From 164886f50b068014d59b2106d2e8a6ae1e47f160 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Fri, 26 Aug 2022 23:25:37 +0200 Subject: [PATCH] new workflow files --- .github/workflows/check-pr.yaml | 78 +++++++++++++++++++++++++++++++++ .github/workflows/check.yaml | 4 +- .github/workflows/codecovr.yaml | 9 ++-- .github/workflows/lintr.yaml | 9 ++-- DESCRIPTION | 2 +- NEWS.md | 2 +- 6 files changed, 89 insertions(+), 15 deletions(-) create mode 100644 .github/workflows/check-pr.yaml diff --git a/.github/workflows/check-pr.yaml b/.github/workflows/check-pr.yaml new file mode 100644 index 00000000..0a51be69 --- /dev/null +++ b/.github/workflows/check-pr.yaml @@ -0,0 +1,78 @@ +# ==================================================================== # +# TITLE # +# Antimicrobial Resistance (AMR) Data Analysis for R # +# # +# SOURCE # +# https://github.com/msberends/AMR # +# # +# LICENCE # +# (c) 2018-2022 Berends MS, Luz CF et al. # +# Developed at the University of Groningen, the Netherlands, in # +# collaboration with non-profit organisations Certe Medical # +# Diagnostics & Advice, and University Medical Center Groningen. # +# # +# 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: '**' + +name: R-code-check-PR + +jobs: + R-code-check-PR: + 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: + - {os: macOS-latest, r: 'devel', allowfail: true} + - {os: macOS-latest, r: 'release', allowfail: false} + - {os: ubuntu-latest, r: 'devel', allowfail: true} + - {os: ubuntu-latest, r: 'release', allowfail: false} + - {os: windows-latest, r: 'devel', allowfail: true} + - {os: windows-latest, r: 'release', 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 diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 26380847..9d845e4e 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -48,6 +48,7 @@ jobs: config: # test all systems against all released versions of R >= 3.0, we support them all! - {os: macOS-latest, r: 'devel', allowfail: true} + - {os: macOS-latest, r: '4.2', allowfail: false} - {os: macOS-latest, r: '4.1', allowfail: false} - {os: macOS-latest, r: '4.0', allowfail: false} - {os: macOS-latest, r: '3.6', allowfail: false} @@ -63,6 +64,7 @@ jobs: - {os: ubuntu-22.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: ubuntu-22.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: windows-latest, r: 'devel', allowfail: true} + - {os: windows-latest, r: '4.2', allowfail: false} - {os: windows-latest, r: '4.1', allowfail: false} - {os: windows-latest, r: '4.0', allowfail: false} - {os: windows-latest, r: '3.6', allowfail: false} @@ -72,7 +74,7 @@ jobs: R_REPOSITORIES: "https://cran.rstudio.com" steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - uses: r-lib/actions/setup-r@v2 with: diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index 318ce55f..cf935069 100644 --- a/.github/workflows/codecovr.yaml +++ b/.github/workflows/codecovr.yaml @@ -25,12 +25,9 @@ on: push: - branches: - - development - - main + branches: '**' pull_request: - branches: - - main + branches: '**' name: code-coverage @@ -40,7 +37,7 @@ jobs: env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - uses: r-lib/actions/setup-r@v2 with: diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml index 365e473e..8f302eed 100644 --- a/.github/workflows/lintr.yaml +++ b/.github/workflows/lintr.yaml @@ -25,12 +25,9 @@ on: push: - branches: - - development - - main + branches: '**' pull_request: - branches: - - main + branches: '**' name: lintr @@ -40,7 +37,7 @@ jobs: env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - uses: r-lib/actions/setup-r@v2 diff --git a/DESCRIPTION b/DESCRIPTION index 501e2a1e..0bbcb928 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.1.9029 +Version: 1.8.1.9030 Date: 2022-08-26 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 0277c3a9..2d3ee2b3 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.1.9029 +# AMR 1.8.1.9030 ### New * EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.