[Bioperl-l] Need CPAN release to clear up CPANtesters test failure reports

Fri May 27 15:45:22 UTC 2016

If folks can send me their PAUSE IDs I can work on adding a few more names.

chris

On May 27, 2016, at 10:23 AM, Mark A Jensen <maj at fortinbras.us<mailto:maj at fortinbras.us>> wrote:

Chris, I don't think it's a problem calling this a developer release. I think we want to get all the myriad patches now in master out and see what people think, in addition to a split. (We are talking about making the split, right? )

Brian, first thing would be to do the mutually exclusive dependency grouping exercise for real, my (and others prob) thought has been this may indicate the natural package clumps. I have some scripts that can do this and also could help create the appropriate package metadata, which is a btch to do by hand, but I think must be done.

If we decide now to release using the group PAUSE id, then we can extend the rollout and give Chris a break. Let's make the first installment the group of mods that includes Bio::Seq and friends. This will be a basic dep for almost everything else.

On Fri, May 27, 2016 at 10:39 AM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:

I can set some time aside later today and this weekend to start on this but we’ll need to go through the process over until we can retrieve the old wiki content.  We may just go ahead and pull the trigger on a 1.7 release unless we *really* need a new 1.6.x.  My only concern with odd-numbered releases w/ bioperl tend to worry folks as they have long been noted as developer releases.

Long-term, what I suggest is (while I’m working on this) we set up a few others under the BIOPERLML PAUSE umbrella ID so we can spread the load a bit more.  My day-to-day schedule has been horrendous, so this would definitely help.

Re: documentation: there was a page on releases on the old wiki, now off-line; since the OBF web server compromise we’ve managed to get dumps of all OBF sites (I still need to upload those to the cloud account).

chris

On May 27, 2016, at 9:22 AM, Brian Osborne <bosborne11 at verizon.net<mailto:bosborne11 at verizon.net>> wrote:

Mark,

Can you start this list on what needs to be done?

BIO

On May 27, 2016, at 10:13 AM, Mark A Jensen <maj at fortinbras.us<mailto:maj at fortinbras.us>> wrote:

I've done some work and thinking (I.e., stewing) about this, if you want help Chris.

On Fri, May 27, 2016 at 10:07 AM, Brian Osborne <bosborne11 at verizon.net<mailto:bosborne11 at verizon.net>> wrote:

Chris,

You are still the de facto leader for CPAN releases, but that does not mean that you have to do all the work. But I think you probably have the most comprehensive view of what needs to be done so I suggest - if we want to get out a release before YAPC - that you list here what needs to be done. Then we’ll put these into Github, sort out who does what, this worked for the Wiki -> GitHub pages tasks.

Thanks again,

Brian O.

> On May 26, 2016, at 8:47 PM, James E Keenan <jkeen at verizon.net<mailto:jkeen at verizon.net>> wrote:
>
> On 05/16/2016 09:52 AM, Fields, Christopher J wrote:
>> Thanks Jim!  We can work on pushing out a new release.
>>
>> One of the long-term problems with BioPerl is the large size of the distribution; we’ve been considering a new 1.7x series to deal with this, but it’s clearly slowed down over the years.  Maybe this will help stimulate that effort again.
>>
>> chris
>>
>>> On May 15, 2016, at 6:41 PM, James E Keenan <jkeen at verizon.net<mailto:jkeen at verizon.net>> wrote:
>>>
>>> [snip]
>
>>> Your last CPAN release was in July 2014.  I strongly advise that you do a CPAN release of BioPerl ASAP so that your project does not suffer reputational damage from all those test failure reports.  At the same time, I urge you to go through the bug reports at https://rt.cpan.org/Public/Dist/Display.html?Name=BioPerl<https://urldefense.proofpoint.com/v2/url?u=https-3A__rt.cpan.org_Public_Dist_Display.html-3FName-3DBioPerl&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=ASh8D2kHlj-3SXVj3DM4iJWuWTPu8T5rBEgXEkaeY7Q&s=Nz6xnaLCX_p9G8jXXgKz4ybAuhnFuSrQEGQEnwP2tYg&e=>.  It's likely that HEAD on github resolves some of these.
>>>
>>> Thank you very much.
>>> Jim Keenan
>
> I'd like to follow up on my recommendation that you try to get a new CPAN release of BioPerl out soon.
>
> The major North American Perl conference, The Perl Conference/YAPC::NA::2016, will be held in Orlando, FL, starting just 26 days from now.
>
> http://www.yapcna.org/yn2016/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.yapcna.org_yn2016_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=ASh8D2kHlj-3SXVj3DM4iJWuWTPu8T5rBEgXEkaeY7Q&s=kmKD7Jir7nJjqg1TBsG9bZmXvaJkk1qL5Ehzr9_LHOA&e=>
>
> A CPAN release before YAPC would be a strong shot in the arm for the visibility of BioPerl within the larger Perl community.  Apart from the fact that there are software engineers who work in the biomedical sciences who frequently attend YAPC, there are also Perl people (like myself) who are in a position to submit patches and pull requests simply for the purpose of improving the quality of the Perl code.  But people in the latter category are unlikely to contribute patches unless they think that there is a realistic chance of the code's being released to CPAN.
>
> So, please take advantage of this time-limited opportunity.
>
> Thank you very much.
> Jim Keenan
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org<mailto:Bioperl-l at mailman.open-bio.org>
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l<https://urldefense.proofpoint.com/v2/url?u=http-3A__mailman.open-2Dbio.org_mailman_listinfo_bioperl-2Dl&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=ASh8D2kHlj-3SXVj3DM4iJWuWTPu8T5rBEgXEkaeY7Q&s=KKo8zqU4bkEC4Y5tYFw4lV85q_cL2Ft2ETk-i6UkLD4&e=>

_______________________________________________
Bioperl-l mailing list
Bioperl-l at mailman.open-bio.org<mailto:Bioperl-l at mailman.open-bio.org>
http://mailman.open-bio.org/mailman/listinfo/bioperl-l<https://urldefense.proofpoint.com/v2/url?u=http-3A__mailman.open-2Dbio.org_mailman_listinfo_bioperl-2Dl&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=ASh8D2kHlj-3SXVj3DM4iJWuWTPu8T5rBEgXEkaeY7Q&s=KKo8zqU4bkEC4Y5tYFw4lV85q_cL2Ft2ETk-i6UkLD4&e=>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/bioperl-l/attachments/20160527/7f3d91d6/attachment.html>