Update GitHub Actions

crp2a · Sep 18, 2024 · 78b72a6 · 78b72a6
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diff --git a/.github/workflows/GitHub_Actions_CI.yaml → .github/workflows/R-CMD-check.yaml b/.github/workflows/GitHub_Actions_CI.yaml → .github/workflows/R-CMD-check.yaml
@@ -1,36 +1,46 @@
-# CI GitHub Action ... adapted from usethis::use_github_actions()
+# 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: [master]
-
+    branches: [main, master]
   pull_request:
-    branches: [master, new_feature]
+    branches: [main, master]
 
-name: GitHub Actions CI
+name: R-CMD-check.yaml
 
-## change if caches needs to be refreshed
-env:
-  cache-version: v4
+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: windows-latest, r: 'release', not_cran: 'true'}
-        - {os: macos-12, r: 'release', not_cran: 'true'}
-        - {os: ubuntu-latest,   r: 'devel', not_cran: 'true'}
-        - {os: ubuntu-latest,   r: 'release', not_cran: 'true'}
-        - {os: ubuntu-latest,   r: 'oldrel', not_cran: 'true'}
+          - {os: macos-12,   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:
-      _R_CHECK_FORCE_SUGGESTS_: true
       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
+
       - name: Install JAGS on macOS
         if: runner.os == 'macOS'
         run: brew install jags
@@ -48,30 +58,12 @@ jobs:
           curl --progress-bar -s -o 'C:\JAGS-4.3.1.exe' -L 'https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/JAGS-4.3.1.exe'
           C:\JAGS-4.3.1.exe /S
 
-      - 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
-            any::XML
-            any::covr
+          extra-packages: any::rcmdcheck
           needs: check
 
-
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-
-      - name: Test coverage
-        run: |
-          covr::codecov()
-        shell: Rscript {0}
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,61 @@
+# 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.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")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          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
diff --git a/README.Rmd b/README.Rmd
@@ -18,7 +18,7 @@ library(BayLum)
 # BayLum <img width=120px src="man/figures/logo_BayLum.png" align="right" />
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml/badge.svg)](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml)
+[![R-CMD-check](https://github.com/crp2a/BayLum/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/crp2a/BayLum/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/crp2a/BayLum/graph/badge.svg?token=cOdZr6imKX)](https://app.codecov.io/gh/crp2a/BayLum)
 
 [![r-universe](https://crp2a.r-universe.dev/badges/BayLum)](https://crp2a.r-universe.dev/BayLum)
@@ -41,32 +41,29 @@ print(cite, bibtex = FALSE)
 
 ## Installation
 
-To install the latest development builds directly from GitHub, run
+**You need to have [JAGS](https://mcmc-jags.sourceforge.io) installed on your computer.**
 
-```{r gh-installation, eval = FALSE}
-if(!require("devtools"))
-  install.packages("devtools")
-devtools::install_github("crp2a/BayLum@master")
-```
-
-To install a developer build other than 'master', replace the term 'master' in the codeline by the name
-of the wanted developer build. 
-
-**Please note that you need to have [JAGS](https://mcmc-jags.sourceforge.io) installed on your computer**
-
-## Note
+You can install the released version of **BayLum** from [CRAN](https://CRAN.R-project.org) with:
 
-**The package comes without any guarantee!**
+```{r cran-installation, eval=FALSE}
+install.packages("BayLum")
+```
 
-Please further note that this version is a development version and may change day by day. For stable branches please visit
-the package on [CRAN 'BayLum'](https://CRAN.R-project.org/package=BayLum ).
+And the development version from [GitHub](https://github.com/) with:
 
-## Funding
+```{r gh-installation, eval=FALSE}
+# install.packages("remotes")
+remotes::install_github("crp2a/BayLum")
+```
 
-The development of `'BayLum'` received a state financial support managed by the Agence Nationale de la Recherche (France) through the program *Investissements d'avenir* (ref. [ANR-10-LABX-52](https://lascarbx.labex.u-bordeaux.fr)) between 2015 and 2018.
+Please note that development versions may change day by day.
 
 ## License
 
 This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.
 
 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the [GNU General Public License](https://github.com/crp2a/BayLum/blob/master/LICENSE) for more details.
+
+## Acknowledgements
+
+The development of **BayLum** received a state financial support managed by the Agence Nationale de la Recherche (France) through the program *Investissements d'avenir* (ref. [ANR-10-LABX-52](https://lascarbx.labex.u-bordeaux.fr)) between 2015 and 2018.
diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml/badge.svg)](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml)
+[![R-CMD-check](https://github.com/crp2a/BayLum/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/crp2a/BayLum/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/crp2a/BayLum/graph/badge.svg?token=cOdZr6imKX)](https://app.codecov.io/gh/crp2a/BayLum)
 
 [![r-universe](https://crp2a.r-universe.dev/badges/BayLum)](https://crp2a.r-universe.dev/BayLum)
@@ -49,35 +49,24 @@ Optically Stimulated (OSL) **Lum**inescence Dating
 
 ## Installation
 
-To install the latest development builds directly from GitHub, run
+**You need to have [JAGS](https://mcmc-jags.sourceforge.io) installed on
+your computer.**
+
+You can install the released version of **BayLum** from
+[CRAN](https://CRAN.R-project.org) with:
 
 ``` r
-if(!require("devtools"))
-  install.packages("devtools")
-devtools::install_github("crp2a/BayLum@master")
+install.packages("BayLum")
 ```
 
-To install a developer build other than ‘master’, replace the term
-‘master’ in the codeline by the name of the wanted developer build.
-
-**Please note that you need to have
-[JAGS](https://mcmc-jags.sourceforge.io) installed on your computer**
-
-## Note
+And the development version from [GitHub](https://github.com/) with:
 
-**The package comes without any guarantee!**
-
-Please further note that this version is a development version and may
-change day by day. For stable branches please visit the package on [CRAN
-‘BayLum’](https://CRAN.R-project.org/package=BayLum).
+``` r
+# install.packages("remotes")
+remotes::install_github("crp2a/BayLum")
+```
 
-## Funding
-
-The development of `'BayLum'` received a state financial support managed
-by the Agence Nationale de la Recherche (France) through the program
-*Investissements d’avenir* (ref.
-[ANR-10-LABX-52](https://lascarbx.labex.u-bordeaux.fr)) between 2015 and
-2018.
+Please note that development versions may change day by day.
 
 ## License
 
@@ -92,3 +81,11 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the [GNU
 General Public
 License](https://github.com/crp2a/BayLum/blob/master/LICENSE) for more
 details.
+
+## Acknowledgements
+
+The development of **BayLum** received a state financial support managed
+by the Agence Nationale de la Recherche (France) through the program
+*Investissements d’avenir* (ref.
+[ANR-10-LABX-52](https://lascarbx.labex.u-bordeaux.fr)) between 2015 and
+2018.