Merge pull request #25 from CausalAIBook/fixed_flaml_update #33
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| name: Strip Python and R Notebooks from Outputs and Transform .irnb to .Rmd | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - gen-Rmd | |
| concurrency: | |
| group: strip-transform-notebooks-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| strip-transform-notebooks: | |
| if: github.event.commits[0].author.name != 'metricsml-bot' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ secrets.BOT_ACCESS_TOKEN }} | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.10' # Use Python 3.10 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install jupyter nbstripout | |
| shell: bash | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Install rmarkdown package | |
| run: | | |
| R -e 'install.packages(c("rmarkdown"), repos="https://cloud.r-project.org")' | |
| - name: Strip outputs from .ipynb files | |
| run: | | |
| git pull | |
| dirs=(PM1 PM2 PM3 PM4 PM5 CM1 CM2 CM3 AC1 AC2 T) | |
| for dir in "${dirs[@]}"; do | |
| # Check if directory exists | |
| if [ -d "$dir" ]; then | |
| echo "Processing directory: $dir" | |
| # Loop over all .ipynb files in the directory (non-recursively) | |
| for notebook in "$dir"/*.ipynb; do | |
| # Check if there are any .ipynb files | |
| if [ -e "$notebook" ]; then | |
| echo "Stripping output from notebook: $notebook" | |
| nbstripout "$notebook" | |
| fi | |
| done | |
| for notebook in "$dir"/*.irnb; do | |
| # Check if there are any .irnb files | |
| if [ -e "$notebook" ]; then | |
| echo "Stripping output from notebook: $notebook" | |
| ipynb_notebook=$(mktemp --suffix=.ipynb) | |
| mv "$notebook" "$ipynb_notebook" | |
| nbstripout "$ipynb_notebook" | |
| mv "$ipynb_notebook" "$notebook" | |
| fi | |
| done | |
| echo "Converting .irnb to .Rmd to update the .Rmd version" | |
| # first we delete all Rmd files and regenerate. This will make sure | |
| # that if a .irnb file is deleted then the corresponding .Rmd file | |
| # will also be removed by this script. | |
| find "$dir" -maxdepth 1 -type f -name '*.Rmd' -exec git rm {} \; | |
| R -e " | |
| files <- list.files(path = '$dir', pattern = '\\\\.irnb$', full.names = TRUE, recursive = FALSE) | |
| lapply(files, function(input) { | |
| rmarkdown::convert_ipynb(input) | |
| }) | |
| " | |
| find "$dir" -maxdepth 1 -type f -name '*.Rmd' -exec git add {} \; | |
| else | |
| echo "Directory $dir does not exist." | |
| fi | |
| done | |
| - name: Check if there are any changes (e.g. stripped outputs) | |
| id: verify_diff | |
| run: | | |
| git pull | |
| git status --porcelain | |
| CHANGES=$(git status --porcelain) | |
| if [ -z "$CHANGES" ]; then | |
| echo "No changes were found" | |
| else | |
| echo "Found changes" | |
| echo "$CHANGES" | |
| echo "changed=true" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Commit and push stripped .ipynb files | |
| if: steps.verify_diff.outputs.changed == 'true' | |
| run: | | |
| git config --global user.name 'metricsml-bot' | |
| git config --global user.email '[email protected]' | |
| git pull | |
| dirs=(PM1 PM2 PM3 PM4 PM5 CM1 CM2 CM3 AC1 AC2 T) | |
| for dir in "${dirs[@]}"; do | |
| # Check if directory exists | |
| if [ -d "$dir" ]; then | |
| echo "Adding changed files from directory: $dir" | |
| git add "$dir"/*.ipynb "$dir"/*.irnb "$dir"/*.Rmd | |
| else | |
| echo "Directory $dir does not exist." | |
| fi | |
| done | |
| git commit -m 'Strip outputs from .ipynb files [skip ci]' | |
| git push --force-with-lease |