[Bioc-devel] svn repository for data experiment packages now having branches too

2014-01-22 Thread Hervé Pagès 

Hi developers,

Taking advantage of this particularly calm week on Bioc-devel,
I'd like to formally announce that we're now using branches
in the svn repo for data experiment packages.

The trunk/branches layout is similar to what we already do in
the software repo. That is:

 - URL for packages in trunk:

 https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/

 - URLs for packages in the branches:


https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs


https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs


https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_15/experiment/pkgs

Only the RELEASE_2_13 branch exists right now. This is where the
packages that are in the current release version of BioC (2.13)
are living. Like for software packages, a new branch will be created
for each new BioC release. For example the RELEASE_2_14 branch will
be created in April one day or so before the BioC 2.14 release,
the RELEASE_2_15 branch in October, etc...

More precisely, at any given time, you only have access to 2
versions of your data experiment package: the "release" and
"devel" versions.

The "release" version of your package is always in the latest
branch (RELEASE_2_13 at the moment) and accessible at:


https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/

Only bug fixes and documentation improvements should go here.

The "devel" version of your package is always available at:

  https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/

One important difference with the svn software repository still
remains though. For data experiment, the recommended way to checkout
a package is:

  1. Checkout a "shallow" working copy of the pkgs/ folder:

   svn co 
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs --depth=files


 Use the URL to the current branch if you need to checkout a
 "release" package.

  2. cd to the pkg/ folder

  3. Fetch the working copy of a particular package:

   svn up 

 (You can list all the folders in pkgs/ with 'svn ls')

 IMPORTANT: This doesn't fetch the data. But most of the
 time you don't need them e.g. if you only need to make a
 change to a man page, the vignette, the DESCRIPTION file,
 the NAMESPACE etc... you can do so and commit.
 But of course, if you didn't fetch the data, it's very
 likely that you won't be able to test your changes with
 'R CMD check'.

  4. If you need to fetch the data:

   (from the pkgs/ folder)

   ./add_data.py 

 This will populate the  folder with the data.
 Note that you need to be in a data folder in order to commit
 any change to the data. Any commit you do from the top level
 folder of the package won't include any change you could have
 made to the data.

We're also wondering whether we should start to use the same x.y.z
versioning scheme as for software packages, that is, an even y in
release, an odd y in devel, with y bump (and z reset to 0) at each
new release. Feedback welcome.

Please let me know if you have questions or concerns about this.

Cheers,
H.

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fhcrc.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
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Re: [Bioc-devel] svn repository for data experiment packages now having branches too

2014-02-07 Thread Bernd Fischer 
Dear Herve!

Please start using the same x.y.z versioning scheme as for software packages 
with the new release
for data experiment packages, with even y for release and odd y for devel. 

I just copied code from devel to the release version of my package and asked 
myself which version
number to use. Automatic version bumping 



--
Bernd Fischer
EMBL Heidelberg
Meyerhofstraße 1
69117 Heidelberg
Tel: +49 [0] 6221 387-8131
E-Mail: bernd.fisc...@embl.de
Homepage: http://www-huber.embl.de/users/befische/




On 22.01.2014, at 23:30, Hervé Pagès  wrote:

> Hi developers,
> 
> Taking advantage of this particularly calm week on Bioc-devel,
> I'd like to formally announce that we're now using branches
> in the svn repo for data experiment packages.
> 
> The trunk/branches layout is similar to what we already do in
> the software repo. That is:
> 
> - URL for packages in trunk:
> 
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
> 
> - URLs for packages in the branches:
> 
> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs
> 
> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs
> 
> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_15/experiment/pkgs
> 
> Only the RELEASE_2_13 branch exists right now. This is where the
> packages that are in the current release version of BioC (2.13)
> are living. Like for software packages, a new branch will be created
> for each new BioC release. For example the RELEASE_2_14 branch will
> be created in April one day or so before the BioC 2.14 release,
> the RELEASE_2_15 branch in October, etc...
> 
> More precisely, at any given time, you only have access to 2
> versions of your data experiment package: the "release" and
> "devel" versions.
> 
> The "release" version of your package is always in the latest
> branch (RELEASE_2_13 at the moment) and accessible at:
> 
> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/
> 
> Only bug fixes and documentation improvements should go here.
> 
> The "devel" version of your package is always available at:
> 
>  https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
> 
> One important difference with the svn software repository still
> remains though. For data experiment, the recommended way to checkout
> a package is:
> 
>  1. Checkout a "shallow" working copy of the pkgs/ folder:
> 
>   svn co https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs 
> --depth=files
> 
> Use the URL to the current branch if you need to checkout a
> "release" package.
> 
>  2. cd to the pkg/ folder
> 
>  3. Fetch the working copy of a particular package:
> 
>   svn up 
> 
> (You can list all the folders in pkgs/ with 'svn ls')
> 
> IMPORTANT: This doesn't fetch the data. But most of the
> time you don't need them e.g. if you only need to make a
> change to a man page, the vignette, the DESCRIPTION file,
> the NAMESPACE etc... you can do so and commit.
> But of course, if you didn't fetch the data, it's very
> likely that you won't be able to test your changes with
> 'R CMD check'.
> 
>  4. If you need to fetch the data:
> 
>   (from the pkgs/ folder)
> 
>   ./add_data.py 
> 
> This will populate the  folder with the data.
> Note that you need to be in a data folder in order to commit
> any change to the data. Any commit you do from the top level
> folder of the package won't include any change you could have
> made to the data.
> 
> We're also wondering whether we should start to use the same x.y.z
> versioning scheme as for software packages, that is, an even y in
> release, an odd y in devel, with y bump (and z reset to 0) at each
> new release. Feedback welcome.
> 
> Please let me know if you have questions or concerns about this.
> 
> Cheers,
> H.
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fhcrc.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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Re: [Bioc-devel] svn repository for data experiment packages now having branches too

2014-02-10 Thread Hervé Pagès 

Hi Bernd and other developers,

On 02/07/2014 04:57 AM, Bernd Fischer wrote:

Dear Herve!

Please start using the same x.y.z versioning scheme as for software
packages with the new release
for data experiment packages, with even y for release and odd y for devel.


Thanks for your feedback! Can anyone think of a reason why we should not
do that? If nobody objects then we'll start using the same x.y.z
versioning scheme as for software for the next BioC release (in April).

Thanks,
H.




I just copied code from devel to the release version of my package and
asked myself which version
number to use. Automatic version bumping



--
Bernd Fischer
EMBL Heidelberg
Meyerhofstraße 1
69117 Heidelberg
Tel: +49 [0] 6221 387-8131
E-Mail: bernd.fisc...@embl.de 
Homepage: http://www-huber.embl.de/users/befische/




On 22.01.2014, at 23:30, Hervé Pagès mailto:hpa...@fhcrc.org>> wrote:


Hi developers,

Taking advantage of this particularly calm week on Bioc-devel,
I'd like to formally announce that we're now using branches
in the svn repo for data experiment packages.

The trunk/branches layout is similar to what we already do in
the software repo. That is:

- URL for packages in trunk:

https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/

- URLs for packages in the branches:

https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs

https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs

https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_15/experiment/pkgs

Only the RELEASE_2_13 branch exists right now. This is where the
packages that are in the current release version of BioC (2.13)
are living. Like for software packages, a new branch will be created
for each new BioC release. For example the RELEASE_2_14 branch will
be created in April one day or so before the BioC 2.14 release,
the RELEASE_2_15 branch in October, etc...

More precisely, at any given time, you only have access to 2
versions of your data experiment package: the "release" and
"devel" versions.

The "release" version of your package is always in the latest
branch (RELEASE_2_13 at the moment) and accessible at:

https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/

Only bug fixes and documentation improvements should go here.

The "devel" version of your package is always available at:

 https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/

One important difference with the svn software repository still
remains though. For data experiment, the recommended way to checkout
a package is:

 1. Checkout a "shallow" working copy of the pkgs/ folder:

  svn co
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs --depth=files

Use the URL to the current branch if you need to checkout a
"release" package.

 2. cd to the pkg/ folder

 3. Fetch the working copy of a particular package:

  svn up 

(You can list all the folders in pkgs/ with 'svn ls')

IMPORTANT: This doesn't fetch the data. But most of the
time you don't need them e.g. if you only need to make a
change to a man page, the vignette, the DESCRIPTION file,
the NAMESPACE etc... you can do so and commit.
But of course, if you didn't fetch the data, it's very
likely that you won't be able to test your changes with
'R CMD check'.

 4. If you need to fetch the data:

  (from the pkgs/ folder)

  ./add_data.py 

This will populate the  folder with the data.
Note that you need to be in a data folder in order to commit
any change to the data. Any commit you do from the top level
folder of the package won't include any change you could have
made to the data.

We're also wondering whether we should start to use the same x.y.z
versioning scheme as for software packages, that is, an even y in
release, an odd y in devel, with y bump (and z reset to 0) at each
new release. Feedback welcome.

Please let me know if you have questions or concerns about this.

Cheers,
H.

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fhcrc.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel




--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fhcrc.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] svn repository for data experiment packages now having branches too

2014-03-31 Thread Andrzej Oleś 
Dear Hervé,

just to make sure: is the the same x.y.z versioning scheme as for
software packages already implemented for experiment data packages,
i.e. will there be an automatic version bump for experiment packages
with the upcoming BioC release?

Cheers,
Andrzej

On Tue, Feb 11, 2014 at 7:18 AM, Hervé Pagès  wrote:
> Hi Bernd and other developers,
>
>
> On 02/07/2014 04:57 AM, Bernd Fischer wrote:
>>
>> Dear Herve!
>>
>> Please start using the same x.y.z versioning scheme as for software
>> packages with the new release
>> for data experiment packages, with even y for release and odd y for devel.
>
>
> Thanks for your feedback! Can anyone think of a reason why we should not
> do that? If nobody objects then we'll start using the same x.y.z
> versioning scheme as for software for the next BioC release (in April).
>
> Thanks,
> H.
>
>
>>
>> I just copied code from devel to the release version of my package and
>> asked myself which version
>> number to use. Automatic version bumping
>>
>>
>>
>> --
>> Bernd Fischer
>> EMBL Heidelberg
>> Meyerhofstraße 1
>> 69117 Heidelberg
>> Tel: +49 [0] 6221 387-8131
>> E-Mail: bernd.fisc...@embl.de 
>>
>> Homepage: http://www-huber.embl.de/users/befische/
>>
>>
>>
>>
>> On 22.01.2014, at 23:30, Hervé Pagès > > wrote:
>>
>>> Hi developers,
>>>
>>> Taking advantage of this particularly calm week on Bioc-devel,
>>> I'd like to formally announce that we're now using branches
>>> in the svn repo for data experiment packages.
>>>
>>> The trunk/branches layout is similar to what we already do in
>>> the software repo. That is:
>>>
>>> - URL for packages in trunk:
>>>
>>> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
>>>
>>> - URLs for packages in the branches:
>>>
>>>
>>> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs
>>>
>>>
>>> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs
>>>
>>>
>>> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_15/experiment/pkgs
>>>
>>> Only the RELEASE_2_13 branch exists right now. This is where the
>>> packages that are in the current release version of BioC (2.13)
>>> are living. Like for software packages, a new branch will be created
>>> for each new BioC release. For example the RELEASE_2_14 branch will
>>> be created in April one day or so before the BioC 2.14 release,
>>> the RELEASE_2_15 branch in October, etc...
>>>
>>> More precisely, at any given time, you only have access to 2
>>> versions of your data experiment package: the "release" and
>>> "devel" versions.
>>>
>>> The "release" version of your package is always in the latest
>>> branch (RELEASE_2_13 at the moment) and accessible at:
>>>
>>>
>>> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/
>>>
>>> Only bug fixes and documentation improvements should go here.
>>>
>>> The "devel" version of your package is always available at:
>>>
>>>  https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
>>>
>>> One important difference with the svn software repository still
>>> remains though. For data experiment, the recommended way to checkout
>>> a package is:
>>>
>>>  1. Checkout a "shallow" working copy of the pkgs/ folder:
>>>
>>>   svn co
>>> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs --depth=files
>>>
>>> Use the URL to the current branch if you need to checkout a
>>> "release" package.
>>>
>>>  2. cd to the pkg/ folder
>>>
>>>  3. Fetch the working copy of a particular package:
>>>
>>>   svn up 
>>>
>>> (You can list all the folders in pkgs/ with 'svn ls')
>>>
>>> IMPORTANT: This doesn't fetch the data. But most of the
>>> time you don't need them e.g. if you only need to make a
>>> change to a man page, the vignette, the DESCRIPTION file,
>>> the NAMESPACE etc... you can do so and commit.
>>> But of course, if you didn't fetch the data, it's very
>>> likely that you won't be able to test your changes with
>>> 'R CMD check'.
>>>
>>>  4. If you need to fetch the data:
>>>
>>>   (from the pkgs/ folder)
>>>
>>>   ./add_data.py 
>>>
>>> This will populate the  folder with the data.
>>> Note that you need to be in a data folder in order to commit
>>> any change to the data. Any commit you do from the top level
>>> folder of the package won't include any change you could have
>>> made to the data.
>>>
>>> We're also wondering whether we should start to use the same x.y.z
>>> versioning scheme as for software packages, that is, an even y in
>>> release, an odd y in devel, with y bump (and z reset to 0) at each
>>> new release. Feedback welcome.
>>>
>>> Please let me know if you have questions or concerns about this.
>>>
>>> Cheers,
>>> H.
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Se

Re: [Bioc-devel] svn repository for data experiment packages now having branches too

2014-03-31 Thread Hervé Pagès 

Hi Andrzej,

On 03/31/2014 02:49 AM, Andrzej Oleś wrote:

Dear Hervé,

just to make sure: is the the same x.y.z versioning scheme as for
software packages already implemented for experiment data packages,
i.e. will there be an automatic version bump for experiment packages
with the upcoming BioC release?


Nobody has objected so far so yes, that's what we're going to do.

Cheers,
H.



Cheers,
Andrzej

On Tue, Feb 11, 2014 at 7:18 AM, Hervé Pagès  wrote:

Hi Bernd and other developers,


On 02/07/2014 04:57 AM, Bernd Fischer wrote:


Dear Herve!

Please start using the same x.y.z versioning scheme as for software
packages with the new release
for data experiment packages, with even y for release and odd y for devel.



Thanks for your feedback! Can anyone think of a reason why we should not
do that? If nobody objects then we'll start using the same x.y.z
versioning scheme as for software for the next BioC release (in April).

Thanks,
H.




I just copied code from devel to the release version of my package and
asked myself which version
number to use. Automatic version bumping



--
Bernd Fischer
EMBL Heidelberg
Meyerhofstraße 1
69117 Heidelberg
Tel: +49 [0] 6221 387-8131
E-Mail: bernd.fisc...@embl.de 

Homepage: http://www-huber.embl.de/users/befische/




On 22.01.2014, at 23:30, Hervé Pagès mailto:hpa...@fhcrc.org>> wrote:


Hi developers,

Taking advantage of this particularly calm week on Bioc-devel,
I'd like to formally announce that we're now using branches
in the svn repo for data experiment packages.

The trunk/branches layout is similar to what we already do in
the software repo. That is:

- URL for packages in trunk:

https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/

- URLs for packages in the branches:


https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs


https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs


https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_15/experiment/pkgs

Only the RELEASE_2_13 branch exists right now. This is where the
packages that are in the current release version of BioC (2.13)
are living. Like for software packages, a new branch will be created
for each new BioC release. For example the RELEASE_2_14 branch will
be created in April one day or so before the BioC 2.14 release,
the RELEASE_2_15 branch in October, etc...

More precisely, at any given time, you only have access to 2
versions of your data experiment package: the "release" and
"devel" versions.

The "release" version of your package is always in the latest
branch (RELEASE_2_13 at the moment) and accessible at:


https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/

Only bug fixes and documentation improvements should go here.

The "devel" version of your package is always available at:

  https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/

One important difference with the svn software repository still
remains though. For data experiment, the recommended way to checkout
a package is:

  1. Checkout a "shallow" working copy of the pkgs/ folder:

   svn co
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs --depth=files

 Use the URL to the current branch if you need to checkout a
 "release" package.

  2. cd to the pkg/ folder

  3. Fetch the working copy of a particular package:

   svn up 

 (You can list all the folders in pkgs/ with 'svn ls')

 IMPORTANT: This doesn't fetch the data. But most of the
 time you don't need them e.g. if you only need to make a
 change to a man page, the vignette, the DESCRIPTION file,
 the NAMESPACE etc... you can do so and commit.
 But of course, if you didn't fetch the data, it's very
 likely that you won't be able to test your changes with
 'R CMD check'.

  4. If you need to fetch the data:

   (from the pkgs/ folder)

   ./add_data.py 

 This will populate the  folder with the data.
 Note that you need to be in a data folder in order to commit
 any change to the data. Any commit you do from the top level
 folder of the package won't include any change you could have
 made to the data.

We're also wondering whether we should start to use the same x.y.z
versioning scheme as for software packages, that is, an even y in
release, an odd y in devel, with y bump (and z reset to 0) at each
new release. Feedback welcome.

Please let me know if you have questions or concerns about this.

Cheers,
H.

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fhcrc.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel





--
Hervé Pagès

Program in Computational Biology
Division of Public Health Scie

Re: [Bioc-devel] svn repository for data experiment packages now having branches too

2014-04-01 Thread Laurent Gatto 

On  1 April 2014 06:23, Hervé Pagès  wrote:

> Hi Andrzej,
>
> On 03/31/2014 02:49 AM, Andrzej Oleś wrote:
>> Dear Hervé,
>>
>> just to make sure: is the the same x.y.z versioning scheme as for
>> software packages already implemented for experiment data packages,
>> i.e. will there be an automatic version bump for experiment packages
>> with the upcoming BioC release?
>
> Nobody has objected so far so yes, that's what we're going to do.

An what about (optionally?) syncing version numbers for packages and
associated data package (typically myPackage and myPackagedata) that
were submitted together?

Laurent

> Cheers,
> H.
>
>>
>> Cheers,
>> Andrzej
>>
>> On Tue, Feb 11, 2014 at 7:18 AM, Hervé Pagès  wrote:
>>> Hi Bernd and other developers,
>>>
>>>
>>> On 02/07/2014 04:57 AM, Bernd Fischer wrote:

 Dear Herve!

 Please start using the same x.y.z versioning scheme as for software
 packages with the new release
 for data experiment packages, with even y for release and odd y for devel.
>>>
>>>
>>> Thanks for your feedback! Can anyone think of a reason why we should not
>>> do that? If nobody objects then we'll start using the same x.y.z
>>> versioning scheme as for software for the next BioC release (in April).
>>>
>>> Thanks,
>>> H.
>>>
>>>

 I just copied code from devel to the release version of my package and
 asked myself which version
 number to use. Automatic version bumping



 --
 Bernd Fischer
 EMBL Heidelberg
 Meyerhofstraße 1
 69117 Heidelberg
 Tel: +49 [0] 6221 387-8131
 E-Mail: bernd.fisc...@embl.de 

 Homepage: http://www-huber.embl.de/users/befische/




 On 22.01.2014, at 23:30, Hervé Pagès >>> > wrote:

> Hi developers,
>
> Taking advantage of this particularly calm week on Bioc-devel,
> I'd like to formally announce that we're now using branches
> in the svn repo for data experiment packages.
>
> The trunk/branches layout is similar to what we already do in
> the software repo. That is:
>
> - URL for packages in trunk:
>
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
>
> - URLs for packages in the branches:
>
>
> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs
>
>
> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs
>
>
> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_15/experiment/pkgs
>
> Only the RELEASE_2_13 branch exists right now. This is where the
> packages that are in the current release version of BioC (2.13)
> are living. Like for software packages, a new branch will be created
> for each new BioC release. For example the RELEASE_2_14 branch will
> be created in April one day or so before the BioC 2.14 release,
> the RELEASE_2_15 branch in October, etc...
>
> More precisely, at any given time, you only have access to 2
> versions of your data experiment package: the "release" and
> "devel" versions.
>
> The "release" version of your package is always in the latest
> branch (RELEASE_2_13 at the moment) and accessible at:
>
>
> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/
>
> Only bug fixes and documentation improvements should go here.
>
> The "devel" version of your package is always available at:
>
>   https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
>
> One important difference with the svn software repository still
> remains though. For data experiment, the recommended way to checkout
> a package is:
>
>   1. Checkout a "shallow" working copy of the pkgs/ folder:
>
>svn co
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs --depth=files
>
>  Use the URL to the current branch if you need to checkout a
>  "release" package.
>
>   2. cd to the pkg/ folder
>
>   3. Fetch the working copy of a particular package:
>
>svn up 
>
>  (You can list all the folders in pkgs/ with 'svn ls')
>
>  IMPORTANT: This doesn't fetch the data. But most of the
>  time you don't need them e.g. if you only need to make a
>  change to a man page, the vignette, the DESCRIPTION file,
>  the NAMESPACE etc... you can do so and commit.
>  But of course, if you didn't fetch the data, it's very
>  likely that you won't be able to test your changes with
>  'R CMD check'.
>
>   4. If you need to fetch the data:
>
>(from the pkgs/ folder)
>
>./add_data.py 
>
>  This will populate the  folder with the data.
>  Note that you need to be in a data folder in order to commit
>  any change to the data. Any commit you

Re: [Bioc-devel] svn repository for data experiment packages now having branches too

2014-04-01 Thread Bernd Fischer 
Dear Laurent!

I would vote against syncing the version numbers of data and corresponding 
software packages.
The two packages are submitted as two, because they should be regarded as 
separate.

It can happen that other people submit a data package using the same software 
package or others
submit a software package using the same data package. Syncing version numbers 
across
packages will cause a lot of trouble. 

You still can do this manually for your own packages, if you like.

Cheers,

Bernd  
 
On 01.04.2014, at 12:22, Laurent Gatto  wrote:
> An what about (optionally?) syncing version numbers for packages and
> associated data package (typically myPackage and myPackagedata) that
> were submitted together?
> 
> Laurent


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