Add Bio::Root back about bioperl-live HOT 19 CLOSED

Chris,

Yes, I can do this. Can the person who did the dissection explain what they did, so I can resect?

Thanks again,

BIO

On Jun 8, 2015, at 4:35 PM, Chris Fields [email protected] wrote:

Consensus (well, handful of on mail list) want this back in. Not sure how easily this can be done; @bosborne https://github.com/bosborne mentioned he could try taking it on?

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from bioperl-live.

The persons would be Rob Buels and myself as part of a GSoC project. The idea was that Bio::Root would effectively become the true core, but in hindsight that's likely way too granular and seems to cause too many problems for others. I think a 'clipping the leaves' approach is working better.

Thanks for taking it on. I think the main changes could probably be pulled back in from the 1.6 branch in bioperl-live, failing that a simple copy (I'm not terribly concerned about loss in history). I don't think there is much in the separate repo that hasn't also been added to 1.6 tho.

Chris

On Jun 9, 2015, at 8:01 AM, Brian Osborne <[email protected]mailto:[email protected]> wrote:

Chris,

Yes, I can do this. Can the person who did the dissection explain what they did, so I can resect?

Thanks again,

BIO

On Jun 8, 2015, at 4:35 PM, Chris Fields <[email protected]mailto:[email protected]> wrote:

Consensus (well, handful of on mail list) want this back in. Not sure how easily this can be done; @bosborne https://github.com/bosborne mentioned he could try taking it on?

—
Reply to this email directly or view it on GitHub #114.

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from bioperl-live.

Brian,
You're the man
MAJ
On 2015-06-09 09:14, Chris Fields wrote:

The persons would be Rob Buels and myself as part of a GSoC project.
The idea was that Bio::Root would effectively become the true core,
but in hindsight thats likely way too granular and seems to cause too
many problems for others. I think a clipping the leaves approach is
working better.

Thanks for taking it on. I think the main changes could probably be
pulled back in from the 1.6 branch in bioperl-live, failing that a
simple copy (Im not terribly concerned about loss in history). I dont
think there is much in the separate repo that hasnt also been added
to
1.6 tho.

Chris

On Jun 9, 2015, at 8:01 AM, Brian Osborne
<[email protected]mailto:[email protected]> wrote:

Chris,

Yes, I can do this. Can the person who did the dissection explain
what they did, so I can resect?

Thanks again,

BIO

On Jun 8, 2015, at 4:35 PM, Chris Fields
<[email protected]mailto:[email protected]> wrote:

Consensus (well, handful of on mail list) want this back in. Not
sure how easily this can be done; @bosborne
https://github.com/bosborne mentioned he could try taking it on?

—
Reply to this email directly or view it on GitHub
#114.

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from bioperl-live.

Hello all!
The last modification to Bio::Root repo was done by me on November last year, and until beginning of January I made sure that the v1.6.x was synched with all the split repos and the main branch, but then I got consumed by job and had to dissappear. =(

Currently the Bio::Root modules from the split repo are almost identical to those on the v1.6.x branch with a few exceptions:

1. v1.6.x branch have a "HTTPget.pm" module that the split branch don't have.
2. v1.6.x branch "Build.pm" module use "=head2" for documentation while the split repo use "=func".
3. v1.6x branch have a "HTTPget.t" test that the split branch don't have and seems like a more developed test file than the split branch extra "xt/RootIO.t" test.
4. v1.6x branch "Exception.t" test use "use lib './examples/root/lib';'" and the split repo use "use lib './eg';" because of their different folder organization.

In summary, I think it would be safe to just copy back the Root from the v1.6.x branch back into master and nothing will be lost.

PD: I would love to include the last months commits from main to the v1.6.x branch, so its fully updated again, but I'm not sure when I will have time to do it. =/

Cheers,

from bioperl-live.

Francisco,

Excellent, those are the details I needed.

Thanks again,

BIO

On Jun 9, 2015, at 10:48 AM, Francisco J. Ossandon [email protected] wrote:

Hello all!
The last modification to Bio::Root repo was done by me on November last year, and until beginning of January I made sure that the v1.6.x was synched with all the split repos and the main branch, but then I got consumed by job and had to dissappear. =(

Currently the Bio::Root modules from the split repo are almost identical to those on the v1.6.x branch with a few exceptions:

1. v1.6.x branch have a "HTTPget.pm" module that the split branch don't have.
2. v1.6.x branch "Build.pm" module use "=head2" for documentation while the split repo use "=func".
3. v1.6x branch have a "HTTPget.t" test that the split branch don't have and seems like a more developed test file than the split branch extra "xt/RootIO.t" test.
4. v1.6x branch "Exception.t" test use "use lib './examples/root/lib';'" and the split repo use "use lib './eg';" because of their different folder organization.

In summary, I think it would be safe to just copy back the Root from the v1.6.x branch back into master and nothing will be lost.

Cheers,

—
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from bioperl-live.

@bosborne cool! Let me know if you need anything 👍

from bioperl-live.

Heh, that was @cjfields replying as @bioperl-guts. Attempting to debug notifications 😏

from bioperl-live.

Lol, good one!

Looks like is working fine ;)

De: bioperl-guts [mailto:[email protected]]
Enviado el: martes, 09 de junio de 2015 13:18
Para: bioperl/bioperl-live
CC: Francisco J. Ossandon
Asunto: Re: [bioperl-live] Add Bio::Root back (#114)

Heh, that was @cjfields https://github.com/cjfields replying as @bioperl-guts https://github.com/bioperl-guts . Attempting to debug notifications https://assets-cdn.github.com/images/icons/emoji/unicode/1f60f.png

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from bioperl-live.

Hmm. I've started working on this, but branched off of master rather than v1.6.x. Was that unwise?

On Jun 9, 2015, at 12:17 PM, bioperl-guts [email protected] wrote:

Heh, that was @cjfields https://github.com/cjfields replying as @bioperl-guts https://github.com/bioperl-guts. Attempting to debug notifications

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from bioperl-live.

I think that's the Right Thing.

On Sat, Jun 20, 2015 at 11:33 AM, Brian Osborne < [email protected] [[email protected]] > wrote:
Hmm. I've started working on this, but branched off of master rather than
v1.6.x. Was that unwise?

On Jun 9, 2015, at 12:17 PM, bioperl-guts [email protected] wrote:

Heh, that was @cjfields https://github.com/cjfields replying as
@bioperl-guts https://github.com/bioperl-guts. Attempting to debug
notifications

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#114 (comment).

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from bioperl-live.

Got it, will proceed ….

On Jun 20, 2015, at 11:52 AM, Mark Jensen [email protected] wrote:

I think that's the Right Thing.

On Sat, Jun 20, 2015 at 11:33 AM, Brian Osborne < [email protected] [[email protected]] > wrote:
Hmm. I've started working on this, but branched off of master rather than
v1.6.x. Was that unwise?

On Jun 9, 2015, at 12:17 PM, bioperl-guts [email protected] wrote:

Heh, that was @cjfields https://github.com/cjfields replying as
@bioperl-guts https://github.com/bioperl-guts. Attempting to debug
notifications

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from bioperl-live.

That’s correct. We’re wanting Root back in master, it’s already in 1.6.x :)

-c

On Jun 20, 2015, at 11:17 AM, Brian Osborne <[email protected]mailto:[email protected]> wrote:

Got it, will proceed ….

On Jun 20, 2015, at 11:52 AM, Mark Jensen <[email protected]mailto:[email protected]> wrote:

I think that's the Right Thing.

On Sat, Jun 20, 2015 at 11:33 AM, Brian Osborne < [email protected]:[email protected] [[email protected]:[email protected]] > wrote:
Hmm. I've started working on this, but branched off of master rather than
v1.6.x. Was that unwise?

On Jun 9, 2015, at 12:17 PM, bioperl-guts <[email protected]mailto:[email protected]> wrote:

Heh, that was @cjfields https://github.com/cjfields replying as
@bioperl-guts https://github.com/bioperl-guts. Attempting to debug
notifications

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#114 (comment).

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from bioperl-live.

OK, the branch is merge_root_into_live.

Those t/Tree/Tree.t and t/Tree/TreeIO.t tests continue to be problematic but all other tests pass.

Notes:

• eg/TestObject.pm is now Bio/Root/TestObject.pm
• eg/TestInterface.pm has been removed, looked like it was not used, add it back if you know better
• references to the old Tutorial have been removed
• HTML::TableExtract is recommended, added that to the long list of recommended modules in Build.PL
• a test or 2 needed minor fixes
• a few POD fixes, here and there

Take a look!

On Jun 20, 2015, at 12:20 PM, Chris Fields [email protected] wrote:

That’s correct. We’re wanting Root back in master, it’s already in 1.6.x :)

-c

On Jun 20, 2015, at 11:17 AM, Brian Osborne <[email protected]mailto:[email protected]> wrote:

Got it, will proceed ….

On Jun 20, 2015, at 11:52 AM, Mark Jensen <[email protected]mailto:[email protected]> wrote:

I think that's the Right Thing.

On Sat, Jun 20, 2015 at 11:33 AM, Brian Osborne < [email protected]:[email protected] [[email protected]:[email protected]] > wrote:
Hmm. I've started working on this, but branched off of master rather than
v1.6.x. Was that unwise?

On Jun 9, 2015, at 12:17 PM, bioperl-guts <[email protected]mailto:[email protected]> wrote:

Heh, that was @cjfields https://github.com/cjfields replying as
@bioperl-guts https://github.com/bioperl-guts. Attempting to debug
notifications

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from bioperl-live.

No problems on the branch, everything is passing, everything looks good. On my Mac all t/Tree/Tree.t and t/Tree/TreeIO.t tests are passing (though I'm running w/o network tests). So, full steam ahead to merge back in to master!

from bioperl-live.

\o/

On Sat, Jun 20, 2015 at 8:07 PM, Chris Fields < [email protected] [[email protected]] > wrote:
No problems on the branch, everything is passing, everything looks good. On my
Mac all t/Tree/Tree. t and t/Tree/TreeIO.t tests are passing (though I'm running w/o network tests). So, full steam ahead
to merge back in to master!

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from bioperl-live.

Go go go!!!

De: Mark Jensen [mailto:[email protected]]
Enviado el: sábado, 20 de junio de 2015 21:09
Para: bioperl/bioperl-live
CC: Francisco J. Ossandon
Asunto: Re: [bioperl-live] Add Bio::Root back (#114)

\o/

On Sat, Jun 20, 2015 at 8:07 PM, Chris Fields < [email protected] [[email protected]] > wrote:
No problems on the branch, everything is passing, everything looks good. On my
Mac all t/Tree/Tree. t and t/Tree/TreeIO.t tests are passing (though I'm running w/o network tests). So, full steam ahead
to merge back in to master!

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from bioperl-live.

Let’s also talk about install documentation, while we’re at it. We have a bunch of Wiki pages and INSTALL* files saying slightly different things, when they should all say the same thing. Not referring to Windows, that’s something I don’t know much about. IMO these are the essential messages, and should be in this order in the file or page:

• use CPAN
• or if you want to manually install do “git clone …", “perl Build.PL”, etc.
• those who want local installation should use local::lib

We have the text for CPAN already, of course. No mention of “git clone” or local::lib anywhere, as far as I can see.

Overall there’s just way too much text on this topic in the Wiki and in the INSTALL files, should be simpler.

Thoughts?

On Jun 20, 2015, at 8:10 PM, Francisco J. Ossandon [email protected] wrote:

Go go go!!!

De: Mark Jensen [mailto:[email protected]]
Enviado el: sábado, 20 de junio de 2015 21:09
Para: bioperl/bioperl-live
CC: Francisco J. Ossandon
Asunto: Re: [bioperl-live] Add Bio::Root back (#114)

\o/

On Sat, Jun 20, 2015 at 8:07 PM, Chris Fields < [email protected] [[email protected]] > wrote:
No problems on the branch, everything is passing, everything looks good. On my
Mac all t/Tree/Tree. t and t/Tree/TreeIO.t tests are passing (though I'm running w/o network tests). So, full steam ahead
to merge back in to master!

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from bioperl-live.

Re: install docs and so on, see issue #116

from bioperl-live.

Lost track of this one 😦 . Merged this into master, so closing ticket. Documentation issues will be in #116.

from bioperl-live.