Update action_BODC_table_generator.yml #39
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| name: Update BODC tables used in the package | |
| on: | |
| # Scheduled to run on the 1st of each month | |
| #schedule: | |
| #- cron: '0 0 1 * *' # Runs at midnight UTC on the 1st of each month | |
| # For testing purposes, also trigger on push to main branch | |
| push: | |
| branches: | |
| - develop | |
| jobs: | |
| generate-table: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| # Step 1: Checkout the repository | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| # Step 2: Set up Python environment | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12.2' | |
| # Step 3: Install required dependencies | |
| - name: Install dependencies | |
| run: | | |
| pip install pandas pysema requests numpy | |
| # Step 4: Run the Python script that generates the table | |
| - name: Run table generator script | |
| run: python files/BODC_tables_generator.py | |
| # Step 5: Set up R environment | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| # Step 6: Install R packages | |
| - name: Install R packages | |
| run: Rscript -e 'install.packages(c("devtools","usethis","RCurl", "httr", "dplyr", "finch", "ggplot2", "leaflet", "skosxml", "rjson", "parsedate", "plyr", "obistools", "tidyr", "stringdist"))' | |
| # Step 7: Read the CSV files in R and run the usethis::use_data() commands | |
| - name: Process CSV files with R | |
| run: | | |
| DATE=$(date +%Y%m%d) | |
| Rscript -e "BODCunits <- read.csv('files/BODCunits_$DATE.csv'); \ | |
| BODCvalues <- read.csv('files/BODCvalues_$DATE.csv'); \ | |
| BODCparameters <- read.csv('files/BODCparameters_$DATE.csv'); \ | |
| usethis::use_data(BODCunits, overwrite = TRUE); \ | |
| usethis::use_data(BODCvalues, overwrite = TRUE); \ | |
| usethis::use_data(BODCparameters, overwrite = TRUE); \ | |
| devtools::document()" | |
| # Configure git | |
| - name: Configure Git | |
| run: | | |
| git config --global user.name "github-actions[bot]" | |
| git config --global user.email "github-actions[bot]@users.noreply.github.com" | |
| # Commit the changes | |
| - name: Commit changes | |
| run: | | |
| git add . | |
| git commit -m "Automated commit by GitHub Action" | |
| # Push changes back to the branch | |
| - name: Push changes | |
| run: git push | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |