add code coverage workflow

.Rbuildignore

@@ -16,3 +16,4 @@
 ^cran-comments\.md$
 ^CRAN-RELEASE$
 ^\.github$
+^codecov\.yml$

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

README.Rmd

@@ -19,6 +19,7 @@ knitr::opts_chunk$set(
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/iglu)](https://cran.r-project.org/package=iglu)[![](https://cranlogs.r-pkg.org/badges/iglu)](https://CRAN.R-project.org/package=iglu)
 [![R-CMD-check](https://github.com/irinagain/iglu/workflows/R-CMD-check/badge.svg)](https://github.com/irinagain/iglu/actions)
 [![R-CMD-check](https://github.com/irinagain/iglu/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/irinagain/iglu/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/irinagain/iglu/branch/master/graph/badge.svg)](https://app.codecov.io/gh/irinagain/iglu?branch=master)
 <!-- badges: end -->
 
 iglu: Interpreting data from Continuous Glucose Monitors (CGMs)

README.md

@@ -7,6 +7,9 @@
 
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/iglu)](https://cran.r-project.org/package=iglu)[![](https://cranlogs.r-pkg.org/badges/iglu)](https://CRAN.R-project.org/package=iglu)
 [![R-CMD-check](https://github.com/irinagain/iglu/workflows/R-CMD-check/badge.svg)](https://github.com/irinagain/iglu/actions)
+[![R-CMD-check](https://github.com/irinagain/iglu/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/irinagain/iglu/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/irinagain/iglu/branch/master/graph/badge.svg)](https://app.codecov.io/gh/irinagain/iglu?branch=master)
 <!-- badges: end -->
 
 # iglu: Interpreting data from Continuous Glucose Monitors (CGMs)
@@ -20,18 +23,17 @@ the package, see [package website](https://irinagain.github.io/iglu/).
 
 To cite:
 
--   Broll S, Urbanek J, Buchanan D, Chun E, Muschelli J, Punjabi N and
-    Gaynanova I (2021). [Interpreting blood glucose data with R package
-    iglu.](https://doi.org/10.1371/journal.pone.0248560) *PLoS One*,
-    Vol. 16, No. 4, e0248560.
+- Broll S, Urbanek J, Buchanan D, Chun E, Muschelli J, Punjabi N and
+  Gaynanova I (2021). [Interpreting blood glucose data with R package
+  iglu.](https://doi.org/10.1371/journal.pone.0248560) *PLoS One*, Vol.
+  16, No. 4, e0248560.
 
--   Broll S, Buchanan D, Chun E, Muschelli J, Fernandes N, Seo J, Shih
-    J, Urbanek J, Schwenck J, Gaynanova I (2021). iglu: Interpreting
-    Glucose Data from Continuous Glucose Monitors. R package version
-    3.0.0.
+- Broll S, Buchanan D, Chun E, Muschelli J, Fernandes N, Seo J, Shih J,
+  Urbanek J, Schwenck J, Gaynanova I (2021). iglu: Interpreting Glucose
+  Data from Continuous Glucose Monitors. R package version 3.0.0.
 
-iglu comes with two example datasets: example_data_1\_subject and
-example_data_5\_subject. These data are collected using Dexcom G4 CGM on
+iglu comes with two example datasets: example_data_1_subject and
+example_data_5_subject. These data are collected using Dexcom G4 CGM on
 subjects with Type II diabetes. Each dataset follows the structure
 iglu’s functions are designed around. Note that the 1 subject data is a
 subset of the 5 subject data. See the examples below for loading and
@@ -54,8 +56,6 @@ devtools::install_github("irinagain/iglu", build_vignettes = TRUE)
 
 ``` r
 library(iglu)
-#> Warning in register(): Can't find generic `scale_type` in package ggplot2 to
-#> register S3 method.
 data(example_data_1_subject) # Load single subject data
 ## Plot data
 
@@ -66,6 +66,7 @@ plot_glu(example_data_1_subject)
 <img src="man/figures/README-unnamed-chunk-3-1.png" width="100%" />
 
 ``` r
+
 # Summary statistics and some metrics
 summary_glu(example_data_1_subject)
 #> # A tibble: 1 × 7
@@ -102,11 +103,13 @@ conga(example_data_1_subject)
 data(example_data_5_subject)
 
 plot_glu(example_data_5_subject, plottype = 'lasagna', datatype = 'average')
+#> Warning: Removed 5 rows containing missing values (`geom_tile()`).
 ```
 
 <img src="man/figures/README-unnamed-chunk-3-2.png" width="100%" />
 
 ``` r
+
 below_percent(example_data_5_subject, targets = c(80,170,260))
 #> # A tibble: 5 × 4
 #>   id        below_170 below_260 below_80

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