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Contributing

Source: .github/CONTRIBUTING.md

Contributions to manyhealth, whether in the form of issue identification, bug fixes, new code or documentation are encouraged and welcome, both from research assistants and (early) users of the package:

This outlines how to propose a change to a package from the Global Governance Observatory’s ecosystem. Please note that the manyhealth project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Issues

Please use the issue tracker on GitHub to identify problems or suggest new functionality, before submitting changes to the code. We use issues to identify bugs and tasks, discuss feature requests, and to track implementation of changes.

When submitting an issue, please provide at least a ‘Type’ label that best describes what the issue is about. The most useful issues are ones that precisely identify a bug, or propose a test that should pass but instead fails.

Adding new code

Independent or assigned code contributions are most welcome. When writing new code, please follow tidyverse style guide which is based on standard R guidelines.

It can help to use packages such as lintr and goodpractice to ensure these are followed. These packages are incorporated into the checks made when a pull request is made. The styler package fixes in a non-invasive way the code to adhere to the tidyverse formatting rules, and it also provides an RStudio Addins to help with this task. To run the lintr and goodpractice checks or use styler in a file run:

# basic lintr checking
lintr::lint_package(path = "manyhealth/")

# goodpractices checks. Exclude length 80
goodpractice::gp(path = "manyhealth/",
   checks = all_checks()[-c(8)])

# styler fix some of the styling issues
styler::style_file("filePath")

Writing in markdown/roxygen

When writing passages of text in markdown or roxygen documents, please consider that text should be written such that sentences, and sometimes clauses of a sentence, start on a new line. This facilitates comparison of documents and feedback on GitHub. Lines of text should, ideally, not be over 80 characters in length.

Pull request process

The title of your PR should briefly describe the change. Please include a summary of the changes and which issues are fixed and the relevant motivation and context. List any dependencies that are required for this change, indicating whether this is a major (breaking), minor, or patch change. The body of your PR should contain Fixes #issue-number. A checklist is provided to check off the cases as the different elements listed have been completed to make sure all the steps have been respected. Make sure the package passes R CMD check by running devtools::check() before committing changes to a pull request.

If you want to make a bigger change, it’s a good idea to first file an issue and make sure someone from the team agrees that it’s needed before opening a pull request. If you’ve found a bug, please file an issue that illustrates the bug with a minimal reprex.

Please follow the manyhealth pull request guideline (https://github.com/globalgov/manyhealth/blob/main/.github/pull_request_template.md)

Branches

We use two main branches in this project:

  1. The origin/main branch is reserved for fully functional releases of the model. When the develop branch reaches a stable point, a code maintainer merges it back into to the master branch, and tags it with a release number there.

  2. The origin/develop branch reflects the latest model development stage. Contributers are encouraged to submit minor changes to this branch that enhance existing functionality. New features that may break existing functionality should be committed to supporting branches.

We use two types of supporting branches:

  1. Feature branches are used to develop new functionality. They exist as long as the feature is developed, and are then either merged into the develop branch for incorporation in a release, or deleted if the feature is abandoned. Feature branches should branch off from origin/develop.

  2. Hotfix branches are used to provide fixes to severe bugs in the main branch. That way, the code maintainer does not have to incorporate (potentially unstable) changes from the develop branch to fix an issue. Branch names should be prefixed with hotfix-.

This branching model is based on: https://nvie.com/posts/a-successful-git-branching-model/.

Main Branch (code maintainer only)

To create a release version of the code:

  1. Ensure that the repository is up-to-date: git pull.
  2. Switch to the main branch: git checkout master.
  3. Merge changes to the develop branch: git merge --no-ff develop.
  4. Tag release version: git tag -a VX.Y.Z -m "VERSION-NAME".
  5. Push changes to this repository git push origin master --tags.

Develop Branch (minor changes to existing functionality)

To make minor changes directly to the develop branch, follow standard git procedures:

  1. Make sure you switched to the develop branch of the project: git checkout -b develop.
  2. Make sure your local version of the code is up-to-date: git pull origin develop.
  3. Make your changes
  4. Stage your changes for a commit: git add PATH-TO-CHANGED-FILE.
  5. Commit your changes using an appropriate message: git commit -m "DESCRIPTION".
  6. Push your commit: git push origin develop.

Feature Branches (new functionality)

To create a new feature branch: git checkout -b myfeature develop.

To merge a feature branch back into develop:

git checkout develop
git merge --no-ff myfeature
git branch -d myfeature
git push origin develop

Hotfix Branches (to fix critical bugs in release versions)

To create a new hotfix branch: git checkout -b hotfix-VERSION master.

To merge a hotfix back into master (code maintainer only):

git checkout master
git merge --no-ff hotfix-VERSION 
git tag -a VERSION
git push origin develop

And into develop:

git checkout develop
git merge --no-ff hotfix-VERSION

Every hotfix should increment the PATCH digit of the version number: a hotfix branch for V1.3.0 is named hotfix-V1.3.1, and the new release is tagged as V1.3.1.

Once merged into master and develop, the hotfix branch can be deleted: git branch -d hotfix-VERSION.

Commit messages

Commits that relate to existing issues should reference the updated status of those issues, and mention the issue number (preceded by a hash symbol: #) in the commit description:

Resolved #31 by adding a new function that does things, also updated documentation

Where the issue hash (i.e. #31) is preceded by resolve, resolves, resolved, close, closes, closed, fix, fixes, or fixed (capitalised or not), the status of the issue(s) mentioned is updated automatically. Our current syntactical standard is to mention the issue first and then provide a short description of what the committed changes do in relation to that issue. Any ancillary changes can be mentioned after a comma.

It should all be written in a single line, like so: #{verb} {issue} {describe main action/changes}, {additional actions/changes}.

Note that it is important to write a structured commit message to improve efficiency in collaboration. Please make sure of: * Making the title clear and concise with correct reference to an issue as described above. * Using a subject line in the description part when the commit message outlines many different changes. * Explaining in details the changes made and why you made them by using bullet points. * Separating each paragraph with a blank line.

To keep the tracking and, if needed, the reversing of changes as easy as possible, please follow the ‘atomic approach’ when committing changes. Each commit should address separate aspects as much as possible, such as making bug fixes and additions of data in separate commits.

Testing

We use the testthat package to write unit tests. By convention, tests are located in testthat/tests/.

You should verify that all tests pass before issuing a commit to existing code. To run all tests for the latest version manually:

git pull
library("testthat")
testthat::test_dir("tests/testthat")

When writing a new function, consider writing a unit test for that function. We follow several conventions for writing tests:

  • A unit test file should test one or more aspects of a single function. This makes it easier to identify the source of bugs, and prevents lower-level tests from failing when higher-level functions change.

  • The naming convention for test files is: test-FILENAME_IN_R_DIRECTORY-FUNCTION_NAME.R, i.e. test files are named after the file containing the original function in the R directory, pre-fixed with “test”, and optionally post-fixed with the name of the function that is being tested.

  • If a test requires auxiliary functions from the package, e.g. to initialize a network with sample data, these belong in a helper file. There should be only one helper file for each R file, named helper-FILENAME_IN_R_DIRECTORY-FUNCTION_NAME.R. Re-using existing test data is preferable to creating new data for every test.

Documentation

A final way of contributing to the package is in developing the vignettes/articles that illustrate the value added in the package. Please contact us directly with proposals for updating the documentation, or submit an issue if existing documentation is unclear.

Versioning

Note that the package is versioned according to semantic versioning. This means that versions follow the Major.Minor.Patch semantic format.

Each minor or major level version is also given a new version name, which should be updated in the zzz.R file.

For developers using MacOS

Develops using MacOS might meet problems compiling the packages since the compiling configuration of R in MacOS is usually incorrect. If one meet an error with error info “/usr/bin/ld: cannot find -lgfortran”, then he can either correct the configuration himself or follows the following steps to solve the problem: 1. Run “.libPaths()” command in R and get a path, e.g. one might get “/Library/Frameworks/R.framework/Versions/3.6/Resources/library” 2. If the path one get in the first step is “something/library”, then open the file “something/etc/Makeconf” and comment out the line starting with “FLIBS”. e.g. one might open the file ” /Library/Frameworks/R.framework/Versions/3.6/Resources/etc/Makeconf” and change the line “FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm” to “#FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath - lm”