Developer documentation

Contributing guidelines

If you haven't, please read the Contributing guidelines first.

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

First time clone

If you have writing rights

If you have writing rights, you don't have to fork. Instead, simply clone and skip ahead. Whenever upstream is mentioned, use origin instead.

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/DEEPDIP-project/AttentionLayer.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.

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

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 create the issue first, so we can properly discuss the changes.
  • 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

Atomic git commits

Try to create "atomic git commits" (recommended reading: The Utopic Git History).

  • Make sure the tests pass.

  • 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()

Making a new release

To create a new release, you can follow these simple steps:

  • Create a branch release-x.y.z
  • Update version in Project.toml
  • Update the CHANGELOG.md:
    • Rename the section "Unreleased" to "[x.y.z] - yyyy-mm-dd" (i.e., version under brackets, dash, and date in ISO format)
    • Add a new section on top of it named "Unreleased"
    • Add a new link in the bottom for version "x.y.z"
    • Change the "[unreleased]" link to use the latest version - end of line, vx.y.z ... HEAD.
  • Create a commit "Release vx.y.z", push, create a PR, wait for it to pass, merge the PR.
  • Go back to main screen and click on the latest commit (link: https://github.com/DEEPDIP-project/AttentionLayer.jl/commit/main)
  • At the bottom, write @JuliaRegistrator register

After that, you only need to wait and verify:

  • Wait for the bot to comment (should take < 1m) with a link to a PR to the registry
  • Follow the link and wait for a comment on the auto-merge
  • The comment should said all is well and auto-merge should occur shortly
  • After the merge happens, TagBot will trigger and create a new GitHub tag. Check on https://github.com/DEEPDIP-project/AttentionLayer.jl/releases
  • After the release is create, a "docs" GitHub action will start for the tag.
  • After it passes, a deploy action will run.
  • After that runs, the stable docs should be updated. Check them and look for the version number.