Using GitHub

Process

	github.com/[org]/[repo] (org web)	github.com/[user]/[repo] (user web)	~/github/[repo] (user local)
->1x		-> fork	-> clone
<-	merge pull request {admin} <-	<- [pull request](Fork & Pull Model)	<- push, <-> commit

where:

• [org] is an organization (eg ohi-science)
• [repo] is a repository in the orgranization (eg ohicore, ohiprep, etc.)
• [user] is your github username

Other workflows

• github-flow
• git-flow

Resolving Conflicts

See:

• Resolving a merge conflict from the command line · GitHub Help:

In this example, pull request ohi-science/ohicore#94 for bbest/ohicore to update ohi-science/ohicore returns the message:

We can’t automatically merge this pull request. Use the command line to resolve conflicts before continuing.

Checkout via command line

If you cannot merge a pull request automatically here, you have the option of checking it out via command line to resolve conflicts and perform a manual merge.

HTTP: https://github.com/bbest/ohicore.git

Step 1: From your project repository, check out a new branch and test the changes.

git checkout -b bbest-master master
git pull https://github.com/bbest/ohicore.git master

Step 2: Merge the changes and update on GitHub.

git checkout master
git merge --no-ff bbest-master
git push origin master

Here are the extra steps to resolve this conflict. First, you need a local copy of ohi-science/ohicore in a temporary directory.

cd /Users/bbest/Github_Mac
mkdir tmp; cd tmp
git clone https://github.com/ohi-science/ohicore.git
cd ohicore

Then checkout a new branch bbest-master based on master, and overwrite with the bbest repo.

git checkout -b bbest-master master
git pull https://github.com/bbest/ohicore.git master

The Auto-merging will then detect CONFLICTs. In this case:

CONFLICT (content): Merge conflict in inst/extdata/tmp/layers_navigation_2012a_2013a.csv

Look at the various versions of the file

# local
open inst/extdata/tmp/layers_navigation_2012a_2013a.csv

# ohi-science web
open https://github.com/ohi-science/ohicore/blob/master/inst/extdata/tmp/layers_navigation_2012a_2013a.csv

# bbest web
open https://github.com/bbest/ohicore/blob/master/inst/extdata/tmp/layers_navigation_2012a_2013a.csv

Let's overwrite with the raw online version of the file from the bbest repo.

curl -L -o inst/extdata/tmp/layers_navigation_2012a_2013a.csv "https://raw.github.com/bbest/ohicore/master/inst/extdata/tmp/layers_navigation_2012a_2013a.csv"

Once the conflicts are resolved, mark the resolved file(s) with git add and then commit with a message.

git add inst/extdata/tmp/layers_navigation_2012a_2013a.csv
git commit -m "resolved conflict with inst/extdata/tmp/layers_navigation_2012a_2013a.csv by overwriting with bbest version"
git status

Finally, merge the branches and push back to github.

git checkout master
git merge --no-ff bbest-master
git push origin master

Issues

• ohicore milestones on HuBoard - excellent overview

  • HuBoard customizations

  • Kanban six core practices

  • maintain ordering by editing order in top comment of issue:

    <!---
    @huboard:{"order":0.01,"custom_state":""}
    -->
    

• GitHub Issues 2.0: The Next Generation - lots of useful tips, including keyboard shortcuts

• GitHub Mention @somebody. They're notified.

  including @user in issue comments notifies that person and subscribes to future updates.

• Trying to enable creation of issues via email alone:

  • Connect GitHub to Email via IFTTT doesn't seem to work based on my recipe: Send [email protected] an email tagged #ohicoreIssue from [email protected].

• Closing Issues Across Repositories

  Now you can include "fixes user/repo#45" in your commit message, and it will close the referenced issue, provided you have the permission to push to that repository.

• GitHub Issues API

  curl -i -u bbest https://api.github.com/issues

• github-issues-import - this Python script allows you to import issues and pull requests from one repository to another

• gissues - GitHub Issues

• GitHub: Merging Repos, Migrating Issues

• tutorial: Team Collaboration With GitHub

Styling

• Emoji cheat sheet for Campfire and GitHub
• Say Hello to Octicons
  • Icon Fonts are Awesome
  • Icons · Styleguide

Markdown

• Mastering Markdown · GitHub Guides

Reproducible Science

• A review paper describing how git can be used to improve reproducibility in science
• Productivity in RStudio [bbest]: data wrangling with dplyr, versioning with github, documenting with markdown (note: presentation itself done in RStudio with markdown in presentation mode)