I love github and RStudio for workflow. Recently, I've created a project template that makes directories and scripts etc. and would like to create locally and push to github.
In the past I created a repo for a project via https://github.com/ used version control in RStudio to create the local repo and then dump all files I already had there.
This seems wasteful of time. How can one to take the directory/repo that's already in RStudio with a .Rproj file and upload to github with out first creating the shell repo at https://github.com/?
I think this could save time in the workflow.
I thought I could just follow the directions -here- (under Adding version control to a project) to add version control but this doesn't allow me to push to github (nor should it because how does RStudio know which git site you want to push to).
The only way you could create a repository on github directly from your computer, without having to create it with their website first, would be to create a remote branch directly from git on your system. This is possible on some git installation, but not on Github.
However, Github provides an API that allows to create the repository from the command line, via a call to curl for example. You will find information on how to do it in this answer (not tested) :
curl -u 'USER:PASS' https://api.github.com/user/repos -d '{"name":"REPO"}'
git remote add origin git#github.com:USER/REPO.git
git push origin master
But I don't think you will be able to do it directly from RStudio : you will need to put your project under version control, and then to execute the three commands provided in the answer in a shell.
Have you seen hub?
hub create
git push -u origin master
will do the job for you, once hub is configured to access your GitHub account. If you want the project to be called different from the name of the parent directory, use
hub create projectname
The general usage is
hub create [NAME] [-p] [-d DESCRIPTION] [-h HOMEPAGE]
(-p -- private repository), and you can access many more GitHub features with this tool.
Related
I have followed every advice on http://r-pkgs.had.co.nz/git.html and on the subsection http://r-pkgs.had.co.nz/git.html#git-branch and I am still getting error.
The steps I need/did (different from what Hadley's page dictates).
grab URL of GitHub repo (e.g, https://github.com/OHDSI/Achilles.git )
create versioned project in RStudio with this URL
set up my global user names for git
select a dev branch here (for example devXYZ)
At this point I got "detached at origin/devXYZ) message.
Per instructions in Hadley book - I tried to do fix this using this command
git push --set-upstream origin devXYZ
but it fails. The error is: origin does not appear to be a git repository or src refspec devXYZ does not match any
I tried fixing it with doing this command (may be wrong)
git remote add origin https://github.com/OHDSI/Achilles.git
I am using windows, latest R, latest RStudio, latest git from https://git-scm.com/download/win
EDIT: I also tried making a new branch using the recommended mechanism but it also fails. The goal is to get instructions where there is not git init and the whole process starts with an URL and new project in RStudio.
The desired future steps to work would be 5. modify and commit into the devXYZ branch.
THIS ONLY APPLIES TO NON-MASTER BRANCHES:
If you are newbie to git - simply don't try to do the git part in R at all.
Instead, use GitHub Desktop or SourceTree.
Point that tool to the desired repo, switch to desired branch
Start RStudio and do any development
Close RStudio and use that external tool to perform any git steps.
FOR MASTER BRANCHES:
integrated RStudio git implementation works great.
I think I might know what the problem is. You're trying to push directly to the main repo. I'm guessing you're not one of the main contributors for that repo so it won't allow you to create a branch there directly. I'm guessing in that book he's probably using his own repository as an example rather than using an existing one
The reason you're getting that error is because that branch doesn't exist on the remote repo so it can't get the reference to it which is inferred from this src refspec devXYZ does not match any
The preferred workflow is to work on a fork of the main repo (basically its your own personal copy of the main repo that is stored on the server). Even if you end up as a contributor at some point I think this is a good workflow to follow
Here's a good explanation on how use the fork workflow. There's other information on stackoverflow as well
Once you've made updates you'd create what's called a pull request to the original repo (commonly referred to as upstream). This basically is a request to merge your changes from the fork into the main repo. This allows the repo owner to review the changes and decide whether to accept them or make changes
Since you're just going over a tutorial I'd say use your fork as the origin wherever its used in the book for now
I have figured out how to create a repository on github. Now I am trying to push the repository to both my macbook pro and my server, which is hosted through http://namecheap.com, and be able to understand how to keep things simple. I am using wordpress on my server and I have a template theme. I want to edit my files on my mac and then push them to the website, keeping everything easy.
There is plenty of information out there on how to get started with github, so I will just focus on clearing up a misconception:
Now I am trying to push the repository to both my macbook pro and my server
You do not push from github to a server. You need to clone your github repo to your development (macbook) and production (server) environments.
git clone https://github.com/USERNAME/REPOSITORY.git
https://help.github.com/articles/fetching-a-remote/
Alternatively, you can push existing code to an empty repository by initializing locally, setting your remote and then pushing
git init
git add -A
git commit -m "Initial commit"
git remote add origin https://github.com/USERNAME/REPOSITORY.git
git push origin master
Once you have your repo setup, your typical workflow will look something like this:
Make changes in your development environment (macbook).
push those changes to github.
pull those changes from github in your production or staging environment (server).
One of the main things you need to use git this way is access to a terminal on the hosting serve, to push your files directly through git that should be installed as well.
Alternatively you can upload file using any available protocol such as (s)FTP or SSH direct to your server. In this case you'll be using git to version and manager your templates but not to upload or release them.
I've seen that cheapnames.com provides Softaculous as a mechanism to manage their servers. This software also provides synch and install scripts.
I want to create a master repository on our server, from which I can clone a local version onto my computer.
I am using R Studio v0.98.994.
So far, this is what I have tried doing:
Create a folder for the master repository to live in. I do this using 'new project' in R studio, and tell it to make a git repository.
I can then open up another new project, located on my C drive, and use R studio to clone, by telling it to open an existing project and setting the URL as the location of the master project.
However, then when I make changes and commit to my local repository (which works fine) I cannot push to the master repository, I get an error exactly as described in this question: git push fails: `refusing to update checked out branch: refs/heads/master`
So it appears that R Studio creates non-bare repositories?
Now I thought, well okay, I will use git bash to initialise the repository and then connect to that within R studio.
I do so, but cannot then find a way to use that repository in R Studio.
I am very new to Git, so it is entirely probable that this is one of those 'read the instructions' questions, in which case I am very sorry - and could someone possibly point me towards some guidance for this situation? I have spent the better half of a day googling around this error and haven't yet managed to pull together the pieces :( I also apologise; this doesn't feel like a very reproducible question.
It sounds like you are using Windows Git, with a setup on a local Windows machine (C: drive) and a server of some kind, mounted as the S: drive. There's a few things you should be aware of when doing this.
Shared Repositories
If you are intending for multiple people to share the same repository, you want to initiate a shared repository. See the --shared option in git-init for more details. Note that I'm not sure how having your repository on a Windows machine affects the sharing options. If you are just trying to keep your repository in two places, that makes things a lot easier.
Bare Repositories
Separate from the discussion of sharing is the discussion of bare repositories. If you don't intend to ever work with files in the server (i.e. it's just going to be a place to push changes so they are safely stored), you could initialize a bare repository. A bare repository contains the database structure of Git, but does not have the actual files in the directory.
A standard Git repository is a directory with a hidden folder in it named .git. This .git folder contains all the various data structures that Git uses to track changes. A bare repository is essentially a folder containing only the contents of .git.
The good thing about a bare repository is that no one can work in the repository itself (since there is no working directory, just the database). This means that no one could log into S: and edit the repository themselves. Instead, they would have to clone the repository, then push their changes back to the origin. The GitGuys have a good article about why this is ideal.
Note that shared repos and bare repos are not dependent or mutually exclusive. As a general practice, if you are having a "server repo" from which you pull and to which you push, you should have it be bare, regardless of whether the project is shared.
A Non-Shared Workflow
Since it's not clear if you are sharing or not sharing and you're on a Windows environment, which I don't know about from a sharing standpoint, I'm going to give you a simple example. Using git-bash, you should be able to change directories to wherever on S: you have your repositories. Then, use git init with the bare options as described by the link above to initialize a bare repository. Navigate to where you want your repository to live on C:, and then do git clone to get a working copy.
Add a README file or something else so you can do your initial commit, and then commit and do git push origin master to push your changes to the S: repository. Once all that is done, THEN initialize the RStudio Git project. RStudio should defer to your existing configuration, and things should hopefully work.
I m writing a web application where it accepts the git URL and file to read and then displays the file on the webpage. I m using JGit for this. I see that JGit needs a local repository to clone before viewing the file. Since this is server, I do not have access to local files. So, is there anyway I can access the git remotely and view the file from there?
Thanks
It's not just JGit that needs a local repository, Git itself requires a local repository. Centralized version control systems like CVS and SVN had remote server viewing built-in, but decentralized systems (such as Git and Mercurial) typically do not.
If you want to browse a Git server, you have to make a local clone, but you could do this in the background for the user.
You might also be interested in the GitHub API, which lets you do what you want, but only for repositories hosted by GitHub.
I want to be able to develop my plugins & themes on my machine and the changes be reflected on my server almost instantly. Also I want a backup plan. So git & github seems a very good solution. I want to make regular changes to the server (push from local) and once in a while upload them on github too (local to github or remote to github).
The question is can I clone the repo from github to my remote server and to my local machine and be able to push from local to remote or pull from github to remote (if I'm not at home)?
Edit: I did a research and I found out that I actually need a bare repo in the server, but i want it to be able to push/pull to/from github.
In github and bitbucket (https://bitbucket.org) you can add any number of ssh keys from different machines and push and pull from anywhere you want. The command to generate such a key is
ssh-keygen
answer the questions with enter and the ssh key will be in /home/user/.ssh/id_rsa.pub. You have to do this for every machine you want to push and when the repository is set to private, yo also have to do it for those machines, you want to pull from.
So the workflow would be
editing locally
pushing to github/butbucket repo: git push -u origin
log in to the machine where wordpress is running: git pull