Update propagate.yml to point to main branch only #488
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 | |
push-templates-data: | |
description: 'Push generated templates data to pharmaverseadam repo' | |
default: false | |
required: false | |
type: boolean | |
exclude-templates-data: | |
description: 'List of data generated by templates to exclude (templates script will run, but results will not be push to pharmaverseadam repo) - comma seperated list' | |
default: '' | |
required: false | |
type: string | |
push: | |
branches: | |
- main | |
- devel | |
- pre-release | |
pull_request: | |
branches: | |
- main | |
- devel | |
- pre-release | |
env: | |
# branch name for PR | |
source-branch: update_templates_data | |
repo: pharmaverseadam | |
target-branch: main | |
reviewers: > | |
{ | |
"admiralonco": { | |
"reviewers": ["bundfussr", "manciniedoardo"] | |
}, | |
"admiralophtha": { | |
"reviewers": ["manciniedoardo"] | |
}, | |
"admiral": { | |
"reviewers": ["manciniedoardo", "bms63"] | |
}, | |
"admiralvaccine": { | |
"reviewers": ["ahasoplakus", "arjoon-r", "manciniedoardo"] | |
} | |
} | |
# data folder name for templates | |
templates_data_folder: ./data/ | |
name: Check Templates | |
concurrency: | |
group: templates-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
jobs: | |
get_r_version: | |
name: Get R version | |
runs-on: ubuntu-latest | |
if: > | |
!contains(github.event.commits[0].message, '[skip check_templates]') | |
outputs: | |
r-version: ${{ steps.normalizer.outputs.R_VERSION }} | |
steps: | |
- name: Normalize inputs | |
id: normalizer | |
run: | | |
R_VERSION="${{ inputs.r-version }}" | |
if [ "$R_VERSION" == "" ] | |
then { | |
R_VERSION="4.1" | |
} | |
fi | |
echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | |
shell: bash | |
check_templates: | |
name: Verify | |
if: > | |
!contains(github.event.commits[0].message, '[skip check_templates]') | |
runs-on: ubuntu-latest | |
container: | |
image: "ghcr.io/pharmaverse/admiralci-${{needs.get_r_version.outputs.r-version}}:latest" | |
needs: get_r_version | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
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: ${{ steps.branch-name.outputs.head_ref_branch }} | |
fetch-depth: 0 | |
- name: Add safe directory | |
run: | | |
git config --global --add safe.directory "${GITHUB_WORKSPACE}" # open issue: git dubious ownership running in docker container context: https://github.com/actions/runner/issues/2033 | |
shell: bash | |
- name: Normalize inputs | |
id: normalizer | |
run: | | |
function remove_substring() { | |
echo "${1//$2}" | |
} | |
BRANCH=${{ steps.branch-name.outputs.head_ref_branch }} | |
if [ "${BRANCH}" == "" ] | |
then { | |
BRANCH=$(git name-rev HEAD | awk '{print $NF}') | |
} | |
fi | |
if [[ $BRANCH == remotes/pull/* ]] | |
then { | |
PR=$(remove_substring "$BRANCH" "/merge") | |
PR=$(remove_substring "$PR" "remotes/") | |
PR=$(echo $PR | sed 's/pull/pulls/') | |
echo "Accessing repos/${GITHUB_REPOSITORY}/${PR}" | |
BRANCH=$(gh api -X GET repos/${GITHUB_REPOSITORY}/${PR} | jq -r '.head.ref') | |
} | |
fi | |
echo "BRANCH is $BRANCH" | |
R_VERSION="${{ inputs.r-version }}" | |
if [ "$R_VERSION" == "" ] | |
then { | |
R_VERSION="4.1" | |
} | |
fi | |
echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | |
echo "SD_GIT_REF=$BRANCH" >> $GITHUB_OUTPUT | |
shell: bash | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
- name: Restore cache | |
uses: actions/cache@v3 | |
with: | |
path: | | |
~/.staged.dependencies | |
key: staged-deps | |
restore-keys: staged-deps | |
- name: Run Staged dependencies | |
uses: insightsengineering/staged-dependencies-action@v1 | |
with: | |
run-system-dependencies: false | |
enable-check: false | |
git-ref: ${{ steps.normalizer.outputs.SD_GIT_REF }} | |
renv-restore: false | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
##################### END boilerplate steps ##################### | |
- name: Install package | |
run: | | |
R CMD build --no-build-vignettes --no-manual . | |
R CMD INSTALL *.tar.gz | |
- name: Run Template Scripts | |
run: | | |
desc <- read.dcf("DESCRIPTION") | |
package_name <- as.character(desc[, "Package"]) | |
templates <- list.files( | |
system.file("templates", package = package_name), | |
pattern = "\\.R$", | |
ignore.case = TRUE, | |
full.names = TRUE | |
) | |
if (length(templates) > 0) { | |
exit_codes <- purrr::map_chr(templates, function(file) { | |
cmd <- sprintf("Rscript --vanilla %s", file) | |
system(cmd) | |
}) | |
if (any(exit_codes == 1L)) { | |
failed_scripts <- basename(templates)[which(exit_codes == 1L)] | |
err_msg <- sprintf( | |
"Executing the following template scripts failed:\n%s", | |
paste("-", failed_scripts, collapse = "\n") | |
) | |
stop(err_msg, call. = FALSE) | |
} | |
} | |
shell: Rscript {0} | |
- name: Add other data formats and suffixes, exclude data | |
if: inputs.push-templates-data | |
run: | | |
library(readxl) | |
library(zip) | |
loadRData <- function(fileName){ | |
load(fileName) | |
get(ls()[ls() != "fileName"]) | |
} | |
print(file.path("${{ github.workspace }}", "tmp")) | |
print(file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp")) | |
folder_path <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp") | |
rda_files <- list.files(path = folder_path, pattern = "\\.rda$") | |
ex_files <- unlist(strsplit("${{ inputs.exclude-templates-data }}", ",")) # files to exclude | |
for (rda_file in rda_files) { | |
# delete file if part of inputs.exclude-templates-data | |
if (gsub("\\.rda$", "", rda_file) %in% ex_files) { | |
file.remove(file.path(folder_path, rda_file)) | |
cat("Deleted:", rda_file, "\n") | |
} | |
else { | |
print(sprintf("converting file %s", rda_file)) | |
data <- loadRData(file.path(folder_path, rda_file)) | |
suffix <- gsub("pharmaverse/admiral", "", "${{ github.repository }}") | |
if (nchar(suffix) > 0) { | |
rda_file_renamed <- gsub("\\.rda$", sprintf("_%s.rda", suffix), rda_file) | |
csv_file <- gsub("\\.rda$", sprintf("_%s.csv", suffix), rda_file) | |
file.rename(file.path(folder_path, rda_file), file.path(folder_path, rda_file_renamed)) | |
} | |
else { | |
csv_file <- gsub("\\.rda$", ".csv", rda_file) | |
rda_file_renamed <- rda_file | |
} | |
write.csv(data, file = file.path(folder_path, csv_file), row.names = FALSE) | |
# rename content of rda file | |
rda_var <- gsub("\\.rda$", "", rda_file_renamed) | |
print(rda_var) | |
assign(rda_var, data) | |
do.call(save, list(rda_var, file = file.path(folder_path, sprintf("%s.rda", rda_var)), compress = "bzip2")) | |
# create associated documentation inside R folder | |
dataset_name <- gsub("\\.rda$", "", rda_file_renamed) | |
doc_string <- paste( | |
sprintf("#' Dataset %s", dataset_name), | |
"#'", | |
sprintf("#' %s dataset", dataset_name), | |
"#'", | |
sprintf("#' @name %s", dataset_name), | |
"#' @docType data", | |
sprintf("#' @format A data frame with %s columns:", ncol(data)), | |
"#' \\describe{", | |
paste(sapply(names(data), function(col_name) { | |
paste(sprintf("#' \\item{ %s }{%s}", col_name, col_name)) | |
}, USE.NAMES = FALSE), collapse="\n"), | |
"#' }", | |
"#'", sprintf("#' @source Generated from ${{ github.repository }}."), | |
"#' @references None", | |
"#'", sprintf("#' @examples\n#' data(\"%s\")", dataset_name), | |
sep = '\n', | |
sprintf("\"%s\"", dataset_name) | |
) | |
doc_dir <- "datasets_doc" | |
if (!file.exists(doc_dir)) { | |
dir.create(doc_dir, recursive = TRUE) | |
} | |
writeLines(doc_string, con = file.path(doc_dir, paste0(dataset_name, ".R"))) | |
} | |
} | |
shell: Rscript {0} | |
# zip templates data | |
- name: zip artifacts data | |
if: inputs.push-templates-data | |
run: | | |
find "$GITHUB_WORKSPACE/tmp" -type f \( -name "*.rda" -o -name "*.csv" \) -exec zip -j "$GITHUB_WORKSPACE/data.zip" {} \; | |
find "$GITHUB_WORKSPACE/datasets_doc" -type f \( -name "*.R" \) -exec zip -j "$GITHUB_WORKSPACE/doc.zip" {} \; | |
# store templates data as artifacts | |
- name: Archive templates data | |
if: inputs.push-templates-data | |
uses: actions/upload-artifact@v3 | |
with: | |
name: data_templates | |
path: ${{ github.workspace }}/data.zip | |
# store templates data as artifacts | |
- name: Archive doc | |
if: inputs.push-templates-data | |
uses: actions/upload-artifact@v3 | |
with: | |
name: doc_templates | |
path: ${{ github.workspace }}/doc.zip | |
- name: Checkout repo (PR) 🛎 | |
if: inputs.push-templates-data | |
uses: actions/checkout@v3 | |
with: | |
ref: main | |
repository: "${{ github.repository_owner }}/${{ env.repo }}" | |
fetch-depth: 2 | |
token: ${{ secrets.PHARMAVERSE_BOT }} | |
- name: Add safe directory | |
if: inputs.push-templates-data | |
run: | | |
git config --global --add safe.directory "${GITHUB_WORKSPACE}" | |
shell: bash | |
- name: Download data artifacts | |
if: inputs.push-templates-data | |
uses: actions/download-artifact@v3 | |
with: | |
name: data_templates | |
- name: Download doc artifacts | |
if: inputs.push-templates-data | |
uses: actions/download-artifact@v3 | |
with: | |
name: doc_templates | |
# detect diffs om templates data | |
- name: Check templates changes | |
if: inputs.push-templates-data | |
id: changes | |
run: | | |
head_data_folder=$(git ls-tree -r HEAD data) # check if data folder exists on remote main branch | |
unzip -o "${GITHUB_WORKSPACE}/data.zip" -d "${GITHUB_WORKSPACE}/inst/extdata/" | |
unzip -o "${GITHUB_WORKSPACE}/doc.zip" -d "${GITHUB_WORKSPACE}/R" | |
# move every rda files inside data folder | |
mkdir -p data | |
for rda_file in inst/extdata/*.rda; do | |
filename=$(basename "$rda_file") | |
mv "$rda_file" "data/$filename" | |
done | |
if [ -z "${head_data_folder}" ] | |
then { | |
echo "data folder not existing on main branch yet - init mode (all templates data files will be pushed)" | |
diff_files=$(ls "${GITHUB_WORKSPACE}/data") | |
} else { | |
git add data R | |
diff_files_data=$(git status data | grep 'data/.*\.rda$') | |
diff_files_doc=$(git status R | grep 'R/.*\.R$') | |
diff_files="${diff_files_data}${diff_files_doc}" | |
} | |
fi | |
if [ -z "$diff_files" ] | |
then { | |
echo "No changes detected after running templates. Stop here" | |
echo "diff=false" >> $GITHUB_OUTPUT | |
} else { | |
echo "Changes detected, new PR will be created" | |
echo "list of files with new updates: $diff_files" | |
echo "diff=true" >> $GITHUB_OUTPUT | |
} | |
fi | |
shell: bash {0} | |
- name: Generate man pages | |
if: inputs.push-templates-data | |
run: | | |
Rscript -e "roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))" | |
git add man | |
shell: bash {0} | |
- name: Update spellchecks list | |
if: inputs.push-templates-data | |
run: | | |
spelling::update_wordlist(pkg=".", confirm=FALSE) | |
shell: Rscript {0} | |
- name: set source-branch name | |
if: inputs.push-templates-data | |
id: branch | |
run: | | |
repo_name=$(basename "${{ github.repository }}") | |
echo "source-branch=${{ env.source-branch }}_${repo_name}@devel" >> $GITHUB_OUTPUT | |
shell: bash {0} | |
# if diff detected, push changes | |
- name: Commit and push changes in {{ env.repo }} | |
if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' }} | |
uses: stefanzweifel/git-auto-commit-action@v4 | |
with: | |
commit_message: templates data updates from ${{ github.repository }} | |
file_pattern: 'inst/extdata/* data/* R/* inst/WORDLIST' | |
commit_user_name: pharmaverse-bot | |
commit_user_email: [email protected] | |
branch: "${{ steps.branch.outputs.source-branch }}" | |
create_branch: true | |
- name: Create Pull Request | |
if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' }} | |
uses: actions/github-script@v6 | |
with: | |
github-token: ${{ secrets.PHARMAVERSE_BOT }} | |
script: | | |
// Look for any open PRs | |
const repo_owner = "${{ github.repository_owner }}"; | |
const target_repo_name = "${{ env.repo }}"; | |
const result = await github.rest.pulls.list({ | |
owner: repo_owner, | |
repo: target_repo_name, | |
state: "open" | |
}) | |
let create_new_pr = true; | |
for (const pr of result.data) { | |
// Look for distinct PR branch name | |
if (pr.head.ref === "${{ steps.branch.outputs.source-branch }}") { | |
console.log("PR with head ref " + pr.head.ref + " already exists"); | |
create_new_pr = false; | |
break; | |
} | |
} | |
// If no PR with distinguished branch name has been found | |
// create a new PR to track changes to renv.lock. | |
if (create_new_pr) { | |
console.log("Creating a new PR"); | |
const result2 = await github.rest.pulls.create({ | |
title: 'Templates data updates from ${{ github.repository }}', | |
owner: repo_owner, | |
repo: target_repo_name, | |
head: '${{ steps.branch.outputs.source-branch }}', | |
base: '${{ env.target-branch }}', | |
body: [ | |
'This PR has been automatically generated by ', | |
'check-templates workflow from ${{ github.repository }}.', | |
'\n\nPlease review the changes.' | |
].join('') | |
}); | |
// Assign reviewers to the PR | |
let rev = process.env.reviewers; | |
let reviewers_dict = JSON.parse(rev); | |
let current_repo_name_full = "${{ github.repository }}"; | |
let current_repo_name = current_repo_name_full.split('/').pop(); | |
const result3 = await github.rest.pulls.requestReviewers({ | |
owner: repo_owner, | |
repo: target_repo_name, | |
pull_number: result2.data.number, | |
reviewers: reviewers_dict[current_repo_name]["reviewers"] | |
}); | |
} |