Summit Microbes

This is a working data repository for the 2019 NEON Science Summit Soil Micro/Biogeochemistry Working Group

Working in this repository

1. To work on this repository fork the repository to your github repo. This acts as a bridge between the original repository and your personal copy. You can submit "pull requests" to offer changes to the original project.
2. Clone your fork. Once you have forked your repository, clone the repository to your desktop
3. Make and push changes. When you're ready to submit your changes, stage and commit your changes and push to your repository.
4. Making a pull request. When you're ready to add your changes to the final project (this repo) go to your forked repository and you will see a banner indicating that you have pushed a new branch and that you can submit this branch "upstream", to the original repository. Type in information and rationale as to why you're making this pull request and then send the pull request to this master repository.

Introduction to Version Control with Git

this link below is a helpful guide https://guides.github.com/activities/hello-world/

first fork the repository to your github account

fork = copy repository on github
clone = copy to local machine

copy to your local machine by moving to the directory you would like to clone to

cd ~/Documents #moves to documents from your home directory
mkdir DirectoryName #make a directory to add your github clone to
cd DirectoryName

clone respository with https link from your forked repository

git clone https://github.com/<username>/GalleryLab.git #should differ in your forked repository
git config --global user.name "<githubusername>"
git config --global user.email <githubemail>
git init . #initialize current wd

Add --> Commit --> Push Data

add is the staging command for git. want to use add the most when working with git
want to add, but not ready to commit
adding means can work on it
commit is where you get to unique id
commit is focal point of version control, where info is being stored forever
with IDs can go back in time to the old versions you have made
push uploads them to github
refer to the guide link at the top of this tutorial on pushing sensitive data, passwds etc.

mkdir example_directory
cd example_directory
nano sometextfile.txt

write some text and save out

git add sometextfile.txt
git status #see everything that has been changed since last commit
git commit -m 'added example text file' # put in some useful comment that has been
 changed since last commit
git push

we have now created a text file with command line in a new directory
added the textfile to the staging area
committed the file with a unique I.D.
and pushed to a publicly available server to be reiterated over

After each push, you can either set up credential caching for HTTPS access or set up SSH keys

http://happygitwithr.com/credential-caching.html #credential-caching
http://happygitwithr.com/ssh-keys.html #ssh-keys https keychain is recommended by github