Delete resources/raw_data/2023/data_entry_biannual_spr2023.xlsx #337
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
| # 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 |