LIMS Developers Workshop

Ettema Lab

Ino de Bruijn / @inodb

Part 1 slightly geeky

Goal - Updating the documentation

• Git
• Github
• Fork & Pull
• Updating documentation

Git (2005)

• Distributed Revision Control System
• Revision control, helps to keep track of history and different versions
• Distributed, everybody has full history of the repository
  • Older centralized versioning systems
  • Concurrent Version System (CVS) 1990
  • Apache Subversion (SVN) 2000
• Linux kernel's revision control system is git (both by Linus Torvalds)

Github (2008)

• Website that hosts Git repositories
• Feautures
  • Browse code
  • Nicely display common formats (MarkDown, ReStructuredText, csv, json, geojson)
  • Issue tracker (comments etc)
  • Unlimited public repositories
  • Private repositories for money (free @ bitbucket)
  • Group repositiories
  • Fork & pull
• The LIMS is hosted here
• The Linux kernel is also hosted there

Making changes to the documentation

• Make a Github account
• Go to the documentation
• Click on Edit on Github at the top
• Edit the file
  • This will fork (copy) the repository to your own account
  • You make your changes there
  • The pull request will be done afterwards
  • Me/Lionel will check whether the pull request is ok or not
  • If the pull request is not okay, you can continue to make changes until it is

Part 2 hella geeky

Goal - Changing zhe code

• Git Basics & Command Line Interface
• LIMS technical breakdown
  • Django
  • Travis Continuous Integration for testing
  • Sphinx Read the Docs
  • LIMS on Helicoprion
• Changing zhe code

Git basics & Command Line Interface

• Fork the repository to your own account (otherwise you can only edit your own repo)
• Clone the repository (aka download it):

USERNAME=inodb
mkdir -p ~/github
cd ~/github
git clone https://github.com/$USERNAME/SCGLIMS
ls SCGLIMS/.git

Git basics & Command Line Interface

• Now you can make some changes to the files
• In this case we edit the README.rst

cd ~/github/SCGLIMS
# checkout which files have changed
git status
# stage the files that you want to commit
git add README.rst
# commit the files
git commit -m "Change Single Cell LIMS to LIMS"
# check out the log
git log
# list remote repositories
git remote -v
# push your local commits to your Github repo
git push origin master

Git basics & Command Line Interface

• Git uses branches
  • each new feauture/bugfix on a different branch
  • merge features to master branch once done

Git basics & Command Line Interface

• List all branches

$ cd ~/github/SCGLIMS
$ git branch -a
* master
remotes/origin/HEAD -> origin/master
remotes/origin/master

Git basics & Command Line Interface

• Create a new branch and switch to it

$ git checkout -b new_feature
$ git branch
master
* new_feature

Git basics & Command Line Interface

• Push the new branch up to your GitHub account

$ git remote -v 
origin  https://github.com/inodb/SCGLIMS (fetch)
origin  https://github.com/inodb/SCGLIMS (push)
$ git push origin new_feature
To https://github.com/inodb/SCGLIMS
 * [new branch]      new_feature -> new_feature
$ git push origin --delete new_feature
$ git branch -D new_feature

Git basics & Command Line Interface

• Merge a branch

$ git checkout master
$ git merge new_feature

Git basics & Command Line Interface

• Delete the branch

$ git push origin --delete new_feature
$ git branch -D new_feature

Git basics & Command Line Interface

• If you are writing scripts without version control
• NOOOOOOO!!!
• Please make at least one repo

LIMS Technical breakdown

• Everything written in Python
  • Django web framework
• Uses database of choice
  • PostgreSQL on Helicoprion
  • SQLite local

LIMS Technical breakdown

• Travis Continuous Integration for testing
  • SCGLIMS/.travis.yml
• Coveralls.io shows test code coverage
• Sphinx in docs/
  • ReadTheDocs hosts the output

LIMS Technical breakdown

• Helicoprion has a PostgreSQL server
• It has a copy of the code on /local/lims
  • hidden production settings

Changing zhe code

• Use your forked repo
• Follow installation instructions from the repo
• Make changes and push them to your repo
• Click on pull request from Github at your own repo
• Merging is decided by me or Lionel

Bugs or features?