True : if line[0]!=">" : raise ValueError("Records in Fasta files should start with '>' character") if title2ids : id, name, descr = title2ids(line[1:].rstrip()) else : descr = line[1:].rstrip() id = descr.split()[0] name = id qualities = [] line = handle.readline() while True: if not line : break if line[0] == ">": break qualities.extend([int(word) for word in line.split()]) line = handle.readline() if qualities : if min(qualities) < 0 or max(qualities) > 90 : raise ValueError(("Quality score range for %s is %i to %i, outside the " \ +"expected 0 to 90. Perhaps these are Solexa/Illumina " \ +"scores, and not PHRED scores?") \ % (id, min(qualities), max(qualities))) #Return the record and then continue... record = SeqRecord(UnknownSeq(len(qualities), alphabet), id = id, name = name, description = descr) record.letter_annotations["phred_quality"] = qualities yield record if not line : return #StopIteration assert False, "Should not reach this line" | ca957491dd42f6d15dc267230d1a6ebbd10491c1 /local1/tlutelli/issta_data/temp/all_python//python/2009_temp/2009/7167/ca957491dd42f6d15dc267230d1a6ebbd10491c1/QualityIO.py | [
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