update CWG2R based on suggestions by @mmlopezu

[zkamvar]

I've added comments to let the user know to start on step 3 if they've already forked and cloned the repository.

Question: should I change the steps to:

• STEP i. Fork
• STEP ii. Clone
• STEP 1. Update
• STEP 2. Branch
• STEP 3. Commit

I think it might be easier this way.

[mmlopezu]

👍

[smanel]

YES!

[smanel]

Yes...If I understand you have not made the change now as suggested above?
If you make the change, you will need to change the 6 below steps?

Perhaps finally better to keep the 6 below steps:

1 Fork the popgenInfo repository*
2 Clone your fork to your local machine.*
3 Checkout your master branch, fetch the changes from NESCent and merge them into your fork.
4 Create a new branch and then add and commit new changes or content.
5 Push your changes to your fork.
6 Open a pull request from your fork to NESCent.

At the moment you have 5 steps in the vignette and there is finally no section 6. It is easy to create one: just before mgs<-

Finally Why not adding this as an additional step?
7-Pull request from your github fork Nescent -->and you can provide some explanations on how to do?
"Once you are finished with all of your changes, you can create a pull request from your GitHub fork to NESCent"

[zkamvar]

@smanel,

Yes...If I understand you have not made the change now as suggested above?

if you look at the commits, I have indeed made the changes as suggested above in c62b06b.

At the moment you have 5 steps in the vignette and there is finally no section 6. It is easy to create one: just before mgs<-

I saw your comment and have started to make changes in 688403e. I'm waiting on @hlapp's answer for #134 to include images.

Finally Why not adding this as an additional step?
7-Pull request from your github fork Nescent -->and you can provide some explanations on how to do?
"Once you are finished with all of your changes, you can create a pull request from your GitHub fork to NESCent"

This is actually redundant with Step 6.

---

The final order is:

i. Fork
ii. Clone

1. Update master
2. Checkout new branch from master
3. Add, commit, and push
4. Make a pull request

The last one is a bit difficult to write as github has no concrete guides that I can point to for this kind of workflow.

[zkamvar]

Note, you can see all of the changes I make by clicking here: https://github.com/NESCent/popgenInfo/pull/132/files

[smanel]

Sorry! I was looking the bad file.

Concerning the last section (I think that this is what I need to do for my vignette), I suggest to develop

"Once your pull request passes peer review and is published, you can update your
+fork by starting from Step 1: checkout your master branch, fetch the changes
+from NESCent, merge those changes, REVISED YOUR VIGNETTE, and push (STEP 3) them up to the master branch on your
+fork to make it even with NESCent." FINALLY CREATE THE PULL REQUEST (STEP 4)

Is it correct? If yes I will try to apply it .

[zkamvar]

"Once your pull request passes peer review and is published, you can update your
+fork by starting from Step 1: checkout your master branch, fetch the changes
+from NESCent, merge those changes, REVISED YOUR VIGNETTE, and push (STEP 3) them up to the master branch on your
+fork to make it even with NESCent." FINALLY CREATE THE PULL REQUEST (STEP 4)

Is it correct? If yes I will try to apply it .

Hi @smanel,

In your case, you should continue to add and commit changes to your vignette and push those changes since your pull request (#121) is still open and has not been published.

I now realize where the confusion lies. You are currently in step 4, but there are no instructions on what to do if changes need to be made (which is to continue adding content, committing, and pushing). I will add these instructions today.

[zkamvar]

@smanel, in other words, no, you do not need to update your branch at this time.

[smanel]

I use the following R script. Now what is missing?

library(git2r)
repo <- repository()
checkout(repo, "26_01_16_Signal_Selection")
repo
status(repo)
add(repo, "*") # adding all new or changed files
status(repo)
msg <- " review signal selection vignette: correction boxplot"
commit(repo, msg, session = TRUE)
status(repo) # should return nothing
repo
summary(commits(repo)[[1]])
push(repo, credentials = cred_token())

[zkamvar]

I use the following R script. Now what is missing?

library(git2r)
repo <- repository()
checkout(repo, "26_01_16_Signal_Selection")
repo
status(repo)
add(repo, "*") # adding all new or changed files
status(repo)
msg <- " review signal selection vignette: correction boxplot"
commit(repo, msg, session = TRUE)
status(repo) # should return nothing
repo
summary(commits(repo)[[1]])
push(repo, credentials = cred_token())

Nothing is missing! 😺

[zkamvar]

@smanel, I have made changes to include instructions on peer review. Are these sufficient?

[smanel]

I think yes. But I probably need to read all the vignette again and not only short revised sections to have a global idea of the vignette. Is it possible?

[zkamvar]

You can download it here. I've rendered it on my machine and placed it in a zip file:
CWG2R.zip

[smanel]

A long vignette!
I will test it again with a new vignette (I hope soon).

[zkamvar]

Yeah, that's what ends up happening with how-to guides. 😐

Sent from my iPhone

On Feb 14, 2016, at 12:41, Stéphanie Manel [email protected] wrote:

A long vignette!

I will test it again with a new vignette (I hope soon).

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

[zkamvar]

If it helps, steps 1-4 in the vignette correspond to steps 1-4 in the figure: https://github.com/NESCent/popgenInfo/pull/143/files

[zkamvar]

@smanel, do you think this version is good enough to merge at the moment? I would argue that it's much improved over the version that exists now.

[smanel]

Where I am sure to read the last changes?
In comment #153? In this case, yes I think that it can be merge.

[zkamvar]

@smanel, #153 is suggesting to change CONTRIBUTING.md, BUT it is a summary of the same flow that CONTRIBUTING_WITH_GIT2R.Rmd has. Given that this is the case, I'll merge it. If you find any problems, please create an issue and I will fix them.