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test-coverage.yaml
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---
name: Coverage 📔
on:
push:
tags:
- "v*"
branches:
- main
pull_request:
types:
- opened
- synchronize
- reopened
- ready_for_review
branches:
- main
workflow_dispatch:
workflow_call:
inputs:
install-system-dependencies:
description: Check for and install system dependencies
required: false
default: false
type: boolean
enable-staged-dependencies-check:
description: Enable staged dependencies YAML check
required: false
default: false
type: boolean
publish-coverage-report:
description: Publish the coverage report as a pull request comment
required: false
default: true
type: boolean
allow-failure:
description: Allow workflow failure if errors from covtracer are generated
required: false
type: boolean
default: false
enable-covtracer:
description: Enable the covtracer job
required: false
type: boolean
default: false
additional-env-vars:
description: |
Extra environment variables, as a 'key=value' pair, with each pair on a new line.
Example usage:
additional-env-vars: |
ABC=123
XYZ=456
required: false
default: ""
type: string
sd-direction:
description: The direction to use to install staged dependencies. Choose between 'upstream', 'downstream' and 'all'
required: false
type: string
default: upstream
publish-coverage-report-gh-pages:
description: Publish HTML coverage report to GitHub pages alongside pkgdown docs.
required: false
type: boolean
default: true
latest-tag-alt-name:
description: |
The name of directory to store coverage report when running for latest tag.
The variable is named this way to keep it consistent with r-pkgdown-multiversion input name.
required: false
type: string
default: "latest-tag"
release-candidate-alt-name:
description: |
The name of directory to store coverage report when running for rc tag.
The variable is named this way to keep it consistent with r-pkgdown-multiversion input name.
required: false
type: string
default: "release-candidate"
package-subdirectory:
description: Subdirectory in the repository, where the R package is located.
required: false
type: string
default: ""
secrets:
REPO_GITHUB_TOKEN:
description: |
Github token with read access to repositories, required
for staged.dependencies installation
required: false
concurrency:
group: coverage-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
coverage:
name: Coverage 📔
runs-on: ubuntu-latest
if: >
github.event.pull_request.draft == false
container:
image: ghcr.io/insightsengineering/rstudio:latest
outputs:
publish-coverage-html-report: ${{ steps.coverage-output.outputs.coverage-upload }}
current-branch-or-tag: ${{ steps.current-branch-or-tag.outputs.ref-name }}
is-latest-tag: ${{ steps.current-branch-or-tag.outputs.is-latest-tag }}
is-rc-tag: ${{ steps.current-branch-or-tag.outputs.is-rc-tag }}
multiversion-docs: ${{ steps.current-branch-or-tag.outputs.multiversion-docs }}
steps:
- name: Setup token 🔑
id: github-token
run: |
if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then
echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN."
echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
else
echo "Using REPO_GITHUB_TOKEN."
echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
fi
shell: bash
- name: Get branch names 🌿
id: branch-name
uses: tj-actions/branch-names@v7
- name: Checkout gh-pages 🛎
if: >-
github.event_name != 'pull_request'
&& inputs.publish-coverage-report-gh-pages == true
id: checkout-gh-pages
uses: actions/checkout@v4
with:
ref: gh-pages
path: gh-pages
repository: ${{ github.event.pull_request.head.repo.full_name }}
- name: Get current branch or tag 🏷️
if: >-
github.event_name != 'pull_request'
&& inputs.publish-coverage-report-gh-pages == true
id: current-branch-or-tag
run: |
if [ "${{ steps.branch-name.outputs.is_tag }}" == "true" ]; then
echo "Current tag: ${{ steps.branch-name.outputs.tag }}"
echo "ref-name=${{ steps.branch-name.outputs.tag }}" >> $GITHUB_OUTPUT
current_tag="${{ steps.branch-name.outputs.tag }}"
if [ "$(echo "$current_tag" | grep -E "^v([0-9]+\.)?([0-9]+\.)?([0-9]+)$")" != "" ]; then
echo "Running for latest-tag."
echo "is-latest-tag=true" >> $GITHUB_OUTPUT
elif [ "$(echo "$current_tag" | grep -E "^v([0-9]+\.)?([0-9]+\.)?([0-9]+)(-rc[0-9]+)$")" != "" ]; then
echo "Running for rc-tag."
echo "is-rc-tag=true" >> $GITHUB_OUTPUT
fi
else
echo "Current branch: ${{ steps.branch-name.outputs.current_branch }}"
echo "ref-name=${{ steps.branch-name.outputs.current_branch }}" >> $GITHUB_OUTPUT
fi
# Check if pkgdown multiversion docs are used at all.
if [ $(grep -rl '<!-- start dropdown for versions -->' gh-pages | wc -l) -gt 0 ]; then
echo "multiversion-docs=true" >> $GITHUB_OUTPUT
else
echo "multiversion-docs=false" >> $GITHUB_OUTPUT
fi
shell: bash
- name: Checkout repo (PR) 🛎
uses: actions/checkout@v4
if: github.event_name == 'pull_request'
with:
ref: ${{ steps.branch-name.outputs.head_ref_branch }}
path: ${{ github.event.repository.name }}
repository: ${{ github.event.pull_request.head.repo.full_name }}
- name: Checkout repo 🛎
uses: actions/checkout@v4
if: github.event_name != 'pull_request'
with:
ref: ${{ steps.branch-name.outputs.head_ref_branch }}
path: ${{ github.event.repository.name }}
- name: Check commit message 💬
run: |
git config --global --add safe.directory $(pwd)
export head_commit_message="$(git show -s --format=%B | tr '\r\n' ' ' | tr '\n' ' ')"
echo "head_commit_message = $head_commit_message"
if [[ $head_commit_message == *"$SKIP_INSTRUCTION"* ]]; then
echo "Skip instruction detected - cancelling the workflow."
curl -s -LJ -o gh.tar.gz https://github.com/cli/cli/releases/download/v${GH_CLI_VERSION}/gh_${GH_CLI_VERSION}_linux_amd64.tar.gz
tar -xzf gh.tar.gz --strip-components 2
./gh version
./gh run cancel ${{ github.run_id }}
./gh run watch ${{ github.run_id }}
fi
shell: bash
env:
GH_TOKEN: ${{ steps.github-token.outputs.token }}
GH_CLI_VERSION: 2.44.1
SKIP_INSTRUCTION: "[skip coverage]"
- name: Normalize inputs ⊳
id: normalizer
shell: bash
run: |
echo "publish-coverage-report=${{ inputs.publish-coverage-report }}" >> $GITHUB_OUTPUT
if [ "${{ inputs.publish-coverage-report }}" == "" ]
then {
echo "publish-coverage-report=true" >> $GITHUB_OUTPUT
}
fi
- name: Restore SD cache 💰
uses: actions/cache@v4
with:
key: sd-${{ runner.os }}-${{ github.event.repository.name }}
path: ~/.staged.dependencies
- name: Run Staged dependencies 🎦
uses: insightsengineering/staged-dependencies-action@v1
env:
GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }}
with:
path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
enable-check: ${{ inputs.enable-staged-dependencies-check }}
run-system-dependencies: ${{ inputs.install-system-dependencies }}
direction: ${{ inputs.sd-direction }}
- name: Install R package 🚧
run: |
if (file.exists("renv.lock")) renv::restore()
install.packages(".", repos=NULL, type="source")
shell: Rscript {0}
working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
- name: Install covr 🎪
run: |
if (file.exists("renv.lock")) {
renv::restore()
if (!require("covr")) renv::install("covr")
}
if (!require("covr")) install.packages("covr")
shell: Rscript {0}
- name: Run coverage 👟
run: |
setwd("${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}")
if (file.exists("renv.lock")) {
renv::restore()
}
# Load extra env vars
extra_env_vars <- "${{ inputs.additional-env-vars }}"
if (extra_env_vars != "") {
writeLines(extra_env_vars, "/tmp/dotenv.env")
if (!require("dotenv")) install.packages("dotenv", repos = "https://cloud.r-project.org")
dotenv::load_dot_env("/tmp/dotenv.env")
}
tryCatch(
expr = {
x <- covr::package_coverage(
clean = FALSE,
quiet = FALSE
)
print(x)
covr::report(
x,
file = "coverage-report.html",
browse = FALSE
)
covr::to_cobertura(x, filename = "coverage.xml")
p <- covr::percent_coverage(x)
cat(p, file = "coverage.txt", sep = "")
},
error = function(e) {
message("Errors generated during coverage analysis:")
print(e)
error_file <- list.files(path = "/tmp", pattern="*.fail$", recursive = T, full.names = T)[1]
if (length(error_file) && file.exists(error_file)) {
cat("__________FULL OUTPUT__________")
writeLines(readLines(error_file))
}
}
)
covr_html <- "coverage-report.html"
if (!file.exists(covr_html)) writeLines(c("No coverage report."), covr_html)
shell: Rscript {0}
- name: Check whether coverage reports exists 💭
id: check_coverage_reports
uses: andstor/file-existence-action@v3
with:
files: >-
${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/coverage.xml,
${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/coverage.txt,
${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/coverage-report.html
- name: Post coverage report 🗞
if: steps.check_coverage_reports.outputs.files_exists == 'true'
uses: insightsengineering/coverage-action@v2
with:
path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/coverage.xml
threshold: 80
fail: false
publish: ${{ steps.normalizer.outputs.publish-coverage-report }}
diff: true
continue-on-error: true
- name: Upload report 🔼
uses: actions/upload-artifact@v4
with:
name: coverage-report
path: |
${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/coverage-report.html
${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/lib/
continue-on-error: true
- name: Set output ⚙️
id: coverage-output
if: >-
github.event_name != 'pull_request'
&& inputs.publish-coverage-report-gh-pages == true
run: echo "coverage-upload=true" >> $GITHUB_OUTPUT
covtracer:
name: Covtracer 🐄
runs-on: ubuntu-latest
if: >
github.event.pull_request.draft == false
&& contains(inputs.enable-covtracer, 'true')
container:
image: ghcr.io/insightsengineering/rstudio:latest
steps:
- name: Get branch names 🌿
id: branch-name
uses: tj-actions/branch-names@v7
- name: Checkout repo (PR) 🛎
uses: actions/checkout@v4
if: github.event_name == 'pull_request'
with:
ref: ${{ steps.branch-name.outputs.head_ref_branch }}
path: ${{ github.event.repository.name }}
repository: ${{ github.event.pull_request.head.repo.full_name }}
- name: Checkout repo 🛎
uses: actions/checkout@v4
if: github.event_name != 'pull_request'
with:
ref: ${{ steps.branch-name.outputs.head_ref_branch }}
path: ${{ github.event.repository.name }}
- name: Check commit message 💬
run: |
git config --global --add safe.directory $(pwd)
export head_commit_message="$(git show -s --format=%B | tr '\r\n' ' ' | tr '\n' ' ')"
echo "head_commit_message = $head_commit_message"
if [[ $head_commit_message == *"$SKIP_INSTRUCTION"* ]]; then
echo "Skip instruction detected - cancelling the workflow."
curl -s -LJ -o gh.tar.gz https://github.com/cli/cli/releases/download/v${GH_CLI_VERSION}/gh_${GH_CLI_VERSION}_linux_amd64.tar.gz
tar -xzf gh.tar.gz --strip-components 2
./gh version
./gh run cancel ${{ github.run_id }}
./gh run watch ${{ github.run_id }}
fi
shell: bash
env:
GH_TOKEN: ${{ steps.github-token.outputs.token }}
GH_CLI_VERSION: 2.44.1
SKIP_INSTRUCTION: "[skip coverage]"
- name: Restore SD cache 💰
uses: actions/cache@v4
with:
key: sd-${{ runner.os }}-${{ github.event.repository.name }}
path: ~/.staged.dependencies
- name: Run Staged dependencies 🎦
uses: insightsengineering/staged-dependencies-action@v1
env:
GITHUB_PAT: ${{ steps.github-token.outputs.token }}
with:
path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
enable-check: ${{ inputs.enable-staged-dependencies-check }}
run-system-dependencies: ${{ inputs.install-system-dependencies }}
direction: ${{ inputs.sd-direction }}
- name: Run Covtracer 🐄
uses: insightsengineering/covtracer-action@v1
env:
GITHUB_PAT: ${{ steps.github-token.outputs.token }}
with:
path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
allow-failure: ${{ inputs.allow-failure }}
publish-coverage-report:
name: Publish coverage report 📰
runs-on: ubuntu-latest
needs: coverage
if: >
needs.coverage.outputs.publish-coverage-html-report == 'true'
&& github.event_name != 'pull_request'
# Only one job can publish to gh-pages branch concurrently.
concurrency:
group: ghpages
steps:
- name: Setup token 🔑
id: github-token
run: |
if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then
echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN."
echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
else
echo "Using REPO_GITHUB_TOKEN."
echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
fi
shell: bash
- name: Download coverage report as artifact ⤵️
uses: actions/download-artifact@v4
with:
name: coverage-report
path: coverage-report
- name: Rename report ⚙️
run: mv coverage-report/coverage-report.html coverage-report/index.html
- name: Upload coverage report to GitHub pages 🗞️
if: needs.coverage.outputs.multiversion-docs == 'true'
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ steps.github-token.outputs.token }}
publish_dir: ./coverage-report
destination_dir: ${{ needs.coverage.outputs.current-branch-or-tag }}/coverage-report
- name: Upload coverage report to GitHub pages (latest-tag) 🏷️
if: >
needs.coverage.outputs.is-latest-tag == 'true'
&& needs.coverage.outputs.multiversion-docs == 'true'
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ steps.github-token.outputs.token }}
publish_dir: ./coverage-report
destination_dir: ${{ inputs.latest-tag-alt-name }}/coverage-report
- name: Upload coverage report to GitHub pages (release-candidate) 🏷️
if: >
needs.coverage.outputs.is-rc-tag == 'true'
&& needs.coverage.outputs.multiversion-docs == 'true'
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ steps.github-token.outputs.token }}
publish_dir: ./coverage-report
destination_dir: ${{ inputs.release-candidate-alt-name }}/coverage-report
- name: Upload coverage report to GitHub pages (non-multiversion) 🗞️
if: needs.coverage.outputs.multiversion-docs == 'false'
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ steps.github-token.outputs.token }}
publish_dir: ./coverage-report
destination_dir: coverage-report