headers
Hilmar Lapp | 1 Jul 01:36
Picon
Gravatar

Re: First cut svn repository


On Jun 28, 2007, at 3:43 PM, George Hartzell wrote:

> I just did the experiment, and filename-insensitivity seems to be
> breaking something.
>
> I'm using an svn I picked up from http://www.codingmonkeys.de/mbo/.
>
> I reformatted a memory stick to be case sensitive and co of
>
>   bioperl/bioperl-live/tags/release-0-9-2/t
>
> worked, then I made a directory in my home dir (normal mac thing) and
> got the same error as above.

You picked up a rename of a file from lower case extension to upper  
case extension. Unfortunately, there are several months between  
adding the upper-case and removing the lower-case version.

We can reconstruct what happened with this using svn log on the  
directory (this does not require a checkout):

$ svn log --verbose svn+ssh://dev.open-bio.org/home/hartzell/bioperl/ 
bioperl-live/trunk/t/data

Searching for HUMBETGLOA yields the following two commits that added  
one and removed the other:

------------------------------------------------------------------------
r2245 | jason | 2001-12-08 11:59:05 -0500 (Sat, 08 Dec 2001) | 2 lines
(Continue reading)

Permalink | Reply | 4 comments |
headers
Chris Fields | 1 Jul 02:40
Picon

Re: First cut svn repository

Checkout worked for me (Mac OS X) using both:

svn co svn+ssh://dev.open-bio.org/home/hartzell/bioperl/bioperl-live/ 
tags/release-0-9-2/t/data
svn co svn+ssh://dev.open-bio.org/home/hartzell/bioperl/bioperl-live/ 
tags/release-0-9-2/

so removing the offending file worked (good catch!).  Haven't run a  
full co but probably isn't necessary.

chris

On Jun 30, 2007, at 6:36 PM, Hilmar Lapp wrote:

>
> On Jun 28, 2007, at 3:43 PM, George Hartzell wrote:
>
>> I just did the experiment, and filename-insensitivity seems to be
>> breaking something.
>>
>> I'm using an svn I picked up from http://www.codingmonkeys.de/mbo/.
>>
>> I reformatted a memory stick to be case sensitive and co of
>>
>>   bioperl/bioperl-live/tags/release-0-9-2/t
>>
>> worked, then I made a directory in my home dir (normal mac thing) and
>> got the same error as above.
>
> You picked up a rename of a file from lower case extension to upper
(Continue reading)

Permalink | Reply | 3 comments |
headers
George Hartzell | 1 Jul 02:48
Gravatar

Take 2 of the new subversion repository.


There's a second cut at the subversion repository.  I've done a better
job of setting svn:keywords and svn:eol-style on various files.  The
defaults were more cautious and I used an auto-props files based on
the wiki version.

  svn+ssh://dev.open-bio.org/home/hartzell/bioperl_take2

The old repository's still around as

  svn+ssh://dev.open-bio.org/home/hartzell/bioperl_take1

I renamed it so that people would work with it by mistake.  If, for
some hard-to-imagine reason, you have a working copy that you want to
run against it, you should be able to do an svn switch --relocate on
your working copy and be back in shape.  In fact, it might be a good
time to give it a try....

g.
Permalink | Reply | 18 comments |
headers
George Hartzell | 1 Jul 03:17
Gravatar

Re: First cut svn repository

Chris Fields writes:
 > Checkout worked for me (Mac OS X) using both:
 > 
 > svn co svn+ssh://dev.open-bio.org/home/hartzell/bioperl/bioperl-live/ 
 > tags/release-0-9-2/t/data
 > svn co svn+ssh://dev.open-bio.org/home/hartzell/bioperl/bioperl-live/ 
 > tags/release-0-9-2/
 > 
 > so removing the offending file worked (good catch!).  Haven't run a  
 > full co but probably isn't necessary.
 > [...]

I'll keep a note of that as something to do when I prepare the final
cut of the repository.

g.
Permalink | Reply | 0 comments |
headers
Jason Stajich | 1 Jul 03:25
Gravatar

Re: Take 2 of the new subversion repository.

Thanks George -
I also did
chgrp -R bioperl /home/hartzell/bioperl_take?
to make sure the group permission was set right.

We may also want to do a chmod g+s on all the dirs in there as well  
so that permissions are preserved when this gets deployed for real.

If anyone wants to make some changes to files and commit them, as  
well as make some branches/tags to play around a little bit since  
we'll likely throw this away and do it again from locked down version  
from CVS at some appointed time.

Do you know how to have svn commit messages generate summary emails  
as well?

-j
On Jun 30, 2007, at 5:48 PM, George Hartzell wrote:

>
> There's a second cut at the subversion repository.  I've done a better
> job of setting svn:keywords and svn:eol-style on various files.  The
> defaults were more cautious and I used an auto-props files based on
> the wiki version.
>
>   svn+ssh://dev.open-bio.org/home/hartzell/bioperl_take2
>
> The old repository's still around as
>
>   svn+ssh://dev.open-bio.org/home/hartzell/bioperl_take1
(Continue reading)

Permalink | Reply | 11 comments |
headers
Hilmar Lapp | 1 Jul 04:21
Picon
Gravatar

Re: Take 2 of the new subversion repository.


On Jun 30, 2007, at 8:48 PM, George Hartzell wrote:

> I renamed it so that people would work with it by mistake.  If, for
> some hard-to-imagine reason, you have a working copy that you want to
> run against it,

It's not so hard to imagine - checking out the entire repository  
takes a long time.

> you should be able to do an svn switch --relocate on
> your working copy and be back in shape.  In fact, it might be a good
> time to give it a try....

It doesn't work:

svn: The repository at 'svn+ssh://dev.open-bio.org/home/hartzell/ 
bioperl_take2' has uuid '31277767-6726-dc11-ab4c-0019e3f901d6', but  
the WC has '27e854f1-f323-dc11-8c1b-0019e3f901d6'

You can't relocate to a totally new repository (relocating to  
bioperl_take1 does work though).

	-hilmar

--

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================
(Continue reading)

Permalink | Reply | 0 comments |
headers
Chris Fields | 1 Jul 04:39
Picon

Re: Take 2 of the new subversion repository.

There are a few CPAN modules available; here's one:

http://search.cpan.org/~dwheeler/SVN-Notify-2.66/lib/SVN/Notify.pm

chris

On Jun 30, 2007, at 8:25 PM, Jason Stajich wrote:

> Thanks George -
> I also did
> chgrp -R bioperl /home/hartzell/bioperl_take?
> to make sure the group permission was set right.
>
> We may also want to do a chmod g+s on all the dirs in there as well
> so that permissions are preserved when this gets deployed for real.
>
> If anyone wants to make some changes to files and commit them, as
> well as make some branches/tags to play around a little bit since
> we'll likely throw this away and do it again from locked down version
> from CVS at some appointed time.
>
> Do you know how to have svn commit messages generate summary emails
> as well?
>
> -j
> On Jun 30, 2007, at 5:48 PM, George Hartzell wrote:
>
>>
>> There's a second cut at the subversion repository.  I've done a  
>> better
(Continue reading)

Permalink | Reply | 0 comments |
headers
Chris Fields | 1 Jul 04:46
Picon

Re: Splits again


On Jun 30, 2007, at 4:32 PM, Sendu Bala wrote:

> Hilmar Lapp wrote:
>> On Jun 28, 2007, at 3:19 PM, Sendu Bala wrote:
>>> [...]
>>> Very definitely the latter. The key benefit of my approach is  
>>> that  the organisation stays as is and that a snapshot of the  
>>> repository  remains a single directory of modules in Bio so that  
>>> people don't  have to 'install' Bioperl, they can still just  
>>> uncompress the  archive (or check out the package from svn) and  
>>> point their  PERL5LIB to the root dir of the package.
> [snip]
>> In this sense, I understand a release pumpkin will generate ~900   
>> packages to upload to CPAN? How much hassle is that compared to  
>> what  uploading a bioperl release means right now?
>
> I'd have to investigate. I did my uploads using the PAUSE website,  
> which for 900 packages would be unfeasible. Will have to see if the  
> process can be automated.

Not that they would care one way or another but maybe we should  
contact the CPAN maintainers to get their thoughts.  They might have  
some ideas...

>> How brittle is all the Build.PL code that will be needed to  
>> automate  all of this, and how difficult will it be to maintain?  
>> For example,  if someone adds in 10 new modules, what Build.PL- 
>> related work will  need to be done?
>
(Continue reading)

Permalink | Reply | 0 comments |
headers
Hilmar Lapp | 1 Jul 04:56
Picon
Gravatar

Re: First cut svn repository

It turns out that both files are also present on the release-0-9-3,  
bioperl-1-0-0, bioperl-1-0-alpha, and bioperl-1-0-alpha2-rc tags, so add

$ svn rm -m "Removing offending duplicate" svn+ssh://dev.open-bio.org/ 
home/hartzell/bioperl/bioperl-live/tags/release-0-9-3/t/data/ 
HUMBETGLOA.fasta
$ svn rm -m "Removing offending duplicate" svn+ssh://dev.open-bio.org/ 
home/hartzell/bioperl/bioperl-live/tags/bioperl-1-0-0/t/data/ 
HUMBETGLOA.fasta
$ svn rm -m "Removing offending duplicate" svn+ssh://dev.open-bio.org/ 
home/hartzell/bioperl/bioperl-live/tags/bioperl-1-0-alpha/t/data/ 
HUMBETGLOA.fasta
$ svn rm -m "Removing offending duplicate" svn+ssh://dev.open-bio.org/ 
home/hartzell/bioperl/bioperl-live/tags/bioperl-1-0-alpha2-rc/t/data/ 
HUMBETGLOA.fasta

to the post-processing commands.

	-hilmar

On Jun 30, 2007, at 8:40 PM, Chris Fields wrote:

> Checkout worked for me (Mac OS X) using both:
>
> svn co svn+ssh://dev.open-bio.org/home/hartzell/bioperl/bioperl- 
> live/tags/release-0-9-2/t/data
> svn co svn+ssh://dev.open-bio.org/home/hartzell/bioperl/bioperl- 
> live/tags/release-0-9-2/
>
> so removing the offending file worked (good catch!).  Haven't run a
(Continue reading)

Permalink | Reply | 1 comment |
headers
David Messina | 1 Jul 07:38
Picon
Favicon

Re: svn auto-properties [was Re: First cut svn repository]


> [Nath]
> I think the list of seq formats recognised by Bioperl in Bio::SeqIO  
> and
> Bio::AlignIO would be a good start. As these are likely to be the ones
> that are sensitive to file format recognition and thus could break  
> tests
> if renamed.

Sounds good to me. I will do a quick tour of the rest of the repo  
looking for other common or important file extensions, but I don't  
expect there to be many if any.

> [still Nath]
> I think a lot of people have used "." in file names as an  
> alternative to
> a space. I think it would be beneficial to use an underscore "_" in
> these cases and leave the "." to represent the beginning of the file
> extension.

That's a great idea.

> [Chris]
> Do we need to define every filetype extension, or can there be a  
> fallback (eg if it isn't on the list or has no extension it's plain  
> text)?

For every file that's added, svn takes a peek to see if it's human- 
readable. If not, it's tagged with the generic MIME type application/ 
octet-stream. (It does this so it knows not to try to do diffs and
(Continue reading)

Permalink | Reply | 0 comments |

Gmane