CONTRIBUTING.md

In r-hyperspec/hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

Contributor Guidelines

:+1::tada: First off, thanks for taking the time to contribute! :tada::+1:

The following is a set of guidelines for contributing to the R package hyperSpec.

Code Licensing

We are in the (slow) process of transitioning the license of the hyperspec project to MIT. By contributing, you understand and agree that your work becomes the part of the hyperSpec project and you grant permission to the hyperSpec project to license your contribution under the GNU GPL v3 or a compatible license and/or under the MIT license or a compatible license.

Reporting Bugs and Submitting Suggestions

• Ensure the bug was not already reported by searching on GitHub under Issues.
• If you're unable to find an open issue addressing the problem, open a new one. Be sure to include a title and clear description, as much relevant information as possible, and a code sample or an executable test case demonstrating the expected behavior that is not occurring.
• Refer to the Bug Reporting in R article for guidance.
• Include minimal working example of data and code that reproduces the problem.

Color Use (Vignettes & Perhaps Examples)

• There is a built-in colorblind friendly qualitative palette palette_colorblind; please use whenever possible.
• These next two palettes are also colorblind-friendly:
• For a diverging palette, please use colorspace::diverging_hcl(n, palette = "Blue-Red2").
• For a sequential palette, please use colorspace::sequential_hcl(n, palette = "viridis").

Code and Documentation Style Guide

• This project adheres to the Tidyverse styleguide.
• This guide applies both to the code and the roxygen2 documentation.
• The documentation is written in markdown

• Whenever touching a function, please take the time to check its documentation. Large parts have been converted automatically from LaTeX, and may still need some manual polishing.

• Use package styler with RStudio add-in to easily re-style your code to comply with the guidelines.

• When appropriate, prefer this naming scheme for the internal functions – .<generic>_<x><y><...> with <x>, <y>, etc. the first, second and later parameter/operand:
• _ ... missing
• a ... array
• d ... data frame
• f ... formula
• h ... hyperSpec object
• m ... matrix

• n ... numeric (scalar, vector, or matrix)

• Each new function should be accompanied with appropriate unit tests.

• If a unit test needs to be disabled temporarily, please use skip("reason for switching off"). This way, we'll be reminded that the test is switched off whenever the unit tests are run.

Vignette Style and Standards

• No multi-line sentences (enter/return after each sentence, extra return starts a new paragraph). This facilitates comparison via version control.
• Package names in text are written in bold.
• Package names in section headings are in bold italic.
• In section headings main words should be capitalized.
• Use the British English variant and corresponding spell checker.
• Function names should be written between backticks with the parentheses and followed by a signal to use syntax formatting (not simply for example texttt or code if one was using pure LaTeX), for example fun(){.r}. The CSS file controls the exact appearance.
• When parts of the hyperSpec objects are mentioned, use the syntax formatting, for instance @data{.r}.
• When parts of a structure such as a column or list element, use the syntax highlighting, e.g. $something{.r}.
• Figures should have captions.
• Every figure should be mentioned in text via reference. This will give automatic numbering.
• Figure and Table should be capitalized when mentioned in text, e.g. Figure 1. Do not use "Fig.".
• Mention of the software R should be formatted with backticks.
• Sourced files should make vignette authors' life easier, and should not contain anything important to end users/readers.
• The first code block should start with rm(list = ls()) to ensure a clean, reproducible workspace.
• NEED TO DISCUSS: formatting of code blocks. Could use tidy = TRUE as one option.
• If you need to leave a note in a vignette, please use this method.
• Figure sizes are largely standardized, via the hook defined in vignette-default-settings.R. See the discussion there.

Working With Git

Branches

This project follows the git flow branching model.

Briefly

The branch master contains stable releases that are tested and guaranteed to work. It is not allowed to contribute directly to master.

The branch develop contains latest delivered development changes for the next release. When develop reaches a stable point and is ready to be released, it gets merged to master and tagged with a version number (e.g. 'v0.99.21'). This procedure is a subject for a strict review.

You should not directly contribute to develop, unless the change is trivial (e.g. a typo). Instead, for any new feature or bugfix, please create a separate supporting branch. We use a default naming convention for them:

• feature/###-<feature_name> for new features. Generally, for a new feature you should open an issue which at least describes the intended feature; it may go further and allow for discussion and refinement before much effort is expended. ### is the corresponding issue number.
• bugfix/###-<bugfix_name> for bugfixes
• release/x.y.z for release preparation, where x.y.z. is the version to be released. See section "Release process" below for details.

It is recommended to use the git flow tool to streamline the process (see Cheatsheet for git flow). However, do not call git flow xxx finish as it makes a merge without the code review - instead, finish your branch by opening a pull request.

Please make sure that the package can be built and and that all checks and unit tests are passed before merging back into develop. The shortcut in RStudio for that is Ctrl+Shift+E.

If you are making a significant change, please also add an entry to NEWS.md.

Wait, What if I'm not Allowed to Create a Branch in the Main Repository?

If you are not a member of the project then you cannot create a branch in the main repository. But this is not a problem! In this case, you simply fork the main repository, make the changes starting off the develop branch, and merge it back into the develop branch of the main repository via a pull request.

After a successful code review the pull request gets accepted, and your changes are represented in the main repo as a separate branch (in accordance with our guidelines). After that you can delete your fork, if you'd like.

Pull Requests

Open a pull request via GitHub interface to let others see your work and review it. It is a collaborative tool, so we encourage you to open a 'draft pull request' as soon as you start working on your part. This provides a place for the community to discuss your work and correct it as you go. Once your part is completed, change the status to “Ready for review”.

The project maintainer may want to merge your pull request when your work is usable, even before it is 100% complete. In such a case, the branch must be deleted and a new one created off the develop branch. You can use the same name for it to indicate that this is a continuation. It will be merged, as usual, via a new pull request. This may seem to be an overhead at first glance, but it leads to a faster integration and makes the the pull requests smaller and less overwhelming.

The merged support branches should be deleted - they're clutter. If you want to keep their name for reference, just apply a git tag after the merge. Never reuse merged branches, it can lead to problems.

Git Commits

Commit often, try to make small atomic commits. An atomic commit addresses only a small separate fix or change and is more or less self-consistent. Every commit should be related to one feature only, but the commit should group strongly related changes together (e.g. when refactoring to rename a function, all files that are affected by this should be in the same commit).

Commit Messages

• Use the present tense ("Add feature" not "Added feature")
• Use the imperative mood ("Move cursor to..." not "Moves cursor to...")
• Limit the first line to 72 characters or less
• Reference issues and pull requests liberally after the first line
• Give a high-level description of the what and why of the changes (similar to good code comments) already in the first line
• Use the most specialized verb that describes the situation

Versioning

The project adheres to the semantic versioning guidelines, as outlined at https://semver.org/ (Work in progress, see #123).

Briefly, the version string has the form x.y.z (or major.minor.patch), where the major number gets incremented if a release introduces breaking changes, the minor one after any changes in functionality (new features of bugfixes), and the patch number is increased after any trivial change. If a major or minor number is incremented, all subsequent ones are set to zero.

The version numbers refer only to commits in the master branch, and get incremented in one of two cases:

• during the release preparation, when a release/x.y.z branch buds off develop and merges into master.
• after a hotfix, which also results in a new commit on master.
• development branches have version x.x.x.9000 (or .9001 and so on - but that is rarely needed). This is important since pkgdown uses the .9000 to distinguish between documentation for the released version vs. the development version.

Release Process

The process starts when the package is in a stable state that can be released to CRAN (release candidate). First, decide on a new version number x.y.z based on the severity of changes. Then:

• Create a release/x.y.z branch using git flow release start <x.y.z> and push it with git flow publish
• Open a pull request that merges into master
• Update the version number in the DESCRIPTION file
• Verify that the changes are listed in NEWS.md
• Confirm that the package can be built for each platform
• Ensure that all check are passed on the tarballs you build (either on your machine or using CI) with R CMD check --as-cran <package.tar.gz>. The checks must pass for R versions R-oldrel, R-release, R-patched, and R-devel.
• If any bugs are found, they must be fixed in the very same branch (see here for details)
• Once everything works use git flow release finish <x.y.z>. It will merge the release branch into both master and develop, and will assign a tag to the newly created commit in the master branch.

Thanks! :heart:

r-hyperspec/hyperSpec documentation built on May 31, 2024, 5:53 p.m.