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check-full.yaml
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---
# Github Actions workflow to check covidregionaldata
name: R-CMD-check
'on':
push:
branches:
- master
schedule:
- cron: '0 0 * * *'
pull_request:
branches:
- '*'
workflow_dispatch:
jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
fail-fast: true
matrix:
config:
- {os: macOS-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-20.04, r: 'release'}
- {os: ubuntu-20.04, r: 'oldrel'}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@v1
with:
r-version: ${{ matrix.config.r }}
- uses: r-lib/actions/setup-pandoc@v1
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
- name: Install system dependencies
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
while read -r cmd
do
eval sudo $cmd
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
sudo apt-get -y install libudunits2-dev libgdal-dev libqpdf-dev libcurl4-openssl-dev
shell: bash
- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0}
- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
- name: Check
env:
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_DONTTEST_EXAMPLES_: false
_R_CHECK_FORCE_SUGGESTS_: false
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
shell: Rscript {0}
- name: Show testthat output
if: always()
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Upload check results
if: failure()
uses: actions/upload-artifact@v2
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check
Lint:
runs-on: ubuntu-20.04
needs: [R-CMD-check]
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@v1
- uses: r-lib/actions/setup-pandoc@v1
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
- name: Install system dependencies
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
while read -r cmd
do
eval sudo $cmd
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
sudo apt-get -y install libudunits2-dev libgdal-dev libqpdf-dev libcurl4-openssl-dev
shell: bash
- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("lintr")
remotes::install_cran("sessioninfo")
remotes::install_local(".")
shell: Rscript {0}
- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
- name: Lint
run: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = lintr::line_length_linter(120)))
shell: Rscript {0}
test-coverage:
if: github.repository == 'epiforecasts/covidregionaldata'
runs-on: macOS-latest
needs: [R-CMD-check]
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@v1
- uses: r-lib/actions/setup-pandoc@v1
- name: Install system dependencies
run: |
brew install udunits harfbuzz fribidi
shell: bash
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
- name: Cache R packages
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: macOS-r-4.0-2-${{ hashFiles('.github/depends.Rds') }}
restore-keys: macOS-r-4.0-2-
- name: Install dependencies
run: |
install.packages(c("remotes"))
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("covr")
shell: Rscript {0}
- name: Test coverage
run: covr::codecov()
shell: Rscript {0}
pkgdown:
if: github.ref == 'refs/heads/master' && github.repository == 'epiforecasts/covidregionaldata'
runs-on: macOS-latest
needs: [R-CMD-check, Lint, test-coverage]
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@v1
- uses: r-lib/actions/setup-pandoc@v1
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
- name: Cache R packages
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: macOS-r-4.0-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: macOS-r-4.0-1-
- name: Install dependencies
run: |
install.packages(c("remotes", "pkgbuild"))
remotes::install_deps(dependencies = TRUE)
remotes::install_dev("pkgdown")
shell: Rscript {0}
- name: Install package
run: R CMD INSTALL .
- name: Deploy package
run: |
git config --local user.email "actions@github.com"
git config --local user.name "GitHub Actions"
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
shell: bash
push_to_registry:
if: github.ref == 'refs/heads/master' && github.repository == 'epiforecasts/covidregionaldata'
name: Push Docker image to GitHub Packages
runs-on: ubuntu-20.04
needs: [R-CMD-check, pkgdown, test-coverage]
steps:
- name: Check out the repo
uses: actions/checkout@v2
- name: Login to GitHub Packages
uses: docker/login-action@v1
with:
registry: docker.pkg.github.com
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Push to GitHub Packages
uses: docker/build-push-action@v2
with:
context: .
push: true
tags: docker.pkg.github.com/epiforecasts/covidregionaldata/covidregionaldata:latest