[Bioperl-l] new bioperl release please?
Carnë Draug
There's currently a lot of changes in bioperl, mainly about
splitting modules into their own separated distributions.
Is there anything preventing a new release? Because the changes
are mostly about splitting bioperl, there should not be any new
issue blocking a release or regression. I got it configured with
dzil so a new release should be as simple as `dzil release`.
I would like to package the chnages it for Debian before their
freeze.
I would also like to avoid mixing code fixes with the split of
into multiple distributions.
David
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Fields, Christopher J
Carnë Draug
<cjfi...@illinois.edu> wrote:
>
> On January 29, 2019 at 9:37:34 AM, Carnë Draug (carandr...@gmail.com) wrote:
>>
>> Hi everyone
>>
>> There's currently a lot of changes in bioperl, mainly about
>> splitting modules into their own separated distributions.
>>
>> Is there anything preventing a new release? Because the changes
>> are mostly about splitting bioperl, there should not be any new
>> issue blocking a release or regression. I got it configured with
>> dzil so a new release should be as simple as `dzil release`.
>>
>> I would like to package the chnages it for Debian before their
>> freeze.
>>
>> I would also like to avoid mixing code fixes with the split of
>> into multiple distributions.
>>
>> David
>
https://release.debian.org/buster/freeze_policy.html
Seems like it's already pass. I thought it was in two weeks time but
that's soft freeze. Debian is already in transition freeze so large
changes are no longer acceptable.
I can still prepare the debian package for unstable.
> [...] There aren’t really
> any true blockers, it’s primarily blocking off some time to do this
> and ensure tests are passing. I wanted to do a release over the
> holiday break, but $job took much more of my time than expected.
> Would you be interested in joining in on releases? It might help
> expediting these.
Sure. I can run 'dzil release' in bioperl-live from my computer, no
problem. It only takes a few minutes. Do I have the permissions in
PAUSE to do it?
Fields, Christopher J
On January 29, 2019 at 11:58:48 AM, Carnë Draug (carandr...@gmail.com) wrote:
On Tue, 29 Jan 2019 at 17:09, Fields, Christopher J
<cjfi...@illinois.edu> wrote:
>
> On January 29, 2019 at 9:37:34 AM, Carnë Draug (carandr...@gmail.com) wrote:
>>
>> Hi everyone
>>
>> There's currently a lot of changes in bioperl, mainly about
>> splitting modules into their own separated distributions.
>>
>> Is there anything preventing a new release? Because the changes
>> are mostly about splitting bioperl, there should not be any new
>> issue blocking a release or regression. I got it configured with
>> dzil so a new release should be as simple as `dzil release`.
>>
>> I would like to package the chnages it for Debian before their
>> freeze.
>>
>> I would also like to avoid mixing code fixes with the split of
>> into multiple distributions.
>>
>> David
>
> When are the dates before the Debian freeze? [...]
https://release.debian.org/buster/freeze_policy.html
Seems like it's already pass. I thought it was in two weeks time but
that's soft freeze. Debian is already in transition freeze so large
changes are no longer acceptable.
I can still prepare the debian package for unstable.
Ah, well unstable is fine. Maybe we can add a milestone for the next stable?
> [...] There aren’t really
> any true blockers, it’s primarily blocking off some time to do this
> and ensure tests are passing. I wanted to do a release over the
> holiday break, but $job took much more of my time than expected.
> Would you be interested in joining in on releases? It might help
> expediting these.
Sure. I can run 'dzil release' in bioperl-live from my computer, no
problem. It only takes a few minutes. Do I have the permissions in
PAUSE to do it?
I could also do this but it would be better to have another dev under the umbrella. Let me try adding you under the BIOPERLML umbrella, or at least give you co-maint on the modules.
Chris
Carnë Draug
<cjfi...@illinois.edu> wrote:
> On January 29, 2019 at 11:58:48 AM, Carnë Draug (carandr...@gmail.com) wrote:
>>> On January 29, 2019 at 9:37:34 AM, Carnë Draug (carandr...@gmail.com) wrote:
>>>> I would like to package the chnages it for Debian before their
>>>> freeze.
>>>
>>> When are the dates before the Debian freeze? [...]
>>
>> https://release.debian.org/buster/freeze_policy.html
>>
>> Seems like it's already pass. I thought it was in two weeks time but
>> that's soft freeze. Debian is already in transition freeze so large
>> changes are no longer acceptable.
>>
>> I can still prepare the debian package for unstable.
>
> Ah, well unstable is fine. Maybe we can add a milestone for the next stable?
Being in unstable during the freeze, then it won't migrate to testing
until the release is done.
I know many people use this via Ubuntu and not Debian directly.
Ubuntu is based on testing. Depending on how long the freeze the
takes then it might migrate just on time to go into the next Ubuntu
LTS (20.04). If it takes too long, then the next buntu LTS to have it
will only be 22.04.
>>> [...] There aren’t really
>>> any true blockers, it’s primarily blocking off some time to do this
>>> and ensure tests are passing. I wanted to do a release over the
>>> holiday break, but $job took much more of my time than expected.
>>> Would you be interested in joining in on releases? It might help
>>> expediting these.
>>
>> Sure. I can run 'dzil release' in bioperl-live from my computer, no
>> problem. It only takes a few minutes. Do I have the permissions in
>> PAUSE to do it?
>
> I could also do this but it would be better to have another dev
> under the umbrella. Let me try adding you under the BIOPERLML
> umbrella, or at least give you co-maint on the modules.
Tried to make the release but it failed to index. Here's the error:
Not indexed because permission missing. Current registered
primary maintainer is BIOPERLML. Hint: you can always find the
legitimate maintainer(s) on PAUSE under "View Permissions".
Can you fix this?
Thank you
Fields, Christopher J
On January 30, 2019 at 8:01:12 AM, Carnë Draug (carandr...@gmail.com) wrote:
On Tue, 29 Jan 2019 at 22:46, Fields, Christopher J
<cjfi...@illinois.edu> wrote:
> On January 29, 2019 at 11:58:48 AM, Carnë Draug (carandr...@gmail.com) wrote:
>> On Tue, 29 Jan 2019 at 17:09, Fields, Christopher J wrote:
>>> On January 29, 2019 at 9:37:34 AM, Carnë Draug (carandr...@gmail.com) wrote:
>>>> [...]
>>>> I would like to package the chnages it for Debian before their
>>>> freeze.
>>>> [...]
>>>
>>> When are the dates before the Debian freeze? [...]
>>
>> https://release.debian.org/buster/freeze_policy.html
>>
>> Seems like it's already pass. I thought it was in two weeks time but
>> that's soft freeze. Debian is already in transition freeze so large
>> changes are no longer acceptable.
>>
>> I can still prepare the debian package for unstable.
>
> Ah, well unstable is fine. Maybe we can add a milestone for the next stable?
Being in unstable during the freeze, then it won't migrate to testing
until the release is done.
I know many people use this via Ubuntu and not Debian directly.
Ubuntu is based on testing. Depending on how long the freeze the
takes then it might migrate just on time to go into the next Ubuntu
LTS (20.04). If it takes too long, then the next buntu LTS to have it
will only be 22.04.
Ok, let’s aim to get a release out ASAP
>
> I could also do this but it would be better to have another dev
> under the umbrella. Let me try adding you under the BIOPERLML
> umbrella, or at least give you co-maint on the modules.
Tried to make the release but it failed to index. Here's the error:
Not indexed because permission missing. Current registered
primary maintainer is BIOPERLML. Hint: you can always find the
legitimate maintainer(s) on PAUSE under "View Permissions".
Can you fix this?
Thank you
Checking on this; PAUSE’s methods for adding co-maint on a primary umbrella account are a little obfuscated.
chris
Carnë Draug
<cjfi...@illinois.edu> wrote:
> On January 30, 2019 at 8:01:12 AM, Carnë Draug (carandr...@gmail.com) wrote:
>> Tried to make the release but it failed to index. Here's the error:
>>
>> Not indexed because permission missing. Current registered
>> primary maintainer is BIOPERLML. Hint: you can always find the
>> legitimate maintainer(s) on PAUSE under "View Permissions".
>>
>> Can you fix this?
>
Is it done? My CPAN Id is CDRAUG
Fields, Christopher J
Carnë Draug
>
> On Tue, 5 Feb 2019 at 19:39, Fields, Christopher J
> <cjfi...@illinois.edu> wrote:
> >
> > On February 5, 2019 at 12:57:06 PM, Carnë Draug (carandr...@gmail.com) wrote:
> >> [...]
> >> I won't be doing a release of BioPerl-Run though. There's a bunch of
> >> other things in the Build.PL that I don't understand. If someone can
> >> make the release that would be better.
> >
> > [...] How pressing is this release? Can
> > it wait a few days?
>
> I guess it depends on who you ask. I'm no longer a user of
> BioPerl-Run so for me it's not important.
>
> However, some of the BioPerl-Run modules have been moved to BioPerl
> and there hasn't been a matching BioPerl-Run release. This may cause
> issues to people trying to install BioPerl-Run.
This is already causing issues to others. Someone already started
upgrading bioperl in Debian and is faced with the issue that it
conflicts with bioperl-run
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=921495
Fields, Christopher J
On Tue, 5 Feb 2019 at 20:17, Carnë Draug <carandr...@gmail.com> wrote:
>
> On Tue, 5 Feb 2019 at 19:39, Fields, Christopher J
> <cjfi...@illinois.edu> wrote:
> >
> > On February 5, 2019 at 12:57:06 PM, Carnë Draug (carandr...@gmail.com) wrote:
> >> [...]
> >> I won't be doing a release of BioPerl-Run though. There's a bunch of
> >> other things in the Build.PL that I don't understand. If someone can
> >> make the release that would be better.
> >
> > [...] How pressing is this release? Can
> > it wait a few days?
>
> I guess it depends on who you ask. I'm no longer a user of
> BioPerl-Run so for me it's not important.
>
> However, some of the BioPerl-Run modules have been moved to BioPerl
> and there hasn't been a matching BioPerl-Run release. This may cause
> issues to people trying to install BioPerl-Run.
This is already causing issues to others. Someone already started
upgrading bioperl in Debian and is faced with the issue that it
conflicts with bioperl-run
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=921495
I’ll push a release out. It looks like this may be an issue with the Debian package as well, so that would also need?
The package can’t be upgraded because one of its files (/usr/share/man/man3/Bio::Tools::Run::Analysis.3pm.gz) conflicts with libbio- perl-run-perl.
Chris