scenario-2-push-to-github-gitbioc.md

Scenario 2: Push to both GitHub and Bioconductor repositories

Goal: During everyday development, you commit changes to your local repository master branch, and wish to push these commits to both GitHub and Bioconductor repositories.

NOTE: See Scenario 3 for best practices for pulling updates from Bioconductor and GitHub before committing local changes.

Steps:

1. We assume you already have a GitHub repository with the right setup to push to Bioconductor's git server (git@git.bioconductor.org). If not please see FAQ's on how to get access and follow Scenario 1. We use a clone of the BiocGenerics package in the following example.

2. To check that remotes are set up properly, run the command inside your local machine's clone.

   git remote -v
   

   which should produce the result (where is your GitHub username):

   origin  git@github.com:<developer>/BiocGenerics.git (fetch)
   origin  git@github.com:<developer>/BiocGenerics.git (push)
   upstream    git@git.bioconductor.org:packages/BiocGenerics.git (fetch)
   upstream    git@git.bioconductor.org:packages/BiocGenerics.git (push)
   

3. Make and commit changes to the master branch

   git checkout master
   ## edit files, etc.
   git add <name of file changed>
   git commit -m "My informative commit message describing the change"
   

4. (Alternatve) When changes are more elaborate, best practice is to use a local branch for development.

   git checkout master
   git checkout -b feature-my-feature
   ## multiple rounds of edit, add, commit
   

   Merge the local branch to master when the feature is 'complete'.

   git checkout master
   git merge feature-my-feature
   

5. Push updates to GitHub's (origin) master branch

   git push origin master
   

6. Next, push updates to Bioconductor's (upstream) master branch

   git push upstream master
   

7. Confirm changes, e.g., by visiting the GitHub web page for the repository.