Coverage (#3)

* add linter to gh actions

* install before lint

* error on note, moved lint to check

* moved tibble, knitr to Suggests

* spellcheck

* removed blank line

* added spelling.R to lint exception

* coverage

* coverage on coverage branch

* finished codcov

Co-authored-by: bjoern <[email protected]>

.github/workflows/coverage.yaml

@@ -0,0 +1,46 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        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}

README.Rmd

@@ -18,6 +18,7 @@ knitr::opts_chunk$set(
 # simaerep <a href='https://openpharma.github.io/simaerep'><img src='man/figures/logo.png' align="right" height="139" /></a>
 <!-- badges: start -->
 [![R build status](https://github.com/openpharma/simaerep/workflows/R-CMD-check/badge.svg)](https://github.com/openpharma/simaerep/actions)
+[![codecov](https://codecov.io/gh/openpharma/simaerep/branch/master/graph/badge.svg)](https://codecov.io/gh/openpharma/simaerep)
 <!-- badges: end -->
 
 Simulate adverse event reporting in clinical trials with the goal of detecting under-reporting sites.

README.md

@@ -7,6 +7,7 @@
 
 [![R build
 status](https://github.com/openpharma/simaerep/workflows/R-CMD-check/badge.svg)](https://github.com/openpharma/simaerep/actions)
+[![codecov](https://codecov.io/gh/openpharma/simaerep/branch/master/graph/badge.svg)](https://codecov.io/gh/openpharma/simaerep)
 <!-- badges: end -->
 
 Simulate adverse event reporting in clinical trials with the goal of