From katel@worldpath.net Sat, 3 Jun 2000 21:58:10 -0400
Date: Sat, 3 Jun 2000 21:58:10 -0400
From: Cayte katel@worldpath.net
Subject: [BioPython] wxpython prototype
This is a multi-part message in MIME format.
------=_NextPart_000_001C_01BFCDA6.CE7E1D60
Content-Type: text/plain;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
I just uploaded a wxpython prototype, SeqGui.py to =
pub/katel/biopython/Bio on the ftp site. After a few hours of =
bafflement, I was able to get wxConstaints to do what I wanted. In the =
same ammount of time, I was able to get the TKinter LayoutGrid to sort =
of do something like I wanted.
> Andrew said
>Okay, then my final statement is that I've
>found that the GUI is not that large a part of applications I've worked
>on, and can be written in such a way that different GUIs can be used
>with only minimal change to the internals.=20
Potentially, the gui can help the researcher visualize hidden =
patterns. Some day, when I'm feeling rich, I',m going to get hold of =
The Display of Visual Information:).
USER STORY:
Ellen Elegans has discovered a new protein, but she is not sure =
what its function is, and her eyes are tired from poring over text. She =
runs the protein through a program that highlights protein motifs in =
color. She recognizes the motifs as appearing often in digestive =
enzymes, so she suspects the protein has to do with digestion.
Cayte
------=_NextPart_000_001C_01BFCDA6.CE7E1D60
Content-Type: text/html;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
I just uploaded a wxpython prototype, =
SeqGui.py to=20
pub/katel/biopython/Bio on the ftp site. After a few hours of =
bafflement,=20
I was able to get wxConstaints to do what I wanted. In the same =
ammount of=20
time, I was able to get the TKinter LayoutGrid to sort of do something =
like I=20
wanted.
> Andrew said
>Okay, then my final statement is that =
I've
>found=20
that the GUI is not that large a part of applications I've =
worked
>on, and=20
can be written in such a way that different GUIs can be used
>with =
only=20
minimal change to the internals.
Potentially, the gui can help the researcher =
visualize=20
hidden patterns. Some day, when I'm feeling rich, I',m going to =
get hold=20
of The Display of Visual =
Information:).
USER STORY:
Ellen Elegans =
has=20
discovered a new protein, but she is not sure what its =
function=20
is, and her eyes are tired from poring over text. =
She=20
runs the protein through a program that highlights protein =
motifs in=20
color. She recognizes the motifs as appearing often in digestive =
enzymes,=20
so she suspects the protein has to do with digestion.
&nbs=
p; =
; =
&=
nbsp; &n=
bsp; =20
Cayte
------=_NextPart_000_001C_01BFCDA6.CE7E1D60--
From katel@worldpath.net Mon, 5 Jun 2000 01:08:11 -0700
Date: Mon, 5 Jun 2000 01:08:11 -0700
From: Cayte katel@worldpath.net
Subject: [BioPython] User stories
This is a multi-part message in MIME format.
------=_NextPart_000_0009_01BFCE8A.84C25440
Content-Type: text/plain;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
The site /www.ncbi.nlm.nih.gov/Coffeebreak has bioinformatics user =
stories. Also, bionet.molbio.computation is a bioinformatics newsgroup.
Cayte
------=_NextPart_000_0009_01BFCE8A.84C25440
Content-Type: text/html;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
The site /www.ncbi.nlm.nih.gov/Coffeebreak has =
bioinformatics user stories. Also, bionet.molbio.computation is a=20
bioinformatics newsgroup.
&nbs=
p; =
; =
&=
nbsp; =20
Cayte
------=_NextPart_000_0009_01BFCE8A.84C25440--
From jchang@SMI.Stanford.EDU Mon, 5 Jun 2000 21:46:36 -0700 (PDT)
Date: Mon, 5 Jun 2000 21:46:36 -0700 (PDT)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] wxpython prototype
Hi Cayte,
I've finally gotten around to installing wxPython. I've started running
your GUI, and I really like where you're goin with it! It's definitely
the first step towards getting these tools out of the hands of the
informaticians and into those of the biologists.
I'd like to check the stuff you have so far into the main development
tree. Would that be ok with you? What would you like to call this
package?
Thanks,
Jeff
On Sat, 3 Jun 2000, Cayte wrote:
> I just uploaded a wxpython prototype, SeqGui.py to pub/katel/biopython/Bio on the ftp site. After a few hours of bafflement, I was able to get wxConstaints to do what I wanted. In the same ammount of time, I was able to get the TKinter LayoutGrid to sort of do something like I wanted.
>
> > Andrew said
>
> >Okay, then my final statement is that I've
> >found that the GUI is not that large a part of applications I've worked
> >on, and can be written in such a way that different GUIs can be used
> >with only minimal change to the internals.
>
> Potentially, the gui can help the researcher visualize hidden patterns. Some day, when I'm feeling rich, I',m going to get hold of The Display of Visual Information:).
>
> USER STORY:
> Ellen Elegans has discovered a new protein, but she is not sure what its function is, and her eyes are tired from poring over text. She runs the protein through a program that highlights protein motifs in color. She recognizes the motifs as appearing often in digestive enzymes, so she suspects the protein has to do with digestion.
>
> Cayte
>
>
>
From katel@worldpath.net Wed, 7 Jun 2000 00:43:55 -0700
Date: Wed, 7 Jun 2000 00:43:55 -0700
From: Cayte katel@worldpath.net
Subject: [BioPython] wxpython prototype
----- Original Message -----
From: Jeffrey Chang
To: Cayte
Cc:
Sent: Monday, June 05, 2000 9:46 PM
Subject: Re: [BioPython] wxpython prototype
> Hi Cayte,
>
> I've finally gotten around to installing wxPython. I've started running
> your GUI, and I really like where you're goin with it! It's definitely
> the first step towards getting these tools out of the hands of the
> informaticians and into those of the biologists.
>
> I'd like to check the stuff you have so far into the main development
> tree. Would that be ok with you? What would you like to call this
> package?
It would be OK, but I just uploaded an alternative gui that is closer to
Andrews ideas. It is called SeqGuiAlt.py. Which should we go with?
Cayte
From jchang@SMI.Stanford.EDU Wed, 7 Jun 2000 22:03:54 -0700 (PDT)
Date: Wed, 7 Jun 2000 22:03:54 -0700 (PDT)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] wxpython prototype
> > I'd like to check the stuff you have so far into the main development
> > tree. Would that be ok with you? What would you like to call this
> > package?
>
> It would be OK, but I just uploaded an alternative gui that is closer to
> Andrews ideas. It is called SeqGuiAlt.py. Which should we go with?
I like SeqGuiAlt.py better. The interface seems more consistent with
other programs. In addition, it'll be easier to add transformations
without ending up with buttons up the wazoo.
I've created a new directory
biopython/Scripts/SeqGui/
and checked SeqGuiAlt.py in there as SeqGui.py. Please start working
against this copy!
Thanks,
Jeff
From katel@worldpath.net Fri, 9 Jun 2000 00:47:12 -0700
Date: Fri, 9 Jun 2000 00:47:12 -0700
From: Cayte katel@worldpath.net
Subject: [BioPython] wxpython prototype
----- Original Message -----
From: Jeffrey Chang
To: Cayte
Cc:
Sent: Wednesday, June 07, 2000 10:03 PM
Subject: Re: [BioPython] wxpython prototype
> I like SeqGuiAlt.py better. The interface seems more consistent with
> other programs. In addition, it'll be easier to add transformations
> without ending up with buttons up the wazoo.
Eventually, I'd also like to add filters, for example, to print all
hydrophobic amino acids in green or sulfter containing amino acids in
purple. I'd like to know Andrews' objections to a tabbed options dialog.
Throwing too many options at a novice user can cause confusion and the
options dialog hides the confusion. In The
Inmates are Running the Asylum, Alan Cooper describes an alarm clock with so
many options, no one could figure out how to use it!
>
> I've created a new directory
> biopython/Scripts/SeqGui/
>
> and checked SeqGuiAlt.py in there as SeqGui.py. Please start working
> against this copy!
>
It woud be convenient to have Transcribe.py, and Translate.py in a
package. Especially in Windows, packages make it easier to import.
>
>
Cayte
From dalke@acm.org Thu, 8 Jun 2000 23:24:16 -0600
Date: Thu, 8 Jun 2000 23:24:16 -0600
From: Andrew Dalke dalke@acm.org
Subject: [BioPython] wxpython prototype
>I'd like to know Andrews' objections to a tabbed options dialog.
>Throwing too many options at a novice user can cause confusion and the
>options dialog hides the confusion. In The
>Inmates are Running the Asylum, Alan Cooper describes an alarm clock with
so
>many options, no one could figure out how to use it!
Pretty much the same reasons as Cooper. Lots of examples at:
http://www.iarchitect.com/tabs.htm
As the page says, it can be done well. Any objections I have would
be because they are too easy to use wrong.
Andrew
From katel@worldpath.net Tue, 13 Jun 2000 22:23:57 -0700
Date: Tue, 13 Jun 2000 22:23:57 -0700
From: Cayte katel@worldpath.net
Subject: [BioPython] glue for Translate
This is a multi-part message in MIME format.
------=_NextPart_000_000D_01BFD586.10B207A0
Content-Type: text/plain;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Over the last couple of evenings, I've been trying to pull Translate =
in the gui. The unambiguous_dna_by_name lookup only seems to work with =
the alternate name. When a picklist is available, I prefer the long =
name, because it reminds you what organism your working with. At first =
I thought it might be because I had old files, but I updated the files =
and reran the unit tests.
The unit tests showed the same problem.
In my opinion, it would be a good idea to have bug tracking like =
bioperl. Bug reports tend to slip through the cracks when they are =
mixed in with discussion.
Cayte
------=_NextPart_000_000D_01BFD586.10B207A0
Content-Type: text/html;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Over the last couple of evenings, I've been =
trying to=20
pull Translate in the gui. The unambiguous_dna_by_name lookup only =
seems=20
to work with the alternate name. When a picklist is available, I =
prefer=20
the long name, because it reminds you what organism your working =
with. At=20
first I thought it might be because I had old files, but I updated =
the=20
files and reran the unit tests.
The unit tests showed the same problem.
In my opinion, it would be a good idea to =
have bug=20
tracking like bioperl. Bug reports tend to slip through the cracks =
when=20
they are mixed in with discussion.
&nbs=
p; =
; =
&=
nbsp; &n=
bsp; =20
Cayte
------=_NextPart_000_000D_01BFD586.10B207A0--
From katel@worldpath.net Mon, 19 Jun 2000 23:44:26 -0700
Date: Mon, 19 Jun 2000 23:44:26 -0700
From: Cayte katel@worldpath.net
Subject: [BioPython] jitterbug
This is a multi-part message in MIME format.
------=_NextPart_000_001D_01BFDA48.4D93DE20
Content-Type: text/plain;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
We need to link the new biopython jitterbug to the web sitem so it's =
visible to the oublic. I can try if no one objects.
Cayte
------=_NextPart_000_001D_01BFDA48.4D93DE20
Content-Type: text/html;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
We need to link the new biopython =
jitterbug to=20
the web sitem so it's visible to the oublic. I can try if no one=20
objects.
&nbs=
p; =
; =
&=
nbsp;=20
Cayte
------=_NextPart_000_001D_01BFDA48.4D93DE20--
From katel@worldpath.net Mon, 19 Jun 2000 23:59:25 -0700
Date: Mon, 19 Jun 2000 23:59:25 -0700
From: Cayte katel@worldpath.net
Subject: [BioPython] scop
This is a multi-part message in MIME format.
------=_NextPart_000_002E_01BFDA4A.655EA600
Content-Type: text/plain;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Browsing through the SCOP database, I don't see dom, lin or location =
files, that the SCOP parser leads me to expect. The site has web pages =
that are roughly like the lin files. If I look at the HTML source, it =
contains text, that resembles location and dom. But I'm not seeing =
files that I can feed directly into the parser?
Cayte
------=_NextPart_000_002E_01BFDA4A.655EA600
Content-Type: text/html;
charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Browsing through the SCOP database, I =
don't see=20
dom, lin or location files, that the SCOP parser leads me to=20
expect. The site has web pages that are roughly like the lin =
files. =20
If I look at the HTML source, it contains text, that resembles location =
and=20
dom. But I'm not seeing files that I can feed directly into the=20
parser?
&nbs=
p; =
; =
&=
nbsp; =20
Cayte
------=_NextPart_000_002E_01BFDA4A.655EA600--
From steve@neomorphic.com Tue, 20 Jun 2000 00:00:19 -0700
Date: Tue, 20 Jun 2000 00:00:19 -0700
From: Steve A. Chervitz steve@neomorphic.com
Subject: [BioPython] scop
Cayte wrote:
> Browsing through the SCOP database, I don't see dom, lin or
> location files, that the SCOP parser leads me to expect. The site has
> web pages that are roughly like the lin files. If I look at the HTML
> source, it contains text, that resembles location and dom. But I'm
> not seeing files that I can feed directly into the
> parser?
> Cayte
Try these URLs for the dom and lin files:
http://scop.berkeley.edu/search.cgi?dir=dom
http://scop.berkeley.edu/search.cgi?dir=lin
The dom file is about 1Mb, the lin file is about 7X that size.
A while back I wrote a bioperl module for working with SCOP data (not
yet contributed, but
possibly soon). It might be useful to compare notes.
Steve
From jchang@SMI.Stanford.EDU Tue, 20 Jun 2000 10:35:24 -0700 (PDT)
Date: Tue, 20 Jun 2000 10:35:24 -0700 (PDT)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] scop
On Tue, 20 Jun 2000, Steve A. Chervitz wrote:
> Cayte wrote:
>
> > Browsing through the SCOP database, I don't see dom, lin or
> > location files, that the SCOP parser leads me to expect. The site has
> > web pages that are roughly like the lin files. If I look at the HTML
> > source, it contains text, that resembles location and dom. But I'm
> > not seeing files that I can feed directly into the
> > parser?
> > Cayte
>
> Try these URLs for the dom and lin files:
>
> http://scop.berkeley.edu/search.cgi?dir=dom
> http://scop.berkeley.edu/search.cgi?dir=lin
Yes. Sorry about that. This should be documented somewhere.
>
> The dom file is about 1Mb, the lin file is about 7X that size.
>
> A while back I wrote a bioperl module for working with SCOP data (not
> yet contributed, but
> possibly soon). It might be useful to compare notes.
Yes, that would be nice. The biopython sources are available in the CVS
tree. As I recall, the sequence locations in SCOP were not trivial to
parse.
Jeff
>
> Steve
>
>
>
> _______________________________________________
> BioPython mailing list - BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
>
From Michael.Poidinger@eBioinformatics.com Thu, 22 Jun 2000 16:04:24 +1000
Date: Thu, 22 Jun 2000 16:04:24 +1000
From: Mike Poidinger Michael.Poidinger@eBioinformatics.com
Subject: [BioPython] Blast Parser broken
The BioPython BlastParser breaks if more than one database is used in the
blast search.
I have modified NCBIStandalone.py and Record.py to accomodate this,
Modified versions or patches available by request.
Mike
____________________________________________________________
Mike Poidinger PhD(Virology) PGDipSci(Computer Science)
Project Manager
eBioinformatics Inc
Suite 104, Bay 16 Australian Technology Park,
Eveleigh, NSW, 1430, Australia
http://www.ebioinformatics.com
Ph: +61-2-9209-4765 Fax: +61-2-9209-4747
From jchang@SMI.Stanford.EDU Thu, 22 Jun 2000 09:52:56 -0700 (PDT)
Date: Thu, 22 Jun 2000 09:52:56 -0700 (PDT)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] Blast Parser broken
Hi Mike,
Can you send me the patches, and an example of an input file that breaks?
Thanks,
Jeff
On Thu, 22 Jun 2000, Mike Poidinger wrote:
> The BioPython BlastParser breaks if more than one database is used in the
> blast search.
>
> I have modified NCBIStandalone.py and Record.py to accomodate this,
> Modified versions or patches available by request.
>
> Mike
>
> ____________________________________________________________
> Mike Poidinger PhD(Virology) PGDipSci(Computer Science)
> Project Manager
> eBioinformatics Inc
> Suite 104, Bay 16 Australian Technology Park,
> Eveleigh, NSW, 1430, Australia
> http://www.ebioinformatics.com
> Ph: +61-2-9209-4765 Fax: +61-2-9209-4747
>
>
>
> _______________________________________________
> BioPython mailing list - BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
>
From jchang@SMI.Stanford.EDU Thu, 22 Jun 2000 10:06:10 -0700 (PDT)
Date: Thu, 22 Jun 2000 10:06:10 -0700 (PDT)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] pending developmental release
Hello all,
There's enough stuff in biopython now that we can start developmental
releases available in formats other than CVS. This will make the code
more accessible for people who don't have access to CVS. This
developmental release will be pre-alpha. The main purpose is to get the
code to a larger audience, who knows that they will be working with
"bleeding edge", slightly broken stuff. For authors, it means that your
API's aren't frozen yet, but you should be developing them with care, and
planning on freezing them soon.
I'm hoping to get this done over the next week, so will authors please let
me know when your respective code is in "good" condition. Brad, I would
like to make a simultaneous release of the CORBA stuff. Please let me
know if that will be possible.
Eventually, I want to start moving toward an alpha 0.9 release. Before
then, we need to:
- finish Seq/SeqFeature interface
- add BLAST access over WWW
- add PDB parser (Andrew's UPDB?)
- add regression tests
- finish documentation
If you're interested in taking one of these on, please let me know!
Thanks,
Jeff
From chapmanb@arches.uga.edu Thu, 22 Jun 2000 14:00:06 -0400
Date: Thu, 22 Jun 2000 14:00:06 -0400
From: Brad Chapman chapmanb@arches.uga.edu
Subject: [BioPython] pending developmental release
> There's enough stuff in biopython now that we can start developmental
> releases available in formats other than CVS.
Thats sounds like a great idea!
> Brad, I would
> like to make a simultaneous release of the CORBA stuff. Please let
me
> know if that will be possible.
Yeah, I don't see a problem with that as long as it is near the later
part of next week. I have some stuff to clean up and also a few ideas
I want to try (which might make omniORB work) but just let me know a
date, and I can make it without a problem.
> Eventually, I want to start moving toward an alpha 0.9 release.
Before
> then, we need to:
> - finish Seq/SeqFeature interface
> - add BLAST access over WWW
> - add PDB parser (Andrew's UPDB?)
> - add regression tests
> - finish documentation
>
> If you're interested in taking one of these on, please let me know!
Jeff, if you want help with docs, this would be something I would be
happy to work on, so just let me know what your plan is for that and
what I can do.
BTW, Jason (from Bioperl) and I have started working on
documentation for biocorba, so I hope that will be done by the time we
are ready for the alpha release.
Brad
From jchang@SMI.Stanford.EDU Thu, 22 Jun 2000 21:16:50 -0700 (PDT)
Date: Thu, 22 Jun 2000 21:16:50 -0700 (PDT)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] Blast Parser broken
Thanks very much, Mike! I've checked your patches into the repository. I
didn't even know that you could search against multiple databases
simultaneously...
Jeff
On Thu, 22 Jun 2000, Mike Poidinger wrote:
> The BioPython BlastParser breaks if more than one database is used in the
> blast search.
>
> I have modified NCBIStandalone.py and Record.py to accomodate this,
> Modified versions or patches available by request.
>
> Mike
>
> ____________________________________________________________
> Mike Poidinger PhD(Virology) PGDipSci(Computer Science)
> Project Manager
> eBioinformatics Inc
> Suite 104, Bay 16 Australian Technology Park,
> Eveleigh, NSW, 1430, Australia
> http://www.ebioinformatics.com
> Ph: +61-2-9209-4765 Fax: +61-2-9209-4747
>
>
>
> _______________________________________________
> BioPython mailing list - BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
>
From jchang@SMI.Stanford.EDU Thu, 22 Jun 2000 23:47:48 -0700 (PDT)
Date: Thu, 22 Jun 2000 23:47:48 -0700 (PDT)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] pending developmental release
> Yeah, I don't see a problem with that as long as it is near the later
> part of next week. I have some stuff to clean up and also a few ideas
> I want to try (which might make omniORB work) but just let me know a
> date, and I can make it without a problem.
Great! We'll make it at the end of the week, then. Friday, or
Saturday...
> Jeff, if you want help with docs, this would be something I would be
> happy to work on, so just let me know what your plan is for that and
> what I can do.
Yes, that would be great. I think what's most important is to have a
Tutorial so that people can pick this package up and immediately see how
to do some things. It's intimidating to be thrown into a pile of modules,
with only docstrings as guides...
I've started the barest outline of a tutorial in
biopython/Doc/Tutorial.txt with some ideas of things to put in. However,
I'm not set on the content. In any case, we should target it toward as
wide an audience as possible, without having to give a CS or biology
lesson.
Is this what you had in mind to do?
Also, if you have any ideas on what kind of format we should use for
documentation (LaTeX, Word, HTML, Text, etc.), please let me know.
Python doesn't have the nice POD or javadoc stuff...
Hmmm... Most of the code does have docstrings, so we should look into the
state of docstring programs.
> BTW, Jason (from Bioperl) and I have started working on
> documentation for biocorba, so I hope that will be done by the time we
> are ready for the alpha release.
Great! Please send me a contributors to biopython-corba, so that I can
add them to the AUTHORS file.
Thanks,
Jeff
From chapmanb@arches.uga.edu Fri, 23 Jun 2000 14:20:58 -0400 (EDT)
Date: Fri, 23 Jun 2000 14:20:58 -0400 (EDT)
From: Brad Chapman chapmanb@arches.uga.edu
Subject: [BioPython] pending developmental release
Jeff Chang wrote:
> Great! We'll make it at the end of the week, then. Friday, or
> Saturday...
That sounds super to me. I'll send you a mail when I think biopython-corba
is ready to go.
> I've started the barest outline of a tutorial in
> biopython/Doc/Tutorial.txt with some ideas of things to put in. However,
> I'm not set on the content. In any case, we should target it toward as
> wide an audience as possible, without having to give a CS or biology
> lesson.
>
> Is this what you had in mind to do?
Yup, you're a mind reader :-). Seriously, the ideas in Tutorial.txt sound
good, so I think a good next step would be to flesh it out into a real
outline of sections, etc. Then we can think about how to divide the work
of writing the documentation up. If you want, I can take a stab at getting
an outline going based on what you already have, and then we can have
your ideas and mine in the first outline. Maybe some other people also
have ideas on what should be included.
> Also, if you have any ideas on what kind of format we should use for
> documentation (LaTeX, Word, HTML, Text, etc.), please let me know.
> Python doesn't have the nice POD or javadoc stuff...
I would very much prefer to write in LaTeX (especially over Word, bleah).
I have had really good luck doing "technical" documentation in it using
verbatim to typeset code examples. In addition, it also produces lots of
nice formats, and I have been converting LaTeX to html regularly using
HeVeA (http://pauillac.inria.fr/~maranget/hevea/index.html) with good
luck.
> Hmmm... Most of the code does have docstrings, so we should look
> into the
> state of docstring programs.
AFAIK, there are three separate implementations to convert docstrings into
some readable output:
pythonddoc -> http://starship.python.net/crew/danilo/pythondoc/
crystal -> http://www.btinternet.com/~tratt/comp/python/crystal/
htmldoc -> http://www.lfw.org/python/ (at the bottom of the page)
I have tried all of these without any success, so I don't have a personal
recommendation :-< (They all seem to not work well on programs with
dependencies on modules that aren't from the core library, but we
shouldn't have these problems with biopython). However, htmldoc should be
easiest since it is only two modules and doesn't try to do anything like
format docstrings (which crystal and pythondoc do).
Brad
From jchang@SMI.Stanford.EDU Wed, 28 Jun 2000 11:55:38 -0700 (PDT)
Date: Wed, 28 Jun 2000 11:55:38 -0700 (PDT)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] jitterbug
Chris Dagdigian has set up jitterbug and a new biopython-dev mailing list.
I would like to move the discussions of the more technical issues, such as
implementation details and bugs, onto this list. In addition, incoming
bugs will be automatically be sent to this list. Thus, it'll be a
high-volume unmoderated list that contains low-level details about the
code. I would like all core developers to sign up on it.
Cayte, can you link Jitterbug now to the main web page? I'll update the
mailing list page with a link to biopython-dev.
Thanks,
Jeff
On Mon, 19 Jun 2000, Cayte wrote:
> We need to link the new biopython jitterbug to the web sitem so
> it's visible to the oublic. I can try if no one objects.
>
>
> Cayte
>
From jchang@SMI.Stanford.EDU Wed, 28 Jun 2000 12:00:49 -0700 (PDT)
Date: Wed, 28 Jun 2000 12:00:49 -0700 (PDT)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] 0.9d01 release
Hello developers,
The first developmental release is coming at the end of the week. Please
let me know whether your code will be in "decent" state by then, or
whether we should push the release back. It does not have to be perfect
or complete, but should at least compile. The purpose of this release is
to make the code more widely available, for developers and power users.
After this release, we should try to follow the "release early, release
often" mantra.
Thanks,
Jeff
From chapmanb@arches.uga.edu Thu, 29 Jun 2000 00:44:13 -0400
Date: Thu, 29 Jun 2000 00:44:13 -0400
From: Brad Chapman chapmanb@arches.uga.edu
Subject: [BioPython] 0.9d01 release
> The first developmental release is coming at the end of the week.
Please
> let me know whether your code will be in "decent" state by then, or
> whether we should push the release back. It does not have to be
perfect
> or complete, but should at least compile. The purpose of this
release is
> to make the code more widely available, for developers and power
users.
I just finished committing the changes I wanted to make to
biopython-corba for the release, so it should be ready to go whenever
everyone else is. If anyone is following biopython-corba (or even if
you aren't) and wants to check this to make sure it runs okay for
someone besides me, I would be very appreciative!
biopython-corba installs using distutils, so making a tarball of
this should be no problem, but it will require that you have either
Fnorb or omniORB installed and run 'python setup.py build' before
running 'python setup.py sdist.'
> After this release, we should try to follow the "release early,
release
> often" mantra.
Sounds like a very good plan :-).
Brad
From chapmanb@arches.uga.edu Fri, 30 Jun 2000 02:00:47 -0400
Date: Fri, 30 Jun 2000 02:00:47 -0400
From: Brad Chapman chapmanb@arches.uga.edu
Subject: [BioPython] 0.9d01 release
I wrote:
> I just finished committing the changes I wanted to make to
> biopython-corba for the release, so it should be ready to go
whenever
> everyone else is. If anyone is following biopython-corba (or even if
> you aren't) and wants to check this to make sure it runs okay for
> someone besides me, I would be very appreciative!
Ooops, darn it, just when you think you are finished, something else
comes along!
They just announced the pre-release of omniORBpy 1.0 (which will
be an official release in a few days, provided there aren't any bad
bugs) and this release version follows the revised python mapping for
CORBA, which includes some changes that break old code. So, I just
updated the CVS version of biopython-corba to use this new standard
and the newly available tools.
Sorry, Jeff, if you've already started packaging stuff, but what
is in cvs now should be my final changes. Really :-).
Please let me know if there are any problems with it.
Brad
From jchang@SMI.Stanford.EDU Fri, 30 Jun 2000 11:28:17 -0700 (PDT)
Date: Fri, 30 Jun 2000 11:28:17 -0700 (PDT)
From: Jeffrey Chang jchang@SMI.Stanford.EDU
Subject: [BioPython] 0.9d01 release
Nah, haven't started packaging yet.
The release is going to be delayed until the beginning of next
week. Cayte has promised to spend the long weekend testing code!
Jeff
On Fri, 30 Jun 2000, Brad Chapman wrote:
> I wrote:
> > I just finished committing the changes I wanted to make to
> > biopython-corba for the release, so it should be ready to go
> whenever
> > everyone else is. If anyone is following biopython-corba (or even if
> > you aren't) and wants to check this to make sure it runs okay for
> > someone besides me, I would be very appreciative!
>
> Ooops, darn it, just when you think you are finished, something else
> comes along!
> They just announced the pre-release of omniORBpy 1.0 (which will
> be an official release in a few days, provided there aren't any bad
> bugs) and this release version follows the revised python mapping for
> CORBA, which includes some changes that break old code. So, I just
> updated the CVS version of biopython-corba to use this new standard
> and the newly available tools.
> Sorry, Jeff, if you've already started packaging stuff, but what
> is in cvs now should be my final changes. Really :-).
> Please let me know if there are any problems with it.
>
> Brad
>
>
>
>
> _______________________________________________
> BioPython mailing list - BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
>