Need CPAN release to clear up CPANtesters test failure reports

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Need CPAN release to clear up CPANtesters test failure reports

James E Keenan
The other day I was looking for unanswered Perl-tagged questions on
stackoverflow.  I came across this one:

http://stackoverflow.com/questions/36985090/extracting-and-joining-exons-from-multiple-sequence-alignments

To answer it I tried to install BioPerl from CPAN but got multiple test
failures.  I then checked out the BioPerl page on CPANtesters and saw
that your latest CPAN distribution has experienced massive test failures
on many versions of Perl and several different operating systems.  See:
  http://matrix.cpantesters.org/?dist=BioPerl+1.6.924

I subsequently located your github site at
https://github.com/bioperl/bioperl-live, from which I was able to fork.
  When I attempted to build locally, I was pleasantly surprised to find
all tests run by ./Build test were PASSing.  The only problem I saw was
a "missing or corrupt MANIFEST" message, for which I have supplied this
pull request:  https://github.com/bioperl/bioperl-live/pull/150.

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.  It's likely
that HEAD on github resolves some of these.

Thank you very much.
Jim Keenan
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Re: Need CPAN release to clear up CPANtesters test failure reports

Fields, Christopher J
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 <[hidden email]> wrote:
>
> The other day I was looking for unanswered Perl-tagged questions on stackoverflow.  I came across this one:
>
> http://stackoverflow.com/questions/36985090/extracting-and-joining-exons-from-multiple-sequence-alignments
>
> To answer it I tried to install BioPerl from CPAN but got multiple test failures.  I then checked out the BioPerl page on CPANtesters and saw that your latest CPAN distribution has experienced massive test failures on many versions of Perl and several different operating systems.  See:  http://matrix.cpantesters.org/?dist=BioPerl+1.6.924
>
> I subsequently located your github site at https://github.com/bioperl/bioperl-live, from which I was able to fork.  When I attempted to build locally, I was pleasantly surprised to find all tests run by ./Build test were PASSing.  The only problem I saw was a "missing or corrupt MANIFEST" message, for which I have supplied this pull request:  https://github.com/bioperl/bioperl-live/pull/150.
>
> 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.  It's likely that HEAD on github resolves some of these.
>
> Thank you very much.
> Jim Keenan
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: Need CPAN release to clear up CPANtesters test failure reports

James E Keenan
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 <[hidden email]> 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.  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/

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
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Re: Need CPAN release to clear up CPANtesters test failure reports

Brian Osborne-2
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 <[hidden email]> 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 <[hidden email]> 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.  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/
>
> 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
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: Need CPAN release to clear up CPANtesters test failure reports

Mark A. Jensen

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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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.  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/
>
> 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
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

_______________________________________________
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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: Need CPAN release to clear up CPANtesters test failure reports

Brian Osborne-2
Mark,

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

BIO


On May 27, 2016, at 10:13 AM, Mark A Jensen <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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.  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/
>
> 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
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

_______________________________________________
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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l



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Re: Need CPAN release to clear up CPANtesters test failure reports

Fields, Christopher J
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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.  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/
>
> 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
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

_______________________________________________
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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l




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Re: Need CPAN release to clear up CPANtesters test failure reports

Mark A. Jensen

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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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.  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/
>
> 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
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

_______________________________________________
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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l




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Re: Need CPAN release to clear up CPANtesters test failure reports

Fields, Christopher J
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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.  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/
>
> 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
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

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Re: Need CPAN release to clear up CPANtesters test failure reports

James E Keenan
In reply to this post by James E Keenan
On 05/26/2016 08:47 PM, James E Keenan 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 <[hidden email]> 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.  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/
>
> 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.
>

Unfortunately, this opportunity was not seized.  YAPC::NA::2016 -- now
re-branded as The Perl Conference 2016 -- has come and gone.  During the
Pull Request Challenge which was part of the conference, I did create
one p.r. against BioPerl, which I'm glad to say has been accepted.
However, we would have been in a better position to advocate for
non-bio-focused Perl programmers to help with BioPerl if we had had an
up-to-date CPAN release.

(By the way, I heard two presentations at the conference that dealt with
genomic data.)

Since AFAICT your github 'master' branch is passing all tests, I would
urge you to simply increment the $VERSION numbers by .001 throughout and
upload to CPAN.  After that's done, you can discuss whether or not you
want to call the next version 1.6 or not.

Thank you very much.
Jim Keenan
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Re: Need CPAN release to clear up CPANtesters test failure reports

Fields, Christopher J

On Jun 27, 2016, at 8:48 PM, James E Keenan <[hidden email]> wrote:

Unfortunately, this opportunity was not seized.  YAPC::NA::2016 -- now re-branded as The Perl Conference 2016 -- has come and gone.  During the Pull Request Challenge which was part of the conference, I did create one p.r. against BioPerl, which I'm glad to say has been accepted. However, we would have been in a better position to advocate for non-bio-focused Perl programmers to help with BioPerl if we had had an up-to-date CPAN release.

(By the way, I heard two presentations at the conference that dealt with genomic data.)

Since AFAICT your github 'master' branch is passing all tests, I would urge you to simply increment the $VERSION numbers by .001 throughout and upload to CPAN.  After that's done, you can discuss whether or not you want to call the next version 1.6 or not.

Thank you very much.
Jim Keenan

Jim,

Though some might consider it a bit pushy we do appreciate the nudge on releases.  I was simply not able to fit this into my schedule, which has become much busier over the last few years.  We also had a major site migration due to a hacked server that forced our hand prematurely, which really didn’t help much.

Saying that, simply pushing out a new 1.6.x is not tenable off the master branch; you will note that we had long ago created a separate release branch for 1.6.x, which has been highly cherry-picked to.  We will be releasing a 1.7 release from 'master' once we have addressed a few minor factors (https://github.com/bioperl/bioperl-live/issues/158).  It’s possible some may be added such as cleaning up access for remote databases, which are not run by default but fail due to changes outside our control.  You’ll also note this hasn’t been announced to the list yet :)

Also, if anyone, including you Jim, want to participate in development to improve BioPerl, I am more than happy to have you on board (you will also note I have the bioperl6 repo as well, which I will likely switch over to the ‘bioperl' organization account).  I have been pretty free about giving out perms for commits to the Github repo for anyone who wants to contribute.  We generally have a few people as release managers though the releases over the last several years have been predominately by me.  I have taken the steps to add two new co-maints to the project, both of whom have long been members of the BioPerl community, who can help act as release managers for future releases.

Thanks,

chris


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Re: Need CPAN release to clear up CPANtesters test failure reports

Hilmar Lapp-5
Perhaps this would be a useful target to address at the upcoming CodeFest in Orlando? Chris, if you’re planning to be there, I’d be willing to work through this with you.

  -hilmar

On Jun 28, 2016, at 12:36 AM, Fields, Christopher J <[hidden email]> wrote:


On Jun 27, 2016, at 8:48 PM, James E Keenan <[hidden email]> wrote:

Unfortunately, this opportunity was not seized.  YAPC::NA::2016 -- now re-branded as The Perl Conference 2016 -- has come and gone.  During the Pull Request Challenge which was part of the conference, I did create one p.r. against BioPerl, which I'm glad to say has been accepted. However, we would have been in a better position to advocate for non-bio-focused Perl programmers to help with BioPerl if we had had an up-to-date CPAN release.

(By the way, I heard two presentations at the conference that dealt with genomic data.)

Since AFAICT your github 'master' branch is passing all tests, I would urge you to simply increment the $VERSION numbers by .001 throughout and upload to CPAN.  After that's done, you can discuss whether or not you want to call the next version 1.6 or not.

Thank you very much.
Jim Keenan

Jim,

Though some might consider it a bit pushy we do appreciate the nudge on releases.  I was simply not able to fit this into my schedule, which has become much busier over the last few years.  We also had a major site migration due to a hacked server that forced our hand prematurely, which really didn’t help much.

Saying that, simply pushing out a new 1.6.x is not tenable off the master branch; you will note that we had long ago created a separate release branch for 1.6.x, which has been highly cherry-picked to.  We will be releasing a 1.7 release from 'master' once we have addressed a few minor factors (https://github.com/bioperl/bioperl-live/issues/158).  It’s possible some may be added such as cleaning up access for remote databases, which are not run by default but fail due to changes outside our control.  You’ll also note this hasn’t been announced to the list yet :)

Also, if anyone, including you Jim, want to participate in development to improve BioPerl, I am more than happy to have you on board (you will also note I have the bioperl6 repo as well, which I will likely switch over to the ‘bioperl' organization account).  I have been pretty free about giving out perms for commits to the Github repo for anyone who wants to contribute.  We generally have a few people as release managers though the releases over the last several years have been predominately by me.  I have taken the steps to add two new co-maints to the project, both of whom have long been members of the BioPerl community, who can help act as release managers for future releases.

Thanks,

chris

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Re: Need CPAN release to clear up CPANtesters test failure reports

Fields, Christopher J
Yep, that’s the plan (doing some of this at CodeFest).  I’m not sure if anyone else is going to be at CodeFest this go around.

chris

On Jun 28, 2016, at 9:03 AM, Hilmar Lapp <[hidden email]> wrote:

Perhaps this would be a useful target to address at the upcoming CodeFest in Orlando? Chris, if you’re planning to be there, I’d be willing to work through this with you.

  -hilmar

On Jun 28, 2016, at 12:36 AM, Fields, Christopher J <[hidden email]> wrote:


On Jun 27, 2016, at 8:48 PM, James E Keenan <[hidden email]> wrote:

Unfortunately, this opportunity was not seized.  YAPC::NA::2016 -- now re-branded as The Perl Conference 2016 -- has come and gone.  During the Pull Request Challenge which was part of the conference, I did create one p.r. against BioPerl, which I'm glad to say has been accepted. However, we would have been in a better position to advocate for non-bio-focused Perl programmers to help with BioPerl if we had had an up-to-date CPAN release.

(By the way, I heard two presentations at the conference that dealt with genomic data.)

Since AFAICT your github 'master' branch is passing all tests, I would urge you to simply increment the $VERSION numbers by .001 throughout and upload to CPAN.  After that's done, you can discuss whether or not you want to call the next version 1.6 or not.

Thank you very much.
Jim Keenan

Jim,

Though some might consider it a bit pushy we do appreciate the nudge on releases.  I was simply not able to fit this into my schedule, which has become much busier over the last few years.  We also had a major site migration due to a hacked server that forced our hand prematurely, which really didn’t help much.

Saying that, simply pushing out a new 1.6.x is not tenable off the master branch; you will note that we had long ago created a separate release branch for 1.6.x, which has been highly cherry-picked to.  We will be releasing a 1.7 release from 'master' once we have addressed a few minor factors (https://github.com/bioperl/bioperl-live/issues/158).  It’s possible some may be added such as cleaning up access for remote databases, which are not run by default but fail due to changes outside our control.  You’ll also note this hasn’t been announced to the list yet :)

Also, if anyone, including you Jim, want to participate in development to improve BioPerl, I am more than happy to have you on board (you will also note I have the bioperl6 repo as well, which I will likely switch over to the ‘bioperl' organization account).  I have been pretty free about giving out perms for commits to the Github repo for anyone who wants to contribute.  We generally have a few people as release managers though the releases over the last several years have been predominately by me.  I have taken the steps to add two new co-maints to the project, both of whom have long been members of the BioPerl community, who can help act as release managers for future releases.

Thanks,

chris

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-- 
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