Update codecov

.github/workflows/Test-coverage.yaml

@@ -1,6 +1,5 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2-branch/examples
+# 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, development]
@@ -10,26 +9,55 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
-    if: "!contains(github.event.commits[0].message, '[skip-ci]')"
     runs-on: ubuntu-latest
-
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - 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
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
-        run: covr::codecov(quiet = FALSE)
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

README.Rmd

@@ -22,8 +22,8 @@ knitr::opts_chunk$set(
 | Development | CI | License |
 |---|---|---|
 | [![Project Status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) | [![R-CMD-check](https://github.com/Allgeier-Lab/arrR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Allgeier-Lab/arrR/actions/workflows/R-CMD-check.yaml) | [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) |
-| [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) | [![codecov](https://codecov.io/gh/Allgeier-Lab/arrR/branch/development/graph/badge.svg?token=Jx7R1vWP3s)](https://codecov.io/gh/Allgeier-Lab/arrR) | [![DOI](https://img.shields.io/badge/DOI-10.1002/eap.2617-blue.svg)](https://doi.org/10.1002/eap.2617) |
-
+| [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) | [![Codecov test coverage](https://codecov.io/gh/Allgeier-Lab/arrR/graph/badge.svg)](https://app.codecov.io/gh/Allgeier-Lab/arrR) | [![DOI](https://img.shields.io/badge/DOI-10.1002/eap.2617-blue.svg)](https://doi.org/10.1002/eap.2617) |
+[![Codecov test coverage](https://codecov.io/gh/Allgeier-Lab/arrR/graph/badge.svg)](https://app.codecov.io/gh/Allgeier-Lab/arrR)
 <!-- badges: end -->
 
 The goal of **arrR** is to simulate seagrass primary production around artificial reefs (ARs). For a more detailed model description, please see `vignette("general-background")`. Please see `vignette("get-started")` for a short tutorial how to use **arrR**.

arrR.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 0b70d906-cc18-4208-be93-731836109db9
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

codecov.yml

@@ -4,12 +4,11 @@ coverage:
   status:
     project:
       default:
-        target: 80%
+        target: auto
         threshold: 1%
+        informational: true
     patch:
       default:
-        target: 80%
+        target: auto
         threshold: 1%
-
-ignore:
-  - "inst/include"
+        informational: true