Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

2017-11-03 Thread Arman Shahrisa 
Thank you very much for all your assistance. Unfortunately, git bash must be 
run as administrator,
otherwise user won’t be able to change the pwd from partition C to another 
partition (It will remain in
the previous directory on partition C). This is why I had to run it as 
administrator.


Best regards,
Arman

From: Martin Morgan
Sent: Friday, November 3, 2017 13:23
To: Arman Shahrisa; 
bioc-devel
Subject: Re: [Bioc-devel] Confusion with how to maintain release/devel files on 
local computer.

Thank you for the detailed description, it is much easier to understand
what is going on. I have made some comments below

On 11/02/2017 11:14 AM, Arman Shahrisa wrote:
>  > There is no branch releas_3_6.
>
>>> I don't know what 'it' is -- I guess your local repository that you
>>> cloned, but where did you clone it from?
>
> I repeated all the process again.
>
> I opened git bash as an administrator and ran commands described here:

it is not necessary or recommended to run these commands as an
administrator; generally all activities should be done as a regular user.

Likely you need, as a regular user, to regenerate your ssh key pair, and
to re-submit the public key to Bioconductor. Alternatively, perhaps as a
regular user you already have an ssh key pair, and you can submit the
public key part of the key pair. Remember that this will take at least
24 hours to process.

>
> https://bioconductor.org/developers/how-to/git/maintain-bioc-only/

This workflow means that you want to maintain only the Bioconductor
version of your repository, you do not want to maintain the github
version of your repository that you used during package submission.

>
>  > Arman@Arman-VAIO MINGW64 ~
>
>  > $ cd /z/cbaf/Source
>
>  > Arman@Arman-VAIO MINGW64 /z/cbaf/Source
>
>  > $ git clone g...@git.bioconductor.org:packages/cbaf
>
>  > Cloning into 'cbaf'...
>
>  > Enter passphrase for key '/c/Users/Arman/.ssh/id_rsa':
>
>  > remote: Counting objects: 732, done.
>
>  > remote: Compressing objects: 100% (218/218), done.
>
>  > remote: Total 732 (delta 503), reused 725 (delta 499)
>
>  > Receiving objects: 100% (732/732), 749.19 KiB | 182.00 KiB/s, done.
>
>  > Resolving deltas: 100% (503/503), done.
>
>  > Arman@Arman-VAIO MINGW64 /z/cbaf/Source
>
>  > $ git remote -v
>
>  > fatal: Not a git repository (or any of the parent directories): .git
>
>  > Arman@Arman-VAIO MINGW64 /z/cbaf/Source
>
>  > $ cd /z/cbaf/Source/cbaf
>
>  > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master)
>
>  > $ git remote -v
>
>  > origin  g...@git.bioconductor.org:packages/cbaf (fetch)
>
>  > origin  g...@git.bioconductor.org:packages/cbaf (push)

ok, all of the above looks good. You cloned the repository, and your ssh
key was recognized.

>
>  > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master)
>
>  > $ git pull
>
>  > Enter passphrase for key '/c/Users/Arman/.ssh/id_rsa':
>
>  > Already up-to-date.
>
> The I ran this one:
>
>  > git remote add upstream g...@git.bioconductor.org:packages/cbaf.git

This step is not required. It is not part of the workflow you cited.
Earlier, when you issued the command 'git remote -v' git indicated that
you already had a remote named 'origin' and referencing the git server
g...@git.bioconductor.org. What the command above does is to add a second
remote pointing to git.bioconductor.org, but this one named 'upstream'.

I can see that the documentation in this work flow needs to be adjusted,
because in other

It would be appropriate to rename the remote, e.g.,

   git remote rename origin upstream

nonetheless, issuing the command should not cause a problem.

It seems like at this stage you should continue with the workflow that
you started, i.e.,

   - 'Commit changes to your local repository' to develop a new feature
or fix a bug, including checking that your code changes are correct by
running R CMD build and R CMD check using the 'devel' version of
Bioconductor, and

   - 'Push your local changes to the Bioconductor repository' to make
your code changes available to the Bioconductor build server. Remember
that builds run once a day, and that you need to confirm that the build
has been successful by visiting http://bioconductor.org/checkResults/.

The steps below are not necessary for you at the moment.

Martin

>
> Then these commands from
> c
>
>  > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master)
>
>  > $ git checkout master
>
>  > Already on 'master'
>
>  > Your branch is up-to-date with 'origin/master'.
>
>  > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master)
>
>  > $ git fetch upstream
>
>  > Enter passphrase for key '/c/Users/Arman/.ssh/id_rsa':
>
>  > From git.bioconductor.org:packages/cbaf
>
>  >  * [new branch]  RELEASE_3_6 -> upstream/RELEASE_3_6
>
>  >  * [new branch]  master  -> upstream/master
>
>  > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master)
>
>  > $ git merge

Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

2017-11-03 Thread Martin Morgan 
Thank you for the detailed description, it is much easier to understand 
what is going on. I have made some comments below


On 11/02/2017 11:14 AM, Arman Shahrisa wrote:

 > There is no branch releas_3_6.

I don't know what 'it' is -- I guess your local repository that you 
cloned, but where did you clone it from?


I repeated all the process again.

I opened git bash as an administrator and ran commands described here:


it is not necessary or recommended to run these commands as an 
administrator; generally all activities should be done as a regular user.


Likely you need, as a regular user, to regenerate your ssh key pair, and 
to re-submit the public key to Bioconductor. Alternatively, perhaps as a 
regular user you already have an ssh key pair, and you can submit the 
public key part of the key pair. Remember that this will take at least 
24 hours to process.




https://bioconductor.org/developers/how-to/git/maintain-bioc-only/


This workflow means that you want to maintain only the Bioconductor 
version of your repository, you do not want to maintain the github 
version of your repository that you used during package submission.




 > Arman@Arman-VAIO MINGW64 ~

 > $ cd /z/cbaf/Source

 > Arman@Arman-VAIO MINGW64 /z/cbaf/Source

 > $ git clone g...@git.bioconductor.org:packages/cbaf

 > Cloning into 'cbaf'...

 > Enter passphrase for key '/c/Users/Arman/.ssh/id_rsa':

 > remote: Counting objects: 732, done.

 > remote: Compressing objects: 100% (218/218), done.

 > remote: Total 732 (delta 503), reused 725 (delta 499)

 > Receiving objects: 100% (732/732), 749.19 KiB | 182.00 KiB/s, done.

 > Resolving deltas: 100% (503/503), done.

 > Arman@Arman-VAIO MINGW64 /z/cbaf/Source

 > $ git remote -v

 > fatal: Not a git repository (or any of the parent directories): .git

 > Arman@Arman-VAIO MINGW64 /z/cbaf/Source

 > $ cd /z/cbaf/Source/cbaf

 > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master)

 > $ git remote -v

 > origin  g...@git.bioconductor.org:packages/cbaf (fetch)

 > origin  g...@git.bioconductor.org:packages/cbaf (push)


ok, all of the above looks good. You cloned the repository, and your ssh 
key was recognized.




 > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master)

 > $ git pull

 > Enter passphrase for key '/c/Users/Arman/.ssh/id_rsa':

 > Already up-to-date.

The I ran this one:

 > git remote add upstream g...@git.bioconductor.org:packages/cbaf.git


This step is not required. It is not part of the workflow you cited. 
Earlier, when you issued the command 'git remote -v' git indicated that 
you already had a remote named 'origin' and referencing the git server 
g...@git.bioconductor.org. What the command above does is to add a second 
remote pointing to git.bioconductor.org, but this one named 'upstream'.


I can see that the documentation in this work flow needs to be adjusted, 
because in other


It would be appropriate to rename the remote, e.g.,

  git remote rename origin upstream

nonetheless, issuing the command should not cause a problem.

It seems like at this stage you should continue with the workflow that 
you started, i.e.,


  - 'Commit changes to your local repository' to develop a new feature 
or fix a bug, including checking that your code changes are correct by 
running R CMD build and R CMD check using the 'devel' version of 
Bioconductor, and


  - 'Push your local changes to the Bioconductor repository' to make 
your code changes available to the Bioconductor build server. Remember 
that builds run once a day, and that you need to confirm that the build 
has been successful by visiting http://bioconductor.org/checkResults/.


The steps below are not necessary for you at the moment.

Martin



Then these commands from 
c


 > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master)

 > $ git checkout master

 > Already on 'master'

 > Your branch is up-to-date with 'origin/master'.

 > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master)

 > $ git fetch upstream

 > Enter passphrase for key '/c/Users/Arman/.ssh/id_rsa':

 > From git.bioconductor.org:packages/cbaf

 >  * [new branch]  RELEASE_3_6 -> upstream/RELEASE_3_6

 >  * [new branch]  master  -> upstream/master

 > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master)

 > $ git merge upstream/master

 > Already up-to-date.



I have attached an screenshot of what I have now. The following is the

Command-line output:

 > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master)

 > $ git branch -a

 > * master

 >   remotes/origin/HEAD -> origin/master

 >   remotes/origin/RELEASE_3_6

 >   remotes/origin/master

 >   remotes/upstream/RELEASE_3_6

 >   remotes/upstream/master

Thank you very much for your help.

Best regards,

Arman

*From: *Martin Morgan 
*Sent: *Thursday, November 2, 2017 17:58
*To: *Arman Shahrisa ; bioc-devel 

*Subject: *Re: [Bioc-devel] Confusion with how to

Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

2017-11-02 Thread Martin Morgan 

On 11/02/2017 10:11 AM, Arman Shahrisa wrote:

I can see two branches master and releas_3_6. I created GMaster to


Again, you need to be very precise here.

There is no branch releas_3_6.

I don't know what 'it' is -- I guess your local repository that you 
cloned, but where did you clone it from?


I don't know what you mean by 'created GMaster'

connect it with GitHub. But as far as it looks like, it’s only a local 
directory.


the cloned repository is a local directory, yes.

Also, I don’t know weather I can remove it or not. Should upsteam appear 
here?


If you remove it, then any changes not 'pushed' to an online repository 
will be lost.


'upstream' would appear with

  git remote -v

if you had added an 'upstream' remote

  git remote add upstream g...@git.bioconductor.org:packages/your-package

or if you had renamed an existing remote

  git rename origin upstream

'origin' and 'upstream' are just names; you can call remotes whatever 
you want.


It would be helpful to report as carefully as possible what your 
configure and commands are. For instance instead of your message, you 
could say


I can see two branches

$ git branch  -a
  RELEASE_3_6
* master

I have created a remote connecting to GitHub

$ git remote -v
origin  g...@github.com:Bioconductor/your-package (fetch)
origin  g...@github.com:Bioconductor/your-package (push)
upstreamg...@git.bioconductor.org:packages/your-package (fetch)
upstreamg...@git.bioconductor.org:packages/your-package (push)

and so on.

Martin



Best regards,

Arman

*From: *Martin Morgan 
*Sent: *Thursday, November 2, 2017 05:00
*To: *Arman Shahrisa ; Stephanie M. 
Gogarten ; bioc-devel 

*Subject: *Re: [Bioc-devel] Confusion with how to maintain release/devel 
files on local computer.


On 11/01/2017 07:53 PM, Arman Shahrisa wrote:
I cloned the package into a clean directory. 


It helps to be more precise here. Were did you clone the package from?
In the simplest case it would be

    git clone g...@git.bioconductor.org:packages/your-package

and you'd have a single remote named 'origin'

    git remote -v

You can add or rename remotes, e.g.,

    git remote rename origin upstream
    git remote add origin g...@github.com:your-name/your-package

and you can pull (or fetch and then merge) from each

    git pull upstream  # pull changes from 'upstream' remote
    git pull origin    # pull changes from 'origin'

Study the how-to documents for different scenarios, and be precise as
possible with what you are trying to do. Also, when learning, it can be
comforting to know that removing your local repository from your disk is
not the end of the world, you can just start over with a new clone from
git.bioconductor.org or from github.


Then I followed �New package workflow� strategy. By checking Description file 
while switching between branches, I can easily see the version change which is 
correct. If I understand it correctly, GitHub can only contain changes I make 
to master branch. If  I want to push changes to GitHub as well, what should I 
do?


You can do whatever you want with your local clone, and with github. The
Bioconductor git repository allows you to push only to 'master' and the
current release, RELEASE_3_6. Suppose you'd made changes to master, and
you named the remotes 'origin' (for github) and 'upstream' (for
bioconductor). Then after after adding (git add ...) and committing (git
commit ...) to the local repository, you'd push to bioconductor with

    git push upstream master

and to github with

    git push origin master

Martin



Best regards,
Arman


From: Stephanie M. Gogarten
Sent: Thursday, November 2, 2017 02:19
To: Arman Shahrisa
Cc: bioc-devel
Subject: Re: [Bioc-devel] Confusion with how to maintain release/devel files on 
local computer.

One possible point of confusion: Laurent's workflow includes maintaining
separate branches "master" and "devel", which he syncs to his own Github
repo and Bioconductor's git repo respectively. However, the
documentation on the bioc website
(https://bioconductor.org/developers/how-to/git/) assumes that you have
only one "master" branch that you push to both remotes.

On 11/1/17 2:33 PM, Laurent Gatto wrote:


On  1 November 2017 20:36, Arman Shahrisa wrote:


I'm confused with development process.

At first, I need to have a folder with accepted packaged. Then I need to pull
origion RELEASE_3_6?

Then in another folder, I need to pull origion master?


No, it all happens in the same folder, but switching between branches
using git. Here's an example of one of my own packages. The first
command list all available branches (all, using -a, means also
remote-only branches). My current branch is noted with an *, and I also
have a feature branch called writeMSData,

Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

2017-11-01 Thread Martin Morgan 

On 11/01/2017 07:53 PM, Arman Shahrisa wrote:
I cloned the package into a clean directory. 


It helps to be more precise here. Were did you clone the package from? 
In the simplest case it would be


  git clone g...@git.bioconductor.org:packages/your-package

and you'd have a single remote named 'origin'

  git remote -v

You can add or rename remotes, e.g.,

  git remote rename origin upstream
  git remote add origin g...@github.com:your-name/your-package

and you can pull (or fetch and then merge) from each

  git pull upstream  # pull changes from 'upstream' remote
  git pull origin# pull changes from 'origin'

Study the how-to documents for different scenarios, and be precise as 
possible with what you are trying to do. Also, when learning, it can be 
comforting to know that removing your local repository from your disk is 
not the end of the world, you can just start over with a new clone from 
git.bioconductor.org or from github.



Then I followed �New package workflow� strategy. By checking Description file 
while switching between branches, I can easily see the version change which is 
correct. If I understand it correctly, GitHub can only contain changes I make 
to master branch. If I want to push changes to GitHub as well, what should I do?


You can do whatever you want with your local clone, and with github. The 
Bioconductor git repository allows you to push only to 'master' and the 
current release, RELEASE_3_6. Suppose you'd made changes to master, and 
you named the remotes 'origin' (for github) and 'upstream' (for 
bioconductor). Then after after adding (git add ...) and committing (git 
commit ...) to the local repository, you'd push to bioconductor with


  git push upstream master

and to github with

  git push origin master

Martin



Best regards,
Arman


From: Stephanie M. Gogarten
Sent: Thursday, November 2, 2017 02:19
To: Arman Shahrisa
Cc: bioc-devel
Subject: Re: [Bioc-devel] Confusion with how to maintain release/devel files on 
local computer.

One possible point of confusion: Laurent's workflow includes maintaining
separate branches "master" and "devel", which he syncs to his own Github
repo and Bioconductor's git repo respectively. However, the
documentation on the bioc website
(https://bioconductor.org/developers/how-to/git/) assumes that you have
only one "master" branch that you push to both remotes.

On 11/1/17 2:33 PM, Laurent Gatto wrote:


On  1 November 2017 20:36, Arman Shahrisa wrote:


I'm confused with development process.

At first, I need to have a folder with accepted packaged. Then I need to pull
origion RELEASE_3_6?

Then in another folder, I need to pull origion master?


No, it all happens in the same folder, but switching between branches
using git. Here's an example of one of my own packages. The first
command list all available branches (all, using -a, means also
remote-only branches). My current branch is noted with an *, and I also
have a feature branch called writeMSData, which also lives on GitHub
(https://github.com/lgatto/MSnbase/, but that's optional).

$ git branch -a
devel
* master
writeMSData
remotes/origin/HEAD -> origin/master
remotes/origin/centroiding
remotes/origin/fixBracketSubset
remotes/origin/issue82
remotes/origin/master
remotes/origin/orbifilter
remotes/origin/processingData
remotes/origin/removePrecMz
remotes/origin/writeMSData
remotes/upstream/RELEASE_2_10
remotes/upstream/RELEASE_2_11
remotes/upstream/RELEASE_2_12
remotes/upstream/RELEASE_2_13
remotes/upstream/RELEASE_2_14
remotes/upstream/RELEASE_2_8
remotes/upstream/RELEASE_2_9
remotes/upstream/RELEASE_3_0
remotes/upstream/RELEASE_3_1
remotes/upstream/RELEASE_3_2
remotes/upstream/RELEASE_3_3
remotes/upstream/RELEASE_3_4
remotes/upstream/RELEASE_3_5
remotes/upstream/master

As you can see (and as specified by Gabe in his earlier reply), I
haven't have pulled all Bioconductor releases. master points to GitHub's
origin/master branch, and devel points to Bioconductor's
upstream/master. As you can see above, I haven't got the latest release
references yet. I can do this with

$ git fetch --all
Fetching origin
Fetching upstream
remote: Counting objects: 6, done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 6 (delta 4), reused 0 (delta 0)
Unpacking objects: 100% (6/6), done.
  From git.bioconductor.org:packages/MSnbase
   * [new branch]  RELEASE_3_6 -> upstream/RELEASE_3_6
 b680678..a98138c  master -> upstream/master

And now

$ git branch -a
devel
* master
writeMSData
remotes/origin/HEAD -> origin/master
remotes/origin/centroiding
remotes/origin/fixBracketSubset
remotes/origin/issue82
remotes/origin/master
remotes/origin/orbifilter
remotes/origin/processingData
remotes/origin/removePrecMz
remotes/origin/writeMSData

Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

2017-11-01 Thread Vincent Carey 
As I plan to "fix a bug" in release version of BiocSklearn, I tried

%vjcair> git checkout remotes/upstream/RELEASE_3_6

Here is the result; what would I do to make some changes, alter DESCRIPTION
version to 1.0.1, commit and push so that the build system

has 1.0.1?

Note: checking out 'remotes/upstream/RELEASE_3_6'.


You are in 'detached HEAD' state. You can look around, make experimental

changes and commit them, and you can discard any commits you make in this

state without impacting any branches by performing another checkout.


If you want to create a new branch to retain commits you create, you may

do so (now or later) by using -b with the checkout command again. Example:


  git checkout -b 


HEAD is now at 98fabcd... bump x.y.z versions to even y prior to creation
of RELEASE_3_6 branch

On Wed, Nov 1, 2017 at 8:19 PM, Arman Shahrisa 
wrote:

> I found how I can create another remote with GitHub using Rstudio. How can
> I merge master and GitHub?
>
> Best regards,
> Arman
>
> From: Arman Shahrisa
> Sent: Thursday, November 2, 2017 03:23
> To: Stephanie M. Gogarten; bioc-devel bioc-devel@r-project.org>
> Subject: RE: [Bioc-devel] Confusion with how to maintain release/devel
> files on local computer.
>
> I cloned the package into a clean directory. Then I followed “New package
> workflow” strategy. By checking Description file while switching between
> branches, I can easily see the version change which is correct. If I
> understand it correctly, GitHub can only contain changes I make to master
> branch. If I want to push changes to GitHub as well, what should I do?
>
> Best regards,
> Arman
>
>
> From: Stephanie M. Gogarten
> Sent: Thursday, November 2, 2017 02:19
> To: Arman Shahrisa
> Cc: bioc-devel
> Subject: Re: [Bioc-devel] Confusion with how to maintain release/devel
> files on local computer.
>
> One possible point of confusion: Laurent's workflow includes maintaining
> separate branches "master" and "devel", which he syncs to his own Github
> repo and Bioconductor's git repo respectively. However, the
> documentation on the bioc website
> (https://bioconductor.org/developers/how-to/git/) assumes that you have
> only one "master" branch that you push to both remotes.
>
> On 11/1/17 2:33 PM, Laurent Gatto wrote:
> >
> > On  1 November 2017 20:36, Arman Shahrisa wrote:
> >
> >> I'm confused with development process.
> >>
> >> At first, I need to have a folder with accepted packaged. Then I need
> to pull
> >> origion RELEASE_3_6?
> >>
> >> Then in another folder, I need to pull origion master?
> >
> > No, it all happens in the same folder, but switching between branches
> > using git. Here's an example of one of my own packages. The first
> > command list all available branches (all, using -a, means also
> > remote-only branches). My current branch is noted with an *, and I also
> > have a feature branch called writeMSData, which also lives on GitHub
> > (https://github.com/lgatto/MSnbase/, but that's optional).
> >
> > $ git branch -a
> >devel
> > * master
> >writeMSData
> >remotes/origin/HEAD -> origin/master
> >remotes/origin/centroiding
> >remotes/origin/fixBracketSubset
> >remotes/origin/issue82
> >remotes/origin/master
> >remotes/origin/orbifilter
> >remotes/origin/processingData
> >remotes/origin/removePrecMz
> >remotes/origin/writeMSData
> >remotes/upstream/RELEASE_2_10
> >remotes/upstream/RELEASE_2_11
> >remotes/upstream/RELEASE_2_12
> >remotes/upstream/RELEASE_2_13
> >remotes/upstream/RELEASE_2_14
> >remotes/upstream/RELEASE_2_8
> >remotes/upstream/RELEASE_2_9
> >remotes/upstream/RELEASE_3_0
> >remotes/upstream/RELEASE_3_1
> >remotes/upstream/RELEASE_3_2
> >remotes/upstream/RELEASE_3_3
> >remotes/upstream/RELEASE_3_4
> >remotes/upstream/RELEASE_3_5
> >remotes/upstream/master
> >
> > As you can see (and as specified by Gabe in his earlier reply), I
> > haven't have pulled all Bioconductor releases. master points to GitHub's
> > origin/master branch, and devel points to Bioconductor's
> > upstream/master. As you can see above, I haven't got the latest release
> > references yet. I can do this with
> >
> > $ git fetch --all
> > Fetching origin
> > Fetching upstream
> > remote: Counting objects: 6, done.
> > remote: Compressing objects: 100% (6/6), done.
> > remote: Total 6 (delta 4), reused 0 (delta 0)
> > Unpacking objects: 100% (6/6), done.
> >  From git.bioconductor.org:packages/MSnbase
> >   * [new branch]  RELEASE_3_6 -> upstream/RELEASE_3_6
> > b680678..a98138c  master -> upstream/master
> >
> > And now
> >
> > $ git branch -a
> >devel
> > * master
> >writeMSData
> >remotes/origin/HEAD -> origin/master
> >remotes/origin/centroiding
> >remotes/origin/fixBracketSubset
> >

Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

2017-11-01 Thread Arman Shahrisa 
I cloned the package into a clean directory. Then I followed �New package 
workflow� strategy. By checking Description file while switching between 
branches, I can easily see the version change which is correct. If I understand 
it correctly, GitHub can only contain changes I make to master branch. If I 
want to push changes to GitHub as well, what should I do?

Best regards,
Arman


From: Stephanie M. Gogarten
Sent: Thursday, November 2, 2017 02:19
To: Arman Shahrisa
Cc: bioc-devel
Subject: Re: [Bioc-devel] Confusion with how to maintain release/devel files on 
local computer.

One possible point of confusion: Laurent's workflow includes maintaining
separate branches "master" and "devel", which he syncs to his own Github
repo and Bioconductor's git repo respectively. However, the
documentation on the bioc website
(https://bioconductor.org/developers/how-to/git/) assumes that you have
only one "master" branch that you push to both remotes.

On 11/1/17 2:33 PM, Laurent Gatto wrote:
>
> On  1 November 2017 20:36, Arman Shahrisa wrote:
>
>> I'm confused with development process.
>>
>> At first, I need to have a folder with accepted packaged. Then I need to pull
>> origion RELEASE_3_6?
>>
>> Then in another folder, I need to pull origion master?
>
> No, it all happens in the same folder, but switching between branches
> using git. Here's an example of one of my own packages. The first
> command list all available branches (all, using -a, means also
> remote-only branches). My current branch is noted with an *, and I also
> have a feature branch called writeMSData, which also lives on GitHub
> (https://github.com/lgatto/MSnbase/, but that's optional).
>
> $ git branch -a
>devel
> * master
>writeMSData
>remotes/origin/HEAD -> origin/master
>remotes/origin/centroiding
>remotes/origin/fixBracketSubset
>remotes/origin/issue82
>remotes/origin/master
>remotes/origin/orbifilter
>remotes/origin/processingData
>remotes/origin/removePrecMz
>remotes/origin/writeMSData
>remotes/upstream/RELEASE_2_10
>remotes/upstream/RELEASE_2_11
>remotes/upstream/RELEASE_2_12
>remotes/upstream/RELEASE_2_13
>remotes/upstream/RELEASE_2_14
>remotes/upstream/RELEASE_2_8
>remotes/upstream/RELEASE_2_9
>remotes/upstream/RELEASE_3_0
>remotes/upstream/RELEASE_3_1
>remotes/upstream/RELEASE_3_2
>remotes/upstream/RELEASE_3_3
>remotes/upstream/RELEASE_3_4
>remotes/upstream/RELEASE_3_5
>remotes/upstream/master
>
> As you can see (and as specified by Gabe in his earlier reply), I
> haven't have pulled all Bioconductor releases. master points to GitHub's
> origin/master branch, and devel points to Bioconductor's
> upstream/master. As you can see above, I haven't got the latest release
> references yet. I can do this with
>
> $ git fetch --all
> Fetching origin
> Fetching upstream
> remote: Counting objects: 6, done.
> remote: Compressing objects: 100% (6/6), done.
> remote: Total 6 (delta 4), reused 0 (delta 0)
> Unpacking objects: 100% (6/6), done.
>  From git.bioconductor.org:packages/MSnbase
>   * [new branch]  RELEASE_3_6 -> upstream/RELEASE_3_6
> b680678..a98138c  master -> upstream/master
>
> And now
>
> $ git branch -a
>devel
> * master
>writeMSData
>remotes/origin/HEAD -> origin/master
>remotes/origin/centroiding
>remotes/origin/fixBracketSubset
>remotes/origin/issue82
>remotes/origin/master
>remotes/origin/orbifilter
>remotes/origin/processingData
>remotes/origin/removePrecMz
>remotes/origin/writeMSData
>remotes/upstream/RELEASE_2_10
>remotes/upstream/RELEASE_2_11
>remotes/upstream/RELEASE_2_12
>remotes/upstream/RELEASE_2_13
>remotes/upstream/RELEASE_2_14
>remotes/upstream/RELEASE_2_8
>remotes/upstream/RELEASE_2_9
>remotes/upstream/RELEASE_3_0
>remotes/upstream/RELEASE_3_1
>remotes/upstream/RELEASE_3_2
>remotes/upstream/RELEASE_3_3
>remotes/upstream/RELEASE_3_4
>remotes/upstream/RELEASE_3_5
>remotes/upstream/RELEASE_3_6
>remotes/upstream/master
>
> If I want to modify the development branch (i.e. Bioconductor's
> upstreams/master), then I checkout devel (that's how I named it
> locally), do changes and push.
>
> $ git checkout devel
> ## do stuff
> $ git push
>
> Same principle for other branches.
>
>> So that by opening each folder, I know what I'm editing.
>> Also during push, I need to be careful about where I'm pushing changes.
>> Origion is bioc's git address of my package whereas master is the package 
>> directory in GitHub?
>
> No - I suggest you read a bit about git (GitHub is a web interface using
> git) to familiarise yourself with the concepts and vocabulary.
>
>> Am I getting it correct?
>> Is there anywhere that contains whole the process and codes in steps?
>
> All the setup and more details are provided in
>
>

Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

2017-11-01 Thread Stephanie M. Gogarten 
One possible point of confusion: Laurent's workflow includes maintaining 
separate branches "master" and "devel", which he syncs to his own Github 
repo and Bioconductor's git repo respectively. However, the 
documentation on the bioc website 
(https://bioconductor.org/developers/how-to/git/) assumes that you have 
only one "master" branch that you push to both remotes.


On 11/1/17 2:33 PM, Laurent Gatto wrote:


On  1 November 2017 20:36, Arman Shahrisa wrote:


I'm confused with development process.

At first, I need to have a folder with accepted packaged. Then I need to pull
origion RELEASE_3_6?

Then in another folder, I need to pull origion master?


No, it all happens in the same folder, but switching between branches
using git. Here's an example of one of my own packages. The first
command list all available branches (all, using -a, means also
remote-only branches). My current branch is noted with an *, and I also
have a feature branch called writeMSData, which also lives on GitHub
(https://github.com/lgatto/MSnbase/, but that's optional).

$ git branch -a
   devel
* master
   writeMSData
   remotes/origin/HEAD -> origin/master
   remotes/origin/centroiding
   remotes/origin/fixBracketSubset
   remotes/origin/issue82
   remotes/origin/master
   remotes/origin/orbifilter
   remotes/origin/processingData
   remotes/origin/removePrecMz
   remotes/origin/writeMSData
   remotes/upstream/RELEASE_2_10
   remotes/upstream/RELEASE_2_11
   remotes/upstream/RELEASE_2_12
   remotes/upstream/RELEASE_2_13
   remotes/upstream/RELEASE_2_14
   remotes/upstream/RELEASE_2_8
   remotes/upstream/RELEASE_2_9
   remotes/upstream/RELEASE_3_0
   remotes/upstream/RELEASE_3_1
   remotes/upstream/RELEASE_3_2
   remotes/upstream/RELEASE_3_3
   remotes/upstream/RELEASE_3_4
   remotes/upstream/RELEASE_3_5
   remotes/upstream/master

As you can see (and as specified by Gabe in his earlier reply), I
haven't have pulled all Bioconductor releases. master points to GitHub's
origin/master branch, and devel points to Bioconductor's
upstream/master. As you can see above, I haven't got the latest release
references yet. I can do this with

$ git fetch --all
Fetching origin
Fetching upstream
remote: Counting objects: 6, done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 6 (delta 4), reused 0 (delta 0)
Unpacking objects: 100% (6/6), done.
 From git.bioconductor.org:packages/MSnbase
  * [new branch]  RELEASE_3_6 -> upstream/RELEASE_3_6
b680678..a98138c  master -> upstream/master

And now

$ git branch -a
   devel
* master
   writeMSData
   remotes/origin/HEAD -> origin/master
   remotes/origin/centroiding
   remotes/origin/fixBracketSubset
   remotes/origin/issue82
   remotes/origin/master
   remotes/origin/orbifilter
   remotes/origin/processingData
   remotes/origin/removePrecMz
   remotes/origin/writeMSData
   remotes/upstream/RELEASE_2_10
   remotes/upstream/RELEASE_2_11
   remotes/upstream/RELEASE_2_12
   remotes/upstream/RELEASE_2_13
   remotes/upstream/RELEASE_2_14
   remotes/upstream/RELEASE_2_8
   remotes/upstream/RELEASE_2_9
   remotes/upstream/RELEASE_3_0
   remotes/upstream/RELEASE_3_1
   remotes/upstream/RELEASE_3_2
   remotes/upstream/RELEASE_3_3
   remotes/upstream/RELEASE_3_4
   remotes/upstream/RELEASE_3_5
   remotes/upstream/RELEASE_3_6
   remotes/upstream/master

If I want to modify the development branch (i.e. Bioconductor's
upstreams/master), then I checkout devel (that's how I named it
locally), do changes and push.

$ git checkout devel
## do stuff
$ git push

Same principle for other branches.


So that by opening each folder, I know what I'm editing.
Also during push, I need to be careful about where I'm pushing changes.
Origion is bioc's git address of my package whereas master is the package 
directory in GitHub?


No - I suggest you read a bit about git (GitHub is a web interface using
git) to familiarise yourself with the concepts and vocabulary.


Am I getting it correct?
Is there anywhere that contains whole the process and codes in steps?


All the setup and more details are provided in

   https://github.com/bioconductor/bioc_git_transition/

in particular the FAQ and all the scenarios at the bottom

   https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/faq.md

Best wishes,

Laurent


Best regards,
Arman



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Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

2017-11-01 Thread Laurent Gatto 

On  1 November 2017 20:36, Arman Shahrisa wrote:

> I'm confused with development process.
>
> At first, I need to have a folder with accepted packaged. Then I need to pull
> origion RELEASE_3_6?
>
> Then in another folder, I need to pull origion master?

No, it all happens in the same folder, but switching between branches
using git. Here's an example of one of my own packages. The first
command list all available branches (all, using -a, means also
remote-only branches). My current branch is noted with an *, and I also
have a feature branch called writeMSData, which also lives on GitHub
(https://github.com/lgatto/MSnbase/, but that's optional).

$ git branch -a
  devel
* master
  writeMSData
  remotes/origin/HEAD -> origin/master
  remotes/origin/centroiding
  remotes/origin/fixBracketSubset
  remotes/origin/issue82
  remotes/origin/master
  remotes/origin/orbifilter
  remotes/origin/processingData
  remotes/origin/removePrecMz
  remotes/origin/writeMSData
  remotes/upstream/RELEASE_2_10
  remotes/upstream/RELEASE_2_11
  remotes/upstream/RELEASE_2_12
  remotes/upstream/RELEASE_2_13
  remotes/upstream/RELEASE_2_14
  remotes/upstream/RELEASE_2_8
  remotes/upstream/RELEASE_2_9
  remotes/upstream/RELEASE_3_0
  remotes/upstream/RELEASE_3_1
  remotes/upstream/RELEASE_3_2
  remotes/upstream/RELEASE_3_3
  remotes/upstream/RELEASE_3_4
  remotes/upstream/RELEASE_3_5
  remotes/upstream/master

As you can see (and as specified by Gabe in his earlier reply), I
haven't have pulled all Bioconductor releases. master points to GitHub's
origin/master branch, and devel points to Bioconductor's
upstream/master. As you can see above, I haven't got the latest release
references yet. I can do this with

$ git fetch --all
Fetching origin
Fetching upstream
remote: Counting objects: 6, done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 6 (delta 4), reused 0 (delta 0)
Unpacking objects: 100% (6/6), done.
>From git.bioconductor.org:packages/MSnbase
 * [new branch]  RELEASE_3_6 -> upstream/RELEASE_3_6
   b680678..a98138c  master -> upstream/master

And now

$ git branch -a  
  devel
* master
  writeMSData
  remotes/origin/HEAD -> origin/master
  remotes/origin/centroiding
  remotes/origin/fixBracketSubset
  remotes/origin/issue82
  remotes/origin/master
  remotes/origin/orbifilter
  remotes/origin/processingData
  remotes/origin/removePrecMz
  remotes/origin/writeMSData
  remotes/upstream/RELEASE_2_10
  remotes/upstream/RELEASE_2_11
  remotes/upstream/RELEASE_2_12
  remotes/upstream/RELEASE_2_13
  remotes/upstream/RELEASE_2_14
  remotes/upstream/RELEASE_2_8
  remotes/upstream/RELEASE_2_9
  remotes/upstream/RELEASE_3_0
  remotes/upstream/RELEASE_3_1
  remotes/upstream/RELEASE_3_2
  remotes/upstream/RELEASE_3_3
  remotes/upstream/RELEASE_3_4
  remotes/upstream/RELEASE_3_5
  remotes/upstream/RELEASE_3_6
  remotes/upstream/master

If I want to modify the development branch (i.e. Bioconductor's
upstreams/master), then I checkout devel (that's how I named it
locally), do changes and push.

$ git checkout devel
## do stuff
$ git push

Same principle for other branches.

> So that by opening each folder, I know what I'm editing.
> Also during push, I need to be careful about where I'm pushing changes.
> Origion is bioc's git address of my package whereas master is the package 
> directory in GitHub?

No - I suggest you read a bit about git (GitHub is a web interface using
git) to familiarise yourself with the concepts and vocabulary.

> Am I getting it correct?
> Is there anywhere that contains whole the process and codes in steps?

All the setup and more details are provided in 

  https://github.com/bioconductor/bioc_git_transition/

in particular the FAQ and all the scenarios at the bottom

  https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/faq.md

Best wishes,

Laurent

> Best regards,
> Arman
>
>
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/

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Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

2017-11-01 Thread Martin Morgan 

On 11/01/2017 04:42 PM, Gabe Becker wrote:

Arman,

Not on the Bioc team per se, but I would say only have a checkout of the
release branch when you need it, ie a bug is reported, you have fixed it in
devel, and you are ready to push the very narrow bugfix to release. I only
keep "master" checkouts of my packages on a permanent basis.


In case Arman is not aware, the basic scenarios are at

  https://bioconductor.org/developers/how-to/git

the most straight-forward of which (a clone of the Bioconductor git 
repository, no GitHub mirror) is


  https://bioconductor.org/developers/how-to/git/maintain-bioc-only/

Generally, one has only a single local git repository, switching between 
branches within that repository.


Martin



You generally shouldn't need a checkout of release, imho, because no
development should be happening there with exception of the case above.

Hope that helps,
~G

On Wed, Nov 1, 2017 at 1:36 PM, Arman Shahrisa 
wrote:


I’m confused with development process.

At first, I need to have a folder with accepted packaged. Then I need to
pull
origion RELEASE_3_6?

Then in another folder, I need to pull origion master?

So that by opening each folder, I know what I’m editing.
Also during push, I need to be careful about where I’m pushing changes.
Origion is bioc’s git address of my package whereas master is the package
directory in GitHub?

Am I getting it correct?
Is there anywhere that contains whole the process and codes in steps?

Best regards,
Arman



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Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

2017-11-01 Thread Gabe Becker 
Arman,

Not on the Bioc team per se, but I would say only have a checkout of the
release branch when you need it, ie a bug is reported, you have fixed it in
devel, and you are ready to push the very narrow bugfix to release. I only
keep "master" checkouts of my packages on a permanent basis.

You generally shouldn't need a checkout of release, imho, because no
development should be happening there with exception of the case above.

Hope that helps,
~G

On Wed, Nov 1, 2017 at 1:36 PM, Arman Shahrisa 
wrote:

> I’m confused with development process.
>
> At first, I need to have a folder with accepted packaged. Then I need to
> pull
> origion RELEASE_3_6?
>
> Then in another folder, I need to pull origion master?
>
> So that by opening each folder, I know what I’m editing.
> Also during push, I need to be careful about where I’m pushing changes.
> Origion is bioc’s git address of my package whereas master is the package
> directory in GitHub?
>
> Am I getting it correct?
> Is there anywhere that contains whole the process and codes in steps?
>
> Best regards,
> Arman
>
>
>
> [[alternative HTML version deleted]]
>
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Gabriel Becker, Ph.D
Scientist
Bioinformatics and Computational Biology
Genentech Research

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