Update action_BODC_table_generator.yml #40
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: ${{ matrix.config.r }} | |
| # Step 6: Install R packages | |
| - name: Install R packages | |
| run: | | |
| Rscript -e 'install.packages(c("RCurl", "httr", "dplyr", "finch", "ggplot2", "leaflet", "rjson", "parsedate", "plyr", "tidyr", "stringdist"))' | |
| Rscript -e 'remotes::install_github("iobis/obistools")' | |
| Rscript -e 'remotes::install_github("iobis/skosxml")' | |
| # Step 7: Read the CSV files in R and run the usethis::use_data() commands | |
| - name: Process CSV files with R | |
| run: | | |
| DATE=$(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 }} |