Merge branch 'main' of https://github.com/SCBI-ForestGEO/SCBImortality #223
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| # This file determines when GitHub Actions (GA) is triggered and if so what | |
| # sequence of steps continous integration takes. | |
| # | |
| # For a video tutorial explaining these steps click: https://youtu.be/JKF6aXtdLHs | |
| # When any of these files are modified trigger GAs (except for the ones with a '!'): | |
| on: | |
| push: | |
| paths: | |
| - 'raw_data/FFF_excel**' | |
| - '!raw_data/README.md' | |
| - 'R_scripts/CI_1_Generate_reports.R' | |
| - 'R_scripts/CI_2_Generate_warnings.R' | |
| - 'R_scripts/CI_3_Generate_map_of_reports.R' | |
| - 'R_scripts/CI_4_Generate_daily_progress_reports.R' | |
| pull_request: | |
| paths: | |
| - 'raw_data/FFF_excel**' | |
| - '!raw_data/README.md' | |
| - 'R_scripts/CI_1_Generate_reports.R' | |
| - 'R_scripts/CI_2_Generate_warnings.R' | |
| - 'R_scripts/CI_3_Generate_map_of_reports.R' | |
| - 'R_scripts/CI_4_Generate_daily_progress_reports.R' | |
| # Name the workflow as it will appear on GA status page | |
| # https://github.com/SCBI-ForestGEO/SCBImortality/actions | |
| name: data-tests | |
| # Here are all the steps GA takes when triggered: | |
| jobs: | |
| data-tests: | |
| # Set the operating system GA assumes: | |
| runs-on: windows-latest | |
| # Allow only authorized collaborators to trigger GA: | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| # All steps in workflow: | |
| steps: | |
| # Housekeeping - Import various actions to make process work: | |
| - uses: actions/checkout@v3 | |
| # Use this action: https://github.com/actions/checkout#checkout-v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| # Use this action: https://github.com/r-lib/actions/tree/v2/setup-r | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| # Housekeeping - Run package check (may not be needed): | |
| # - name: Check | |
| # run: | | |
| # options(crayon.enabled = TRUE) | |
| # rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error") | |
| # shell: Rscript {0} | |
| # Run R script to generate error reports: | |
| - name: Generate reports | |
| id: Generate_reports | |
| run: | | |
| source("R_scripts/CI_1_Generate_reports.R") | |
| shell: Rscript {0} | |
| # Run R script to generate warning reports: | |
| - name: Generate warnings | |
| id: Generate_warnings | |
| run: | | |
| source("R_scripts/CI_2_Generate_warnings.R") | |
| shell: Rscript {0} | |
| # Run R script to generate map of reports: | |
| - name: Generate map of reports | |
| id: Generate_map_of_reports | |
| run: | | |
| source("R_scripts/CI_3_Generate_map_of_reports.R") | |
| shell: Rscript {0} | |
| # Run R script to generate daily progress reports: | |
| - name: Generate daily progress reports | |
| id: Generate_daily_progress_reports | |
| run: | | |
| source("R_scripts/CI_4_Generate_daily_progress_reports.R") | |
| shell: Rscript {0} | |
| # Commit and push all new files, where commits are assigned to GA bot: | |
| - name: Commit new files | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Actions" | |
| git pull | |
| git add --all | |
| git commit -am "add data" | |
| git push | |
| # Use testthat package to issue notifications of any data collection errors: | |
| - name: Run tests | |
| run: Rscript testthat.R |