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CONTRIBUTING.md

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How to contribute github

Prerequistes

Make a github user account and clone this repository https://github.com/CC-RMD-EpiBio/autoencirt.git

git clone https://github.com/CC-RMD-EpiBio/autoencirt.git

git fetch --all

Tutorials

Github guides in general are informative: https://guides.github.com/

  1. Basic Hello World with github https://guides.github.com/activities/hello-world/ (10 - 30 minutes)
  2. Understanding the github flow https://guides.github.com/introduction/flow/ (10 - 30 minutes)
  3. Making your code citable https://guides.github.com/activities/citable-code/
  4. Documenting projects https://guides.github.com/features/wikis/

Contributing

Simple Merge and Pull request

  1. git checkout -b <new branch>

  2. Make some modifications

  3. git add <you the files you want to stage>

  4. Add a commit message git commit

  • If needed to reference an issue, write Issue #<issue number> on the bottom
  • If needed to close an issue, write Fixes #<issue number> on the bottom
    • close
    • closes
    • resolves
    • resolved
    • fixed

  1. Squash commits git rebase -i <hash or HEAD~2>

    • Use git log to find the hash number
    • HEAD~# is the last number of commits
    • the UI is interactive and help guide you to squashing your commits

  2. git fetch --all Grab the master branch

  3. Attempt to merge the master branch git merge upstream/master

  • See Cherry Picking when you want your commits to exist on the end

  1. git push Push it to your git account

    • If it doesn't exist git will complain and print out a command to run
    • The command is git push --set-upstream origin <branch_name>

  2. Make a pull request on github

Contributing with cherry picking - Please follow these directions when you have a merge conflict

Most open source projects encourage contributers to cherrypick because git place the commit on the end rather than somewhere in the middle. This project do not require cherry picking except for any changes which has a large impact on other users such as refactoring or merge conflicts with pr requests.

  1. git checkout -b <new_dev_branch>

  2. Make some modifications

  3. git add <you the files you want to stage>

  4. Add a commit message git commit

  • If needed to reference an issue, write Issue #<issue number> on the bottom
  • If needed to close an issue, write Fixes #<issue number> on the bottom
    • close
    • closes
    • resolves
    • resolved
    • fixed

  1. Squash commits git rebase -i <hash or HEAD~2>

    • Use git log to find the hash number
    • HEAD~# is the last number of commits
    • the UI is interactive and help guide you to squashing your commits

  2. git fetch --all Grab the master branch

  3. git checkout upstream/master Checkout the upstream master

  4. git checkout -b <cherry_pick> Create a branch

  5. git log <new_dev_branch>

  • You can run git log --oneline <new_dev_branch> for a more condensed log
  1. git cherry-pick <hash>
  • You can pick a range of commits with git cherry-pick <hash_A>...<hash_B>
  1. git push --set-upstream origin <cherry_pick>
  2. Make a pull request on github

Keeping up with the master branch

First, rebase your commits

Clutter commit logs with merge 'user/branch'

I would not recommend merging during development. These commands will clutter your commits with upstreams.

git checkout master
git fetch --all
git merge upstream/master
git push

Cherry-picking

git checkout master
git fetch --all
git checkout upstream/master
git checkout -b <up_branch>
git log <dev_branch> ## remember the commit hash
git cherry-pick <Hash>
git push --set-upstream origin <up_branch>
## Make a pull request

For maintainers

Combining two forks

When two forks are in active development, git merge may combine the commits in a sequential order between the two forks. In some cases, this merge will be harmless. In other cases, the files change randomly. The best solution is to cherry-pick one fork commits into the other fork.

  1. Choose a fork you want to merge into
    • See the commits *git log --left-right --graph --cherry-pick --oneline fork1...fork2
    • I choose fork one
  2. See fork2 commits only
    • git log --left-right --graph --cherry-pick --oneline fork1...fork2 | grep '>'
    • Reverse > when you want to see only fork 1 commits
  3. git checkout fork1
  4. git checkout -b cherrypick-fork2
  5. git cherry-pick <fork1-hash>
  6. git cherry-pick <fork1-hash>
  7. ....
  8. ....
  9. git cherry-pick <fork1-hash>

Links

https://lwn.net/Articles/328436/

Common git commands

  • Change branches git checkout <branch name>
  • View branch git branch
  • View all branches git branch -a
  • Delete branches git branch -d <branch name>
  • View log git log
  • View commit git status
  • Undo Staging git reset