inference-ci.yml

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}