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check-and-transform-R-notebooks.yml
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name: Check R Notebooks
on:
pull_request:
branches:
- main
schedule:
- cron: '0 12 * * 0' # Runs every Sunday at 12 PM UTC
concurrency:
group: test-R-notebooks-${{ github.ref }}
cancel-in-progress: true
jobs:
test-R-notebooks:
runs-on: ubuntu-latest
strategy:
matrix:
directory: ['PM1', 'PM2', 'PM3', 'PM4', 'PM5', 'CM1', 'CM2', 'CM3', 'AC1', 'AC2', 'T']
steps:
- name: Checkout repository
uses: actions/checkout@v3
with:
fetch-depth: ${{ github.event_name == 'pull_request' && 2 || 0 }}
- name: Find changed notebooks in PR
if: github.event_name == 'pull_request'
id: find_notebooks_pr
run: |
# git fetch origin ${{ github.event.pull_request.base.ref }} ${{ github.event.pull_request.head.ref }}
# git diff --name-only origin/${{ github.event.pull_request.base.ref }}...origin/${{ github.event.pull_request.head.ref }} > changed_files.txt
git diff --name-only -r HEAD^1 HEAD > changed_files.txt
grep -E '\.irnb$|\.Rmd$|\.github/workflows/check-and-transform-R-notebooks.yml$' changed_files.txt > changed_notebooks.txt || echo "No notebooks changed" > changed_notebooks.txt
- name: Find changed notebooks in Push
if: github.event_name == 'push'
id: find_notebooks_push
run: |
git diff --name-only ${{ github.event.before }} ${{ github.event.after }} > changed_files.txt
grep -E '\.irnb$|\.Rmd$|\.github/workflows/check-and-transform-R-notebooks.yml$' changed_files.txt > changed_notebooks.txt || echo "No notebooks changed" > changed_notebooks.txt
- name: Check if any notebooks changed in PR or Push
if: (github.event_name == 'push') || (github.event_name == 'pull_request')
id: check_notebooks
run: |
cat changed_notebooks.txt
if grep -q -E '^${{ matrix.directory }}/.*\.irnb$|^${{ matrix.directory }}/.*\.Rmd$|\.github/workflows/check-and-transform-R-notebooks.yml$' changed_notebooks.txt; then
echo "notebooks_changed=true" >> $GITHUB_ENV
else
echo "notebooks_changed=false" >> $GITHUB_ENV
echo "No R notebooks changed in folder ${{ matrix.directory }} in this PR."
fi
- name: Set notebooks changed to true for schedule
if: "! ((github.event_name == 'push') || (github.event_name == 'pull_request'))"
id: set_check_notebooks_true
run: |
# we run all folders if it is the weekly scheduled run to
# check if something broke due to changes in dependencies
echo "notebooks_changed=true" >> $GITHUB_ENV
- name: Install system dependencies
if: env.notebooks_changed == 'true'
run: |
sudo apt-get update
sudo apt-get install -y libcurl4-openssl-dev
- name: Set up Python
if: env.notebooks_changed == 'true'
uses: actions/setup-python@v2
with:
python-version: '3.10' # Specify your Python version here
- name: Install Python dependencies
if: env.notebooks_changed == 'true'
run: |
python -m pip install --upgrade pip
pip install nbstripout
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
shell: bash
- name: Set up R
if: env.notebooks_changed == 'true'
uses: r-lib/actions/setup-r@v2
- name: Install rmarkdown, knitr, and lintr packages
if: env.notebooks_changed == 'true'
run: |
R -e 'install.packages(c("rmarkdown", "knitr", "lintr", "xfun", "remotes"), repos="https://cloud.r-project.org")'
- name: Strip outputs from .irnb files
if: env.notebooks_changed == 'true'
run: |
for notebook in ${{ matrix.directory }}/*.irnb; do
ipynb_notebook="${notebook%.irnb}.ipynb"
mv "$notebook" "$ipynb_notebook"
nbstripout "$ipynb_notebook"
mv "$ipynb_notebook" "$notebook"
done
- name: Convert .irnb to .Rmd and .R
if: env.notebooks_changed == 'true'
run: |
R -e '
files <- list.files(path = "${{ matrix.directory }}", pattern = "\\.irnb$", full.names = TRUE, recursive = FALSE)
lapply(files, function(input) {
rmarkdown::convert_ipynb(input)
rmd_file <- xfun::with_ext(input, "Rmd")
knitr::purl(rmd_file, output = xfun::with_ext(input, "R"))
})
'
- name: Lint .Rmd files
if: env.notebooks_changed == 'true'
id: lint
run: |
R -e '
library(lintr)
linters <- with_defaults(line_length_linter = line_length_linter(120),
object_name_linter = object_name_linter(styles = c("snake_case", "CamelCase", "camelCase")),
object_usage_linter = NULL)
rmd_files <- list.files(path = "${{ matrix.directory }}", pattern = "\\.Rmd$", full.names = TRUE)
results <- lapply(rmd_files, function(file) {
lints <- lint(file, linters)
if (length(lints) > 0) {
cat("Warnings found during linting:\n")
print(lints)
stop("Linting failed with warnings")
}
})
'
- name: Execute R scripts and log output
if: env.notebooks_changed == 'true'
id: execute
run: |
log_file="${{ matrix.directory }}_r_script_execution.log"
R -e '
options(show.error.locations = TRUE)
files <- list.files(path = "${{ matrix.directory }}", pattern = "\\.R$", full.names = TRUE, recursive = FALSE)
log_con <- file("'$log_file'", open = "wt")
sink(log_con, type = "output")
sink(log_con, type = "message")
errors <- list()
for (gitrfile in files) {
withCallingHandlers(
withRestarts(
source(gitrfile),
muffleStop = function() NULL
),
error = function(e) {
traceback_info <- sys.calls()
errors[[length(errors) + 1]] <<- list(gitrfile = gitrfile, location = capture.output(print(e$call)), message = e$message, traceback = traceback_info)
invokeRestart("muffleStop")
}
)
}
sink(type = "output")
sink(type = "message")
close(log_con)
if (length(errors) > 0) {
for (error in errors) {
cat("Error found in file:", error$gitrfile, "\n")
cat("at line::", error$location, "\n")
cat("Error message:", error$message, "\n")
print("Traceback:\n")
cat(paste(error$traceback, collapse = "\n"))
print("\n")
}
quit(status = 1, save = "no") # Exit with an error status if errors are found
}
' 2>/dev/null
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
- name: Upload execution log
if: env.notebooks_changed == 'true'
uses: actions/upload-artifact@v2
with:
name: ${{ matrix.directory }}-r-script-execution-log
path: ${{ matrix.directory }}_r_script_execution.log
- name: Zip .R files
if: env.notebooks_changed == 'true'
run: |
mkdir r_scripts
mv ${{ matrix.directory }}/*.R r_scripts/
zip -r ${{ matrix.directory }}_r_scripts.zip r_scripts
- name: Upload artifact
if: env.notebooks_changed == 'true'
uses: actions/upload-artifact@v2
with:
name: ${{ matrix.directory }}-r-scripts
path: ${{ matrix.directory }}_r_scripts.zip
- name: Delete .R files and zip
if: env.notebooks_changed == 'true'
run: |
rm -rf r_scripts
rm ${{ matrix.directory }}_r_scripts.zip
# - name: Check out the branch for pull request
# if: "(github.event_name == 'pull_request') && (env.notebooks_changed == 'true')"
# run: |
# git fetch --all
# git checkout ${{ github.event.pull_request.head.ref }}
# - name: Check if there are any changes
# if: env.notebooks_changed == 'true'
# id: verify_diff
# run: |
# git pull
# git diff --quiet ${{ matrix.directory }}/*.irnb ${{ matrix.directory }}/*.Rmd || echo "changed=true" >> $GITHUB_OUTPUT
# - name: Commit and push stripped .irnb and .Rmd files
# if: "(env.notebooks_changed == 'true') && (steps.verify_diff.outputs.changed == 'true')"
# run: |
# git config --global user.name 'github-actions[bot]'
# git config --global user.email 'github-actions[bot]@users.noreply.github.com'
# git pull
# git add ${{ matrix.directory }}/*.irnb ${{ matrix.directory }}/*.Rmd
# git commit -m 'Strip outputs from .irnb, convert to .Rmd, lint .Rmd files, and execute .R files in ${{ matrix.directory }} [skip ci]'
# git push --force-with-lease
# env:
# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}