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Ann Loraine | 6 May 2007 15:40
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[BioPython] advice on structuring packages

Dear friends,

My group is getting ready to distribute some python modules and also to
migrate some of our code to a publicly-accessible cvs repository.

For the migration, we would like to restructure our cvs directory layout so
as to be more compatible with community standards.

We could really use some good ideas and suggestions on how to do this. Do
you have any recommendations for books or other documentation we could read
to bring ourselves up to speed on this topic?

Looking at how the biopython code is organized has been very helpful, as
well, of course!

Thank you very much for your time,

Ann Loraine

--

-- 
Ann Loraine
Assistant Professor
University of Alabama at Birmingham
http://www.transvar.org
205-996-4155
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Julius Lucks | 6 May 2007 17:19
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Re: [BioPython] advice on structuring packages

Hi Ann,

If you are going to do a major restructuring, I HIGHLY recommend you  
switch from CVS to Subversion as well.  Subversion works a lot like  
CVS but has many more nice features and is just structured better -  
it allows you to version binary files as well as text files, it has a  
better back end allowing the repository to be more space-efficient  
and speedy, and many more nice things.

To that end, there is an EXCELLENT book called 'Pragmatic Version  
Control Using Subversion'

http://www.pragmaticprogrammer.com/titles/svn/index.html

I highly recommend this book - I went through the whole thing and it  
really taught be a lot about the best way to use subversion, as well  
as a whole chapter on how to structure the repository, manage tags  
and branches, etc.

If you want to stick with CVS, Pragmatic Bookshelf also has the same  
book, but with CVS

http://www.pragmaticprogrammer.com/starter_kit/vcc/index.html

Hope this helps,

Julius

-----------------------------------------------------
http://openwetware.org/wiki/User:Lucks
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Jean Lechner | 9 May 2007 10:14
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[BioPython] bio.pdb.mmcif does not exist

Hello

I have installed Biopython without any problems but when I try tu use
the mmcif parser or the mmcif2dict, I have a error saying the mmcif
package does not exist.

How can I install this package ?
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Peter | 9 May 2007 12:59
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Re: [BioPython] bio.pdb.mmcif does not exist

(Forgot to reply to the mainling list last time, sending again)

Jean Lechner wrote:
> Hello
> 
> 
> I have installed Biopython without any problems but when I try tu use
> the mmcif parser or the mmcif2dict, I have a error saying the mmcif
> package does not exist.
> 
> How can I install this package ?

Hi Jean,

Are you using Windows, Linux, MacOS, other?
How did you install Biopython? (and out of interest, which version?)

As you can read on the download page, you will need flex (The Fast
Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On Linux
(and other Unix like systems) this is actually very straight forward.
This may be the same issue here...

Peter

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Jean Lechner | 9 May 2007 14:10
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Re: [BioPython] bio.pdb.mmcif does not exist

Hi Peter
Thank you for answering

I m using MacOS X
And I have installed BioPython(version 1,43) following the steps
listed on biopython.org website
I have installed flex and the directory has been created.
But when I try tu use the MMCIF2Dict this error stay :
 "ImportError: No module named mmCIF.MMCIFlex"

When I look in the Bio.PDB.mmCIF folder, MMCIFlex is here but it is a
MMCIFlex.so
and there is no __init__.py file

So I don t know what to do now ...

If you have any Idea please answer me

Jean

2007/5/9, Peter <biopython <at> maubp.freeserve.co.uk>:
> Jean Lechner wrote:
> > Hello
> >
> >
> > I have installed Biopython without any problems but when I try tu use
> > the mmcif parser or the mmcif2dict, I have a error saying the mmcif
> > package does not exist.
> >
> > How can I install this package ?
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Alex Lancaster | 9 May 2007 14:20
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Re: [BioPython] bio.pdb.mmcif does not exist

>>>>> "P" == Peter   writes:
>> I have installed Biopython without any problems but when I try tu
>> use the mmcif parser or the mmcif2dict, I have a error saying the
>> mmcif package does not exist.
>> 
>> How can I install this package ?

P> Hi Jean,

P> Are you using Windows, Linux, MacOS, other?  How did you install
P> Biopython? (and out of interest, which version?)

P> As you can read on the download page, you will need flex (The Fast
P> Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On
P> Linux (and other Unix like systems) this is actually very straight
P> forward.  This may be the same issue here...

On this issue, it appears that in biopython 1.43 compilation of the
mmCIF module is actually commented-out in the setup.py (which would
account for the lack of the Bio.PDB.mmCIF module noted by Jean, even
if flex was installed).  It was removed in this commit:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/setup.py.diff?r1=1.108&r2=1.109&cvsroot=biopython

with the somewhat confusing note:

"Uncommented mmCIF module because of problems if GNU's Flex is
missing"

because it actually commented it out, not uncommented it! ;) It seems
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Peter | 9 May 2007 15:01
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Re: [BioPython] bio.pdb.mmcif does not exist

Alex Lancaster wrote:
> On this issue, it appears that in biopython 1.43 compilation of the
> mmCIF module is actually commented-out in the setup.py (which would
> account for the lack of the Bio.PDB.mmCIF module noted by Jean, even
> if flex was installed).

Well spotted - I had forgotten about that!

 > It was removed in this commit:
> 
> http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/setup.py.diff?r1=1.108&r2=1.109&cvsroot=biopython
> 
> with the somewhat confusing note:
> 
> "Uncommented mmCIF module because of problems if GNU's Flex is
> missing"
> 
> because it actually commented it out, not uncommented it! ;)

That does sound like a simple typing error given the change made.

 > It seems
> to me that the setup.py should test whether GNU Flex is there and then
> enable the module compilation if it is (as is done for reportlab),
> rather than force the user to uncomment sections in the setup.py.  

That sounds reasonable - do you happen to know how to check for the flex 
headers cleanly?

The way the setup.py script prompts the user about building Bio.KDTree
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Alex Lancaster | 9 May 2007 15:13
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Re: [BioPython] bio.pdb.mmcif does not exist

>>>>> "P" == Peter   writes:

[...]

>> It seems to me that the setup.py should test whether GNU Flex is
>> there and then enable the module compilation if it is (as is done
>> for reportlab), rather than force the user to uncomment sections in
>> the setup.py.

P> That sounds reasonable - do you happen to know how to check for the
P> flex headers cleanly?

You could just test for the flex binary, the headers should be there,
but that's probably fragile.  Have to dig into my fading knowledge of
distutils...

P> The way the setup.py script prompts the user about building
P> Bio.KDTree with a simple yes/no prompt is a simple short term
P> solution.  I could certainly manage to make that change.

I would prefer to that it also be a command-line options so that a
biopython build can be automated by a build system, when making RPM
packages.  (Currently the Fedora package has to simulate the user
typing "yes" to the Bio.KDTree question which is fragile).

P> Jean - this issue had slipped my mind (but I don't use this
P> module). If you edit the setup.py file to uncomment the mmCIF
P> extension lines, and retry the build/install that should fix your
P> missing module problem:
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Jean Lechner | 9 May 2007 15:18
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[BioPython] Fwd: bio.pdb.mmcif does not exist

Hum I ve uncommented the lines and reinstalled all.
But the problem stay the same.
The directory Bio.PDB.mmCIF il here and there is a file named
MMCIFlex.so into it
But python can not load it... it is said that there is no module named
mmCIF.MMCIFlex
so i don t know what to do now ...
If you know answer me please

Jean

2007/5/9, Alex Lancaster <alexl <at> users.sourceforge.net>:
> >>>>> "P" == Peter   writes:
> >> I have installed Biopython without any problems but when I try tu
> >> use the mmcif parser or the mmcif2dict, I have a error saying the
> >> mmcif package does not exist.
> >>
> >> How can I install this package ?
>
> P> Hi Jean,
>
> P> Are you using Windows, Linux, MacOS, other?  How did you install
> P> Biopython? (and out of interest, which version?)
>
> P> As you can read on the download page, you will need flex (The Fast
> P> Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On
> P> Linux (and other Unix like systems) this is actually very straight
> P> forward.  This may be the same issue here...
>
> On this issue, it appears that in biopython 1.43 compilation of the
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Michiel de Hoon | 9 May 2007 15:54
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Re: [BioPython] Fwd: bio.pdb.mmcif does not exist

Jean Lechner wrote:
> Hum I ve uncommented the lines and reinstalled all.
> But the problem stay the same.
> The directory Bio.PDB.mmCIF il here and there is a file named
> MMCIFlex.so into it
> But python can not load it... it is said that there is no module named
> mmCIF.MMCIFlex

How exactly are you trying to import MMCIFlex (which command exactly do 
you type into Python)?
On my Mac, I can import MMCIFlex with no problems. So it may be a path 
problem instead of a problem with MMCIFlex.so itself. Try going to the 
directory that contains MMCIFlex.so and try to import it there.

--Michiel.
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Gmane