Developer documentation

If you want to make contributions to this package that involves code, then this guide is for you.

First time clone

If this is the first time you work with this repository, follow the instructions below to clone the repository.

1. Fork this repo

2. Clone your repo (this will create a git remote called origin)

3. Add this repo as a remote:

   git remote add upstream https://github.com/unfoldtoolbox/UnfoldMixedModels.jl

This will ensure that you have two remotes in your git: origin and upstream. You will create branches and push to origin, and you will fetch and update your local main branch from upstream.

!!! tip "dev commandYou can also recommend to use]dev –local UnfoldMixedModels.jlto clone the package to./dev/UnfoldMixedModelsand add automatically add it to your julia project environment. You could also]dev –local https://link.com/myFork/UnfoldMixedModels.jl/`

Linting and formatting

Install a plugin on your editor to use EditorConfig. This will ensure that your editor is configured with important formatting settings.

We use https://pre-commit.com to run the linters and formatters. In particular, the Julia code is formatted using JuliaFormatter.jl, so please install it globally first:

julia> # Press ]
pkg> activate
pkg> add JuliaFormatter

To install pre-commit, we recommend using pipx as follows:

# Install pipx following the link
pipx install pre-commit

With pre-commit installed, activate it as a pre-commit hook:

pre-commit install

To run the linting and formatting manually, enter the command below:

pre-commit run -a

Now, you can only commit if all the pre-commit tests pass.

Testing

As with most Julia packages, you can just open Julia in the repository folder, activate the environment, and run test:

julia> # press ]
pkg> activate .
pkg> test

Instead fo running all tests, you can also run the test/setup.jl to load all required packages, and subsequently run single tests manually either by include("test/test-fit.jl") or by opening the file and running the specific test/testblock you want to run.

Working on a new issue

We try to keep a linear history in this repo, so it is important to keep your branches up-to-date.

1. Fetch from the remote and fast-forward your local main

   git fetch upstream
   git switch main
   git merge --ff-only upstream/main

2. Branch from main to address the issue (see below for naming)

   git switch -c 42-add-answer-universe

3. Push the new local branch to your personal remote repository

   git push -u origin 42-add-answer-universe

4. Create a pull request to merge your remote branch into the org main.

Branch naming

• If there is an associated issue, add the issue number.
• If there is no associated issue, and the changes are small, add a prefix such as "typo", "hotfix", "small-refactor", according to the type of update.
• If the changes are not small and there is no associated issue, then either create an issue first, or discuss in another channel with the maintainers.
• Use dash separated imperative wording related to the issue (e.g., 14-add-tests, 15-fix-model, 16-remove-obsolete-files).

Commit message

• Use imperative or present tense, for instance: Add feature or Fix bug.
• Have informative titles.
• When necessary, add a body with details.
• If there are breaking changes, add the information to the commit message.

Before creating a pull request

• Ideally: locally run the tests.

• Ideally: Make sure the pre-commit tests pass.

• Fetch any main updates from upstream and rebase your branch, if necessary:

  git fetch upstream
  git rebase upstream/main BRANCH_NAME

• Then you can open a pull request and work with the reviewer to address any issues.

Building and viewing the documentation locally

Following the latest suggestions, we recommend using LiveServer to build the documentation. Here is how you do it:

1. Run julia --project=docs to open Julia in the environment of the docs.
2. If this is the first time building the docs
   1. Press ] to enter pkg mode
   2. Run pkg> dev . to use the development version of your package
   3. Press backspace to leave pkg mode
3. Run julia> using LiveServer
4. Run julia> servedocs()