How to Contribute to Development

Step 1: Set up a development environment (OSX and Linux only)

  • If needed, install miniconda by following the steps here.

  • If needed, install mamba: conda install mamba

  • Clone a copy of this repo:

git clone https://gitlab.com/data-analysis5/phenotypes/process.phenotypes.git
# or 
git clone git@gitlab.com:data-analysis5/phenotypes/process.phenotypes.git

  • Navigate into the repo directory: cd process.phenotypes

  • Create a conda environment with, minimally, the dependencies defined in r-dev.yaml. Make sure to activate your dev environment whenever you are writing/committing code!

# create the env
mamba env create -f r-dev.yaml

# activate the env
conda activate r-dev

npm install -g commitizen cz-conventional-changelog
commitizen init cz-conventional-changelog --save-dev --save-exact

  • Set up pre-commit hook scripts. This will apply linting and check for some common code formatting errors every time you commit. See https://pre-commit.com/ for more details.

pre-commit install

  • Install pre-commit in R (either in an R terminal or in Rstudio):

install.packages("precommit")

Step 2: Select an issue to work on, or submit one that you’d like to address

See the current issues for this project.

Step 3: Contribute code

  • All development work should branch off of the dev branch. Make sure you’re on the right branch: git checkout dev

  • Make sure your repository is up-to-date with the remote: git pull origin dev

  • Create a new branch named for the feature you’re going to work on: git checkout <feature_branch>

  • Write code and commit often!

    • Stage changes with git add .

    • Commit code with git cz; make sure to cite the issue number you’re working on

    • Push your changes to the remote repository with git push origin <feature_branch>

  • When you’re all done, submit a merge request here. Other developers will review your code, make comments, and merge in your changes when ready!