BAIT - a tool for breakpoint analysis and inference of time series

• Created by: Ines Adriaens (adria036)
  • Collaborators: Harmen Doekes, Malou van der Sluis
• Created on: April 15, 2022

For questions, please contact ines.adriaens@wur.nl

Project description

[to be added]

Furthermore, we refer to following sources:

• Manuscript
• Repo
• Changepoint analysis, PELT

Project structure + roadmap

1. Project initialisation and plan
2. Code modules:
   • Preprocessing (+ generalisation / requirements)
   • Segmentation (changepoint analysis)
   • Classification (ML - decision trees or more)
3. Validation of the tool
   • Dataset 1
   • Dataset 2
4. Documentation + dissemination
   • Manuals
   • Code documentation / docstrings
   • Presentation

Scripts - files

• README.md (this file)
• .gitignore (local files not version controlled)
• CHANGELOG.md (can also contain #todo or roadmaps)
• Tool module:
  • Input & preprocessing
    • Data quality + structure
    • Requirements and environment (code)
  • Segmentation
  • Classification
• Validation scripts:
  • Dataset I
  • Dataset II
• Manual and documentation

Using this repo (development only)

Configuration

Requirements

Download in this order:

• Notepad++
• Putty/PuttyGen
• [Git for windows] (https://gitforwindows.org/)

Configuration

1. Create GitLab account on wur gitlab
2. Open PuttyGen and generate a public-private key pair, for example a ssh-ed25519.
   • save both in a folder on your computer, e.g. in "C:/users/user_name/.ssh/"
   • copy the public key to your GitLab profile in Preferences > SSH Keys > Add an SSH key
     • the format is as follows: "ssh-ed25519 AAAAC3NzaC1lZDI1NTExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
     • or "ssh-rsa AAAAAxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
3. go to Access Tokens > Add a personal access token > select all options > create. Save your token in a password manager and keep it close
4. For enabling two-factor authentication, scan the code with your authenticator app (plus in right upper corner > other)
   • save the recovery codes in a safe place or passwork manager

Connect

1. create group on gitlab for your project
2. create a repository (= project) on GitLab
3. click "clone" + copy link to clone with https
4. open git bash in your local folder where you want to put the repository (right mouse click > Git Bash Here)
5. type "git clone copied_link_to_repo "
6. enter your wur mailadress and NOT the password, but the TOKEN you copied in the previous part step 3.

Initialisation

• on your local computer: go to project folder (in my case: C:\Users\adria036\OneDrive - Wageningen University & Research\iAdriaens_doc\Projects\iAdriaens\bait\code)
• open git Bash (Git Bash Here)
• git clone this repo (a new folder "bait" will appear)

git clone https://git.wur.nl/iadriaens/bait.git
cd bait

Working with git (if alone)

• make changes locally and commit them
• this will only keep track of your changes locally (on your own pc)
• git status = which changes have or have not been committed

git status  
git add .
git commit -m "meaningful_message"

• to make changes without interference with other people's work
  • BEFORE starting to work: pull last version of the project in "main"
  • create + checkout your local branch
  • "git add ." + "git commit -m "message""
• the changes in your local branch need to be merged into main in the remote
  • push local branch and ask for merge (or merge yourself)

Working with git (if others work with you)

git pull
git checkout -b new_branch_name

commit changes:

git status  
git add .
git commit -m "meaningful_message"

• to push your local changes to the remote, depending whether you worked in 'main' branch or a local branch

git push origin new_branch_name (or main)

In the remote, you can now create a merge request to add your changes to the main.

Contributing

Once the tool is developed, we will be open for collaborations:

• to test the tool on new applications / validation
• to point out bugs / generalisation issues
• any other comments are always welcome

License

TBD