reorder data by area #301
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| # Set the list of files that when modified will trigger GitHub Actions | |
| # (GA) continuous integration (CI) to run | |
| # For a video tutorial explaining these steps for the similarly structured | |
| # SCBI mortality census (https://github.com/SCBI-ForestGEO/SCBImortality), | |
| # click this link to YouTube: https://youtu.be/JKF6aXtdLHs | |
| on: | |
| push: | |
| paths: | |
| - 'resources/raw_data/**' | |
| - 'Rscripts/survey_forms/create_master_csv_2021_and_after.R' | |
| - 'Rscripts/Generate_reports.R' | |
| - 'Rscripts/Generate_warnings.R' | |
| - 'README.Rmd' | |
| pull_request: | |
| paths: | |
| - 'resources/raw_data/**' | |
| - 'Rscripts/survey_forms/create_master_csv_2021_and_after.R' | |
| - 'Rscripts/Generate_reports.R' | |
| - 'Rscripts/Generate_warnings.R' | |
| - 'README.Rmd' | |
| # Name the workflow as it will appear on GA status page | |
| # https://github.com/SCBI-ForestGEO/Dendrobands/actions | |
| name: QA_QC_checks | |
| jobs: | |
| QA_QC_checks: | |
| # Set the operating system CI assumes: | |
| runs-on: macOS-latest | |
| # Allow only authorized collaborators to trigger GA: | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| # All steps in workflow: | |
| steps: | |
| # Housekeeping: Use various GA tools, install R, install pandoc | |
| # (to be able to use RMarkdown) | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| # Housekeeping: Install all packages listed in DESCRIPTION file | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("remotes", "rcmdcheck", "rmarkdown")) | |
| remotes::install_deps(dependencies = TRUE) | |
| shell: Rscript {0} | |
| # 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} | |
| # Create data/scbi.dendroAll_YEAR.csv from resources/raw_data/YEAR/ | |
| # csv's | |
| - name: Create current year's master data csv | |
| id: create_master_csv | |
| run: | | |
| source("Rscripts/survey_forms/create_master_csv_2021_and_after.R") | |
| shell: Rscript {0} | |
| # Test for data collection errors that require field fixes, outputs | |
| # saved in testthat/reports/ | |
| - name: Generate error reports | |
| id: generate_error_reports | |
| run: | | |
| source("Rscripts/Generate_reports.R") | |
| shell: Rscript {0} | |
| # Test for warnings, outputs saved in testthat/reports/ | |
| - name: Generate warning reports | |
| id: generate_warning_reports | |
| run: | | |
| source("Rscripts/Generate_warnings.R") | |
| shell: Rscript {0} | |
| # Recompute annual summaries in results/dendro_trees_dbhcount/ | |
| - name: Recompute annual summaries | |
| run: | | |
| source("Rscripts/analysis/dendrotrees_by_sp-survey-dbh.R") | |
| shell: Rscript {0} | |
| # Update dashboard: repository README.md front page | |
| - name: Update README | |
| run: | | |
| Rscript -e 'rmarkdown::render("README.Rmd")' | |
| rm README.html | |
| # Commit and push all new files, assigned to GA bot | |
| - name: Commit and push all new files | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Actions" | |
| git add --all || echo "No changes to commit" | |
| git commit -m "Added/modified files and updated README" || echo "No changes to commit" | |
| git push origin | |
| # Use testthat package to issue notifications of any data collection errors | |
| - name: Are there any data collection? | |
| run: Rscript testthat.R |