new setup unit tests

2026-03-16 02:47:52 +01:00 · 2023-01-05 15:03:18 +01:00
parent a98d0d75ea
commit 51c0f0814e
5 changed files with 32 additions and 27 deletions
--- a/.github/workflows/check-recent.yaml
+++ b/.github/workflows/check-recent.yaml
@@ -0,0 +1,106 @@
+# ==================================================================== #
+# TITLE                                                                #
+# AMR: An R Package for Working with Antimicrobial Resistance Data     #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# CITE AS                                                              #
+# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C    #
+# (2022). AMR: An R Package for Working with Antimicrobial Resistance  #
+# Data. Journal of Statistical Software, 104(3), 1-31.                 #
+# doi:10.18637/jss.v104.i03                                            #
+#                                                                      #
+# Developed at the University of Groningen and the University Medical  #
+# Center Groningen in The Netherlands, in collaboration with many      #
+# colleagues from around the world, see our website.                   # 
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
+# ==================================================================== #
+
+on:
+  pull_request:
+    # run in each PR in this repo
+    branches: '**'
+  push:
+    branches: '**'
+  schedule:
+    # run a schedule everyday at 1 AM.
+    # this is to check that all dependencies are still available (see R/zzz.R)
+    - cron:  '0 1 * * *'
+
+name: check-recent
+
+jobs:
+  R-code-check:
+    runs-on: ${{ matrix.config.os }}
+
+    continue-on-error: ${{ matrix.config.allowfail }}
+
+    name: ${{ matrix.config.os }} (R-${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          # current development version:
+          - {os: macOS-latest,   r: 'devel', allowfail: false}
+          - {os: windows-latest, r: 'devel', allowfail: false}
+          - {os: ubuntu-latest,  r: 'devel', allowfail: false}
+          # current 'release' version:
+          - {os: macOS-latest,   r: '4.2', allowfail: false}
+          - {os: windows-latest, r: '4.2', allowfail: false}
+          - {os: ubuntu-latest,  r: '4.2', allowfail: false}
+          # older versions:
+          - {os: macOS-latest,   r: '4.1', allowfail: false}
+          - {os: windows-latest, r: '4.1', allowfail: false}
+          - {os: ubuntu-latest,  r: '4.1', allowfail: false}
+          
+          - {os: macOS-latest,   r: '4.0', allowfail: false}
+          - {os: windows-latest, r: '4.0', allowfail: false}
+          - {os: ubuntu-latest,  r: '4.0', allowfail: false}
+          
+          - {os: macOS-latest,   r: '3.6', allowfail: false}
+          - {os: windows-latest, r: '3.6', allowfail: false}
+          - {os: ubuntu-latest,  r: '3.6', allowfail: false}
+          
+          - {os: macOS-latest,   r: '3.5', allowfail: false}
+          - {os: windows-latest, r: '3.5', allowfail: false}
+          - {os: ubuntu-latest,  r: '3.5', allowfail: false}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          # use RStudio Package Manager to quickly install packages
+          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
+        env:
+          _R_CHECK_LENGTH_1_CONDITION_: verbose
+          _R_CHECK_LENGTH_1_LOGIC2_: verbose
+          # during 'R CMD check', R_LIBS_USER will be overwritten, so:
+          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
+          R_RUN_TINYTEST: true