Spatiotemporal exposures and toxicology patch 2

.github/workflows/codecov.yaml

@@ -0,0 +1,53 @@
+name: R Package CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: 4.1  # You can change this to the R version you need
+
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libudunits2-dev libgdal-dev
+
+
+    - name: Install dependencies
+      run: |
+        R -e 'install.packages("remotes")'
+        R -e 'remotes::install_deps()'
+
+    - name: Install dependencies for covr and testthat
+      run: R -e 'install.packages(c("covr", "testthat"), dependencies = TRUE)'
+
+
+    - name: Run tests and calculate coverage
+      run: |
+        R -e 'library(covr); covr::package_coverage()'
+
+    - name: Upload coverage to Codecov
+      run: |
+        echo "CODECOV_TOKEN: $CODE_COV"
+        R -e 'library(covr); covr::codecov(token = Sys.getenv("CODE_COV"))'
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODE_COV }}
+
+
+
+    - name: Cleanup
+      run: |
+        R -e 'remove.packages("remotes")'