Github Actions rcmdcheck and codecov

.Rbuildignore

@@ -34,3 +34,4 @@ results/
 cran-comments.md
 ^doc$
 ^Meta$
+^\.github$

.github/.gitignore

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

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,52 @@
+# 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, dev]
+  pull_request:
+    branches: [main, master, dev]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+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: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,63 @@
+# 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, dev]
+  pull_request:
+    branches: [main, master, dev]
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - 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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          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

@@ -17,6 +17,11 @@ knitr::opts_chunk$set(
 # plantR
 <img src="https://raw.githubusercontent.com/liibre/plantR_logo/master/figs/plantR_logo.png?token=AA4OYDE3TMIXBWRYVMNCINC72PIUY" align="right" alt="" width="120" />
 
+<!-- badges: start -->
+[![R-CMD-check: master](https://github.com/LimaRAF/plantR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/LimaRAF/plantR/actions/workflows/R-CMD-check.yaml)
+[![R-CMD-check: dev](https://github.com/LimaRAF/plantR/actions/workflows/R-CMD-check.yaml/badge.svg?branch=dev)](https://github.com/LimaRAF/plantR/actions/workflows/R-CMD-check.yaml?branch=dev)
+[![Codecov test coverage](https://codecov.io/gh/LimaRAF/plantR/graph/badge.svg)](https://app.codecov.io/gh/LimaRAF/plantR)
+<!-- badges: end -->
 
 An R Package for Managing Species Records from Biological Collections
 
@@ -29,7 +34,7 @@ species occurrences from biological collections.
 
 Please read the package [Introduction](https://github.com/LimaRAF/plantR/blob/dev/vignettes/plantR.pdf)
 and detailed [Tutorial](https://github.com/LimaRAF/plantR/blob/dev/vignettes/articles/plantR_tutorial.pdf) for more details.
- 
+
 #### Installation
 
 The package can be installed in R from [github](https://github.com/) with: