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actions.yml
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on:
push:
branches-ignore:
- updateREADME
pull_request:
branches:
- master
workflow_dispatch: # Allow manual triggers
schedule:
- cron: '0 8 * * 4'
name: R-CMD-check
jobs:
## pre-job to determine if a job has been run for the same SHA (e.g. on a different branch)
gatekeeper:
runs-on: ubuntu-latest
outputs:
should_skip: ${{ steps.skip_check.outputs.should_skip }}
steps:
- id: skip_check
uses: fkirc/skip-duplicate-actions@master
with:
github_token: ${{ github.token }}
versions:
needs: gatekeeper
if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name != 'schedule' && (needs.gatekeeper.outputs.should_skip == 'false') && !contains(github.event.head_commit.message, 'worksave') && !contains(github.event.head_commit.message, 'skip-ci'))
runs-on: ubuntu-latest
outputs:
r: ${{ steps.setup.outputs.r }}
bioc: ${{ steps.setup.outputs.bioc }}
dockerise: ${{ steps.setup.outputs.dockerise }}
docker_tag: ${{ steps.setup.outputs.docker_tag }}
steps:
- uses: rlespinasse/github-slug-action@v3.x
- uses: r-lib/actions/setup-r@v2
- name: Get R/Bioc versions
id: setup
run: |
BRANCH_NAME="${{ env.GITHUB_REF_SLUG }}"
## R and Bioc versions
Rscript -e "install.packages('BiocManager', Ncpus=2)"
r_devel=$(Rscript -e "vm=BiocManager:::.version_map(); cat(as.character(vm[vm\$BiocStatus == 'devel',]\$R))")
r_release=$(Rscript -e "vm=BiocManager:::.version_map(); cat(as.character(vm[vm\$BiocStatus == 'release',]\$R))")
if [[ $BRANCH_NAME =~ "release_" ]]
then
bioc="latest"
r="$r_release"
else
bioc="devel"
r="$r_devel"
fi
echo "r=$r" >> $GITHUB_OUTPUT
echo "bioc=$bioc" >> $GITHUB_OUTPUT
## Docker
# Only Dockerise for 'master' or 'RELEASE_*' branches
dockerise='false'
[[ github.event_name != 'schedule' && ($BRANCH_NAME == "master" || $BRANCH_NAME =~ "release_") ]] && dockerise='true'
echo "dockerise=$dockerise" >> $GITHUB_OUTPUT
# Docker tag is 'github' for master and the branch name for release branches
docker_tag="github"
[[ $BRANCH_NAME =~ "release_" ]] && docker_tag=$BRANCH_NAME
echo "docker_tag=$docker_tag" >> $GITHUB_OUTPUT
R-CMD-check:
needs: [gatekeeper, versions]
## run scheduled jobs only on main repo - do not run a duplicate job for merges etc. Do not run if commit messages include any of 'worksave' or 'skip-ci'
if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name != 'schedule' && (needs.gatekeeper.outputs.should_skip == 'false') && !contains(github.event.head_commit.message, 'worksave') && !contains(github.event.head_commit.message, 'skip-ci'))
runs-on: ${{ matrix.config.os }}
container: ${{ matrix.config.image }}
name: ${{ matrix.config.os }} (r_${{ matrix.config.r }} - bioc_${{ matrix.config.bioc }} - image_${{ matrix.config.image }})
strategy:
fail-fast: false
matrix:
config:
- { os: windows-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'}
- { os: macOS-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'}
- { os: ubuntu-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}', image: 'bioconductor/bioconductor_docker:${{ needs.versions.outputs.bioc }}'}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
CRAN: ${{ matrix.config.cran }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- name: Check out repo ⬇️
uses: actions/checkout@v2
- name: Set up R ▶️
uses: r-lib/actions/setup-r@v2
if: matrix.config.image == null
with:
r-version: ${{ matrix.config.r }}
- name: Create slug/short variables
uses: rlespinasse/github-slug-action@v3.x
- name: Install remotes 🔭
run: |
install.packages('remotes', Ncpus=2)
shell: Rscript {0}
- name: Set BiocManager version 📆
if: matrix.config.image == null
run: |
install.packages('BiocManager', Ncpus=2)
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, Ncpus=2)
shell: Rscript {0}
- name: Query dependencies ❓
run: |
saveRDS(remotes::dev_package_deps(dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2)
shell: Rscript {0}
- name: Cache R packages 💾
if: runner.os != 'Windows' && matrix.config.image == null
uses: actions/cache@v1
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}
restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-
- name: Install system and package dependencies using github action 🔧
uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-repositories: 'https://cloud.r-project.org'
- name: Install extra dependencies for macOS
if: runner.os == 'macOS'
run: |
brew install --cask xquartz
brew install gcc
- name: Install extra dependencies for linux
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
sudo apt-get update
sudo apt-get install -y pandoc-citeproc
sudo apt-get install -y qpdf
- name: Install R dependencies 🔨
run: |
options(repos = c(CRAN = "https://cran.r-project.org"))
remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories(), Ncpus=2)
remotes::install_cran("rcmdcheck", Ncpus=2)
remotes::install_cran("covr", Ncpus=2)
shell: Rscript {0}
- name: Session info 🖥️
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
# runs rmdcheck, first runs 'devtools::install to make sure there is a copy of mixOmics the parallel workers can access'
- name: Check ✅
if: (!contains(github.event.head_commit.message, 'skip-check'))
run: |
remotes::install_cran("devtools", Ncpus=2)
devtools::install()
devtools::check(args = c("--no-manual"), error_on = "warning", check_dir = "check")
shell: Rscript {0}
- name: Check --as-cran ✅ ✅
if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
env:
_R_CHECK_CRAN_INCOMING_: false
run: |
options(devtools.check.dir = "check/asCRAN", devtools.check.warning = "never")
devtools::check(args = c("--no-manual", "--as-cran", "--ignore-vignettes", "--run-dontrun"), build_args = c("--no-build-vignettes"))
shell: Rscript {0}
- name: BiocCheck 🧬 ✅
if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
run: |
BiocManager::install("BiocCheck", Ncpus=2)
BiocCheck::BiocCheck(".")
shell: Rscript {0}
- name: Upload check results ⬆️
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check
- name: Show testthat output 📖
if: always()
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Push to DockerHub 📦
if: runner.os == 'Linux' && needs.versions.outputs.dockerise == 'true' && !contains(github.event.head_commit.message, 'skip-docker')
uses: docker/build-push-action@v1
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_PASSWORD }}
repository: mixomicsteam/mixomics
tags: ${{ needs.versions.outputs.docker_tag }}
build_args: BIOC_VERSION=${{ needs.versions.outputs.bioc }}
- name: Test coverage 🔍
if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
# the commands between 'set +e' and 'set -e' are run without throwing any error
run: |
set +e
Rscript -e "covr::codecov(type = c('tests', 'examples'))"
set -e
# - name: Notify Slack 📣
# uses: 8398a7/action-slack@v3
# with:
# status: ${{ job.status }}
# fields: repo,message,commit,author,action,eventName,ref,workflow,job,took # selectable (default: repo,message)
# env:
# SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} # set in rep's setting >> secrets