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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| name: flepicommon-ci | ||
|
|
||
| on: | ||
| workflow_dispatch: | ||
| push: | ||
| paths: | ||
| - flepimop/R_packages/flepicommon/**/* | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| paths: | ||
| - flepimop/R_packages/flepicommon/**/* | ||
| branches: | ||
| - main | ||
|
|
||
| jobs: | ||
| tests: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| R-version: ["4.3.3"] | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| lfs: true | ||
| sparse-checkout: | | ||
| * | ||
| !documentation/ | ||
| sparse-checkout-cone-mode: false | ||
| - 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" >> $GITHUB_ENV | ||
| - name: R Library Cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| key: flepicommon-rlibs-${{ runner.os }}-${{ matrix.R-version }}-${{ hashFiles('flepimop/R_packages/flepicommon/DESCRIPTION', 'flepimop/R_packages/flepicommon/NAMESPACE') }}-${{ env.R_LIBPATH_CKSUM }}-${{ env.CACHE_DATE }} | ||
| path: ${{ env.R_LIBPATH }} | ||
| - name: Install R Dependencies | ||
| 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", | ||
| 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("flepicommon") | ||
| shell: Rscript {0} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| name: gempyor-ci | ||
|
|
||
| on: | ||
| workflow_dispatch: | ||
| push: | ||
| paths: | ||
| - examples/**/* | ||
| - flepimop/gempyor_pkg/**/* | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| paths: | ||
| - examples/**/* | ||
| - flepimop/gempyor_pkg/**/* | ||
| branches: | ||
| - main | ||
|
|
||
| jobs: | ||
| tests: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| 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: Run gempyor tests | ||
| run: | | ||
| cd flepimop/gempyor_pkg | ||
| pytest --exitfirst | ||
| shell: bash | ||
| - name: Run gempyor-cli integration tests from examples | ||
| run: | | ||
| cd examples | ||
| pytest --exitfirst | ||
| shell: bash |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,112 @@ | ||
| name: inference-ci | ||
|
|
||
| on: | ||
| workflow_dispatch: | ||
| workflow_run: | ||
| workflows: ['flepicommon-ci', 'gempyor-ci'] | ||
| types: | ||
| - completed | ||
| push: | ||
| paths: | ||
| - flepimop/R_packages/inference/**/* | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| paths: | ||
| - flepimop/R_packages/inference/**/* | ||
| branches: | ||
| - main | ||
|
|
||
| jobs: | ||
| tests: | ||
| runs-on: ubuntu-latest | ||
| if: ${{ github.event_name != 'workflow_run' || github.event.workflow_run.conclusion == 'success' }} | ||
| 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} |
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