Add initial testing framework along with automated testing and code coverage (fix #27)

.Rbuildignore

@@ -38,3 +38,5 @@ R/TAGS
 ^data-raw$
 ^doc$
 ^Meta$
+^codecov\.yml$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.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

.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}

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

README.md

@@ -1,6 +1,11 @@
 ciTools: An **R** Package for Quick Uncertainty Intervals
 =========================================================
 
+<!-- badges: start -->
+[![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)
+<!-- badges: end -->
+
 ![](lmer.png)
 
 [As seen at RStudio::conf2018!](https://github.com/matthewravery/ciTools/blob/master/RStudio-conf-slides.pdf)

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

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(ciTools)
+
+test_check("ciTools")

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"
+  )
+})