diff --git a/.Rbuildignore b/.Rbuildignore index 6ce84b8..9b29466 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -38,3 +38,5 @@ R/TAGS ^data-raw$ ^doc$ ^Meta$ +^codecov\.yml$ +^\.github$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..fb4fc50 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,107 @@ +# NOTE: This workflow is overkill for most R packages +# check-standard.yaml is likely a better choice +# usethis::use_github_action("check-standard") will install it. +# +# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. +# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions +on: + push: + branches: + - main + - master + pull_request: + branches: + - main + - master + +name: R-CMD-check + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macOS-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: windows-latest, r: '3.6'} + - {os: ubuntu-18.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" } + - {os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} + - {os: ubuntu-18.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} + - {os: ubuntu-18.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} + - {os: ubuntu-18.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} + - {os: ubuntu-18.04, r: '3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} + + env: + RSPM: ${{ matrix.config.rspm }} + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-r@v1 + id: install-r + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + + - uses: r-lib/actions/setup-pandoc@v1 + + - name: Install pak and query dependencies + run: | + install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/") + saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds") + shell: Rscript {0} + + - name: Restore R package cache + uses: actions/cache@v2 + with: + path: | + ${{ env.R_LIBS_USER }}/* + !${{ env.R_LIBS_USER }}/pak + key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }} + restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1- + + - name: Install system dependencies + if: runner.os == 'Linux' + run: | + pak::local_system_requirements(execute = TRUE) + pak::pkg_system_requirements("rcmdcheck", execute = TRUE) + shell: Rscript {0} + + - name: Install dependencies + run: | + pak::local_install_dev_deps(upgrade = TRUE) + pak::pkg_install("rcmdcheck") + shell: Rscript {0} + + - name: Session info + run: | + options(width = 100) + pkgs <- installed.packages()[, "Package"] + sessioninfo::session_info(pkgs, include_base = TRUE) + shell: Rscript {0} + + - name: Check + env: + _R_CHECK_CRAN_INCOMING_: false + run: | + options(crayon.enabled = TRUE) + rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") + shell: Rscript {0} + + - name: Show testthat output + if: always() + run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload check results + if: failure() + uses: actions/upload-artifact@main + with: + name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results + path: check diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100644 index 0000000..ba1f94f --- /dev/null +++ b/.github/workflows/test-coverage.yaml @@ -0,0 +1,48 @@ +on: + push: + branches: + - main + - master + pull_request: + branches: + - main + - master + +name: test-coverage + +jobs: + test-coverage: + runs-on: macOS-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-r@v1 + + - uses: r-lib/actions/setup-pandoc@v1 + + - name: Query dependencies + run: | + install.packages('remotes') + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + shell: Rscript {0} + + - name: Restore R package cache + uses: actions/cache@v2 + with: + path: ${{ env.R_LIBS_USER }} + key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + + - name: Install dependencies + run: | + install.packages(c("remotes")) + remotes::install_deps(dependencies = TRUE) + remotes::install_cran("covr") + shell: Rscript {0} + + - name: Test coverage + run: covr::codecov() + shell: Rscript {0} diff --git a/DESCRIPTION b/DESCRIPTION index 2ddb7fa..0fdaabe 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -33,7 +33,9 @@ Suggests: ggplot2, knitr, rmarkdown, - SPREDA + SPREDA, + testthat (>= 3.0.0), + covr VignetteBuilder: rmarkdown, knitr @@ -43,3 +45,4 @@ License: GPL (>=3) Encoding: UTF-8 LazyData: true RoxygenNote: 7.1.1 +Config/testthat/edition: 3 diff --git a/README.md b/README.md index 6d9b6a1..15a9f23 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,11 @@ ciTools: An **R** Package for Quick Uncertainty Intervals ========================================================= + +[![R-CMD-check](https://github.com/jthaman/ciTools/workflows/R-CMD-check/badge.svg)](https://github.com/jthaman/ciTools/actions) +[![Codecov test coverage](https://codecov.io/gh/jthaman/ciTools/branch/master/graph/badge.svg)](https://codecov.io/gh/jthaman/ciTools?branch=master) + + ![](lmer.png) [As seen at RStudio::conf2018!](https://github.com/matthewravery/ciTools/blob/master/RStudio-conf-slides.pdf) diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..04c5585 --- /dev/null +++ b/codecov.yml @@ -0,0 +1,14 @@ +comment: false + +coverage: + status: + project: + default: + target: auto + threshold: 1% + informational: true + patch: + default: + target: auto + threshold: 1% + informational: true diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..c8053c0 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(ciTools) + +test_check("ciTools") diff --git a/tests/testthat/test-helper_functions.R b/tests/testthat/test-helper_functions.R new file mode 100644 index 0000000..a4a1450 --- /dev/null +++ b/tests/testthat/test-helper_functions.R @@ -0,0 +1,24 @@ +# from ?lm (reformatted a bit) +d_d9 <- + data.frame( + weight=c(c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14), + c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)), + group=gl(2, 10, 20, labels = c("Ctl","Trt")) + ) +test_lm_model <- lm(weight ~ group, data=d_d9) + +test_that("add_predictions2", { + expect_equal( + add_predictions2(data=d_d9, model=test_lm_model)$pred, + unname(predict(test_lm_model)) + ) + expect_equal( + add_predictions2(data=d_d9, model=test_lm_model, var="newpred")$newpred, + unname(predict(test_lm_model)), + info="var is respected" + ) + expect_s3_class( + add_predictions2(data=d_d9, model=test_lm_model, var="newpred"), + "data.frame" + ) +})