[octave forge] new external package

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[octave forge] new external package

JuanPi
Hi all,

I want to contribute the gpml (Gaussian Processes for Machine
Learning) package to the octave ecosystem.
I keep a repository here[1], which is a snapshot of the released version [2].

Since the original developer contributed (and might do it in the
future), I keep the structure of the original code, but provide an
extra folder 'pkg_octave' with files used by 'Makefile' to generate
the package, i.e. only the result of 'make release' has the octave
forge package structure.

I am still struggling to converge to a method to include test and
demos and to improve the documentation. Oliver has gave me some nice
clues, but any suggestion is welcome. See [3] for the mailing list
thread.

In [4] you will find a file that should be installable using 'pkg
install gpml-4.0.0'

Regards,

JPi

[1]: https://bitbucket.org/KaKiLa/gpml
[2]: http://gaussianprocess.org/gpml/
[3]: http://octave.1599824.n4.nabble.com/OF-Docs-Demos-and-Test-for-External-package-td4681888.html
[4]:https://bitbucket.org/KaKiLa/gpml/downloads/gpml-4.0.0.tar.gz
--
JuanPi Carbajal
https://goo.gl/ayiJzi
Public GnuPG key: 9C5B72BF
-----
"Why is thought, being a secretion of the brain, more wonderful than
gravity, a property of matter?"
- C. Darwin

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Re: [octave forge] new external package

jbect
Le 20/08/2017 à 23:21, JuanPi a écrit :

> I want to contribute the gpml (Gaussian Processes for Machine
> Learning) package to the octave ecosystem.
> I keep a repository here[1], which is a snapshot of the released version [2].
>
> Since the original developer contributed (and might do it in the
> future), I keep the structure of the original code, but provide an
> extra folder 'pkg_octave' with files used by 'Makefile' to generate
> the package, i.e. only the result of 'make release' has the octave
> forge package structure.
>
> I am still struggling to converge to a method to include test and
> demos and to improve the documentation. Oliver has gave me some nice
> clues, but any suggestion is welcome. See [3] for the mailing list
> thread.
>
> In [4] you will find a file that should be installable using 'pkg
> install gpml-4.0.0'
>
> Regards,
>
> JPi
>
> [1]: https://bitbucket.org/KaKiLa/gpml
> [2]: http://gaussianprocess.org/gpml/
> [3]: http://octave.1599824.n4.nabble.com/OF-Docs-Demos-and-Test-for-External-package-td4681888.html
> [4]:https://bitbucket.org/KaKiLa/gpml/downloads/gpml-4.0.0.tar.gz

Hi JPi,

Cool.  Having GPML readily available in Octave would be nice.  A few
ideas / remarks :

* I wouldn't block the release for problems related to tests / demos /
etc.  You can improve these aspects later.

* Is startup.m (at the root) needed in the octave package ?  If not, I
would remove it.  If yes, perhaps rename it to a less generic name ?

* The developper manual should be in /doc, not inst/doc, I think.

* The m-files that only provide documentation (such as meanFunctions.m,
covFunctions.m...) could perhaps be renamed with a "gpml_" prefix.  This
would make them much easier to find using completion.

* Same remark for demoClassificaton, usagePrior, etc.

* inst/doc/changelog -> ChangeLog (at the root) ?

@++
Julien


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Re: [octave forge] new external package

Juan Pablo Carbajal-2
On Tue, Aug 29, 2017 at 7:32 PM, Julien Bect
<[hidden email]> wrote:

> Le 20/08/2017 à 23:21, JuanPi a écrit :
>>
>> I want to contribute the gpml (Gaussian Processes for Machine
>> Learning) package to the octave ecosystem.
>> I keep a repository here[1], which is a snapshot of the released version
>> [2].
>>
>> Since the original developer contributed (and might do it in the
>> future), I keep the structure of the original code, but provide an
>> extra folder 'pkg_octave' with files used by 'Makefile' to generate
>> the package, i.e. only the result of 'make release' has the octave
>> forge package structure.
>>
>> I am still struggling to converge to a method to include test and
>> demos and to improve the documentation. Oliver has gave me some nice
>> clues, but any suggestion is welcome. See [3] for the mailing list
>> thread.
>>
>> In [4] you will find a file that should be installable using 'pkg
>> install gpml-4.0.0'
>>
>> Regards,
>>
>> JPi
>>
>> [1]: https://bitbucket.org/KaKiLa/gpml
>> [2]: http://gaussianprocess.org/gpml/
>> [3]:
>> http://octave.1599824.n4.nabble.com/OF-Docs-Demos-and-Test-for-External-package-td4681888.html
>> [4]:https://bitbucket.org/KaKiLa/gpml/downloads/gpml-4.0.0.tar.gz
>
>
> Hi JPi,
>
> Cool.  Having GPML readily available in Octave would be nice.  A few ideas /
> remarks :
>
> * I wouldn't block the release for problems related to tests / demos / etc.
> You can improve these aspects later.
>
> * Is startup.m (at the root) needed in the octave package ?  If not, I would
> remove it.  If yes, perhaps rename it to a less generic name ?
>
> * The developper manual should be in /doc, not inst/doc, I think.
>
> * The m-files that only provide documentation (such as meanFunctions.m,
> covFunctions.m...) could perhaps be renamed with a "gpml_" prefix.  This
> would make them much easier to find using completion.
>
> * Same remark for demoClassificaton, usagePrior, etc.
>
> * inst/doc/changelog -> ChangeLog (at the root) ?
>
> @++
> Julien
>
>

Hi Julien,
Thanks for the feedback. I will implement your suggestions.

How should I proceed with the release? Shall I upload code and html to
the sf as we do with community packages?

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Re: [octave forge] new external package

jbect
Le 31/08/2017 à 01:13, Juan Pablo Carbajal a écrit :

> On Tue, Aug 29, 2017 at 7:32 PM, Julien Bect
> <[hidden email]> wrote:
>> Le 20/08/2017 à 23:21, JuanPi a écrit :
>>> I want to contribute the gpml (Gaussian Processes for Machine
>>> Learning) package to the octave ecosystem.
>>> I keep a repository here[1], which is a snapshot of the released version
>>> [2].
>>>
>>> Since the original developer contributed (and might do it in the
>>> future), I keep the structure of the original code, but provide an
>>> extra folder 'pkg_octave' with files used by 'Makefile' to generate
>>> the package, i.e. only the result of 'make release' has the octave
>>> forge package structure.
>>>
>>> I am still struggling to converge to a method to include test and
>>> demos and to improve the documentation. Oliver has gave me some nice
>>> clues, but any suggestion is welcome. See [3] for the mailing list
>>> thread.
>>>
>>> In [4] you will find a file that should be installable using 'pkg
>>> install gpml-4.0.0'
>>>
>>> Regards,
>>>
>>> JPi
>>>
>>> [1]: https://bitbucket.org/KaKiLa/gpml
>>> [2]: http://gaussianprocess.org/gpml/
>>> [3]:
>>> http://octave.1599824.n4.nabble.com/OF-Docs-Demos-and-Test-for-External-package-td4681888.html
>>> [4]:https://bitbucket.org/KaKiLa/gpml/downloads/gpml-4.0.0.tar.gz
>>
>> Hi JPi,
>>
>> Cool.  Having GPML readily available in Octave would be nice.  A few ideas /
>> remarks :
>>
>> * I wouldn't block the release for problems related to tests / demos / etc.
>> You can improve these aspects later.
>>
>> * Is startup.m (at the root) needed in the octave package ?  If not, I would
>> remove it.  If yes, perhaps rename it to a less generic name ?
>>
>> * The developper manual should be in /doc, not inst/doc, I think.
>>
>> * The m-files that only provide documentation (such as meanFunctions.m,
>> covFunctions.m...) could perhaps be renamed with a "gpml_" prefix.  This
>> would make them much easier to find using completion.
>>
>> * Same remark for demoClassificaton, usagePrior, etc.
>>
>> * inst/doc/changelog -> ChangeLog (at the root) ?
>>
>> @++
>> Julien
>>
>>
> Hi Julien,
> Thanks for the feedback. I will implement your suggestions.
>
> How should I proceed with the release? Shall I upload code and html to
> the sf as we do with community packages?

I think that first you have to ask the admins for a repo on OF, and
synchronize your external repo with it.

Then you can create your first release candidate and ask for a review on
the release tracker.

Olaf or Oliver should be able to tell you more about this.


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Re: [octave forge] new external package

Juan Pablo Carbajal-2
Hi,

I have implemented all Julien's suggestions and improved the structure
of the package. Please test installation and look at html [1].

> I think that first you have to ask the admins for a repo on OF, and
> synchronize your external repo with it.
>
By OF you mean the website? or a repo in sourceforge? I thought
external packages wouldn't have repos in SF.

I am waiting for the green light to release.

[1]: https://bitbucket.org/KaKiLa/gpml/downloads/

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Re: [octave forge] new external package

jbect
Le 01/09/2017 à 00:32, Juan Pablo Carbajal a écrit :
> I have implemented all Julien's suggestions and improved the structure
> of the package. Please test installation and look at html [1].
>
>> I think that first you have to ask the admins for a repo on OF, and
>> synchronize your external repo with it.
>>
> By OF you mean the website? or a repo in sourceforge? I thought
> external packages wouldn't have repos in SF.

Yes, a repo hosted on SF (see the "common requirements":
https://octave.sourceforge.io/common-requirements.php).

You must ask the admins to create one (hg in your case).

It doesn't have to become you main repo, but you need to synchronize it
at least when you want to make a release.


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Re: [octave forge] new external package

Juan Pablo Carbajal-2
Hi,

> Yes, a repo hosted on SF (see the "common requirements":
> https://octave.sourceforge.io/common-requirements.php).
>
> You must ask the admins to create one (hg in your case).
>
I can do that myself, I have push access. I guess I will wait for
Olaf's green light.

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Re: [octave forge] new external package

Olaf Till-2
On Fri, Sep 01, 2017 at 11:27:56AM +0200, Juan Pablo Carbajal wrote:
> Hi,
>
> > Yes, a repo hosted on SF (see the "common requirements":
> > https://octave.sourceforge.io/common-requirements.php).
> >
> > You must ask the admins to create one (hg in your case).
> >
> I can do that myself, I have push access. I guess I will wait for
> Olaf's green light.

I've seen it, please allow some time, I'm currently caught by 'real
life' and still have some OF things in the queue. Julien has already
cared about this, but the formal checks have to be done still... A
first thing to note: This package is exceptional in that 'licensecheck
-r' returns 'UNKNOWN' for almoust all files, which requires much
manual checking. (The license of the original files has to be checked
also, not only of the files in the generated release.)

Yes, I've seen you have 'release technician' rights, but this would
only spare us the work of creating a repository, which is only a small
part.

Olaf

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Re: [octave forge] new external package

Juan Pablo Carbajal-2
> I've seen it, please allow some time, I'm currently caught by 'real
> life' and still have some OF things in the queue. Julien has already
> cared about this, but the formal checks have to be done still...
Sure, it is not that I am not waiting. Just wanted to make sure is in
your (or admins) list.

>A
> first thing to note: This package is exceptional in that 'licensecheck
> -r' returns 'UNKNOWN' for almoust all files, which requires much
> manual checking. (The license of the original files has to be checked
> also, not only of the files in the generated release.)
Files do not have the license header. Shall I add the header to all files?
>
> Yes, I've seen you have 'release technician' rights, but this would
> only spare us the work of creating a repository, which is only a small
> part.
>
If there is a concrete list where the check s are described I can help
with the other things. I cannot guess out of the blue what's needed.

> Olaf
>
> --
> public key id EAFE0591, e.g. on x-hkp://pool.sks-keyservers.net

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Re: [octave forge] new external package

Olaf Till-2
On Fri, Sep 01, 2017 at 03:45:46PM +0200, Juan Pablo Carbajal wrote:
> >A
> > first thing to note: This package is exceptional in that 'licensecheck
> > -r' returns 'UNKNOWN' for almoust all files, which requires much
> > manual checking. (The license of the original files has to be checked
> > also, not only of the files in the generated release.)
>
> Files do not have the license header. Shall I add the header to all
> files?

Yes, that is necessary for the package to be distributed by OF. But be
sure that the added license information is correct.

As I understand it, if you add something to the original files, you
deviate from your stated strategy to keep two-way-synchronized with
the original package of the creator. Maybe you can keep it
one-way-synchronized, generating your repository from the original by
scripts. If you do this, it could be worth considering (for the
future) to let the scripts also generate more Octave-like files.

It's possibly not strictly necessary, but have you contacted the
original author?

Olaf

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Re: [octave forge] new external package

Juan Pablo Carbajal-2
> As I understand it, if you add something to the original files, you
> deviate from your stated strategy to keep two-way-synchronized with
> the original package of the creator. Maybe you can keep it
> one-way-synchronized, generating your repository from the original by
> scripts. If you do this, it could be worth considering (for the
> future) to let the scripts also generate more Octave-like files.
>
Yes, this will be the case. I have to do this anyways to add demos, so
maybe I can start with the license.
We already have a perl script by Carne to add licenses automatically
so I will use it.

> It's possibly not strictly necessary, but have you contacted the
> original author?
>
Yes, I am in contact with him. He doesn't want to add the headers
because the package grows unnecessarily (in his opinion)

Thanks