Cleanup installs happening in the github workflows #433
Workflow file for this run
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| name: run unit tests | |
| on: pull_request | |
| jobs: | |
| run-unit-tests: | |
| name: run unit tests | |
| runs-on: macOS-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Cache R packages | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: r-${{ hashFiles('DESCRIPTION') }} | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("devtools")) | |
| devtools::install_github("epiforecasts/[email protected]") | |
| devtools::install_deps(dependencies = TRUE) | |
| shell: Rscript {0} | |
| - name: Run unit tests | |
| run: | | |
| devtools::test_active_file("tests/testthat/test-align.R", stop_on_failure = TRUE) | |
| devtools::test_active_file("tests/testthat/test-date_management.R", stop_on_failure = TRUE) | |
| devtools::test_active_file("tests/testthat/test-score_forecasts.R", stop_on_failure = TRUE) | |
| devtools::test_active_file("tests/testthat/test-load_forecast_files_repo.R", stop_on_failure = TRUE) | |
| devtools::test_active_file("tests/testthat/test-get_model_designations.R", stop_on_failure = TRUE) | |
| devtools::test_active_file("tests/testthat/test-get_model_metadata.R", stop_on_failure = TRUE) | |
| devtools::test_active_file("tests/testthat/test-load_as_of.R", stop_on_failure = TRUE) | |
| devtools::test_active_file("tests/testthat/test-load_forecasts.R", stop_on_failure = TRUE) | |
| devtools::test_active_file("tests/testthat/test-calc_cramers_dist_equal_space.R", stop_on_failure = TRUE) | |
| devtools::test_active_file("tests/testthat/test-calc_cramers_dist_unequal_space.R", stop_on_failure = TRUE) | |
| devtools::test_active_file("tests/testthat/test-calc_cramers_dist_one_model_pair.R", stop_on_failure = TRUE) | |
| devtools::test_active_file("tests/testthat/test-name_to_fips.R", stop_on_failure = TRUE) | |
| shell: Rscript {0} | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/[email protected] | |
| - name: Checkout covidData when get_truth.R, aggregate_to_weekly.R or load_truth.R has changed | |
| if: >- | |
| ${{ contains(steps.changed-files.outputs.modified_files, 'R/get_truth.R') || | |
| contains(steps.changed-files.outputs.modified_files, | |
| 'R/aggregate_to_weekly.R') || | |
| contains(steps.changed-files.outputs.modified_files, | |
| 'R/load_truth.R')}} | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: reichlab/covidData | |
| path: covidData | |
| - name: Install covidData when get_truth.R, aggregate_to_weekly.R or load_truth.R has changed | |
| if: >- | |
| ${{ contains(steps.changed-files.outputs.modified_files, 'R/get_truth.R') || | |
| contains(steps.changed-files.outputs.modified_files, | |
| 'R/aggregate_to_weekly.R') || | |
| contains(steps.changed-files.outputs.modified_files, | |
| 'R/load_truth.R')}} | |
| run: make recent_data | |
| working-directory: ./covidData/code/data-processing | |
| - name: Run unit test for get_truth.R | |
| if: contains(steps.changed-files.outputs.modified_files, 'R/get_truth.R') | |
| run: | | |
| devtools::test_active_file("tests/testthat/test-get_truth.R", stop_on_failure = TRUE) | |
| shell: Rscript {0} | |
| - name: Run unit test for aggregate_to_weekly.R | |
| if: contains(steps.changed-files.outputs.modified_files, 'R/aggregate_to_weekly.R') | |
| run: | | |
| devtools::test_active_file("tests/testthat/test-aggregate_to_weekly.R", stop_on_failure = TRUE) | |
| shell: Rscript {0} | |
| - name: Run unit test for load_truth.R | |
| if: contains(steps.changed-files.outputs.modified_files, 'R/load_truth.R') | |
| run: | | |
| devtools::test_active_file("tests/testthat/test-load_truth.R", stop_on_failure = TRUE) | |
| shell: Rscript {0} | |
| - name: Render vignettes | |
| run: | | |
| devtools::build_vignettes() | |
| shell: Rscript {0} | |