modified to capture stdout and stderr to log in using system2() being… #97
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| name: inference CI | |
| on: | |
| workflow_dispatch: | |
| workflow_run: | |
| workflows: ['flepicommon-ci', 'gempyor-ci'] | |
| types: | |
| - completed | |
| push: | |
| paths: | |
| - flepimop/R_packages/inference/**/* | |
| branches: | |
| - dev | |
| pull_request: | |
| paths: | |
| - flepimop/R_packages/inference/**/* | |
| branches: | |
| - dev | |
| - main | |
| jobs: | |
| tests: | |
| runs-on: ubuntu-latest | |
| if: (github.event_name != 'workflow_run' || github.event.workflow_run.conclusion == 'success') && (github.event_name != 'pull_request' || github.event.pull_request.draft == false) | |
| strategy: | |
| matrix: | |
| R-version: ["4.3.3"] | |
| python-version: ["3.10", "3.11"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| sparse-checkout: | | |
| * | |
| !documentation/ | |
| sparse-checkout-cone-mode: false | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install gempyor | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install "flepimop/gempyor_pkg[test]" | |
| shell: bash | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.R-version }} | |
| update-rtools: true | |
| - name: Install System Dependencies | |
| run: sudo apt install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libtiff5-dev libudunits2-dev libgdal-dev libgeos-dev libproj-dev | |
| - name: Determine R Library Location | |
| run: | | |
| R_LIBPATH=$( R -s -e "cat(.libPaths()[1L])" | xargs ) | |
| echo "R_LIBPATH=$R_LIBPATH" >> $GITHUB_ENV | |
| R_LIBPATH_CKSUM=$( echo "$R_LIBPATH" | cksum | cut -d ' ' -f 1 ) | |
| echo "R_LIBPATH_CKSUM=$R_LIBPATH_CKSUM" >> $GITHUB_ENV | |
| CACHE_DATE=$( date -d "last Sunday" +%Y%m%d ) | |
| echo "CACHE_DATE=$CACHE_DATE" >> $GITHUB_ENV | |
| - name: R Library Cache | |
| uses: actions/cache@v4 | |
| with: | |
| key: inference-rlibs-${{ runner.os }}-${{ matrix.R-version }}-${{ hashFiles('flepimop/R_packages/flepicommon/DESCRIPTION', 'flepimop/R_packages/flepicommon/NAMESPACE', 'flepimop/R_packages/inference/DESCRIPTION', 'flepimop/R_packages/inference/NAMESPACE') }}-${{ env.R_LIBPATH_CKSUM }}-${{ env.CACHE_DATE }} | |
| path: ${{ env.R_LIBPATH }} | |
| - name: Install R Dependencies For flepicommon | |
| if: steps.r-library-cache.outputs.cache-hit != 'true' | |
| run: | | |
| install.packages( | |
| "devtools", | |
| repos = "https://cloud.r-project.org", | |
| ) | |
| library(devtools) | |
| devtools::install_deps( | |
| pkg = "flepimop/R_packages/flepicommon", | |
| dependencies = TRUE | |
| ) | |
| install.packages("covidcast", repos = "https://cloud.r-project.org") | |
| shell: Rscript {0} | |
| - name: Install The flepicommon Package | |
| run: | | |
| devtools::install( | |
| pkg = "flepimop/R_packages/flepicommon", | |
| quick = TRUE, | |
| dependencies = TRUE, | |
| force = TRUE | |
| ) | |
| shell: Rscript {0} | |
| - name: Install R Dependencies For inference | |
| if: steps.r-library-cache.outputs.cache-hit != 'true' | |
| run: | | |
| devtools::install_deps( | |
| pkg = "flepimop/R_packages/inference", | |
| dependencies = TRUE | |
| ) | |
| install.packages("covidcast", repos = "https://cloud.r-project.org") | |
| shell: Rscript {0} | |
| - name: Install The inference Package | |
| run: | | |
| devtools::install( | |
| pkg = "flepimop/R_packages/inference", | |
| args = c(getOption("devtools.install.args"), "--install-tests"), | |
| quick = TRUE, | |
| dependencies = TRUE, | |
| force = TRUE | |
| ) | |
| shell: Rscript {0} | |
| - name: Run Tests | |
| run: | | |
| library(testthat) | |
| test_package("inference") | |
| shell: Rscript {0} |