Reference: A Quick Guide to Organizing Computational Biology Projects http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424
Learn more about markdown:
https://help.github.com/articles/github-flavored-markdown/
https://daringfireball.net/projects/markdown/
http://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf
Github websites and blogs: https://pages.github.com/
The website for today's lesson can be found here: http://chendaniely.github.io/2015-11-23-harvard/.
The repository for the git stuff done in class is here: https://github.com/chendaniely/2015-11-23-harvard-git
You can read up on the software carpentry Git lesson here: http://swcarpentry.github.io/git-novice/
Link to the etherpad: http://pad.software-carpentry.org/2015-11-23-harvard I will save this after the workshop into the course website so it's backed up in multiple places.
We will learn not to do this anymore: https://xkcd.com/1597/
Please write good commit messages: https://xkcd.com/1296/
Git will help you version control so you you really do end up with 1 final doc: http://www.phdcomics.com/comics/archive.php?comicid=1531
Interactive tutorial on git and branching: http://pcottle.github.io/learnGitBranching/
Some links about the git flow model of collaboration. Don't feel the need to follow this model right away. It took me a good year or so with git to start to understand what the model is trying to accomplish. As you get more confortable with Git, it'll be easier to pick up a new topic within Git.
http://nvie.com/posts/a-successful-git-branching-model/
https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow
The stream seemed to work!
Git collboration: https://www.livecoding.tv/video/2015-11-23-harvard-git/
Git branching: https://www.livecoding.tv/video/2015-11-23-harvard-git-branches/
Pair up, into person A and person B
Part I
1. person-A fork person-B's repository
2. person-A clone the forked repository to your local computer
3. person-A make a change to the repository
4. person-A push the change to your github account
5. person-A create a pull request to person-B
5.1. collaborate
6. person-B accept the change
Part II
1. person-B make a new change after your pull request
2. person-A add person-B's repository as a new remote (upstream)
`git remote add upstream GIT_URL`
3. person-A get the new changes from person-B
4. person-A update your github fork so it is the same as Person-B
part III
1. switch roles.
Pair up, into person A and person B
Part I
1. person-A make a change to the repository (use a branch)
this repo will be the cloned branch you used earlier in part II
from person-B
git checkout -b BRANCH_NAME
make some changes and commits
2. person-A push the change to your github account
git push origin (master) *this is what you did before
git push origin BRANCH_NAME *this is what you will do now
3. person-A create a pull request to person-B
4.1. collaborate
5. person-B accept the change
This change will take the branch from person A
and merge it into person B's master branch
Part II
1. person-B make a new change after your pull request
Either do it on a new branch
2. person-B send yourself a pull request and have person a collaborate, and merge
3. person-A get the new changes from person-B
(git pull upstream)
4. person-A update your github fork so it is the same as Person-B
Reference: A Quick Guide to Organizing Computational Biology Projects http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424
http://software-carpentry.org/ go to lessons: http://software-carpentry.org/lessons.html go to the git site: http://swcarpentry.github.io/git-novice/ Git configurations: http://swcarpentry.github.io/git-novice/02-setup.html
learn git branching: http://pcottle.github.io/learnGitBranching/
git flow workflow: https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow
http://nvie.com/posts/a-successful-git-branching-model/x`
git setup:
$ git config --global user.name "Vlad Dracula"
$ git config --global user.email "vlad@tran.sylvan.ia"
$ git config --global color.ui "auto"
$ git config --global core.editor "nano -w"git init
this will turn the current folder into a git repository, everything from here on will be tracked
git status
ls -a will let you see hidden folders - e.g. the .git folder
git status allows us to see what's being tracked and anything that has changed
example:
git add README.md
This adds the file to the staging area. This only needs to be done once. You can also use: git add .
git config --list This lets you see what commands you have run
.gitignore
Git will not track what's specified in here
git log will let you see the log of all the work you had done in reverse chronological order
git log --oneline to see with less whitespace
exiting using "Q" if running the log opens a new file
git diff to see the differences between two files
use this if you're not sure why a file is being shown as 'modified'
git diff HEAD~1 this lets us check what the file looked like two commits behind us
git diff --stage for one commit behind when you staged files
Use touch to create a file
Track a deleted file by adding the file after git status just like any other action with a file. You can "undelete" using checkout
checkout
git checkout is used to take your "head" and point it somewhere else, like to your old commits
You can do this using either ~ or the hash from the log
Panic button
git reset --hard
Moving a git tracked folder (entire repo) to another folder is fine. Git only tracks what's happening within the repo
GitHub in the cloud (BitBucket is an alternative) Unlimited free public repos with GitHub can distribute "raw" by just right clicking raw button and sharing that link
Remote origin
"origin" --> where
"master" --> what
push to the cloud
pull to bring it back to your local repo
Adding a remote repo:
git remote add origin [webaddress.git]
insert your repo address (https) in the brackets
Use git remote -v to check whether or not you have connected to your remote repo on GitHub
git push origin master
this is used to push your local repo to your remote; you may initially be prompted to enter your username and password
Unstaging a file
git reset
git pull origin master
"pulling" the changes that exist in the remote repo to your local machine
Fast forward message == extending our local master branch one commit
Fixing conflicts within a file done manually -- you clean this up in your text editor Then you need to push back to the remote
Live Coding Stream: https://www.livecoding.tv/chendaniely/
Cloning - one time download from GitHub to local computer downloading and initiating repo into your local machine
Fork - one time download from GitHub to GitHub Click the "fork" button to make a copy of the repo you want to contribute to in your account You can then edit this version of the code and eventually submit a pull request to the original repo owner
Pull Request - please accept my changes from my fork back into your repo *Always add a clear message to the person who's repo you forked.
3 Part Exercise for Collaborating with Others:
Branching- a way to give a series of commits and easy to remember name e.g. simulation with two different parameters; you could create a branch for each version of the simulation
log and show everthing: git log --oneline --graph --decorate --all * hit q to exit the log
Creating a new branch
git checkout -b something_else
replace "something_else" with the name of your new branch
git branch -a
lists all the branches
git checkout branch_name
used to move between branches. Replace branch_name with the name of your branch or master.
- using git branch will let you create a branch but will not move you to that branch
Can use cat to see the changes in the repo
To merge branches you must be on the branch you want to merge into e.g. to merge branches into master, you much checkout master before you merge
git branch -d
deletes the branch -- lowercase is safer as you'll be prompted to make sure you're ready to delete. Don't use uppercase.
git push origin --delete [branch_name]
will delete the remote branch
git rebase
e.g. git rebase master
re-writting history - rewind and move forward to the head of master then replay commits