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• Reordering matrix elements to reflect column and row clustering in naiive python

  - by bgbg

  Hello, I'm looking for a way to perform clustering separately on matrix rows and than on its columns, reorder the data in the matrix to reflect the clustering and putting it all together. The clustering problem is easily solvable, so is the dendrogram creation (for example in this blog or in "Programming collective intelligence"). However, how to reorder the data remains unclear for me. Eventually, I'm looking for a way of creating graphs similar to the one below using naive Python (with any "standard" library such as numpy, matplotlib etc, but without using R or other external tools).

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• python variable scope

  - by Oscar Reyes

  I'm teaching my self python and I was translating some sample class Student: def __init__( self, name, a,b,c ): self.name = name self.a = a self.b = b self.c = c def average(self): return ( a+b+c ) / 3.0 Which is pretty much my intended class definition Later in the main method I create an instance and call it a if __name__ == "__main__" : a = Student( "Oscar", 10, 10, 10 ) That's how I find out that the variable a declared in main is available to the method average and that to make that method work , I have to type self.a + self.b + self.c instead What's the rationale of this? I found related questions, but I don't really know if they are about the same

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• Python (pdb) - Queueing up commands to execute

  - by kpatelPro

  I am implementing a "breakpoint" system for use in my Python development that will allow me to call a function that, in essence, calls pdb.set_trace(); Some of the functionality that I would like to implement requires me to control pdb from code while I am within a set_trace context. Example: disableList = [] def breakpoint(name=None): def d(): disableList.append(name) #**** #issue 'run' command to pdb so user #does not have to type 'c' #**** if name in disableList: return print "Use d() to disable breakpoint, 'c' to continue" pdb.set_trace(); In the above example, how do I implement the comments demarked by the #**** ? In other parts of this system, I would like to issue an 'up' command, or two sequential 'up' commands without leaving the pdb session (so the user ends up at a pdb prompt but up two levels on the call stack. Thanks!

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• do-while loop in Python?

  - by Eye of Hell

  I need to emulate a do-while loop in a python. But, unfortunately, following straightforward code does not work: l = [ 1, 2, 3 ] i = l.__iter__() s = None while True : if s : print s try : s = i.next() except StopIteration : break print "done" Instead of "1,2,3,done" I have the following output: [stdout:]1 [stdout:]2 [stdout:]3 None['Traceback (most recent call last): ', ' File "test_python.py", line 8, in <module> s = i.next() ', 'StopIteration '] What can I do in order to catch 'stop iteration' excepton and break a while loop properly? Example why such thing may be needed. State machine: s = "" while True : if state is STATE_CODE : if "//" in s : tokens.add( TOKEN_COMMENT, s.split( "//" )[1] ) state = STATE_COMMENT else : tokens.add( TOKEN_CODE, s ) if state is STATE_COMMENT : if "//" in s : tokens.append( TOKEN_COMMENT, s.split( "//" )[1] ) else state = STATE_CODE # re-evaluate same line continue try : s = i.next() except StopIteration : break

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• python blocking sockets, send returns immediately

  - by Mark

  Hi, I am writing a multithreaded socket application in Python using the socket module. the server listens for connections and when it gets one it spawns a thread for that socket. the server thread sends some data to the client. but the client is not yet ready to receive it. I thought this would have caused the server to wait until the client starts recv but instead returns immediately the client then calls recv which is blocking and no data is ever received. client socket constructor self.__clientSocket = socket.socket(socket.AF_INET, socket.SOCK_STREAM) self.__clientSocket.connect((server, port)) server socket constructor self.servSock = socket.socket(socket.AF_INET, socket.SOCK_STREAM) self.servSock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1) #self.servSock.settimeout(None) self.servSock.setblocking(1) self.servSock.bind((self.addr,self.port)) self.servSock.listen(5) listening accept thread try: (cs, address) = self.servSock.accept() except socket.timeout: return threadName = '\r\nClient %s:%s\r\n' % (cs, address) print threadName clientSocketHandler = ClientSocket() clientSocketHandler.setClientSocket(cs) self.clients.newThread(self.clientFunc, {clientSocketHandler : "1"}, threadName).start() server and clients send/rec methods from inside ClientSocket receivedData = self.__clientSocket.recv(1024*1024) self.__clientSocket.send(s) any ideas why send() is returning straight away?

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• Python Tkinter - Edit external object within event handler?

  - by M3RPHY

  Hey all, As the title says, I'm grabbing the cursor location within a motion triggered event handler in Tkinter. I'd like to update an existing label widget with the location, however I cannot for the life of me figure out how to edit the label's text field (or any external object for that matter) within the event handler. From what I understand, event is the only argument passed to the handler, which means I can't pass the label object. How do I access objects outside of the handler? Apologize for the noobish question as I'm a C programmer new to Python. Thanks!

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• Desktop Application Development with Javascript, Python / Ruby

  - by Chris

  Hello, Besides using Appcelerator's Titanium Desktop, are there other approaches to integrating Javascript and Ruby/Python into cross-platform desktop applications? Just trying to get a sense of the landscape here. From searching the web, it seems Titanium may be leading the charge in terms of this type of integration. I wasn't able to find references that suggest you can do something similar in Adobe AIR. I am interested in building desktop applications that exploit Protovis and possibly other Javascript interactive vis packages for the UI. At the end of the day, I can go the web app route if need be, but being able to develop desktop apps is helpful. Would appreciate your perspective on this... Chris

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• Python-daemon doesn't kill its kids

  - by Brian M. Hunt

  When using python-daemon, I'm creating subprocesses likeso: import multiprocessing class Worker(multiprocessing.Process): def __init__(self, queue): self.queue = queue # we wait for things from this in Worker.run() ... q = multiprocessing.Queue() with daemon.DaemonContext(): for i in xrange(3): Worker(q) while True: # let the Workers do their thing q.put(_something_we_wait_for()) When I kill the parent daemonic process (i.e. not a Worker) with a Ctrl-C or SIGTERM, etc., the children don't die. How does one kill the kids? My first thought is to use atexit to kill all the workers, likeso: with daemon.DaemonContext(): workers = list() for i in xrange(3): workers.append(Worker(q)) @atexit.register def kill_the_children(): for w in workers: w.terminate() while True: # let the Workers do their thing q.put(_something_we_wait_for()) However, the children of daemons are tricky things to handle, and I'd be obliged for thoughts and input on how this ought to be done. Thank you.

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• Translate Java to Python -- signing strings with PEM certificate files

  - by erikcw

  I'm trying to translate the follow Java into its Python equivalent. // certificate is contents of https://fps.sandbox.amazonaws.com/certs/090909/PKICert.pem // signature is a string that I need to verify. CertificateFactory factory = CertificateFactory.getInstance("X.509"); X509Certificate x509Certificate = (X509Certificate) factory.generateCertificate(new ByteArrayInputStream(certificate.getBytes())); Signature signatureInstance = Signature.getInstance(signatureAlgorithm); signatureInstance.initVerify(x509Certificate.getPublicKey()); signatureInstance.update(stringToSign.getBytes(UTF_8_Encoding)); return signatureInstance.verify(Base64.decodeBase64(signature.getBytes())); This is for the PKI signature verification used by AWS FPS. http://docs.amazonwebservices.com/AmazonFPS/latest/FPSAccountManagementGuide/VerifyingSignature.html Thanks for your help!

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• python urllib post question

  - by paul

  hello ALL im making some simple python post script but it not working well. there is 2 part to have to login. first login is using 'http://mybuddy.buddybuddy.co.kr/userinfo/UserInfo.asp' this one. and second login is using 'http://user.buddybuddy.co.kr/usercheck/UserCheckPWExec.asp' i can login first login page, but i couldn't login second page website. and return some error 'illegal access' such like . i heard this is related with some cooke but i don't know how to implement to resolve this problem. if anyone can help me much appreciated!! Thanks! import re,sys,os,mechanize,urllib,time import datetime,socket params = urllib.urlencode({'ID':'ph896011', 'PWD':'pk1089' }) rq = mechanize.Request("http://mybuddy.buddybuddy.co.kr/userinfo/UserInfo.asp", params) rs = mechanize.urlopen(rq) data = rs.read() logged_fail = r';history.back();</script>' in data if not logged_fail: print 'login success' try: params = urllib.urlencode({'PASSWORD':'pk1089'}) rq = mechanize.Request("http://user.buddybuddy.co.kr/usercheck/UserCheckPWExec.asp", params ) rs = mechanize.urlopen(rq) data = rs.read() print data except: print 'error'

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• Python Instance Variable as Default Parameter

  - by DuneBug

  Hello, I have am writing a Python function that takes a timeout value as a parameter. Normally, the user will always use the same timeout value, but on occasion he may want to wait slightly longer. The timeout value is stored as a class instance variable. I want to use the class' timeout instance variable as the default parameter. Currently, I am implementing this as follows: def _writeAndWait (self, string, timeout = -1): if (timeout == -1): timeout = self._timeout I was just wondering, is the proper way to use an instance variable as a default parameter? Or is there a better way that would avoid the "if" check? Thanks, Ryan

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• Which Python API should be used with Mongo DB and Django

  - by Thomas

  I have been going back and forth over which Python API to use when interacting with Mongo. I did a quick survey of the landscape and identified three leading candidates. PyMongo MongoEngine Ming If you were designing a new content-heavy website using the django framework, what API would you choose and why? MongoEngine looks like it was built specifically with Django in mind. PyMongo appears to be a thin wrapper around Mongo. It has a lot of power, though loses a lot of the abstractions gained through using django as a framework. Ming represents an interesting middle ground between PyMongo and MongoEngine, though I haven't had the opportunity to take it for a test drive.

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• using a "temporary files" folder in python

  - by zubin71

  I recently wrote a script which queries PyPI and downloads a package; however, the package gets downloaded to a user defined folder. I`d like to modify the script in such a way that my downloaded files go into a temporary folder, if the folder is not specified. The temporary-files folder in *nix machines is "/tmp" ; would there be any Python method I could use to find out the temporary-files folder in a particular machine? If not, could someone suggest an alternative to this problem?

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• Assignment in python for loop possible?

  - by flyingcrab

  I have a dictionary d (and a seperate sorted list of keys, keys). I wanted the loop to only process entries where the value is False - so i tried the following: for key in keys and not d[key]: #do foo I suppose my understanding of python sytax is not what i thought it was - because the assignment doesnt suppose to have happened above, and a i get an instanciation error. The below works of course, but I'd really like to be able to use something like the code above.. possible? for key in keys: if d[key]: continue #foo time! Thanks!

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• Python virtualenv conflicting

  - by Fernando

  I'm trying to learn Django, so I started by reading about virtualenv. After installing it with pip (, I end up with: ... sudo pip install virtualenv) ... virtualenv paths virtualenv at /usr/local/bin/virtualenv and virtualenv-2.7 at /usr/local/bin/virtualenv-2.7 If I use virtualenv-2.7 it seems to work fine, but if I use virtualenv, new modules get added to /usr/local/bin, instead of being inside the environment. Example cd ~ virtualenv v1 source v1/bin/activate easy_install yolk which yolk # /usr/local/bin If I use virtualenv-2-7, yolk gets installed correctly inside v1. Did I mess up the installation? How can I fix this? (maybe uninstall virtualenv and start over). Thanks for any help! Edit: I figured i have two easy_install bins /usr/bin/easy_install-2.7 and /usr/bin/easy_install easy_install --version distribute 0.6.24dev-r0 easy_install-2.7 --version distribute 0.6.24dev-r0 so this may be the cause of problems. More info: python version: 2.7.3 virtualenv version: 1.10.1

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• Python urllib2 Basic Auth Problem

  - by Simon

  I'm having a problem sending basic AUTH over urllib2. I took a look at this article, and followed the example. My code: passman = urllib2.HTTPPasswordMgrWithDefaultRealm() passman.add_password(None, "api.foursquare.com", username, password) urllib2.install_opener(urllib2.build_opener(urllib2.HTTPBasicAuthHandler(passman))) req = urllib2.Request("http://api.foursquare.com/v1/user") f = urllib2.urlopen(req) data = f.read() I'm seeing the following on the Wire via wireshark: GET /v1/user HTTP/1.1 Host: api.foursquare.com Connection: close Accept-Encoding: gzip User-Agent: Python-urllib/2.5 You can see the Authorization is not sent, vs. when I send a request via curl: curl -u user:password http://api.foursquare.com/v1/user GET /v1/user HTTP/1.1 Authorization: Basic =SNIP= User-Agent: curl/7.19.4 (universal-apple-darwin10.0) libcurl/7.19.4 OpenSSL/0.9.8k zlib/1.2.3 Host: api.foursquare.com Accept: */* For some reason my code seems to not send the authentication - anyone see what I'm missing? thanks -simon

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• A question about "empty" lists in Python

  - by bitrex

  I've started teaching myself Python, and as an exercise I've set myself the task of generating lookup tables I need for another project. I need to generate a list of 256 elements in which each element is the value of math.sin(2pi/256). The problem is I don't know how to generate a list initialized to "dummy" values that I can then use a for loop to step through and assign the values of the sin function. Using list[] seems to create an "empty" list, but with no elements so I get a "list assignment index out of range" error in the loop. Is there a way to this other than explicitly creating a list declaration containing 256 elements all with "0" as a value? Thanks!

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• Dynamically evaluating simple boolean logic in Python

  - by a paid nerd

  I've got some dynamically-generated boolean logic expressions, like: (A or B) and (C or D) A or (A and B) A empty - evaluates to True The placeholders get replaced with booleans. Should I, Convert this information to a Python expression like True or (True or False) and eval it? Create a binary tree where a node is either a bool or Conjunction/Disjunction object and recursively evaluate it? Convert it into nested S-expressions and use a Lisp parser? Something else? Suggestions welcome.

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• Python + MySQLdb executemany

  - by lhahne

  I'm using Python and its MySQLdb module to import some measurement data into a Mysql database. The amount of data that we have is quite high (currently about ~250 MB of csv files and plenty of more to come). Currently I use cursor.execute(...) to import some metadata. This isn't problematic as there are only a few entries for these. The problem is that when I try to use cursor.executemany() to import larger quantities of the actual measurement data, MySQLdb raises a TypeError: not all arguments converted during string formatting My current code is def __insert_values(self, values): cursor = self.connection.cursor() cursor.executemany(""" insert into values (ensg, value, sampleid) values (%s, %s, %s)""", values) cursor.close() where values is a list of tuples containing three strings each. Any ideas what could be wrong with this? Edit: The values are generated by yield (prefix + row['id'], row['value'], sample_id) and then read into a list one thousand at a time where row is and iterator coming from csv.DictReader.

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• Python script to get the datas from the flex application

  - by nimmyliji

  Hi, I am making a simple Python CGI script that collects data(in xml format) from a flex application and I want to insert it into the mysql database . In perl The script is looks like the following... my @samplexml=$cgi-param("Items"); my $data=$xml-XMLin("@samplexml"); foreach my $e(@{$data-{Group}}) { my $sample="Insert into details(title,Parent,Istreeitem) Values('$e-{title}','$e-{Parent}','$e-{IsTreeItem}')"; my $sam=$dbo-prepare($sample); $sam-execute(); } But I want to know how to write these codes in pytrhon script.... Any one can help me? Thanks in advance. Nimmy.

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• python global variable trouble

  - by Guanidene

  I am having troubles using global variables in python... In my program, i have declared 2 global variables, global SYNC_DATA and global SYNC_TOTAL_SIZE Now in one of my functions, I am able to use the global variable SYNC_DATA without declaring it as global again in the function; however , I am not able to use the other global variable SYNC_TOTAL_SIZE in the same way. I have to declare the latter as global in the function again to use it. I get this error if i use it without declaring as global in the function - "UnboundLocalError: local variable 'SYNC_TOTAL_SIZE' referenced before assignment" Why is it so that sometimes I can access global variables without declaring them as global in functions and sometimes not? And why Is it that we have to again declare it as global in the function when it is already declared once in the beginning... Why doesn`t the function just check the variable in the global namespace if it does not find it in its namespace directly?

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• How to stop Python program execution in IDLE

  - by joaoc

  I have a python script that uses plt.show() as it's last instruction. When it runs IDLE just hangs after the last instruction. I get the image but I don't get the prompt back. On other scripts I typically use ctrl-c to break the program (sometimes doesn't work immediately) but how do I get the prompt back with the plt.show()? Ctrl-c doesn't work... Are there other ways to stop the program? This is IDLE on Windows, if it makes any difference.

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• Python "Every Other Element" Idiom

  - by Matt Luongo

  Hey guys, I feel like I spend a lot of time writing code in Python, but not enough time creating Pythonic code. Recently I ran into a funny little problem that I thought might have an easy, idiomatic solution. Paraphrasing the original, I needed to collect every sequential pair in a list. For example, given the list [1,2,3,4,5,6], I wanted to compute [(1,2),(3,4),(5,6)]. I came up with a quick solution at the time that looked like translated Java. Revisiting the question, the best I could do was l = [1,2,3,4,5,6] [(l[2*x],l[2*x+1]) for x in range(len(l)/2)] which has the side effect of tossing out the last number in the case that the length isn't even. Is there a more idiomatic approach that I'm missing, or is this the best I'm going to get?

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• Python Windows File Copy with Wildcard Support

  - by Wang Dingwei

  I've been doing this all the time: result = subprocess.call(['copy', '123*.xml', 'out_folder\\.', '/y']) if result == 0: do_something() else: do_something_else() Until today I started to look into pywin32 modules, then I saw functions like win32file.CopyFiles(), but then I found it may not support copying files to a directory. Maybe this functionality is hidden somewhere, but I haven't found it yet. I've also tried "glob" and "shutil" combination, but "glob" is incredibly slow if there are many files. So, how do you emulate this Windows command with Python? copy 123*.xml out_folder\. /y

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• How to import classes into other classes within the same file in Python

  - by Chris

  I have the file below and it is part of a django project called projectmanager, this file is projectmanager/projects/models.py . Whenever I use the python interpreter to import a Project just to test the functionality i get a name error for line 8 that FileRepo() cannot be found. How Can I import these classes correctly? Ideally what I am looking for is each Project to contain multiple FileRepos which each contain and unknown number of files. Thanks for any assistance in advance. #imports from django.db import models from django.contrib import admin #Project is responsible for ensuring that each project contains all of the folders and file storage #mechanisms a project needs, as well as a unique CCL# class Project(models.Model): ccl = models.CharField(max_length=30) Techpacks = FileRepo() COAS = FileRepo() Shippingdocs = FileRepo() POchemspecs = FileRepo() Internalpos = FileRepo() Finalreports = FileRepo() Batchrecords = FileRepo() RFPS = FileRepo() Businessdev = FileRepo() QA = FileRepo() Updates = FileRepo() def __unicode__(self): return self.ccl #ProjectFile is the file object used by each FileRepo component class ProjectFile(models.Model): file = models.FileField(uploadto='ProjectFiles') def __unicode__(self): return self.file #FileRepo is the model for the "folders" to be used in a Project class FileRepo(models.Model): typeOf = models.CharField(max_length=30) files = models.ManyToManyField(ProjectFile) def __unicode__(self): return self.typeOf

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