diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index cb05e30..effcaf7 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,63 +1,8 @@ -# Contributing to the hoad project +# Contributing to openairegraph -This outlines how to propose a change to the hybrid open access dashboard (hoad). - - -## Project Structure - -Because hoad is not only a research project, but primarily a data product meant to be used by many, hoad is organised as an R package. - -Please adhere by the package development best practices laid out in: - -- Hadley Wickham's [R Packages](https://r-pkgs.org/index.html) -- [rOpenSci Development Guide](https://devguide.ropensci.org/) - - -### Documentation - -Individual functions are documented using [{roxygen2}](https://roxygen2.r-lib.org). -Functions can be further organised using curated reference index in [{pkgdown}](https://pkgdown.r-lib.org/). - -Scientific articles, blog posts or any other long-form documentation is written as a [{pkgdown}](https://pkgdown.r-lib.org/) *article* inside the packages `/vignettes/` folder. -These articles are written as `bookdown::html_document2()` documents *not* as proper R vignettes, to avoid duplicate publication and to allow more expensive computations. - - -### Shiny Application - -tba. - - -### Computing Environments - -There are two sets of computing environments on which this project is guaranteed to work as per the CI setup: - -1. The {hoad} package, including all its functions, is guaranteed to work (pass `R CMD check`) on a wide variety of computing environments as per the CI setup, a subset of the [tidyverse setup](https://github.com/r-lib/actions/tree/master/examples#quickstart-ci-workflow) and [r-hub linux builders](https://github.com/r-hub/rhub-linux-builders). - Because these tests can be quite extensive, they are only run on commits to `master`, as well as pull requests to `master`. - Other branches are thus not guaranteed to work. -2. All other elements of this projects can be reproduced using a custom docker image in the `Dockerfile`: - - the [{pkgdown}](http://pkgdown.r-lib.org) website for hoad (https://subugoe.github.io/hoad/), including its articles (~ vignettes) - - the shiny web application - - (batch) jobs to reproduce more expensive analyses - - This image is also published on every commit to [docker hub](https://hub.docker.com/repository/docker/subugoe/hoad), tagged by git sha and reference (branch, release). - - This image also includes the RStudio IDE, so you can also develop *inside* this image. - - To run this image, navigate your shell to the root of the repository on your machine and run: - - ``` - docker run --env DISABLE_AUTH=true \ - --publish 8787:8787 \ - --volume $(pwd):/home/rstudio/Documents - subugoe/hoad:refactor-as-pkg - ``` - - This will automatically download the build image from Docker Hub. - You can also rebuild it locally by running - - ``` - docker build --tag hoad . - ``` +This outlines how to propose a change to openairegraph. +For more detailed info about contributing to this, and other tidyverse packages, please see the +[**development contributing guide**](https://rstd.io/tidy-contrib). ## Fixing typos @@ -71,12 +16,9 @@ If you want to make a bigger change, it's a good idea to first file an issue and If you’ve found a bug, please file an issue that illustrates the bug with a minimal [reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed). - ### Pull request process -This requires kno - -* Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("subugoe/hoad", fork = TRUE)`. +* Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("subugoe/openairegraph", fork = TRUE)`. * Install all development dependences with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. @@ -93,14 +35,13 @@ This requires kno * New code should follow the tidyverse [style guide](https://style.tidyverse.org). You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR. -* We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/markdown.html), for documentation. +* We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation. * We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. Contributions with test cases included are easier to accept. - ## Code of Conduct -Please note that the hoad project is released with a +Please note that the openairegraph project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project you agree to abide by its terms. diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index ff751af..bc3df10 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -56,17 +56,6 @@ jobs: - name: Copy dependencies to working directory run: | cp --recursive --force /usr/local/lib/R/site-library/* deps/ - - name: Build and push docker image - uses: docker/build-push-action@v1 - with: - username: ${{ secrets.DOCKER_USERNAME }} - password: ${{ secrets.DOCKER_TOKEN }} - repository: subugoe/openairegraph - tag_with_sha: true - tag_with_ref: true - add_git_labels: true - tags: ${{ github.sha }} - push: ${{ github.event_name != 'pull_request' }} - name: Build pkgdown website run: pkgdown::build_site() shell: Rscript {0} diff --git a/DESCRIPTION b/DESCRIPTION index 75ddf5a..cfe78fe 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -37,7 +37,7 @@ Imports: progress (>= 1.2.2), base64enc (>= 0.1.3), methods (>= 3.6.3) -RoxygenNote: 7.1.0 +RoxygenNote: 7.1.1 Suggests: testthat (>= 2.1.0), future (>= 1.17.0),