No R version get for all jobs #481
Workflow file for this run
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on: | |
workflow_dispatch: | |
workflow_call: | |
inputs: | |
r-version: | |
description: 'The version of R to use' | |
default: '4.1' | |
required: false | |
type: string | |
skip-coverage-badges: | |
description: 'Skip code coverage badge creation' | |
default: false | |
required: false | |
type: boolean | |
push: | |
branches: | |
- main | |
- devel | |
- pre-release | |
pull_request: | |
branches: | |
- main | |
- devel | |
- pre-release | |
name: Code Coverage | |
concurrency: | |
group: coverage-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
jobs: | |
coverage: | |
name: Test Coverage | |
runs-on: ubuntu-latest | |
container: | |
image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest" | |
if: > | |
!contains(github.event.commits[0].message, '[skip coverage]') | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
outputs: | |
coverage-percent: ${{ steps.set-coverage-percentage.outputs.coverage-percentage }} | |
steps: | |
##################### BEGIN boilerplate steps ##################### | |
- name: Get branch names | |
id: branch-name | |
uses: tj-actions/[email protected] | |
- name: Checkout repo (PR) 🛎 | |
uses: actions/checkout@v3 | |
if: github.event_name == 'pull_request' | |
with: | |
ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
repository: ${{ github.event.pull_request.head.repo.full_name }} | |
- name: Checkout repository | |
uses: actions/checkout@v3 | |
if: github.event_name != 'pull_request' | |
with: | |
ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
- name: Normalize inputs | |
id: normalizer | |
run: | | |
R_VERSION="${{ inputs.r-version }}" | |
if [ "$R_VERSION" == "" ] | |
then { | |
R_VERSION="4.1" | |
} | |
fi | |
echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | |
shell: bash | |
- name: Restore cache | |
uses: actions/cache@v3 | |
with: | |
path: | | |
~/.staged.dependencies | |
key: staged-deps | |
- name: Setup Pandoc | |
uses: r-lib/actions/setup-pandoc@v2 | |
- name: Run Staged dependencies | |
uses: insightsengineering/staged-dependencies-action@v1 | |
with: | |
run-system-dependencies: false | |
renv-restore: false | |
enable-check: false | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
##################### END boilerplate steps ##################### | |
- name: Run coverage 👟 | |
run: | | |
tryCatch( | |
expr = { | |
x <- covr::package_coverage( | |
path=".", | |
clean = FALSE, | |
quiet = FALSE | |
) | |
print(x) | |
covr::to_cobertura(x, filename = "coverage.xml") | |
p <- round(covr::percent_coverage(x)) | |
cat(p, file = "coverage.txt", sep = "") | |
covr::report( | |
x, | |
file = "coverage-report.html", | |
browse = FALSE | |
) | |
}, | |
error = function(e) { | |
message("Errors generated during coverage analysis:") | |
print(e) | |
error_file <- list.files(path = "/tmp", pattern="*.fail$", recursive = T, full.names = T)[1] | |
if (length(error_file) && file.exists(error_file)) { | |
cat("__________FULL OUTPUT__________") | |
writeLines(readLines(error_file)) | |
} | |
}, | |
warning = function(w) { | |
message("Warnings generated during coverage analysis:") | |
print(w) | |
} | |
) | |
shell: Rscript {0} | |
- name: Check whether coverage reports exists | |
id: check_coverage_reports | |
uses: andstor/file-existence-action@v1 | |
with: | |
files: "coverage.xml, coverage.txt, coverage-report.html" | |
- name: Set coverage percentage as output | |
id: set-coverage-percentage | |
run: echo "coverage-percentage=$(cat coverage.txt)" >> $GITHUB_OUTPUT | |
if: steps.check_coverage_reports.outputs.files_exists == 'true' | |
- name: Generate Coverage Summary Report | |
if: steps.check_coverage_reports.outputs.files_exists == 'true' && github.event_name == 'pull_request' | |
uses: irongut/[email protected] | |
with: | |
filename: coverage.xml | |
badge: true | |
fail_below_min: false | |
format: markdown | |
hide_branch_rate: true | |
hide_complexity: true | |
indicators: true | |
output: both | |
thresholds: '60 80' | |
- name: Upload report for review | |
if: steps.check_coverage_reports.outputs.files_exists == 'true' && github.event_name == 'pull_request' | |
uses: actions/upload-artifact@v2 | |
with: | |
name: coverage-report | |
path: "coverage-report.html" | |
continue-on-error: true | |
- name: Add Coverage PR Comment | |
if: steps.check_coverage_reports.outputs.files_exists == 'true' && github.event_name == 'pull_request' | |
uses: marocchino/sticky-pull-request-comment@v2 | |
with: | |
header: code-coverage | |
path: code-coverage-results.md | |
continue-on-error: true | |
badge: | |
name: Generate badge for coverage | |
needs: [coverage] | |
runs-on: ubuntu-20.04 | |
if: > | |
inputs.skip-coverage-badges != 'true' || | |
!contains(github.event.commits[0].message, '[skip coverage]') | |
steps: | |
- name: Checkout the badges branch in repo | |
uses: actions/checkout@v3 | |
with: | |
ref: badges | |
path: badges | |
# Use the output from the `coverage` step | |
- name: Generate the badge SVG image | |
uses: emibcn/badge-action@v1 | |
id: badge | |
with: | |
label: 'Test Coverage' | |
status: "${{ needs.coverage.outputs.coverage-percent }}%" | |
color: ${{ | |
needs.coverage.outputs.coverage-percent > 90 && 'green' || | |
needs.coverage.outputs.coverage-percent > 80 && 'yellow,green' || | |
needs.coverage.outputs.coverage-percent > 70 && 'yellow' || | |
needs.coverage.outputs.coverage-percent > 60 && 'orange,yellow' || | |
needs.coverage.outputs.coverage-percent > 50 && 'orange' || | |
needs.coverage.outputs.coverage-percent > 40 && 'red,orange' || | |
needs.coverage.outputs.coverage-percent > 30 && 'red,red,orange' || | |
needs.coverage.outputs.coverage-percent > 20 && 'red,red,red,orange' || | |
'red' }} | |
path: badges/test-coverage.svg | |
- name: Commit badge | |
working-directory: ./badges | |
run: | | |
git config --local user.email "[email protected]" | |
git config --local user.name "GitHub Actions" | |
BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}} | |
mkdir -p "${BRANCH}" | |
mv test-coverage.svg "${BRANCH}" | |
git add "${BRANCH}/test-coverage.svg" | |
git commit -m "Add/Update badge" || true | |
- name: Push badges | |
uses: ad-m/github-push-action@master | |
with: | |
github_token: ${{ secrets.GITHUB_TOKEN }} | |
branch: badges | |
directory: badges | |
continue-on-error: true |