Update R/dbetabinom.R #33
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--- | ||
name: Coverage π | ||
on: | ||
push: | ||
branches: | ||
- main | ||
- pre-release | ||
pull_request: | ||
types: | ||
- opened | ||
- synchronize | ||
- reopened | ||
- ready_for_review | ||
branches: | ||
- main | ||
- pre-release | ||
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 | ||
secrets: | ||
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 π | ||
runs-on: ubuntu-latest | ||
if: > | ||
!contains(github.event.commits[0].message, '[skip coverage]') | ||
&& github.event.pull_request.draft == false | ||
container: | ||
image: ghcr.io/insightsengineering/rstudio_4.2.1_bioc_3.15:latest | ||
steps: | ||
- name: Get branch names πΏ | ||
id: branch-name | ||
uses: tj-actions/branch-names@v5 | ||
- name: Checkout repo π | ||
uses: actions/checkout@v3 | ||
with: | ||
ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
path: ${{ github.event.repository.name }} | ||
- name: Run Staged dependencies π¦ | ||
uses: insightsengineering/staged-dependencies-action@v1 | ||
with: | ||
run-system-dependencies: ${{ inputs.install-system-dependencies }} | ||
env: | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
SD_REPO_PATH: ${{ github.event.repository.name }} | ||
SD_ENABLE_CHECK: ${{ inputs.enable-staged-dependencies-check }} | ||
- name: Install R package π§ | ||
run: | | ||
setwd("${{ github.event.repository.name }}") | ||
if (file.exists("renv.lock")) renv::restore() | ||
install.packages(".", repos=NULL, type="source") | ||
shell: Rscript {0} | ||
- name: Install covr πͺ | ||
run: if (!require("covr")) install.packages("covr") | ||
shell: Rscript {0} | ||
- name: Run coverage π | ||
run: | | ||
oldwd <- getwd() | ||
setwd("${{ github.event.repository.name }}") | ||
if (file.exists("renv.lock")) { | ||
renv::restore() | ||
} | ||
setwd(oldwd) | ||
tryCatch( | ||
expr = { | ||
x <- covr::package_coverage( | ||
path="${{ github.event.repository.name }}", | ||
clean = FALSE, | ||
quiet = FALSE | ||
) | ||
print(x) | ||
covr::to_cobertura(x, filename = "coverage.xml") | ||
p <- 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 <- stringr::str_match(e, "\`(.*?)\`")[, 2] | ||
if (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 π | ||
id: check_coverage_reports | ||
uses: andstor/file-existence-action@v1 | ||
with: | ||
files: "coverage.xml, coverage.txt, coverage-report.html" | ||
- name: Post coverage report π | ||
if: steps.check_coverage_reports.outputs.files_exists == 'true' | ||
uses: insightsengineering/coverage-action@v1 | ||
with: | ||
path: coverage.xml | ||
threshold: 80 | ||
fail: false | ||
publish: ${{ inputs.publish-coverage-report }} | ||
- name: Upload report πΌ | ||
if: steps.check_coverage_reports.outputs.files_exists == 'true' | ||
uses: actions/upload-artifact@v2 | ||
with: | ||
name: coverage-report | ||
path: "coverage-report.html" | ||
covtracer: | ||
name: Covtracer π | ||
runs-on: ubuntu-latest | ||
if: > | ||
!contains(github.event.commits[0].message, '[skip coverage]') | ||
&& github.event.pull_request.draft == false | ||
&& contains(inputs.enable-covtracer, 'true') | ||
container: | ||
image: ghcr.io/insightsengineering/rstudio_4.2.1_bioc_3.15:latest | ||
steps: | ||
- name: Get branch names πΏ | ||
id: branch-name | ||
uses: tj-actions/branch-names@v5 | ||
- name: Checkout repo π | ||
uses: actions/checkout@v2 | ||
with: | ||
ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
path: ${{ github.event.repository.name }} | ||
- name: Run Staged dependencies π¦ | ||
uses: insightsengineering/staged-dependencies-action@v1 | ||
with: | ||
run-system-dependencies: ${{ inputs.install-system-dependencies }} | ||
env: | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
SD_REPO_PATH: ${{ github.event.repository.name }} | ||
SD_ENABLE_CHECK: ${{ inputs.enable-staged-dependencies-check }} | ||
- name: Run Covtracer π | ||
uses: insightsengineering/covtracer-action@v1 | ||
env: | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
with: | ||
path: ${{ github.event.repository.name }} | ||
allow-failure: ${{ inputs.allow-failure }} |