date:20060911

Hendrik van Rooyen wrote:
 Hi,
 
 It is possible to build a system where the fields are self defining : -
 
 One way is to keep a dictionary of tags and descriptors, and to keep the 
 data
 in a dictionary using the same tags as keys, with values - an oversimplified
 example:
 
 DefinitionDict = {1:'Quantity',2:'Price',3:'Value'}
 
 DataItemDict = {1:10,2:3.50,3:35.00}
 
 This is conceptually not much different to putting headers on columns in a
 database table or a spreadsheet, with the data item being a row, or to HT or
 XML.
 
 Now obviously the definitions need not be single valued strings, but could be
 multivalues, for use at different times, such as for gui displaying, for
 printing, etc, and could also hold type information, as most databases do.
 
 Up to this point, there is no a priori human knowledge mixed in with the data
 that has not been written down.
 
 However, when we want to make say a validation rule, such as Quantity times
 Price must equal Value, then we are using a priori knowledge about the data to
 formulate this.
 
 At this point, if a routine is written to check that DataItemDict[1] 
 multiplied
 by DataItemDict[2] is indeed equal to DataItemDict[3], then we are casting the
 meanings into stone, and the flexibility of the structure is to a large extent
 lost.
 
 Now if I want to make a system where these sort of rules, as well as more
 complicated ones, are also definable - Is there a way to do it simply and
 cleanly - a way to expand the DefinitionDict so that it contains all of what 
 we
 know about the structure and relationships of and between the items of data?
 
 It seems to me that if this could be done, then it could be used to 
 dynamically
 generate the routines needed for validation, update, etc...
 
 But my brain strains when I try to think about how to do it...
 
You need to look at properties. The property() function allows you to 
define methods that are called (and which can therefore perform access 
control and/or semantic checks) when attributes are accessed.

regards
  Steve
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Re: RuPy 2007 - Python Ruby Conference

2006-09-11 Thread Kay Schluehr


Magnus Lycka wrote:
 Jakub Piotr Nowak wrote:
  RuPy 2007
  Python  Ruby Conference
 
  Poznan, Poland
  April 7-8, 2007

 Are you aware of the EuroPython Conference which
 will take place in Vilnius three months later?

If I understand the intention right its kind of a peace pipe
cross-community conference. This is somewhat uncommon these days
regarding language community tribalism. So what to do if one has to
polite to each other? As a joint enemy Java might be appropriate?

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Re: egg and modpython

2006-09-11 Thread Paul Boddie

Bruno Desthuilliers wrote:
 Wensheng a écrit :
  I installed pysqlite2 using easy_install.
  and got this when using it from modpython:
  --
  Mod_python error: PythonHandler etc.modpython

[...]

I applaud you for studying the traceback in more depth than I can find
the motivation for, Bruno. ;-) However, this looks like a program using
some package installed by setuptools/easy_install needs to unpack that
package when running.

  ExtractionError: Can't extract file(s) to egg cache

  The following error occurred while trying to extract file(s) to the
  Python egg cache:

[Errno 13] Permission denied: '/var/www/.python-eggs'

And this wants to happen apparently in the home directory of the Web
server user, whose rights may be somewhat limited. Or perhaps one has
to initialise setuptools for any particular user by running it first as
that user: something that isn't a particularly common thing to do with
non-interactive users on UNIX-like systems.

[...]

  Can peak developers fix this please?

 Why should they fix something that's
 1/ documented
 - http://peak.telecommunity.com/DevCenter/EggFormats#zip-file-issues

The Internal Structure of Python Eggs / STOP! This is not the first
document you should read! A case of Beware of the Leopard perhaps?

 2/ not a an egg specific issue

In my experience, most other package managers actually unpack their
resources when invoked, rather than leaving the programs to attempt
such things when running. Debian packages even compile the bytecode
files to ensure that nothing tries (and fails) to write them to
privileged locations afterwards.

 3/ really just a configuration/permission problem

Which should have been solved when the package manager was invoked,
especially since this was most likely done as root.

[...]

  in the mean time, I just have to use old download, unzip/untar 
  python setup.py install way.

 No - you have to read the manual and fix you configuration. FWIW, the
 above traceback gives far enough clues (it's even written in all letters).

The various ways to deal with this include running easy_install as the
Web server user so that it can touch the directory and whatever else it
needs, and perhaps to set up various permissions - something you
wouldn't usually do; running easy_install with the --always-unzip flag
when installing the package as root; using python setup.py install as
usual.

This situation looks either a lot like a use case whose popularity has
been underestimated by the developers - intriguing given the number of
people supposedly using setuptools for their Web application
deployments - or a packaging mistake with the pysqlite2 .egg file.
Either way, system packages rarely suffer from this kind of problem,
and it's quite understandable (and justifiable) to consider this bad
behaviour.

 Or you may read easy_install's doc to avoid installing zipped eggs:
 http://peak.telecommunity.com/DevCenter/EasyInstall#compressed-installation

Perhaps the developers should reverse their defaults and emulate the
usual behaviour of package managers, unfashionable as that may seem.

Paul

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Re: What algorithm does Python use to evaluate: if substring in string

2006-09-11 Thread Fredrik Lundh

Tor Erik wrote:

 I would be surprised if it is the naive:

2.4 and earlier uses that algorithm (but with a better implementation).

And naive isn't really the right word here; on average, a brute force search 
is pretty
good for the find/index/in use case.  Most fancy algorithms ignore the setup 
costs and
other overhead, which works well in theory, but not that well in practice.

/F 



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efficient text file search.

2006-09-11 Thread noro

Is there a more efficient method to find a string in a text file then:

f=file('somefile')
for line in f:
if 'string' in line:
 print 'FOUND'

?

BTW:
does for line in f:  read a block of line to te memory or is it
simply calls f.readline() many times?

thanks
amit

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Re: efficient text file search.

2006-09-11 Thread Luuk


noro [EMAIL PROTECTED] schreef in bericht 
news:[EMAIL PROTECTED]
 Is there a more efficient method to find a string in a text file then:

 f=file('somefile')
 for line in f:
if 'string' in line:
 print 'FOUND'



yes, more efficient would be:
grep (http://www.gnu.org/software/grep/)



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Re: Ann: CoreBio 0.4

2006-09-11 Thread km

On 11 Sep 2006 00:59:30 -0700, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:

 Announcing CoreBio 0.4
 
 CoreBio home page:
 http://code.google.com/p/corebio/

 Download:
 http://corebio.googlecode.com/svn/dist/CoreBio-0.4.1.tar.gz

 CoreBio is an open source python library for bioinformatics and
 computational biology, designed to be fast, compact, reliable and easy
 to use. Currently, CoreBio includes code to store and manipulate
 protein and DNA sequences, read and write many common biological
 sequence formats, read blast reports and access other computational and
 database resources.

 The CoreBio project welcomes additional suggestions, code and
 participants.

 This release includes the following modules:

 - data: Standard information used in computational biology.
 - matrix: Arrays indexed by alphabetic strings.
 - moremath: Various bits of useful math not in the standard

 python library.
 - resource: Access to programs, complex file formats and
 databases
 - astral: ASTRAL dataset IO.
 - scop: SCOP: Structural Classification of Proteins IO.
 - stride: STRIDE: Protein secondary structure assignment

 from atomic coordinates.
 - seq: Alphabetic sequences and associated tools and data.
 - seq_io: Sequence file reading and writing.
 - array_io: Read and write arrays of sequence data.
 - clustal_io: Read the CLUSTAL sequence file format.
 - fasta_io: Read and write FASTA format.
 - genbank_io: Read GenBank flat files.
 - intelligenetics_io: Read IntelliGenetics format.
 - msf_io: Read sequence information in MSF format.
 - nbrf_io: Sequence IO for NBRF/PIR format.
 - nexus_io: Read the sequence data from a nexus file.
 - null_io: Null sequence IO.
 - phylip_io: Read Sequences in interleaved Phylip format.
 - plain_io: Read and write raw, unformatted sequence data.
 - stockholm_io: Read a STOCKHOLM format.
 - table_io: Read  tab delimited format.
 - ssearch_io: Parse sequence search analysis reports.
 - blastxml: Read BLAST XML output.
 - fasta: Read the output of a fasta similarity search.
 - transform: Transformations of Seqs (alphabetic sequences),
 including translation with a full suite of
 GeneticCode's.


 Gavin Crooks and John Gilman

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Hi,why are u reinventing the wheel when Biopython[1] is already existing ? is there any specific reason u wanted to develop this CoreBio ? why dont u just extend the existing BioPython package itself ?regards,KM
[1]http://biopython.org---On 9/11/06, km
[EMAIL PROTECTED] wrote:On 11 Sep 2006 00:59:30 -0700,
[EMAIL PROTECTED][EMAIL PROTECTED] wrote: Announcing CoreBio 0.4 CoreBio home page:
http://code.google.com/p/corebio/ Download: http://corebio.googlecode.com/svn/dist/CoreBio-0.4.1.tar.gz
CoreBio is an open source python library for bioinformatics and computational biology, designed to be fast, compact, reliable and easy to use. Currently, CoreBio includes code to store and manipulate
protein and DNA sequences, read and write many common biological sequence formats, read blast reports and access other computational and database resources. The CoreBio project welcomes additional suggestions, code and
participants. This release includes the following modules: - data: Standard information used in computational biology. - matrix: Arrays indexed by alphabetic strings.
- moremath: Various bits of useful math not in the standard python library. - resource: Access to programs, complex file formats and databases
- astral: ASTRAL dataset IO. - scop: SCOP: Structural Classification of Proteins IO. - stride: STRIDE: Protein secondary structure assignment from atomic coordinates.
- seq: Alphabetic sequences and associated tools and data. - seq_io: Sequence file reading and writing. - array_io: Read and write arrays of sequence data. - clustal_io: Read the CLUSTAL sequence file format.
- fasta_io: Read and write FASTA format. - genbank_io: Read GenBank flat files. - intelligenetics_io: Read IntelliGenetics format. - msf_io: Read sequence information in MSF format.
- nbrf_io: Sequence IO for NBRF/PIR format. - nexus_io: Read the sequence data from a nexus file. - null_io: Null sequence IO. - phylip_io: Read Sequences in interleaved Phylip format.
- plain_io: Read and write raw, unformatted sequence data. - stockholm_io: Read a STOCKHOLM format. - table_io: Readtab delimited format. - ssearch_io: Parse sequence search analysis reports.
- blastxml: Read BLAST XML output. - fasta: Read the output of a fasta similarity search. - transform: Transformations of Seqs (alphabetic sequences), including translation with a full suite of
GeneticCode's. Gavin Crooks and John Gilman -- http://mail.python.org/mailman/listinfo/python-list

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Re: efficient text file search.

2006-09-11 Thread noro

:)

via python...

Luuk wrote:
 noro [EMAIL PROTECTED] schreef in bericht
 news:[EMAIL PROTECTED]
  Is there a more efficient method to find a string in a text file then:
 
  f=file('somefile')
  for line in f:
 if 'string' in line:
  print 'FOUND'
 


 yes, more efficient would be:
 grep (http://www.gnu.org/software/grep/)

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strange DOM behaviour when using minidom

2006-09-11 Thread JoReiners

Hello, I have a really strange problem. I'm unable to figure it out on
my own.

I parse very simple xml documents, without any check for their form.
These files look very similar and are encoded in UTF-8.

Now minidom is always able to parse these files with
minidom.parse(file) .
Now when fetching I use this expression:
xmldoc.getElementsByTagName('DocNumb')[0].firstChild.data.encode('latin1')

(I know it's not beautiful but convenient. )

It always work, but sometimes it simply fails to fetch any element.
Redoing it from hand in the python console with the same file always
works.

I have no idea what the error is. I compared working and not working
files with the hex editor. I couldn't find any significant change. It's
too strange. If anybody has any clue, hint or anything, please let me
know.

Regards, Jonatan

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Re: Looking for the Perfect Editor

2006-09-11 Thread Kent Johnson

Dick Moores wrote:
 At 06:30 PM 9/10/2006, Kent Johnson wrote:
 Dick Moores wrote:
 Also, why do you use TextPad instead of IDLE?
 You're kidding, right?
 
 No. Tell me, please. Macros? Comparing files? What else?

OK...please, no one interpret this as IDLE bashing or attempt to show me 
a better way. I'm happy with TextPad and just writing this because I was 
asked...

In my opinion:

- Most of my Python work is actually in Jython. I can run a Jython 
program with a tool in TP. Actually I have separate tools for each 
active project that set the correct working directory and invoke a batch 
file with the right jars. Can't do that in IDLE.

- TextPad is a good general-purpose editor, not just for Python. All the 
following reasons really come under this heading. I have an editor I 
like, it works great for Python, there is really no reason to use IDLE.

- Fast and powerful multi-file search (easily specify the directory and 
file types to search)

- Syntax highlighting for XML, HTML, Velocity templates, Ruby, Java, 
JavaScript, R, SQL, CSS...all file types I use more or less frequently.

- Word wrap

- Show invisibles

- Customizable with macros and external tools

- Open as binary

etc...

Kent
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Re: efficient text file search.

2006-09-11 Thread Luuk


noro [EMAIL PROTECTED] schreef in bericht 
news:[EMAIL PROTECTED]
 :)

 via python...

 Luuk wrote:
 noro [EMAIL PROTECTED] schreef in bericht
 news:[EMAIL PROTECTED]
  Is there a more efficient method to find a string in a text file then:
 
  f=file('somefile')
  for line in f:
 if 'string' in line:
  print 'FOUND'
 


 yes, more efficient would be:
 grep (http://www.gnu.org/software/grep/)


ok, a more serious answer:

some googling turned op the following.
Second paragraph of chapter 14 of http://www.amk.ca/python/2.1/

a.. The speed of line-oriented file I/O has been improved because people 
often complain about its lack of speed, and because it's often been used as 
a naïve benchmark. The readline() method of file objects has therefore been 
rewritten to be much faster. The exact amount of the speedup will vary from 
platform to platform depending on how slow the C library's getc() was, but 
is around 66%, and potentially much faster on some particular operating 
systems. Tim Peters did much of the benchmarking and coding for this change, 
motivated by a discussion in comp.lang.python.
A new module and method for file objects was also added, contributed by Jeff 
Epler. The new method, xreadlines(), is similar to the existing xrange() 
built-in. xreadlines() returns an opaque sequence object that only supports 
being iterated over, reading a line on every iteration but not reading the 
entire file into memory as the existing readlines() method does. You'd use 
it like this:


for line in sys.stdin.xreadlines():
# ... do something for each line ...
...
For a fuller discussion of the line I/O changes, see the python-dev summary 
for January 1-15, 2001 at http://www.amk.ca/python/dev/2001-01-1.html.



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Re: efficient text file search.

2006-09-11 Thread Kent Johnson

noro wrote:
 Is there a more efficient method to find a string in a text file then:
 
 f=file('somefile')
 for line in f:
 if 'string' in line:
  print 'FOUND'

Probably better to read the whole file at once if it isn't too big:
f = file('somefile')
data = f.read()
if 'string' in data:
print 'FOUND'
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Re: get the en of a program running in background

2006-09-11 Thread awalter1

Hi,

It works when a click on a button launches a program P.
Now, I want that a click on another button launches another program P'

In this case there is only one signal for two events : the end of P and
the end of P'.
How can distinct the two cases.

In addition, what is the use of the frame parameter of the logsignal
procedure ?
It seems to be a little bit complicated to manipulate it.

Thank for your help


oripel a écrit :

 Module 'subprocess' may be a better fit for you than fork+exec.
 Here's an example with a signal handler
 (1) use subprocess, don't fork and exec
 (2) maybe this will help:

 ---
 import signal, subprocess

 # define the signal handler
 def logsignal(signum, frame):
print Caught signal

 # register the signal handler for SIGCHLD
 signal.signal(signal.SIGCHLD, logsignal)

 # run the subprocess in the background
 subprocess.Popen([sleep, 3])

 # Do more stuff
 ---

 The signal handler will be called when the child process ends. Just
 register your own handler.

 You only need to register the handler once.
 If you need this for a single run only, or need different behavior for
 different subprocesses, have your signal handler re-register the old
 handler (see the docs for module 'signal').

 A note about the example: if you run it as is, the parent process will
 end before the child process does. Add a call to 'os.wait()' to have it
 wait for the child. In your GUI you probably won't want it.

 Hope this helps.

 awalter1 wrote:
  Hi,
  I develop a graphical user interface (with pyGTK) where a click on a
  button shall launch a program P in background. I want to get the end of
  this program P but I don't want that my HMI be freezed while P is
  running.
  I try to use fork examplesI found on the web, but it seems to not run
  as expected.
  I am not familiar with these techniques in unix as well as python.
  But I suppose that my needs are usual, despite that I don't find
  anything on the web ...
  Is someone can give me a standard way to call a background program,
  wait its end, with an IHM still active ?
  
  Thank a lot for any idea.

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Re: strange DOM behaviour when using minidom

2006-09-11 Thread JoReiners

Sorry, I just found the error. Simple an empty attribute. Python showed
me strange row numbers. I used a multi line initialization of a dict.
The error always appeared on the first line although I was on an other
line.

Interesting behavior.

Jonatan

JoReiners schrieb:

 Hello, I have a really strange problem. I'm unable to figure it out on
 my own.

 I parse very simple xml documents, without any check for their form.
 These files look very similar and are encoded in UTF-8.

 Now minidom is always able to parse these files with
 minidom.parse(file) .
 Now when fetching I use this expression:
 xmldoc.getElementsByTagName('DocNumb')[0].firstChild.data.encode('latin1')

 (I know it's not beautiful but convenient. )

 It always work, but sometimes it simply fails to fetch any element.
 Redoing it from hand in the python console with the same file always
 works.

 I have no idea what the error is. I compared working and not working
 files with the hex editor. I couldn't find any significant change. It's
 too strange. If anybody has any clue, hint or anything, please let me
 know.
 
 Regards, Jonatan

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extracting substrings from a file

2006-09-11 Thread sofiafig

Hi,

I have a file with several entries in the form:

AFFX-BioB-5_at   E. coli  /GEN=bioB  /gb:J04423.1  NOTE=SIF
corresponding to nucleotides 2032-2305 of /gb:J04423.1  DEF=E.coli
7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
dethiobiotin synthetase (bioD), complete cds.

1415785_a_at /gb:NM_009840.1 /DB_XREF=gi:6753327 /GEN=Cct8 /FEA=FLmRNA
/CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
/DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
/PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1

and I would like to create a file that has only the following:

AFFX-BioB-5_at  /GEN=bioB  /gb:J04423.1

1415785_a_at /gb:NM_009840.1 /GEN=Cct8

Could anyone please tell me how can I do it?

Many thanks in advance
Sofia

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A cross platform systray icon

2006-09-11 Thread Nick Craig-Wood

Does anyone have some hints / tips / experience with making a cross
platform systray icon?  It should work on Windows, Gnome and KDE at
minimum.

I've seen the win32all code which is very similar to the C code I've
written before for Windows.  It would be a small irritation to have to
integrate its event loop with whichever GUI framework I'm using for
the rest of it though.

I don't know how to make a systray under KDE/Gnome though, but I think
freedesktop has made it a lot easier now.  I didn't manage to find a
python example - does anyone have one?

Ideally I'd like someone to tell me that PyQT, tkinter or PyGTK does
it all for me, but from my searching on the subject I doubt it is
going to be that easy!

Thanks
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inserting into a file

2006-09-11 Thread Sai Krishna M

I want to insert a string in a file after a particular line.

I thought of using seek() function but on opening the file in append
mode the seek value is undone.
One crude idea i had was to read the file in a list and insert the
string correspondingly.

Is there any other way to do this?
Please help...

Sai krishna M
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Re: SQLwaterheadretard3 (Was: Is it just me, or is Sqlite3 goofy?)

2006-09-11 Thread Bruno Desthuilliers

[EMAIL PROTECTED] wrote:
 Bruno Desthuilliers wrote:
 [EMAIL PROTECTED] wrote:
 Probably just me. I've only been using Access and SQL Server
 for 12 years, so I'm sure my opinions don't count for anything.

 SQLite never pretended to be a full-blown RDBMS - just a lightweight
 simple embedded database as SQL-compliant as possible.
 
 Ah, *you* haven't read the documentation either!

I use SQLite and PgSQL (and, alas, MySQL) on a daily basis. So I've *of
course* read the doc (and frequently re-read it).

 as SQL-compliant as possible?

Yes. And yes, I know about the typing issue. If you want to make sure
you can migrate your data to a real RDBMS, then it's up to you to take
appropriate precautions (FormEncode can be a real helper here...).

This (documented enough) issue apart, we have far less troubles with
SQLite than we have with MySQL, on both the dev and admin sides.

And FWIW, insulting peoples won't buy you much.

(snip useless rant again)

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python -c print '@'.join(['.'.join([w[::-1] for w in p.split('.')]) for
p in '[EMAIL PROTECTED]'.split('@')])
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Re: efficient text file search.

2006-09-11 Thread Bill Scherer

noro wrote:

Is there a more efficient method to find a string in a text file then:

f=file('somefile')
for line in f:
if 'string' in line:
 print 'FOUND'

?

BTW:
does for line in f:  read a block of line to te memory or is it
simply calls f.readline() many times?

thanks
amit
  

If your file is sorted by some key in the data, you can build a very 
fast binary search with mmap in Python.
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Re: efficient text file search.

2006-09-11 Thread Ant


noro wrote:
 Is there a more efficient method to find a string in a text file then:

 f=file('somefile')
 for line in f:
 if 'string' in line:
  print 'FOUND'
break
  ^^^
Add a 'break' after the print statement - that way you won't have to
read the entire file unless the string isn't there. That's probably not
the sort of advice you're after though :-)

Can't see why reading the entire file in as the other poster suggested
would help, and seeing as for line in f: is now regarded as the
pythonic way of working with lines of text in a file, then I'd assume
that the implementation would be at least as fast as for line in
f.xreadlines(): 

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Re: Can I make unicode in a repr() print readably?

2006-09-11 Thread Terry Hancock

Martin v. Löwis wrote:
  Terry Hancock schrieb:
  Or, put another way, what exactly does 'print' do when it gets a
  class instance to print? It seems to do the right thing if given a
  unicode or string object, but I cant' figure out how to make it do
  the same thing for a class instance.

  It won't. PyFile_WriteObject checks for Unicode objects, and whether
  the file has an encoding attribute set, and if so, encodes the
  Unicode object.

  If it is not a Unicode object, it falls through to PyObject_Print,
  which first checks for the tp_print slot (which can't be set in
  Python), then uses PyObject_Str (which requires that the __str__
  result is a true byte string), or PyObject_Repr (if the RAW flag
  isn't set - it is when printing). PyObject_Str first checks for
  tp_str; if that isn't set, it falls back to PyObject_Repr.

  You can save some typing, of course, with a helper function:

  def p(o): print unicode(o)

Yeah, that's what I've done as it stands.  I think it's actually fewer
keystrokes that way, but it is still inconsistent* with other objects,
of course.

  I agree that this is not optimal; contributions are welcome. It would
  probably be easiest to drop the guarantee that PyObject_Str returns a
  true string, or use _PyObject_Str (which does not make this
  guarantee) in PyObject_Print. One would have to think what the effect
  on backwards compatibility is of such a change.

Ah, contribute to Python itself.  I'll have to think about it -- I don't do
a lot of C programming these days, but it sounds like an idea.

I don't know about the backwards compatibility issue. I'm not sure
what would be affected.  But print frequently generates encoded
Unicode output if the stream supports it, so there is no guarantee
whether it produces unicode or string output now.  I think it's clear
that str() *must* return an ordinary Python string.

I think what would make sense is for the print statement to attempt
to call __unicode__ on an instance before attempting to call __str__
(just as it currently falls back from __str__ to __repr__).  That seems like
it would be pretty consistent, right?

Cheers,
Terry

*Okay, actually it is perfectly consistent in a technical sense, but not in
the utility, this is what you do to examine the object, sense.

-- 
Terry Hancock ([EMAIL PROTECTED])
Anansi Spaceworks http://www.AnansiSpaceworks.com

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Re: Looking for the Perfect Editor

2006-09-11 Thread mystilleef

If you have those requirements installed, it does not need anything
else.

mystilleef wrote:
 I recommend Scribes.

 http://scribes.sf.net

 Flash Demo: http://scribes.sf.net/snippets.htm

 GIF Demo: http://www.minds.may.ie/~dez/images/blog/scribes.html

 Omar wrote:
  I'd love the perfect editor that would be:
 
  a) free
 
  b) enable me to drag and drop code snippets from a sort of browser into
  the code
 
  c) can run programs right from within
 
  d) can edit
- PYTHON
- Javascript
- HTML
- actionscript (since I'm also learning flash)
  
  e) easy to learn
  
  suggestions?

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Re: inserting into a file

2006-09-11 Thread Fredrik Lundh

Sai Krishna M wrote:

 One crude idea i had was to read the file in a list and insert the
 string correspondingly.

file systems usually don't support insertion and deletion, so if you want to 
move
things around, you have to do that yourself.

reading and writing lists (using readlines/writelines) works well, as long as 
the files
aren't too large.

 Is there any other way to do this?

not with plain files.  if you need to do lots of inserts/deletes, you should 
probably
use a database manager instead (which uses more elaborate data structures on
disk).  see e.g. the dbm and bsddb modules in the standard library.

/F 



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Re: Problems with email.Generator.Generator

2006-09-11 Thread Peter Otten

Chris Withers wrote:

 The following piece of code is giving me issues:
 
 from email.Charset import Charset,QP
 from email.MIMEText import MIMEText
 charset = Charset('utf-8')
 charset.body_encoding = QP
 msg = MIMEText(
  u'Some text with chars that need encoding: \xa3',
  'plain',
  )
 msg.set_charset(charset)
 print msg.as_string()
 
 Under Python 2.4.2, this produces the following output, as I'd expect:
 
 MIME-Version: 1.0
 Content-Transfer-Encoding: 8bit
 Content-Type: text/plain; charset=utf-8
 
 Some text with chars that need encoding: =A3
 
 However, under Python 2.4.3, I now get:
 
 Traceback (most recent call last):
File test_encoding.py, line 14, in ?
  msg.as_string()
File c:\python24\lib\email\Message.py, line 129,
 in
 as_string
  g.flatten(self, unixfrom=unixfrom)
File c:\python24\lib\email\Generator.py, line 82,
 in flatten
  self._write(msg)
File c:\python24\lib\email\Generator.py, line 113,
 in _write
  self._dispatch(msg)
File c:\python24\lib\email\Generator.py, line 139,
 in
 _dispatch
  meth(msg)
File c:\python24\lib\email\Generator.py, line 182,
 in
 _handle_text
  self._fp.write(payload)
 UnicodeEncodeError: 'ascii' codec can't encode
 character
 u'\xa3' in position 41:
   ordinal not in range(128)
 
 This seems to be as a result of this change:
 

http://svn.python.org/view/python/branches/release24-maint/Lib/email/Generator.py?rev=42272r1=37910r2=42272
 
 ...which is referred to as part of a fix for this bug:
 

http://sourceforge.net/tracker/?func=detailaid=1409455group_id=5470atid=105470
 
 Now, is this change to Generator.py in error or am I doing something
 wrong?

I'm not familiar enough with the email package to answer that.
 
 If the latter, how can I change my code such that it works as I'd expect?

email.Generator and email.Message use cStringIO.StringIO internally, which
can't cope with unicode. A quick fix might be to monkey-patch:

from StringIO import StringIO
from email import Generator, Message
Generator.StringIO = Message.StringIO = StringIO
# your code here

Peter
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best small database?

2006-09-11 Thread David Isaac

I have no experience with database applications.
This database will likely hold only a few hundred items,
including both textfiles and binary files.

I would like a pure Python solution to the extent reasonable.

Suggestions?

Thank you,
Alan Isaac


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Re: best small database?

2006-09-11 Thread km

checkout gadfly database.regards,KMOn 9/11/06, David Isaac [EMAIL PROTECTED] wrote:
I have no experience with database applications.This database will likely hold only a few hundred items,including both textfiles and binary files.I would like a pure Python solution to the extent reasonable.
Suggestions?Thank you,Alan Isaac--http://mail.python.org/mailman/listinfo/python-list
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Re: extracting substrings from a file

2006-09-11 Thread Tim Chase

 I have a file with several entries in the form:
 
 AFFX-BioB-5_at E. coli  /GEN=bioB  /gb:J04423.1  NOTE=SIF
 corresponding to nucleotides 2032-2305 of /gb:J04423.1  DEF=E.coli
 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
 dethiobiotin synthetase (bioD), complete cds.
 
 1415785_a_at   /gb:NM_009840.1 /DB_XREF=gi:6753327 /GEN=Cct8 /FEA=FLmRNA
 /CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
 /DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
 /PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1
 
 and I would like to create a file that has only the following:
 
 AFFX-BioB-5_at  /GEN=bioB  /gb:J04423.1
 
 1415785_a_at   /gb:NM_009840.1 /GEN=Cct8
 
 Could anyone please tell me how can I do it?

The following seems to do it for me...

outfile = file('out.txt', 'w')
for line in file('in.txt'):
 if '/GEN' in line and '/gb:' in line:
 newline = []
 for index, item in enumerate(line.split()):
 if index == 0 or item.startswith('/GEN') 
or item.startswith('/gb:'):
 newline.append(item)
 outfile.write('\t'.join(newline))
 outfile.write('\n')
outfile.close()


There are some underdefined conditions...I presume that both the 
GEN and gb: have to appear in the line.  If only one of them is 
required, change the and to an or.

-tkc



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Re: best small database?

2006-09-11 Thread Andre Meyer

buzhug is a nice one: http://buzhug.sourceforge.net/ (not sure about binaries, though).greetingsAndreOn 9/11/06, 
km [EMAIL PROTECTED] wrote:
checkout gadfly database.regards,KMOn 9/11/06, David Isaac
 [EMAIL PROTECTED] wrote:

I have no experience with database applications.This database will likely hold only a few hundred items,including both textfiles and binary files.I would like a pure Python solution to the extent reasonable.
Suggestions?Thank you,Alan Isaac--http://mail.python.org/mailman/listinfo/python-list


--http://mail.python.org/mailman/listinfo/python-list
-- Dr. Andre P. Meyerhttp://python.openspace.nl/meyerTNO Defence, Security and Safety
http://www.tno.nl/Delft Cooperation on Intelligent Systemshttp://www.decis.nl/Ah, this is obviously some strange usage of the word 'safe' that I wasn't previously aware of. - Douglas Adams
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Re: win32service (wxpython) -- i cannot install service

I believe you misunderstand services.  They don't
have user interfaces (UIs) like other programs.
They run without any UI as background processes that
are in basically in an infinite loop but with a way
to break out of the loop (stop service).  If you wish
to have a background service that has some sort of
control UI, you need to write it as two parts.  The
service and a UI that communicates with the service
either through a shared file, pipe, or socket server/
client interface.

You should pick up a copy of Python Programming on
Win32 which is an excellent reference book for writing
Windows services.

-Larry Bates
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Re: extracting substrings from a file

2006-09-11 Thread John Machin

[EMAIL PROTECTED] wrote:
 Hi,

 I have a file with several entries in the form:

 AFFX-BioB-5_at E. coli  /GEN=bioB  /gb:J04423.1  NOTE=SIF
 corresponding to nucleotides 2032-2305 of /gb:J04423.1  DEF=E.coli
 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
 dethiobiotin synthetase (bioD), complete cds.

 1415785_a_at   /gb:NM_009840.1 /DB_XREF=gi:6753327 /GEN=Cct8 /FEA=FLmRNA
 /CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
 /DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
 /PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1

 and I would like to create a file that has only the following:

 AFFX-BioB-5_at  /GEN=bioB  /gb:J04423.1

 1415785_a_at   /gb:NM_009840.1 /GEN=Cct8

 Could anyone please tell me how can I do it?

 Many thanks in advance
 Sofia

Here's my first iteration:
C:\junktype sofia.py
prefixes = ['/GEN=', '/gb:']

def extract(fname):
f = open(fname, 'r')
chunks = [[]]
for line in f:
words = line.split()
if words:
chunks[-1].extend(words)
else:
chunks.append([])
for chunk in chunks:
if not chunk:
continue
output = [chunk[0]]
for word in chunk:
for prefix in prefixes:
if word.startswith(prefix):
output.append(word)
break
print ' '.join(output)

if __name__ == __main__:
import sys
extract(sys.argv[1])

C:\junksofia.py sofia.txt
AFFX-BioB-5_at /GEN=bioB /gb:J04423.1 /gb:J04423.1
1415785_a_at /gb:NM_009840.1 /GEN=Cct8 /gb:BC009007.1

Before I fix the duplicate in the first line, you need to say whether
you really want the
/gb:BC009007.1 in the second line thrown away -- IOW, what's the rule?
For each prefix, either (1) get the first word that starts with that
prefix or (2) get all unique such words. You choose.

Cheers,
John

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Re: Refactoring Dilemma

2006-09-11 Thread Steven Bethard

Kamilche wrote:
 Is there any reason NOT to do this that I may be unaware of?
[snip]
 # --- Module 2.py 
 # 'Self' module processing
 import sys
 var = 0
 self = sys.modules[__name__]
 
 def MyRoutine():
 self.var = 1
 
 MyRoutine()
 print var

Looks basically fine to me, but I'd probably write it as::

 _self = __import__(__name__)

Then you don't need to import sys.  I'd also use a leading underscore 
for self so that it's clearly marked as a module-internal attribute.

STeVe
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Re: best small database?

2006-09-11 Thread Thorsten Kampe

* David Isaac (2006-09-11 14:23 +0100)
 I have no experience with database applications.
 This database will likely hold only a few hundred items,
 including both textfiles and binary files.
 
 I would like a pure Python solution to the extent reasonable.

Gadfly?
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Re: extracting substrings from a file

[EMAIL PROTECTED] wrote:
 Hi,
 
 I have a file with several entries in the form:
 
 AFFX-BioB-5_at E. coli  /GEN=bioB  /gb:J04423.1  NOTE=SIF
 corresponding to nucleotides 2032-2305 of /gb:J04423.1  DEF=E.coli
 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
 dethiobiotin synthetase (bioD), complete cds.
 
 1415785_a_at   /gb:NM_009840.1 /DB_XREF=gi:6753327 /GEN=Cct8 /FEA=FLmRNA
 /CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
 /DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
 /PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1
 
 and I would like to create a file that has only the following:
 
 AFFX-BioB-5_at  /GEN=bioB  /gb:J04423.1
 
 1415785_a_at   /gb:NM_009840.1 /GEN=Cct8
 
 Could anyone please tell me how can I do it?
 
 Many thanks in advance
 Sofia
 
What have your tried so far?

Hint: split line on spaces, the first pieces is the first item you want,
then iterate over the pieces looking for the /GEN and /gb: pieces that
you are interested in keeping.  I am assuming that /GEN= and /gb: data
doesn't have any spaces in them.  If they do, you will need to use
regular expressions instead of split.

-Larry Bates
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Re: inserting into a file

Sai Krishna M wrote:
 I want to insert a string in a file after a particular line.
 
 I thought of using seek() function but on opening the file in append
 mode the seek value is undone.
 One crude idea i had was to read the file in a list and insert the
 string correspondingly.
 
 Is there any other way to do this?
 Please help...
 
 Sai krishna M
No magic way to insert lines.  If file is small, read into
memory, insert line, write to disk.  If it is large, read and
write lines to secondary file, insert line, read remaining lines,
delete old file and rename to new file.

-Larry Bates
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Re: Python on handhelds

2006-09-11 Thread Luke Dunstan


Paul Rubin http://[EMAIL PROTECTED] wrote in message 
news:[EMAIL PROTECTED]
 Nick [EMAIL PROTECTED] writes:
 I have never programmed in Python a day in my life. My group is working
 on developing an application on the Dell Axim hand held that has a
 tight deadline. I have heard that Python is particularly advantageous
 in rapid prototyping and deployment. I would like to lean this way if I
 can. Does anyone know if I can run Python on the Dell Axim handheld. It
 runs Windows CE. If so, what all is needed to make this possible.

 Someone did a WinCE port a while back, but I don't think it's actively
 used much.  The approach might be reasonable if you're an expert with
 some time on your hands, but for a newcomer with an onrushing
 deadline, you may be better off using whatever you're already using
 (VB or whatever), and keeping Python in mind for some future project.

I agree that it is much less active than Python on other platforms, and in 
some areas it lags behind the PC, e.g. in GUI toolkits. However, if you want 
to try it go here:

http://sourceforge.net/projects/pythonce

See also the mailing list:

http://mail.python.org/mailman/listinfo/pythonce


Luke Dunstan


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Re: efficient text file search.

2006-09-11 Thread John Machin


Luuk wrote:
[snip]
 some googling turned op the following.
 Second paragraph of chapter 14 of http://www.amk.ca/python/2.1/
[snip]
 For a fuller discussion of the line I/O changes, see the python-dev summary
 for January 1-15, 2001 at http://www.amk.ca/python/dev/2001-01-1.html.

That is *HISTORY*. That is Python 2.1. That is the year 2001.
xreadlines is as dead as a dodo.

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Re: get the en of a program running in background

2006-09-11 Thread Damjan


 It works when a click on a button launches a program P.
 Now, I want that a click on another button launches another program P'
 
 In this case there is only one signal for two events : the end of P and
 the end of P'.
 How can distinct the two cases.

Remember the PIDs of the forked procesess and in your signal handler use
os.wait() to see which one has died. 
BTW os.wait() can work in non-blocking mode .


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Re: extracting substrings from a file

2006-09-11 Thread Paul McGuire

[EMAIL PROTECTED] wrote in message 
news:[EMAIL PROTECTED]
 Hi,

 I have a file with several entries in the form:

 AFFX-BioB-5_at E. coli  /GEN=bioB  /gb:J04423.1  NOTE=SIF
 corresponding to nucleotides 2032-2305 of /gb:J04423.1  DEF=E.coli
 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
 dethiobiotin synthetase (bioD), complete cds.

 1415785_a_at /gb:NM_009840.1 /DB_XREF=gi:6753327 /GEN=Cct8 /FEA=FLmRNA
 /CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
 /DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
 /PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1

 and I would like to create a file that has only the following:

 AFFX-BioB-5_at  /GEN=bioB  /gb:J04423.1

 1415785_a_at /gb:NM_009840.1 /GEN=Cct8

Here's a pyparsing solution that will address your immediate question, and 
also gives you some leeway for adding other / options to your search. 
Pyparsing's home page is at pyparsing.wikispaces.com.

-- Paul


data = 
AFFX-BioB-5_at E. coli  /GEN=bioB  /gb:J04423.1  NOTE=SIF
corresponding to nucleotides 2032-2305 of /gb:J04423.1  DEF=E.coli
7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
dethiobiotin synthetase (bioD), complete cds.

1415785_a_at /gb:NM_009840.1 /DB_XREF=gi:6753327 /GEN=Cct8 /FEA=FLmRNA
/CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
/DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
/PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1


from pyparsing import *

# create expression we are looking for:
#   name [ junk word... ] /qualifier...
name = Word(alphanums,printables).setResultsName(name)
junkWord = ~(Literal(/)) + Word(printables)
qualifier = (/ + Word(alphas+_-.).setResultsName(key) + \
oneOf(= :) + \
Word(printables).setResultsName(value))
expr = name + ZeroOrMore(junkWord) + \
Dict(ZeroOrMore(qualifier)).setResultsName(quals)

# use parse action to repackage qualifier data to support dict-like
# access to qualifiers
qualifier.setParseAction( lambda t: (t.key,.join(t)) )

# use this parse action instead if you just want whatever is
# after the '=' or ':' delimiter in the qualifier
# qualifier.setParseAction( lambda t: (t.key,t.value) )

# parse data strings, showing returned data structure
# (just to show what pyparsing results structure looks like)
for d in data.split(\n\n):
res = expr.parseString(d)
print res.dump()
print
print

# now just do what the OP wanted in the first place
for d in data.split(\n\n):
res = expr.parseString(d)
print res.name, res.quals[gb], res.quals[GEN]


Gives these results:
['AFFX-BioB-5_at', 'E.', 'coli', [('GEN', '/GEN=bioB'), ('gb', 
'/gb:J04423.1')]]
- name: AFFX-BioB-5_at
- quals: [('GEN', '/GEN=bioB'), ('gb', '/gb:J04423.1')]
  - GEN: /GEN=bioB
  - gb: /gb:J04423.1

['1415785_a_at', [('gb', '/gb:NM_009840.1'), ('DB_XREF', 
'/DB_XREF=gi:6753327'), ('GEN', '/GEN=Cct8'), ('FEA', '/FEA=FLmRNA'), 
('CNT', '/CNT=482'), ('TID', '/TID=Mm.17989.1'), ('TIER', '/TIER=FL+Stack'), 
('STK', '/STK=281'), ('UG', '/UG=Mm.17989'), ('LL', '/LL=12469'), ('DEF', 
'/DEF=Mus')]]
- name: 1415785_a_at
- quals: [('gb', '/gb:NM_009840.1'), ('DB_XREF', '/DB_XREF=gi:6753327'), 
('GEN', '/GEN=Cct8'), ('FEA', '/FEA=FLmRNA'), ('CNT', '/CNT=482'), ('TID', 
'/TID=Mm.17989.1'), ('TIER', '/TIER=FL+Stack'), ('STK', '/STK=281'), ('UG', 
'/UG=Mm.17989'), ('LL', '/LL=12469'), ('DEF', '/DEF=Mus')]
  - CNT: /CNT=482
  - DB_XREF: /DB_XREF=gi:6753327
  - DEF: /DEF=Mus
  - FEA: /FEA=FLmRNA
  - GEN: /GEN=Cct8
  - LL: /LL=12469
  - STK: /STK=281
  - TID: /TID=Mm.17989.1
  - TIER: /TIER=FL+Stack
  - UG: /UG=Mm.17989
  - gb: /gb:NM_009840.1


AFFX-BioB-5_at /gb:J04423.1 /GEN=bioB
1415785_a_at /gb:NM_009840.1 /GEN=Cct8 


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Re: best small database?

David Isaac wrote:
 I have no experience with database applications.
 This database will likely hold only a few hundred items,
 including both textfiles and binary files.
 
 I would like a pure Python solution to the extent reasonable.
 
 Suggestions?
 
 Thank you,
 Alan Isaac
 
 
If they are files, just use the filesyatem, you don't need a
database.  If you need multiple indexes into these files, then
use a database, but only for the indexes that point to the
files on the filesystem.  The filesystem is almost always the
most efficient place to store files, not as blobs in a
database.

The answer about which database depends on your target
platform but you could consider gadfly.

-Larry Bates

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Re: egg and modpython

2006-09-11 Thread Damjan

 I applaud you for studying the traceback in more depth than I can find
 the motivation for, Bruno. ;-) However, this looks like a program using
 some package installed by setuptools/easy_install needs to unpack that
 package when running.

See news:[EMAIL PROTECTED]

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Re: A cross platform systray icon

2006-09-11 Thread TheSeeker


Nick Craig-Wood wrote:
 Does anyone have some hints / tips / experience with making a cross
 platform systray icon?  It should work on Windows, Gnome and KDE at
 minimum.

 I've seen the win32all code which is very similar to the C code I've
 written before for Windows.  It would be a small irritation to have to
 integrate its event loop with whichever GUI framework I'm using for
 the rest of it though.
 
You might do a search for TaskBarIcon in the wxPython toolkit.

Duane

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Re: A cross platform systray icon

Nick Craig-Wood wrote:
 Does anyone have some hints / tips / experience with making a cross
 platform systray icon?  It should work on Windows, Gnome and KDE at
 minimum.
 
 I've seen the win32all code which is very similar to the C code I've
 written before for Windows.  It would be a small irritation to have to
 integrate its event loop with whichever GUI framework I'm using for
 the rest of it though.
 
 I don't know how to make a systray under KDE/Gnome though, but I think
 freedesktop has made it a lot easier now.  I didn't manage to find a
 python example - does anyone have one?
 
 Ideally I'd like someone to tell me that PyQT, tkinter or PyGTK does
 it all for me, but from my searching on the subject I doubt it is
 going to be that easy!
 
 Thanks
Google turned this up.

http://radio.weblogs.com/0110159/gems/systray_py.txt

Hope it helps.

-Larry
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Re: best small database?

2006-09-11 Thread Paul Watson

David Isaac wrote:
 I have no experience with database applications.
 This database will likely hold only a few hundred items,
 including both textfiles and binary files.
 
 I would like a pure Python solution to the extent reasonable.
 
 Suggestions?
 
 Thank you,
 Alan Isaac

If you want really simple, look at the anydbm module.  If nothing better 
is available, anydbm will use dumbdbm.  All of these are in the Python 
build, so you do not need to fetch/read/install anything additional.

Doing the DB-API would be much stronger, but might be overkill in your 
situation.
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Re: extracting substrings from a file

2006-09-11 Thread Tim Williams

On 11 Sep 2006 05:29:17 -0700, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
 Hi,

 I have a file with several entries in the form:

 AFFX-BioB-5_at   E. coli  /GEN=bioB  /gb:J04423.1  NOTE=SIF
 corresponding to nucleotides 2032-2305 of /gb:J04423.1  DEF=E.coli
 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
 dethiobiotin synthetase (bioD), complete cds.

 1415785_a_at /gb:NM_009840.1 /DB_XREF=gi:6753327 /GEN=Cct8 /FEA=FLmRNA
 /CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
 /DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
 /PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1

 and I would like to create a file that has only the following:

 AFFX-BioB-5_at  /GEN=bioB  /gb:J04423.1

 1415785_a_at /gb:NM_009840.1 /GEN=Cct8

 Could anyone please tell me how can I do it?

If each entry is a single line, then the following is just to give you
some ideas.  It is not robust enough for production though.

The 2nd input line has 2 /gb fields, and your script would need to
have some way of knowing which one to pick.

 for x in s.splitlines():
... data = x.split()
... output = [ data[0] ]
... for z in data[1:]:
... if (z.startswith('/GEN') or z.startswith('/gb'))and z not in 
output:
... output.append(z)
... print ' '.join(output)
... 
AFFX-BioB-5_at /GEN=bioB /gb:J04423.1
1415785_a_at /gb:NM_009840.1 /GEN=Cct8 /gb:BC009007.1

HTH :)
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Re: Simple regex with whitespaces

2006-09-11 Thread Paul McGuire

[EMAIL PROTECTED] wrote in message 
news:[EMAIL PROTECTED]
 Hello,

  I cannot figure out a way to find a regular expression that would
 match one and only one of these two strings:

 s1 = '  how are you'
 s2 = 'hello world   how are you'

  All I could come up with was:
 patt = re.compile('^[ ]*([A-Za-z]+)[  ]+([A-Za-z]+)$')

  Which of course does not work. I cannot express the fact: sentence
 have 0 or 1 whitespace, separation of group have two or more
 whitespaces.

 Any suggestion ? Thanks a bunch !
 Mathieu

A pyparsing approach is not as terse as regexp's, but it's not terribly long 
either.  Following John Machin's submission as a pattern:

s1 = '  how are you'
s2 = 'hello world   how are you'

from pyparsing import *

wd = Word(printables)
# this is necessary to suppress pyparsing's built-in whitespace skipping
wd.leaveWhitespace()
sentence = delimitedList(wd, delim=White(' ',exact=1))

for test in (s1,s2):
print sentence.searchString(test)


Pyparsing returns data as ParseResults objects, which can be accessed as 
lists or dicts.  From this first cut, we get:
[['how', 'are', 'you']]
[['hello', 'world'], ['how', 'are', 'you']]

These aren't really sentences any more, but we can have pyparsing put them 
back into sentences, by adding a parse action to sentence.

sentence.setParseAction(lambda toks:  .join(toks))

Now our results are:
[['how are you']]
[['hello world'], ['how are you']]


If you really want to get fancy, and clean up some of that capitalization 
and lack of punctuation, you can add a more elaborate parse action instead:
ispunc = lambda s: s in .!?;:,
sixLoyalServingMen = ('What','Why','When','How','Where','Who')
def cleanup(t):
t[0] = t[0].title()
if not ispunc( t[-1][-1] ):
if t[0] in sixLoyalServingMen:
punc = ?
else:
punc = .
else:
punc = 
return  .join(t) + punc
sentence.setParseAction(cleanup)

This time we get:
[['How are you?']]
[['Hello world.'], ['How are you?']]


The pyparsing home page is at pyparsing.wikispaces.com.

-- Paul


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Re: efficient text file search.

2006-09-11 Thread noro

can you add some more info, or point me to a link, i havn't found
anything about binary search in mmap() in python documents.

the files are very big...

thanks
amit
Bill Scherer wrote:
 noro wrote:

 Is there a more efficient method to find a string in a text file then:
 
 f=file('somefile')
 for line in f:
 if 'string' in line:
  print 'FOUND'
 
 ?
 
 BTW:
 does for line in f:  read a block of line to te memory or is it
 simply calls f.readline() many times?
 
 thanks
 amit
 
 
 If your file is sorted by some key in the data, you can build a very
 fast binary search with mmap in Python.

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Re: Algorithm Question

2006-09-11 Thread Neil Cerutti

On 2006-09-10, Andrew McLean [EMAIL PROTECTED] wrote:
 This really an algorithm question more that a Python question,
 but it would be implemented in Python

In that case, try comp.programming.  But still...

 I have a list of strings, A. I want to find a set of strings B
 such that for any a in A there exists b in B such that b is
 a sub-string of a. But I also want to minimise T = sum_j t_j
 where

 t_j = count of the number of elements in A which have b[j] as a
 sub-string

 My guess is that finding the smallest possible T satisfying the
 constraint would be hard. However, for my application just
 keeping it reasonably small would help.

 In my case the list A contains over two million addresses.

I'm afraid I don't understand your description.

How about an example of B for some A?

A = [abb, bbc]
B = [a, ab, abb, b, bb, bbc, bc, c]

Is that what you're after?

-- 
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best way of testing a program exists before using it?

I am writing a wrapper to a binary command to run it and then do 
something with the xml output from it.

What is the best way of making sure that the command is installed on the 
system before I try to execute it, like the python equivalent of the 
unix command which?

Otherwise I'd have to do something like:

if os.system('which somecommand') != 0:
print you don't have %s installed % somecommand
sys.exit(1)

I know that isn't portable which is why a python solution would be 
better (although this will run on unix anyway, but it'd be nice if it 
ran on windows too).


-h

-- 
Hari Sekhon

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Re: efficient text file search.

noro wrote:
 Bill Scherer wrote:
 
noro wrote:


Is there a more efficient method to find a string in a text file then:

f=file('somefile')
for line in f:
   if 'string' in line:
print 'FOUND'

?

BTW:
does for line in f:  read a block of line to te memory or is it
simply calls f.readline() many times?

thanks
amit



If your file is sorted by some key in the data, you can build a very
fast binary search with mmap in Python.
 
 
  can you add some more info, or point me to a link, i haven't found
  anything about binary search in mmap() in python documents.
 
  the files are very big...
 
[please don't top-post: add your latest comments at the end so the 
story reads from the beginning].

I think this is probably not going to help you. A binary search is only 
useful if you want to locate a value in an ordered list. Since your 
original posting made it seem like the text you are looking for could 
appear in any position in any line of the file a binary search doesn't 
do you any good at all (in fact it complicates things and slows them 
down unnecessarily) because you'd still need to look at all lines.

Plus, if the lines are of variable length then you'd need to start by 
creating an index of them, meaning you'd have to go right through the 
file anyway.

regards
  Steve
-- 
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Holden Web LLC/Ltd  http://www.holdenweb.com
Skype: holdenweb   http://holdenweb.blogspot.com
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Re: efficient text file search.

2006-09-11 Thread Luuk


John Machin [EMAIL PROTECTED] schreef in bericht 
news:[EMAIL PROTECTED]

 Luuk wrote:
 [snip]
 some googling turned op the following.
 Second paragraph of chapter 14 of http://www.amk.ca/python/2.1/
 [snip]
 For a fuller discussion of the line I/O changes, see the python-dev 
 summary
 for January 1-15, 2001 at http://www.amk.ca/python/dev/2001-01-1.html.

 That is *HISTORY*. That is Python 2.1. That is the year 2001.
 xreadlines is as dead as a dodo.


Thats's why i started my reply with:
some googling turned op the following.
i did not state that further googling was unneeded ;-)


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ANN: ChiPy Thurs. September 14, 2006. 7pm @ Google, Chicago

2006-09-11 Thread bray

Chicago Python User Group
=

Come join us for our best meeting ever!

Topics
--

* Google Code (Brian Fitzpatrick and Ben Collins-Sussman)
* Trac + Subversion + doctests (Garrett Smith)
* Special method names for operator overloading (Brian Ray)

Location


Google's Chicago office
20 West Kinzie Street, 9th Floor
Chicago, IL 60610

Location description:
18 story glass and steel building on the Northwest corner of Dearborn
and Kinzie.
Across the street from Harry Carey's
Upstairs from Keefer's restaurant

* Map http://tinyurl.com/ee8my

Enter via the lobby on the South side of the building, between Keefer's
restaurant and Keefer's cafe.

Street (meter) parking is kinda sorta available in the area. Garage and
lot parking is also available Southwest and East of our building.

 1. The closest L stop is Grand on the Red Line and Clark/Lake on the
 Blue/Green/Orange/Brown/Purple Line. (All are about an 8 minute walk
 from Google)
 2. The closest Metra station is the Ogilvie Transportation Center (in
 the Citibank building) (about 20 minutes walk or take the Riverbus)
 3. The closest River Bus stop is at Michigan Avenue (By the Wrigley
 Building at 2 North Riverside Plaza.
 (http://www.wendellariverbus.com/rbdock.htm) ;-)
 4. The nearest helipad is at the mouth of the river, near Navy Pier. 
 Obtain security clearance before landing.

*** A Special Note from Fitz::

  I'm going to need a list of all people attending to give to building
  security, so if you're thinking of coming, please send me your name
  (just to me--use my fitz at google dot com address please).

About ChiPy
---

ChiPy is a group of Chicago Python Programmers, l33t, and n00bs.
Meetings are held monthly at various locations around Chicago.
Also, ChiPy is a proud sponsor of many Open Source and Educational
efforts in Chicago. Stay tuned to the mailing list for more info.

ChiPy website: http://chipy.org
ChiPy Mailing List: http://mail.python.org/mailman/listinfo/chicago
Python website: http://python.org



Forward this on.


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Re: egg and modpython

2006-09-11 Thread Wensheng


Paul Boddie wrote:
 Bruno Desthuilliers wrote:
  Wensheng a écrit :
   I installed pysqlite2 using easy_install.
   and got this when using it from modpython:
   --
   Mod_python error: PythonHandler etc.modpython

 [...]

 I applaud you for studying the traceback in more depth than I can find
 the motivation for, Bruno. ;-) However, this looks like a program using
 some package installed by setuptools/easy_install needs to unpack that
 package when running.

   ExtractionError: Can't extract file(s) to egg cache
 
   The following error occurred while trying to extract file(s) to the
   Python egg cache:
 
 [Errno 13] Permission denied: '/var/www/.python-eggs'

 And this wants to happen apparently in the home directory of the Web
 server user, whose rights may be somewhat limited. Or perhaps one has
 to initialise setuptools for any particular user by running it first as
 that user: something that isn't a particularly common thing to do with
 non-interactive users on UNIX-like systems.

 [...]

   Can peak developers fix this please?
 
  Why should they fix something that's
  1/ documented
  - http://peak.telecommunity.com/DevCenter/EggFormats#zip-file-issues

 The Internal Structure of Python Eggs / STOP! This is not the first
 document you should read! A case of Beware of the Leopard perhaps?

  2/ not a an egg specific issue

 In my experience, most other package managers actually unpack their
 resources when invoked, rather than leaving the programs to attempt
 such things when running. Debian packages even compile the bytecode
 files to ensure that nothing tries (and fails) to write them to
 privileged locations afterwards.

  3/ really just a configuration/permission problem

 Which should have been solved when the package manager was invoked,
 especially since this was most likely done as root.

 [...]

   in the mean time, I just have to use old download, unzip/untar 
   python setup.py install way.
 
  No - you have to read the manual and fix you configuration. FWIW, the
  above traceback gives far enough clues (it's even written in all letters).

 The various ways to deal with this include running easy_install as the
 Web server user so that it can touch the directory and whatever else it
 needs, and perhaps to set up various permissions - something you
 wouldn't usually do; running easy_install with the --always-unzip flag
 when installing the package as root; using python setup.py install as
 usual.

 This situation looks either a lot like a use case whose popularity has
 been underestimated by the developers - intriguing given the number of
 people supposedly using setuptools for their Web application
 deployments - or a packaging mistake with the pysqlite2 .egg file.
 Either way, system packages rarely suffer from this kind of problem,
 and it's quite understandable (and justifiable) to consider this bad
 behaviour.

  Or you may read easy_install's doc to avoid installing zipped eggs:
  http://peak.telecommunity.com/DevCenter/EasyInstall#compressed-installation

 Perhaps the developers should reverse their defaults and emulate the
 usual behaviour of package managers, unfashionable as that may seem.

 Paul

Thank you for clarification and other info/sugguestions.

As I read the document, if package author set zip_safe = false in
their setup.py, there would be no such problem.

I also second the idea of making --always-unzip the default.

It's EASY_install and EZ_setup, should be EASY so that we don't have to
read the document:), right?

If it's turbogears, yes, I would definitely read the document, but a
package manager...

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Re: best small database?

2006-09-11 Thread Laurent Pointal

David Isaac a écrit :
 I have no experience with database applications.
 This database will likely hold only a few hundred items,
 including both textfiles and binary files.
 
 I would like a pure Python solution to the extent reasonable.
 
 Suggestions?

May take a look at buzhug (very pythonic way to manipulate data in the
base).

http://buzhug.sourceforge.net/

 
 Thank you,
 Alan Isaac
 
 
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Re: best way of testing a program exists before using it?

Hari Sekhon wrote:
 I am writing a wrapper to a binary command to run it and then do 
 something with the xml output from it.
 
 What is the best way of making sure that the command is installed on the 
 system before I try to execute it, like the python equivalent of the 
 unix command which?
 
 Otherwise I'd have to do something like:
 
 if os.system('which somecommand') != 0:
 print you don't have %s installed % somecommand
 sys.exit(1)
 
 I know that isn't portable which is why a python solution would be 
 better (although this will run on unix anyway, but it'd be nice if it 
 ran on windows too).
 
The easiest way to test whether the command will run is to try and run 
it. If the program doesn't exist then you'll get an exception, which you 
can catch. Otherwise you'll be stuck with non-portable mechanisms for 
each platform anyway ...

regards
  Steve
-- 
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Holden Web LLC/Ltd  http://www.holdenweb.com
Skype: holdenweb   http://holdenweb.blogspot.com
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Re: PIL cannot open TIFF image in Windows

2006-09-11 Thread Iain King


Michele Petrazzo wrote:
 Rob Williscroft wrote:

  I downloaded some test images from:
 
  url:http://www.remotesensing.org/libtiff/images.html
 

 I do the same and modified your code for try FreeImagePy and the results
 are:

 ok: 41  error: 20   total: 61

 Better than PIL, but a lot of problems with

 lower-rgb-planar-  8 and flower-rgb-contig-  8

 IrfanView seem that can load all the images...

  Rob.

 Bye,
 Michele

I've been working with tifs a lot, and I've yet to find a perfect
python solution to them.  The usual images to screw things up for me
are jpeg encoded pages.  Best solution I've found is a try/except fall
through:
try:
  open image with PIL
except:
try:
  open image with FreeImagePy
except:
  try:
open image with wxPython
  except:
fail

Right now my program to compile multipage tiffs no longer does any of
the image work itself - it processes the index file, and then generates
a batch file.  The batch file is a lot of calls to irfanview /append.
I've yet to find a tiff irfanview can't open.

Iain

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Re: best small database?

2006-09-11 Thread Aahz

In article [EMAIL PROTECTED],
Paul Watson  [EMAIL PROTECTED] wrote:
David Isaac wrote:

 I have no experience with database applications.
 This database will likely hold only a few hundred items,
 including both textfiles and binary files.
 
 I would like a pure Python solution to the extent reasonable.
 
 Suggestions?

If you want really simple, look at the anydbm module.  If nothing better 
is available, anydbm will use dumbdbm.  All of these are in the Python 
build, so you do not need to fetch/read/install anything additional.

Doing the DB-API would be much stronger, but might be overkill in your 
situation.

Once Python 2.5 comes out, I recommend using sqlite because it avoids
the mess that dbm can cause.
-- 
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LL YR VWL R BLNG T S  -- www.nancybuttons.com
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Re: Problems with email.Generator.Generator

2006-09-11 Thread Chris Withers

Peter Otten wrote:
 http://sourceforge.net/tracker/?func=detailaid=1409455group_id=5470atid=105470
 Now, is this change to Generator.py in error or am I doing something
 wrong?
 
 I'm not familiar enough with the email package to answer that.

I'm hoping someone around here is ;-)

 If the latter, how can I change my code such that it works as I'd expect?
 
 email.Generator and email.Message use cStringIO.StringIO internally, which
 can't cope with unicode. A quick fix might be to monkey-patch:

I'm not sure that's correct, but I'm happy to stand corrected.

My understanding is that the StringIO's don't mind as long as they type 
is consistent - ie: con't mix unicode and encoded strings, 'cos it 
forced python's default ascii codec to kick in and spew unicode errors.

Now, I want to know what I'm supposed to do when I have unicode source 
and want it to end up as either a text/plain or text/html mime part.

Is there a how-to for this anywhere? The email package's docs are short 
on examples involving charsets, unicode and the like :-(

Chris

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- http://www.simplistix.co.uk
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Re: best way of testing a program exists before using it?





Steve Holden wrote:

  Hari Sekhon wrote:
  
  
I am writing a wrapper to a binary command to run it and then do 
something with the xml output from it.

What is the best way of making sure that the command is installed on the 
system before I try to execute it, like the python equivalent of the 
unix command "which"?

Otherwise I'd have to do something like:

if os.system('which somecommand') != 0:
print "you don't have %s installed" % somecommand
sys.exit(1)

I know that isn't portable which is why a python solution would be 
better (although this will run on unix anyway, but it'd be nice if it 
ran on windows too).


  
  The easiest way to test whether the command will run is to try and run 
it. If the program doesn't exist then you'll get an exception, which you 
can catch. Otherwise you'll be stuck with non-portable mechanisms for 
each platform anyway ...

regards
  Steve
  


Yeah, this occurred to me just after I sent the mail, but I don't
really want to run the program because it will go off and do some work
and take time to come back. If there is a better way then that would be
great. I can't think of anything other than what you have suggested
with a message saying that the program wasn't found in the path which
would be the most appropriate error since the path could also be wrong.

Perhaps I'll just bite the bullet and get the program to do something
as small as possible to test it.

I guess I'll just have to continue to miss my unix commands...

-h

-- 
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Re: best way of testing a program exists before using it?

2006-09-11 Thread Rob Wolfe


Hari Sekhon wrote:
 I am writing a wrapper to a binary command to run it and then do
 something with the xml output from it.

 What is the best way of making sure that the command is installed on the
 system before I try to execute it, like the python equivalent of the
 unix command which?

 Otherwise I'd have to do something like:

 if os.system('which somecommand') != 0:
 print you don't have %s installed % somecommand
 sys.exit(1)

 I know that isn't portable which is why a python solution would be
 better (although this will run on unix anyway, but it'd be nice if it
 ran on windows too).

IMHO this is pretty portable:

 def is_on_path(fname):
... for p in os.environ['PATH'].split(os.pathsep):
... if os.path.isfile(os.path.join(p, fname)):
... return True
... return False

HTH,
Rob

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Re: Algorithm Question

2006-09-11 Thread Carl Banks

Andrew McLean wrote:
 I have a list of strings, A. I want to find a set of strings B such that
 for any a in A there exists b in B such that b is a sub-string of a.

B=A?

 But I also want to minimise T = sum_j t_j where
 t_j = count of the number of elements in A which have b[j] as a sub-string

If there not elements in A that are substrings of any other element in
A, and if B=A, then t_j would be 1 for all j.  Which means B=A would be
optimal (since elements of B have to be substring of at least one
element in A).  It looks like the B={set of all elements in A that are
not a substring of any other element in A} is the generally optimal
solution.

I suspect you mistyped or omitted something--problem is underspecified
at best.


Carl Banks

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Re: Problems with email.Generator.Generator

Chris Withers wrote:
 Peter Otten wrote:
 
http://sourceforge.net/tracker/?func=detailaid=1409455group_id=5470atid=105470

Now, is this change to Generator.py in error or am I doing something
wrong?

I'm not familiar enough with the email package to answer that.
 
 
 I'm hoping someone around here is ;-)
 
 
If the latter, how can I change my code such that it works as I'd expect?

email.Generator and email.Message use cStringIO.StringIO internally, which
can't cope with unicode. A quick fix might be to monkey-patch:
 
 
 I'm not sure that's correct, but I'm happy to stand corrected.
 
 My understanding is that the StringIO's don't mind as long as they type 
 is consistent - ie: con't mix unicode and encoded strings, 'cos it 
 forced python's default ascii codec to kick in and spew unicode errors.
 
 Now, I want to know what I'm supposed to do when I have unicode source 
 and want it to end up as either a text/plain or text/html mime part.
 
 Is there a how-to for this anywhere? The email package's docs are short 
 on examples involving charsets, unicode and the like :-(
 
Well, it would seem like the easiest approach is to monkey-patch the use 
of cStringIO to StringIO as recommended and see if that fixes your 
problem. Wouldn't it?

regards
  Steve
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Cool! A python course!

2006-09-11 Thread Neal Becker

http://www.epp.jhu.edu/schedule/courseinfo.php?deptid=525coursenum=492

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RE: best way of testing a program exists before using it?

2006-09-11 Thread Tim Golden

[Rob Wolfe]
| Hari Sekhon wrote:
|  I am writing a wrapper to a binary command to run it and then do
|  something with the xml output from it.
| 
|  What is the best way of making sure that the command is 
| installed on the
|  system before I try to execute it, like the python equivalent of the
|  unix command which?
| 
|  Otherwise I'd have to do something like:
| 
|  if os.system('which somecommand') != 0:
|  print you don't have %s installed % somecommand
|  sys.exit(1)
| 
|  I know that isn't portable which is why a python solution would be
|  better (although this will run on unix anyway, but it'd be 
| nice if it
|  ran on windows too).
| 
| IMHO this is pretty portable:
| 
|  def is_on_path(fname):
| ... for p in os.environ['PATH'].split(os.pathsep):
| ... if os.path.isfile(os.path.join(p, fname)):
| ... return True
| ... return False
| 

Depends on how fname is specified: on Win32, the filename 
itself will have one of the PATHEXT extensions, even though you
conventionally don't specify it (and if you're after
portability you certainly won't). On *nix, tho', you almost
certainly won't have the extension.

As it happens I wrote a script similar to yours this morning
which takes account of the PATHEXT, but because of that, it's
obviously win-specific. Maybe it could be made a bit smarter
to account for the possible absence of the env var.

(This is a cut-down version)

code
import os, sys

class x_finished (Exception): pass

paths = [.] + os.environ.get (PATH, ).split (;)
exts = [e.lower () for e in os.environ.get (PATHEXT, .exe).split
(;)]

if __name__ == '__main__':
  if len (sys.argv)  1:
search_for = sys.argv[1]
  else:
search_for = raw_input (Search for:)
  
  base, ext = os.path.splitext (search_for)
  if ext:
exts = [ext]

  try:
for path in paths:
  for ext in exts:
filepath = os.path.join (path, %s%s % (base, ext))
if os.path.isfile (filepath):
  print filepath
  raise x_finished
  except x_finished:
pass

/code

TJG


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Re: best way of testing a program exists before using it?





Rob Wolfe wrote:

  Hari Sekhon wrote:
  
  
I am writing a wrapper to a binary command to run it and then do
something with the xml output from it.

What is the best way of making sure that the command is installed on the
system before I try to execute it, like the python equivalent of the
unix command "which"?

Otherwise I'd have to do something like:

if os.system('which somecommand') != 0:
print "you don't have %s installed" % somecommand
sys.exit(1)

I know that isn't portable which is why a python solution would be
better (although this will run on unix anyway, but it'd be nice if it
ran on windows too).

  
  
IMHO this is pretty portable:

  
  

  
def is_on_path(fname):

  

  
  ... for p in os.environ['PATH'].split(os.pathsep):
... if os.path.isfile(os.path.join(p, fname)):
... return True
... return False

HTH,
Rob

  


That works well and is portable, fits nicely. I was actually curious if
somebody already came across this and perhaps put a func like this in
the standard modules...

Thanks.

-h

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Re: best way of testing a program exists before using it?

2006-09-11 Thread Steven Bethard

Hari Sekhon wrote:
 I am writing a wrapper to a binary command to run it and then do 
 something with the xml output from it.
 
 What is the best way of making sure that the command is installed on the 
 system before I try to execute it, like the python equivalent of the 
 unix command which?

There is the which module:

 http://trentm.com/projects/which/

But I'd probably just try the command and catch the exception, e.g.:

  import subprocess
  try:
... subprocess.call(['foo'])
... except OSError:
... print you don't have foo installed
...
you don't have foo installed
  try:
... subprocess.call(['svm_learn'])
... except OSError:
... print you don't have svm_learn installed
...
1

STeVe
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Behaviour of classes (tired of writing too much)

2006-09-11 Thread mpn

How do I catch any reference to an instance of a class, i.e., I want to
run some code as soon as an instance of a class is used in any way.
(and I don't want to define all of __add__, __ge__ etc etc etc etc etc)

The reason for the question is that I want to simplify the Message
Passing Interface (MPI) calls. I find it irritating that I have to
start a non-blocking send/receive and then check that the data has
arrived. Why not automagically check/wait for the data when it is
needed?

The second part that I also need to make that idea work is the ability
to change the instance to the received data, i.e., self=received data,
and then launch the original reference.

So I guess that the code I want to write is:

class MPI_tmp:
   # temporary object that changes ITSELF into another object when
called in any way
   def __on_any_call__(self):
   self=newobject()
   self.__run_the_anycall__()

which probably doesn't work :-)

Greatful for any ideas / Magnus

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Re: best way of testing a program exists before using it?

Rob Wolfe wrote:
 Hari Sekhon wrote:
 
I am writing a wrapper to a binary command to run it and then do
something with the xml output from it.

What is the best way of making sure that the command is installed on the
system before I try to execute it, like the python equivalent of the
unix command which?

Otherwise I'd have to do something like:

if os.system('which somecommand') != 0:
print you don't have %s installed % somecommand
sys.exit(1)

I know that isn't portable which is why a python solution would be
better (although this will run on unix anyway, but it'd be nice if it
ran on windows too).
 
 
 IMHO this is pretty portable:
 
 
def is_on_path(fname):
 
  for p in os.environ['PATH'].split(os.pathsep):
  if os.path.isfile(os.path.join(p, fname)):
  return True
  return False
 
Except that the fname will then have to be a .exe on Windows and not 
on Unix.

regards
  Steve
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Re: best way of testing a program exists before using it?

Hari Sekhon wrote:
 Steve Holden wrote:
 
Hari Sekhon wrote:
  

I am writing a wrapper to a binary command to run it and then do 
something with the xml output from it.

What is the best way of making sure that the command is installed on the 
system before I try to execute it, like the python equivalent of the 
unix command which?

Otherwise I'd have to do something like:

if os.system('which somecommand') != 0:
print you don't have %s installed % somecommand
sys.exit(1)

I know that isn't portable which is why a python solution would be 
better (although this will run on unix anyway, but it'd be nice if it 
ran on windows too).



The easiest way to test whether the command will run is to try and run 
it. If the program doesn't exist then you'll get an exception, which you 
can catch. Otherwise you'll be stuck with non-portable mechanisms for 
each platform anyway ...

regards
  Steve
  

 
 Yeah, this occurred to me just after I sent the mail, but I don't really 
 want to run the program because it will go off and do some work and take 
 time to come back. If there is a better way then that would be great. I 
 can't think of anything other than what you have suggested with a 
 message saying that the program wasn't found in the path which would be 
 the most appropriate error since the path could also be wrong.
 
 Perhaps I'll just bite the bullet and get the program to do something as 
 small as possible to test it.
 
 I guess I'll just have to continue to miss my unix commands...
 
Erm, but don't you *have* to run the program anyway to produce the 
required XML output? So, if the attempt to run it fails then you know it 
isn't installed, and if it succeeds then you should have the required 
output (I'm presuming either the output will appear in a file or you'll 
be using the subprocess module or similar to capture its standard output).

To be specific: I wasn't suggesting that you try to run the program 
first just to see whether it existed, I was suggesting you try to run it 
to produce the XML, and if it fails then you know you can't.

regards
  Steve
-- 
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Recent Ramblings http://del.icio.us/steve.holden

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Re: best way of testing a program exists before using it?





Steven Bethard wrote:

  Hari Sekhon wrote:
  
  
I am writing a wrapper to a binary command to run it and then do 
something with the xml output from it.

What is the best way of making sure that the command is installed on the 
system before I try to execute it, like the python equivalent of the 
unix command "which"?

  
  
There is the which module:

 http://trentm.com/projects/which/

But I'd probably just try the command and catch the exception, e.g.:

  import subprocess
  try:
... subprocess.call(['foo'])
... except OSError:
... 	print "you don't have foo installed"
...
you don't have foo installed
  try:
... subprocess.call(['svm_learn'])
... except OSError:
... 	print "you don't have svm_learn installed"
...
1

STeVe
  

looks good, although I agree with you on the try it and see simplicity.
I think if the which.py was part of the standard lib then I would use
it, but as it is I will stick to the original path search that you
recommended (I'm not gonna both dealing with the pathext just yet)

-- 
Hari Sekhon


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Re: Problems with email.Generator.Generator

2006-09-11 Thread Gerard Flanagan


Chris Withers wrote:

 Now, I want to know what I'm supposed to do when I have unicode source
 and want it to end up as either a text/plain or text/html mime part.

 Is there a how-to for this anywhere? The email package's docs are short
 on examples involving charsets, unicode and the like :-(

no expert in this, but have you tried the codecs module?

http://docs.python.org/lib/codec-objects.html

( with 'xmlcharrefreplace' for the html )?

Gerard

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Re: PyPy with a smaller PVM for the full Python?

2006-09-11 Thread John Roth


Casey Hawthorne wrote:
 Currently PyPy is working toward compiling to C a restricted subset of
 Python, called RPython.

 Would it be possible for PyPy to compile the full subset of Python
 by also using a lot smaller version of the PVM (Python Virtual
 Machine) to go with the compiled code?
 So, the user would be running the C object code and also a smaller
 PVM!

 Or would this completely remove or severely reduce any speed advantage
 of the compiled code?


 Similarly, for JPython (which is at Python 2.2?), could one also use a
 lot smaller accompanying PVM with the JPython source code and JVM to
 use Python 2.5 in its entirety?

 --
 Regards,
 Casey

The PyPy project, as I understand it, is to have a version
of Python that's entirely written in Python. The RPython
modules are the ones that will be compiled into C so that
they can then be compiled into a virtual machine. I doubt
very much if there's anything that can be done to subset
it further. Their direction on performance is toward a JIT
(Just In Time compiler), not to put lots of code in C so
that it runs fast.

The same goes for both Java and the CLR (IronPython).
I believe there are plans to subset the JVM in the
2.7 release, but I have my doubts whether that will reduce
the JVM footprint as far as running Jython is concerned.
The intention is to reduce the initial footprint for runing the
JVM under a browser.

John Roth

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Re: best way of testing a program exists before using it?

2006-09-11 Thread Tim Williams

On 11/09/06, Hari Sekhon [EMAIL PROTECTED] wrote:

  Steve Holden wrote:
  Hari Sekhon wrote:


  The easiest way to test whether the command will run is to try and run
 it. If the program doesn't exist then you'll get an exception, which you
 can catch. Otherwise you'll be stuck with non-portable mechanisms for
 each platform anyway ...

 regards
  Steve


  Yeah, this occurred to me just after I sent the mail, but I don't really
 want to run the program because it will go off and do some work and take
 time to come back. If there is a better way then that would be great. I
 can't think of anything other than what you have suggested with a message
 saying that the program wasn't found in the path which would be the most
 appropriate error since the path could also be wrong.


If you run your wrapper and the program exists then you don't have to
test for it,  so the overall process is quicker and cleaner than
testing-for *then* running the program

If you run your wrapper and the program doesn't exist, then you have
performed your if exists  test without extra code and with very
little processing, and the raised exception will lead you nicely into
your not exists scenario.

try:
run_somecommand
except:
print you don't have %s installed % somecommand


HTH :)
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Re: Behaviour of classes (tired of writing too much)

2006-09-11 Thread Brian Quinlan

[EMAIL PROTECTED] wrote:
 How do I catch any reference to an instance of a class, i.e., I want to
 run some code as soon as an instance of a class is used in any way.
 (and I don't want to define all of __add__, __ge__ etc etc etc etc etc)

What do you mean by used in any way? Which of these are considered usage:

  a = Foo()   # obviously
  b = a   # ?
  a.__gt__(5) # apparently
  a.__gt__# ?

Anyway, look into __getattr__

Cheers,
Brian
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Re: best way of testing a program exists before using it?

2006-09-11 Thread Tim Chase

 Erm, but don't you *have* to run the program anyway to produce
 the required XML output? So, if the attempt to run it fails
 then you know it isn't installed, and if it succeeds then you
 should have the required output (I'm presuming either the
 output will appear in a file or you'll be using the subprocess
 module or similar to capture its standard output).

While it may not be the case for the OP, it's not entirely 
unreasonable there might be some intermediate process that is 
time-consuming...something like

def do_stuff():
data = gather_data_from_user_for_x_days(7)
do_something_with(data)
os.system('program.exe') # to process the gathered data

If it's going to bomb out in step #3, it might be nice to know 
before you start the 7-days worth of data-gathering/sampling in 
step #1.

def do_stuff():
if exists_in_path('program.exe'):
data = gather_data_from_user_for_x_days(7)
do_something_with(data)
os.system('program.exe')
else:
let_user_know_cant_find_program()

That way, they can remedy the situtation before wasting their 
time with a laborious process.

Granted, there's a race condition, that if the program exists and 
the user starts gathering data, and then deletes the program 
before the completion of the data-gathering, it will bomb out. 
However, I'd chalk that up to a 
stupid-user-for-shooting-themselves-in-the-foot exception. :)

Sure, it's a bit contrived in this case, but I've had too many 
applications that do exactly this, and would have welcomed 
information that a piece was missing *before* I had invested time 
in the app.

-tkc





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Re: best small database?

2006-09-11 Thread Paul McGuire

Aahz [EMAIL PROTECTED] wrote in message 
news:[EMAIL PROTECTED]
 In article [EMAIL PROTECTED],
 Once Python 2.5 comes out, I recommend using sqlite because it avoids
 the mess that dbm can cause.
 -- 
 Aahz ([EMAIL PROTECTED])   * 
 http://www.pythoncraft.com/

and if you don't want to wait for 2.5, you can install pysqlite without too 
much trouble - and it is *very* easy to use!

For SQLite design and data browsing, check out the SQLite Browser at 
http://sqlitebrowser.sourceforge.net.

-- Paul


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Re: Is it just me, or is Sqlite3 goofy?

2006-09-11 Thread Gerhard Häring

Kay Schluehr wrote:
 [EMAIL PROTECTED] wrote:
 
 I wouldn't be at all surprised if the pysqlite author operated under that
 assumption.  That the Python developers didn't pick up on the issue is not
 surprising.  I'm not sure how many of them are (py)sqlite users, probably
 relatively few.

 Skip
 
 Who has reviewed sqlite/pysqlite after all? 

pysqlite was actually reviewed by several Python core developers before 
becoming a part of the Python standard library, most prominently Neil 
Norwitz and Anthony Baxter.

 Reading the passage in the
 sqlite FAQ I can hardly believe that passing errors silently and
 coercing everything to string when it fails to be coerced to INTEGER
 although INTEGER was an invariant declared in the create command is on
 par with Pythons design philosophy. [...]

Unfortunately, third-party library authors don't first check with 
Python's design philosophy in case their software will be wrapped as a 
Python module ;-)

I did my best to combine both SQLite's and Python's type system though, 
including a discussion with pysqlite 1.x users before the grand rewrite 
for version 2, which is the one that ended up in the Python standard 
library now.

 In other cases doctoral dissertations are written about whether a
 keyword or some punctuation shall be used for decorator syntax and in
 this case everything must be rushed into the code base of the
 standard library?

There was no rush at all.

-- Gerhard

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Re: best way of testing a program exists before using it?

Tim Williams wrote:
 On 11/09/06, Hari Sekhon [EMAIL PROTECTED] wrote:

  Steve Holden wrote:
  Hari Sekhon wrote:


  The easiest way to test whether the command will run is to try and run
 it. If the program doesn't exist then you'll get an exception, which you
 can catch. Otherwise you'll be stuck with non-portable mechanisms for
 each platform anyway ...

 regards
  Steve


  Yeah, this occurred to me just after I sent the mail, but I don't 
 really
 want to run the program because it will go off and do some work and take
 time to come back. If there is a better way then that would be great. I
 can't think of anything other than what you have suggested with a 
 message
 saying that the program wasn't found in the path which would be the most
 appropriate error since the path could also be wrong.


 If you run your wrapper and the program exists then you don't have to
 test for it,  so the overall process is quicker and cleaner than
 testing-for *then* running the program

 If you run your wrapper and the program doesn't exist, then you have
 performed your if exists  test without extra code and with very
 little processing, and the raised exception will lead you nicely into
 your not exists scenario.

 try:
run_somecommand
 except:
print you don't have %s installed % somecommand


 HTH :)

The down side to that is the program has to be run which consumes time 
and slows the script down a fair bit (as well as outputting garbage to 
the screen)

-h

-- 
Hari Sekhon

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Re: Ann: CoreBio 0.4

2006-09-11 Thread GavinCrooks

km wrote:
 Hi,
 why are u reinventing the wheel when Biopython[1] is already existing ? is
 there any specific reason u wanted to develop this CoreBio ? why dont u just
 extend the existing BioPython package itself ?
 regards,
 KM
 [1]http://biopython.org  [EMAIL PROTECTED] wrote:



Biopython is a fine project which I have used and contributed to in the
past. Unfortunately, Biopython suffers form a lack of focus. It is a
huge heap of code, some of which is well written, but of lot of which
is not, and a significant portion doesn't work as advertised. There is
no consistency, the code-base is idiosyncratic, the documentation is
spotty, and it is very hard to actually discover and use the
functionality that you need. For some common tasks there are three ways
of doing things, only one of which is supported.

CoreBio is intended to be a high-quality, easy to use collection of the
core functionality needed for bioinformatics and computational biology.
Compared to biopython, we are taking a narrow, quality first, rather
than breadth first, approach with simple API's that hide as much
complexity as reasonable possible.

As an example of simple API's consider the common task of reading a
file of protein sequences:

 from corebio import seq_io
 afile = open(human.fa)
 list_of_sequences = seq_io.read(afile)

CoreBio will figure out the file format, so 'seq_io.read()' will parse
sequence data from  fasta, clustal, genbank, intelligenetics, msf,
nbrf/pir, nexus or phylip formatted files.



Gavin Crooks

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Re: Behaviour of classes (tired of writing too much)