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Merge pull request #280 from HopkinsIDD/split-up-unit-tests-action
Split `ci.yml` into separate actions
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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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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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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} |